Psyllid ID: psy3016

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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
MSLGREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLRASAL
Secondary Structure (PSIPRED)
cccccEEEEccccccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEcccccccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEcccccccccccccEEEEccccHHHcHHHHHHHHHHccccEEccEEEccEEcccccEEEccccccccccccccEEEEEccccccccccccccccEEEEEEcccHHHHHHHHHHHcccccccEEEEEEccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccEEEEcccccccHHHHHHHHHcccHccccccEEEEccccccccHHHHHHHHcccccEEEEEEEccccccccccEEEEEcccHHHHHHHHHHHcccEccccEEEEEEccccHHHHccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEccccccccEEEEcccccHHHHHHHHccccEEccccEEEEcccccccccEEEEEcccHHHHHHHHHHHcccEcccccEEEEEHccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mslgreiqagistpclqslsqtklegggesgdgdatiYVGGLDDKVSETLMWELFVqsgpvvnvhmpkdrvtqthqGYGFiefmgeedADYAIKIMNMIKLYgkpirvnkasshqknldvganifignldpevdeKLLYDTFSAFGVILQTPKIMNMIKLYgkpirvnkasshqknldvganifignldpeimrdpdtgnskgfAFINYasfeasdasiDAMHGQylcnrpisvsyafkkdskgdrhGSAAERLLAAqnplsqadrphqlfadapppaplppppppinimglpppppsglrasal
Flexible Loop (DISEMBL)
mslgreiqagistpclqSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKAsshqknldvgaNIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLRASAL
Low Complexity Region (SEG)
MSLGREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFADapppaplppppppinimglpppppSGLRASAL
Disordered region (IsUnstruct)
**********************************ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR****GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF*******************************************************************
Disordered Region (DISOPRED)
***GREI*****************************IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR*****************FIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY*********************************************************************
Disordered Region (DISEMBL)
MSLGREIQAGISTPCLQSLSQT********GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK**********AAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLRASAL
Disordered Region (DISPRO)
***GREIQAGISTP***************SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQN****************PPAPLPP***********************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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)
MSLGREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLRASAL
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]
Q15427	424	Splicing factor 3B subuni	yes	N/A	0.655	0.471	0.743	4e-99
Q6AYL5	424	Splicing factor 3B subuni	yes	N/A	0.655	0.471	0.743	5e-99
Q8QZY9	424	Splicing factor 3B subuni	yes	N/A	0.655	0.471	0.743	5e-99
Q09442	388	Splicing factor 3B subuni	yes	N/A	0.760	0.597	0.615	1e-93
O14102	335	Spliceosome-associated pr	yes	N/A	0.593	0.540	0.457	2e-55
Q55GD6	359	Splicing factor 3B subuni	yes	N/A	0.596	0.506	0.455	2e-48
Q99181	213	Protein HSH49 OS=Saccharo	yes	N/A	0.609	0.873	0.305	1e-26
Q13310	644	Polyadenylate-binding pro	no	N/A	0.668	0.316	0.298	2e-25
A1CRM1	754	Polyadenylate-binding pro	N/A	N/A	0.727	0.294	0.285	2e-24
P11940	636	Polyadenylate-binding pro	no	N/A	0.672	0.322	0.292	5e-24

>sp|Q15427|SF3B4_HUMAN Splicing factor 3B subunit 4 OS=Homo sapiens GN=SF3B4 PE=1 SV=1

 Score =  361 bits (926), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 177/238 (74%), Positives = 194/238 (81%), Gaps = 38/238 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct: 12  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KIMNMIKLYGKPIRVNKAS+H KNLDVGANIFIGNLDPE+DEKLLYDTFSAFGVILQTPK
Sbjct: 72  KIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRDPDTGNSKG+AFIN+ASF+
Sbjct: 132 --------------------------------------IMRDPDTGNSKGYAFINFASFD 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLF 271
           ASDA+I+AM+GQYLCNRPI+VSYAFKKDSKG+RHGSAAERLLAAQNPLSQADRPHQLF
Sbjct: 154 ASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQLF 211

Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.
Homo sapiens (taxid: 9606)

>sp|Q6AYL5|SF3B4_RAT Splicing factor 3B subunit 4 OS=Rattus norvegicus GN=Sf3b4 PE=2 SV=1

 Score =  360 bits (925), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 177/238 (74%), Positives = 194/238 (81%), Gaps = 38/238 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct: 12  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KIMNMIKLYGKPIRVNKAS+H KNLDVGANIFIGNLDPE+DEKLLYDTFSAFGVILQTPK
Sbjct: 72  KIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRDPDTGNSKG+AFIN+ASF+
Sbjct: 132 --------------------------------------IMRDPDTGNSKGYAFINFASFD 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLF 271
           ASDA+I+AM+GQYLCNRPI+VSYAFKKDSKG+RHGSAAERLLAAQNPLSQADRPHQLF
Sbjct: 154 ASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQLF 211

Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.

Rattus norvegicus (taxid: 10116)

>sp|Q8QZY9|SF3B4_MOUSE Splicing factor 3B subunit 4 OS=Mus musculus GN=Sf3b4 PE=2 SV=1

 Score =  360 bits (925), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 177/238 (74%), Positives = 194/238 (81%), Gaps = 38/238 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct: 12  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KIMNMIKLYGKPIRVNKAS+H KNLDVGANIFIGNLDPE+DEKLLYDTFSAFGVILQTPK
Sbjct: 72  KIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRDPDTGNSKG+AFIN+ASF+
Sbjct: 132 --------------------------------------IMRDPDTGNSKGYAFINFASFD 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLF 271
           ASDA+I+AM+GQYLCNRPI+VSYAFKKDSKG+RHGSAAERLLAAQNPLSQADRPHQLF
Sbjct: 154 ASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQLF 211

Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.

Mus musculus (taxid: 10090)

>sp|Q09442|SF3B4_CAEEL Splicing factor 3B subunit 4 OS=Caenorhabditis elegans GN=sap-49 PE=1 SV=2

 Score =  343 bits (879), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 173/281 (61%), Positives = 205/281 (72%), Gaps = 49/281 (17%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DATIYVGGLD+KVSE+++WEL VQ+GPVV+V+MPKDRVT  HQG+GF+EFMGEEDADYAI
Sbjct: 12  DATIYVGGLDEKVSESILWELMVQAGPVVSVNMPKDRVTANHQGFGFVEFMGEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KI+NMIKLYGKPI+VNKAS+H+KN+DVGANIF+GNLDPEVDEKLLYDTFSAFGVILQ PK
Sbjct: 72  KILNMIKLYGKPIKVNKASAHEKNMDVGANIFVGNLDPEVDEKLLYDTFSAFGVILQVPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRD D+G SKGFAFIN+ASFE
Sbjct: 132 --------------------------------------IMRDVDSGTSKGFAFINFASFE 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFAD 273
           ASD +++AM+GQ+LCNR I+VSYAFK+DSKG+RHG+AAER+LAAQNPL   DRPHQ+F+D
Sbjct: 154 ASDTALEAMNGQFLCNRAITVSYAFKRDSKGERHGTAAERMLAAQNPLFPKDRPHQVFSD 213

Query: 274 AP--PPAPLPPPPPPINIM---------GLPPPPPSGLRAS 303
            P   PA  P   P ++           G  PPP  G+  S
Sbjct: 214 VPLGVPANTPLAMPGVHAAIAAHATGRPGYQPPPLMGMAQS 254

Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.

Caenorhabditis elegans (taxid: 6239)

>sp|O14102|SAP49_SCHPO Spliceosome-associated protein 49 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=sap49 PE=3 SV=2

 Score =  216 bits (550), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 101/221 (45%), Positives = 150/221 (67%), Gaps = 40/221 (18%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
           E  + DATIY+G LD+KV++++++EL +Q+GPVVN+H+P+DRV  +H G+GF EF+ E+D
Sbjct: 5   EDRNQDATIYLGNLDEKVTDSILFELCLQAGPVVNIHIPRDRVRNSHNGFGFCEFLHEQD 64

Query: 89  ADYAIKIMNMIKLYGKPIRVNKASSHQK-NLDVGANIFIGNLDPEVDEKLLYDTFSAFGV 147
            +YA +I+N +KL+GKPIRVN+AS  +  N  +GAN+F+GNLDP VDE++LYDTFSA G 
Sbjct: 65  VEYACQILNQVKLFGKPIRVNRASQDRGVNTLIGANLFVGNLDPLVDERVLYDTFSALGQ 124

Query: 148 ILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFI 207
           +++                                       P++ RD + G SKG+ F+
Sbjct: 125 LVKA--------------------------------------PQVARD-ENGRSKGYGFV 145

Query: 208 NYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHG 248
           +Y SFE +DA+I+AM+ Q+L N+PI+VSYAFK++ KG+RHG
Sbjct: 146 SYDSFETADAAIEAMNNQFLMNKPITVSYAFKREGKGERHG 186

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q55GD6|SF3B4_DICDI Splicing factor 3B subunit 4 OS=Dictyostelium discoideum GN=sf3b4 PE=3 SV=1

 Score =  192 bits (489), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 102/224 (45%), Positives = 146/224 (65%), Gaps = 42/224 (18%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           +A + +  LD  V+E+L+ ELF+Q+ PVV V +PKD++TQ H G  ++EF    DA+YA+
Sbjct: 12  EACLLIRDLDPMVTESLLMELFIQAAPVVKVFIPKDKLTQQHSGRAYVEFQSSSDAEYAL 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           K+M  ++L+ K I++ K +  +  +D+GAN+FIGNLD +VDE++L+DTFS FG I+ TPK
Sbjct: 72  KVMKFVRLFNKEIKIKKENKDK--VDIGANLFIGNLDADVDERILHDTFSRFGTIIFTPK 129

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 +MRD + G SKGFAFIN+ SFE
Sbjct: 130 --------------------------------------VMRD-ENGVSKGFAFINFDSFE 150

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAA 257
           ASDA+I+AM+ Q+LCN+PISV+YA KKDS  +RHGS+AER++AA
Sbjct: 151 ASDAAIEAMNSQFLCNKPISVTYARKKDS-NERHGSSAERIIAA 193

Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. Has been found in complex 'B' and 'C' as well.

Dictyostelium discoideum (taxid: 44689)

>sp|Q99181|HSH49_YEAST Protein HSH49 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=HSH49 PE=1 SV=1

 Score =  120 bits (300), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 121/239 (50%), Gaps = 53/239 (22%)

Query: 30  SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA 89
           S D   T+YVG +D ++++  ++ELF+Q  PV+ +  PKD+V Q +QGY FIEF  + DA
Sbjct: 4   SADSGNTVYVGNIDPRITKEQLYELFIQINPVLRIKYPKDKVLQAYQGYAFIEFYNQGDA 63

Query: 90  DYAIKIM-NMIKLYGKPIRVNKASSHQKNLDVGANI-----------FIGNLDPEVDEKL 137
            YAIKIM N ++LY + I+V + ++     ++ +NI           FI NL   +D   
Sbjct: 64  QYAIKIMNNTVRLYDRLIKVRQVTNSTGTTNLPSNISKDMILPIAKLFIKNLADSIDSDQ 123

Query: 138 LYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD 197
           L   F+ FG +++ P+I                             ++ N          
Sbjct: 124 LVKIFNKFGKLIREPEIF----------------------------YLSN---------- 145

Query: 198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGD-RHGSAAERLL 255
            G  K  A++ +  FE +D +I +++ Q + N  I+V YAFK++ KG+ ++G   +RLL
Sbjct: 146 -GKLKC-AYVYFEDFEKADLAIKSLNNQLVANNRITVDYAFKENGKGNAKYGDDVDRLL 202

Possible SF3b-like factor.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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

 Score =  116 bits (290), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 78/261 (29%), Positives = 127/261 (48%), Gaps = 57/261 (21%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           A++YVG L   V+E +++E F  +GPV+++ + +D +T+   GY ++ F    DA+ A+ 
Sbjct: 11  ASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70

Query: 95  IMNMIKLYGKPIRV--NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
            MN   + GKPIR+  ++     +   VG N+FI NLD  +D K LYDTFSAFG IL   
Sbjct: 71  TMNFDVIKGKPIRIMWSQRDPSLRKSGVG-NVFIKNLDKSIDNKALYDTFSAFGNILSCK 129

Query: 153 KI--------------------------MNMIKLYGKPIRVNK-ASSHQKNLDVGA---- 181
            +                          MN + L  + + V +  S  ++  ++GA    
Sbjct: 130 VVCDENGSKGYAFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKE 189

Query: 182 --NIFIGNLDPE--------------------IMRDPDTGNSKGFAFINYASFEASDASI 219
             N++I N   E                    +MRDP+ G SKGF F++Y   E ++ ++
Sbjct: 190 FTNVYIKNFGEEVDDESLKELFSQFGKTLSVKVMRDPN-GKSKGFGFVSYEKHEDANKAV 248

Query: 220 DAMHGQYLCNRPISVSYAFKK 240
           + M+G+ +  + I V  A KK
Sbjct: 249 EEMNGKEISGKIIFVGRAQKK 269

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

Homo sapiens (taxid: 9606)

>sp|A1CRM1|PABP_ASPCL Polyadenylate-binding protein, cytoplasmic and nuclear OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) GN=pab1 PE=3 SV=1

 Score =  113 bits (282), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 80/280 (28%), Positives = 131/280 (46%), Gaps = 58/280 (20%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           A++YVG LD  V+E +++ELF   G V ++ + +D VT+   GY ++ +    D + A++
Sbjct: 51  ASLYVGELDPSVTEAMLYELFSSIGQVASIRVCRDAVTRRSLGYAYVNYNNTADGERALE 110

Query: 95  IMNMIKLYGKPIRVNKASSHQKNLDVG-ANIFIGNLDPEVDEKLLYDTFSAFGVILQTP- 152
            +N   + GKP R+  +         G  N+FI NLD  +D K L+DTF+AFG IL    
Sbjct: 111 DLNYTLIKGKPCRIMWSQRDPALRKTGQGNVFIKNLDSAIDNKALHDTFAAFGNILSCKV 170

Query: 153 --------------------------KIMNMIKLYGKPI----RVNKASSHQKNLDVGA- 181
                                     K +N + L  K +     ++K     K  ++ A 
Sbjct: 171 AQDEFGNSKGYGFVHYETAEAANNAIKHVNGMLLNDKKVFVGHHISKKDRQSKFDEMKAN 230

Query: 182 --NIFIGNLDPEIM--------------------RDPDTGNSKGFAFINYASFEASDASI 219
             NI+I N+DP++                     RDP+ G S+GF F+NY++ E++ A++
Sbjct: 231 FTNIYIKNIDPDVTEEEFRKIFEQFGEITSATLSRDPE-GKSRGFGFVNYSTHESAQAAV 289

Query: 220 DAMHGQYLCNRPISVSYAFKKDSKGD--RHGSAAERLLAA 257
           D MH + +  + + V  A KK  + +  R    A RL  A
Sbjct: 290 DEMHDKEVKTQKLYVGRAQKKHEREEELRKQYEAARLEKA 329

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) (taxid: 344612)

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

 Score =  111 bits (278), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 76/260 (29%), Positives = 127/260 (48%), Gaps = 55/260 (21%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           A++YVG L   V+E +++E F  +GP++++ + +D +T+   GY ++ F    DA+ A+ 
Sbjct: 11  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70

Query: 95  IMNMIKLYGKPIRV--NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
            MN   + GKP+R+  ++     +   VG NIFI NLD  +D K LYDTFSAFG IL   
Sbjct: 71  TMNFDVIKGKPVRIMWSQRDPSLRKSGVG-NIFIKNLDKSIDNKALYDTFSAFGNILSCK 129

Query: 153 KI--------------------------MNMIKLYGKPIRVNK-ASSHQKNLDVGA---- 181
            +                          MN + L  + + V +  S  ++  ++GA    
Sbjct: 130 VVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKE 189

Query: 182 --NIFIGN----LDPEIMRD---------------PDTGNSKGFAFINYASFEASDASID 220
             N++I N    +D E ++D                ++G SKGF F+++   E +  ++D
Sbjct: 190 FTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVD 249

Query: 221 AMHGQYLCNRPISVSYAFKK 240
            M+G+ L  + I V  A KK
Sbjct: 250 EMNGKELNGKQIYVGRAQKK 269

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

Homo sapiens (taxid: 9606)

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
91079430	393	PREDICTED: similar to spliceosome associ	0.724	0.562	0.754	1e-107
347966116	408	AGAP001538-PA [Anopheles gambiae str. PE	0.675	0.504	0.778	1e-105
170057743	360	splicing factor 3B subunit 4 [Culex quin	0.665	0.563	0.784	1e-105
157137418	362	spliceosome associated protein [Aedes ae	0.665	0.560	0.784	1e-105
112983328	342	spliceosomal protein on the X [Bombyx mo	0.672	0.599	0.761	1e-104
312375219	413	hypothetical protein AND_14423 [Anophele	0.691	0.510	0.763	1e-104
307167809	409	Splicing factor 3B subunit 4 [Camponotus	0.655	0.488	0.785	1e-104
380011609	413	PREDICTED: splicing factor 3B subunit 4-	0.655	0.484	0.785	1e-104
357614441	334	spliceosomal protein on the X [Danaus pl	0.672	0.613	0.757	1e-104
350406084	413	PREDICTED: splicing factor 3B subunit 4-	0.655	0.484	0.785	1e-104

>gi|91079430|ref|XP_968120.1| PREDICTED: similar to spliceosome associated protein [Tribolium castaneum] gi|270004395|gb|EFA00843.1| hypothetical protein TcasGA2_TC003731 [Tribolium castaneum]

 Score =  392 bits (1008), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 200/265 (75%), Positives = 213/265 (80%), Gaps = 44/265 (16%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DATIYVGGLDDKV+E+L+WELFVQSGP+VNVHMPKDRVT  HQGYGF+EFMGEEDADYAI
Sbjct: 12  DATIYVGGLDDKVTESLLWELFVQSGPLVNVHMPKDRVTMMHQGYGFVEFMGEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KIMNMIKLYGKPIRVNKAS+HQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK
Sbjct: 72  KIMNMIKLYGKPIRVNKASAHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRDPDTGNSKGFAFIN+ASFE
Sbjct: 132 --------------------------------------IMRDPDTGNSKGFAFINFASFE 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFAD 273
           ASDASI+AM+GQYLCNRPISVSYAFKKDSKG+RHGSAAERLLAAQNPLSQADRPHQLFAD
Sbjct: 154 ASDASIEAMNGQYLCNRPISVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQLFAD 213

Query: 274 A------PPPAPLPPPPPPINIMGL 292
           A      PP   L PPPPP+ + G+
Sbjct: 214 APPMGMMPPGMTLAPPPPPVILAGM 238

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347966116|ref|XP_321584.5| AGAP001538-PA [Anopheles gambiae str. PEST] gi|333470203|gb|EAA00839.5| AGAP001538-PA [Anopheles gambiae str. PEST]

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 190/244 (77%), Positives = 202/244 (82%), Gaps = 38/244 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DATIYVGGLDDKV+ETL+WELFVQSGPVVNVHMPKDRVTQ HQGYGF+EF+GEEDADYAI
Sbjct: 12  DATIYVGGLDDKVTETLLWELFVQSGPVVNVHMPKDRVTQMHQGYGFVEFLGEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KIMNMIKLYGKPIRVNKAS+HQK+LDVGANIFIGNLD EVDEKLLYDTFSAFGVILQTPK
Sbjct: 72  KIMNMIKLYGKPIRVNKASAHQKSLDVGANIFIGNLDLEVDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRDP+TGNSKGFAFIN+ASFE
Sbjct: 132 --------------------------------------IMRDPETGNSKGFAFINFASFE 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFAD 273
           ASDA++DAM+GQYLCNRPISVSYAFKKDSKG+RHGSAAERLLAAQNPLS ADRPHQLFAD
Sbjct: 154 ASDAAMDAMNGQYLCNRPISVSYAFKKDSKGERHGSAAERLLAAQNPLSHADRPHQLFAD 213

Query: 274 APPP 277
           AP P
Sbjct: 214 APAP 217

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170057743|ref|XP_001864617.1| splicing factor 3B subunit 4 [Culex quinquefasciatus] gi|167877079|gb|EDS40462.1| splicing factor 3B subunit 4 [Culex quinquefasciatus]

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 189/241 (78%), Positives = 201/241 (83%), Gaps = 38/241 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DATIYVGGLDDKVSETL+WE+FVQ+GPVVNVHMPKDRVTQ HQGYGF+EF+GEEDADYAI
Sbjct: 12  DATIYVGGLDDKVSETLLWEMFVQAGPVVNVHMPKDRVTQMHQGYGFVEFLGEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KIMNMIKLYGKPIRVNKAS+HQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK
Sbjct: 72  KIMNMIKLYGKPIRVNKASAHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRDP+TGNSKGFAFIN+ASFE
Sbjct: 132 --------------------------------------IMRDPETGNSKGFAFINFASFE 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFAD 273
           ASDA++DAM+GQYLCNRPISVSYAFKKDSKG+RHGSAAERLLAAQNPLS ADRPHQLFAD
Sbjct: 154 ASDAAMDAMNGQYLCNRPISVSYAFKKDSKGERHGSAAERLLAAQNPLSHADRPHQLFAD 213

Query: 274 A 274
           A
Sbjct: 214 A 214

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157137418|ref|XP_001663981.1| spliceosome associated protein [Aedes aegypti] gi|108869713|gb|EAT33938.1| AAEL013795-PA [Aedes aegypti]

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 189/241 (78%), Positives = 201/241 (83%), Gaps = 38/241 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DATIYVGGLDDKVSETL+WE+FVQ+GPVVNVHMPKDRVTQ HQGYGF+EF+GEEDADYAI
Sbjct: 12  DATIYVGGLDDKVSETLLWEMFVQAGPVVNVHMPKDRVTQMHQGYGFVEFLGEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KIMNMIKLYGKPIRVNKAS+HQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK
Sbjct: 72  KIMNMIKLYGKPIRVNKASAHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRDP+TGNSKGFAFIN+ASFE
Sbjct: 132 --------------------------------------IMRDPETGNSKGFAFINFASFE 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFAD 273
           ASDA++DAM+GQYLCNRPISVSYAFKKDSKG+RHGSAAERLLAAQNPLS ADRPHQLFAD
Sbjct: 154 ASDAAMDAMNGQYLCNRPISVSYAFKKDSKGERHGSAAERLLAAQNPLSHADRPHQLFAD 213

Query: 274 A 274
           A
Sbjct: 214 A 214

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|112983328|ref|NP_001037646.1| spliceosomal protein on the X [Bombyx mori] gi|109706833|gb|ABG43003.1| spliceosomal protein on the X [Bombyx mori]

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 185/243 (76%), Positives = 201/243 (82%), Gaps = 38/243 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DATIYVGGLDD+V+E+L+WELFVQSGPVVNVHMPKDRVTQTHQGYGF+EFMGEEDADYAI
Sbjct: 12  DATIYVGGLDDRVTESLLWELFVQSGPVVNVHMPKDRVTQTHQGYGFVEFMGEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           K+MNMIKLYGKP+RVNKAS+HQKNLDVGAN+FIGNLDPEVDEKLLYDTFSAFGVILQTPK
Sbjct: 72  KVMNMIKLYGKPVRVNKASAHQKNLDVGANVFIGNLDPEVDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 +MRDP+TGNSK FAFIN+ASFE
Sbjct: 132 --------------------------------------VMRDPETGNSKAFAFINFASFE 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFAD 273
           ASDA+I+AM+ QYLCNRPISVSYAFKKD KG+RHGSAAERLLAAQNPLS ADRPHQLFAD
Sbjct: 154 ASDAAIEAMNNQYLCNRPISVSYAFKKDVKGERHGSAAERLLAAQNPLSHADRPHQLFAD 213

Query: 274 APP 276
           APP
Sbjct: 214 APP 216

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312375219|gb|EFR22634.1| hypothetical protein AND_14423 [Anopheles darlingi]

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 190/249 (76%), Positives = 203/249 (81%), Gaps = 38/249 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DATIYVGGLDDK +ETL+WELFVQSGPVVNVHMPKDRVTQ HQGYGF+EF+GEEDADYAI
Sbjct: 12  DATIYVGGLDDKATETLLWELFVQSGPVVNVHMPKDRVTQMHQGYGFVEFLGEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KIMNMIKLYGKPIRVNKAS+HQK+LDVGANIFIGNLD EVDEKLLYDTFSAFGVILQTPK
Sbjct: 72  KIMNMIKLYGKPIRVNKASAHQKSLDVGANIFIGNLDLEVDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRDP+TGNSKGFAFIN+ASFE
Sbjct: 132 --------------------------------------IMRDPETGNSKGFAFINFASFE 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFAD 273
           ASDA++DAM+GQYLCNRPISVSYAFKKDSKG+RHGSAAERLLAAQNPLS ADRPHQLFAD
Sbjct: 154 ASDAAMDAMNGQYLCNRPISVSYAFKKDSKGERHGSAAERLLAAQNPLSHADRPHQLFAD 213

Query: 274 APPPAPLPP 282
           AP P  + P
Sbjct: 214 APVPPSMHP 222

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307167809|gb|EFN61250.1| Splicing factor 3B subunit 4 [Camponotus floridanus]

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 187/238 (78%), Positives = 199/238 (83%), Gaps = 38/238 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DATIYVGGLDDKV+E+LMWELFVQSGPVVNVHMPKDRVTQ HQGYGF+EFMGEEDADYAI
Sbjct: 12  DATIYVGGLDDKVTESLMWELFVQSGPVVNVHMPKDRVTQMHQGYGFVEFMGEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KIMNMIKLYGKPIRVNKAS+HQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK
Sbjct: 72  KIMNMIKLYGKPIRVNKASAHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRDP+TGNSKGFAFIN+ASF+
Sbjct: 132 --------------------------------------IMRDPETGNSKGFAFINFASFD 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLF 271
           ASDASI+AM+GQYLCNRPISVSYAFK+D+KG+RHGSAAERLLAAQNPLSQADRPHQLF
Sbjct: 154 ASDASIEAMNGQYLCNRPISVSYAFKRDAKGERHGSAAERLLAAQNPLSQADRPHQLF 211

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380011609|ref|XP_003689892.1| PREDICTED: splicing factor 3B subunit 4-like [Apis florea]

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 187/238 (78%), Positives = 199/238 (83%), Gaps = 38/238 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DATIYVGGLDDKV+E+LMWELFVQSGPVVNVHMPKDRVTQ HQGYGF+EFMGEEDADYAI
Sbjct: 12  DATIYVGGLDDKVTESLMWELFVQSGPVVNVHMPKDRVTQMHQGYGFVEFMGEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KIMNMIKLYGKPIRVNKAS+HQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK
Sbjct: 72  KIMNMIKLYGKPIRVNKASAHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRDP+TGNSKGFAFIN+ASF+
Sbjct: 132 --------------------------------------IMRDPETGNSKGFAFINFASFD 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLF 271
           ASDASI+AM+GQYLCNRPISVSYAFK+D+KG+RHGSAAERLLAAQNPLSQADRPHQLF
Sbjct: 154 ASDASIEAMNGQYLCNRPISVSYAFKRDAKGERHGSAAERLLAAQNPLSQADRPHQLF 211

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357614441|gb|EHJ69078.1| spliceosomal protein on the X [Danaus plexippus]

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 184/243 (75%), Positives = 201/243 (82%), Gaps = 38/243 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DATIYVGGLDD+V+E+L+WELFVQ+GPVVNVHMPKDRVTQTHQGYGF+EFMGEEDADYAI
Sbjct: 12  DATIYVGGLDDRVTESLLWELFVQAGPVVNVHMPKDRVTQTHQGYGFVEFMGEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           K+MNMIKLYGKP+RVNKAS+HQKNLDVGAN+FIGNLDPEVDEKLLYDTFSAFGVILQTPK
Sbjct: 72  KVMNMIKLYGKPVRVNKASAHQKNLDVGANVFIGNLDPEVDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 +MRDP+TGNSK FAFIN+ASFE
Sbjct: 132 --------------------------------------VMRDPETGNSKAFAFINFASFE 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFAD 273
           ASDA+I+AM+ QYLCNRPISVSYAFKKD KG+RHGSAAERLLAAQNPLS ADRPHQLFAD
Sbjct: 154 ASDAAIEAMNNQYLCNRPISVSYAFKKDVKGERHGSAAERLLAAQNPLSHADRPHQLFAD 213

Query: 274 APP 276
           APP
Sbjct: 214 APP 216

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350406084|ref|XP_003487648.1| PREDICTED: splicing factor 3B subunit 4-like [Bombus impatiens]

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 187/238 (78%), Positives = 199/238 (83%), Gaps = 38/238 (15%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DATIYVGGLDDKV+E+LMWELFVQSGPVVNVHMPKDRVTQ HQGYGF+EFMGEEDADYAI
Sbjct: 12  DATIYVGGLDDKVTESLMWELFVQSGPVVNVHMPKDRVTQMHQGYGFVEFMGEEDADYAI 71

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           KIMNMIKLYGKPIRVNKAS+HQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK
Sbjct: 72  KIMNMIKLYGKPIRVNKASAHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 131

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 IMRDP+TGNSKGFAFIN+ASF+
Sbjct: 132 --------------------------------------IMRDPETGNSKGFAFINFASFD 153

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLF 271
           ASDASI+AM+GQYLCNRPISVSYAFK+D+KG+RHGSAAERLLAAQNPLSQADRPHQLF
Sbjct: 154 ASDASIEAMNGQYLCNRPISVSYAFKRDAKGERHGSAAERLLAAQNPLSQADRPHQLF 211

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	305
UNIPROTKB|H9L019	418	SF3B4 "Uncharacterized protein	0.4	0.291	0.877	3.7e-97
UNIPROTKB|F1MWR2	424	SF3B4 "Uncharacterized protein	0.4	0.287	0.877	3.7e-97
UNIPROTKB|E2R5T2	424	SF3B4 "Uncharacterized protein	0.4	0.287	0.877	3.7e-97
UNIPROTKB|Q15427	424	SF3B4 "Splicing factor 3B subu	0.4	0.287	0.877	3.7e-97
UNIPROTKB|F1SDG0	424	SF3B4 "Uncharacterized protein	0.4	0.287	0.877	3.7e-97
MGI|MGI:109580	424	Sf3b4 "splicing factor 3b, sub	0.4	0.287	0.877	3.7e-97
RGD|1309667	424	Sf3b4 "splicing factor 3b, sub	0.4	0.287	0.877	3.7e-97
ZFIN|ZDB-GENE-020419-22	400	sf3b4 "splicing factor 3b, sub	0.4	0.305	0.868	1.3e-96
FB|FBgn0015818	366	Spx "Spliceosomal protein on t	0.308	0.256	0.925	1.4e-94
WB|WBGene00004723	388	sap-49 [Caenorhabditis elegans	0.4	0.314	0.844	3.9e-89

UNIPROTKB|H9L019 SF3B4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 580 (209.2 bits), Expect = 3.7e-97, Sum P(2) = 3.7e-97
 Identities = 107/122 (87%), Positives = 116/122 (95%)

Query:    34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
             DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct:    12 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 71

Query:    94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
             KIMNMIKLYGKPIRVNKAS+H KNLDVGANIFIGNLDPE+DEKLLYDTFSAFGVILQTPK
Sbjct:    72 KIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPK 131

Query:   154 IM 155
             IM
Sbjct:   132 IM 133

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

UNIPROTKB|F1MWR2 SF3B4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 580 (209.2 bits), Expect = 3.7e-97, Sum P(2) = 3.7e-97
 Identities = 107/122 (87%), Positives = 116/122 (95%)

Query:    34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
             DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct:    12 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 71

Query:    94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
             KIMNMIKLYGKPIRVNKAS+H KNLDVGANIFIGNLDPE+DEKLLYDTFSAFGVILQTPK
Sbjct:    72 KIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPK 131

Query:   154 IM 155
             IM
Sbjct:   132 IM 133

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2R5T2 SF3B4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 580 (209.2 bits), Expect = 3.7e-97, Sum P(2) = 3.7e-97
 Identities = 107/122 (87%), Positives = 116/122 (95%)

Query:    34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
             DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct:    12 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 71

Query:    94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
             KIMNMIKLYGKPIRVNKAS+H KNLDVGANIFIGNLDPE+DEKLLYDTFSAFGVILQTPK
Sbjct:    72 KIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPK 131

Query:   154 IM 155
             IM
Sbjct:   132 IM 133

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q15427 SF3B4 "Splicing factor 3B subunit 4" [Homo sapiens (taxid:9606)]

 Score = 580 (209.2 bits), Expect = 3.7e-97, Sum P(2) = 3.7e-97
 Identities = 107/122 (87%), Positives = 116/122 (95%)

Query:    34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
             DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct:    12 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 71

Query:    94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
             KIMNMIKLYGKPIRVNKAS+H KNLDVGANIFIGNLDPE+DEKLLYDTFSAFGVILQTPK
Sbjct:    72 KIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPK 131

Query:   154 IM 155
             IM
Sbjct:   132 IM 133

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IDA

GO:0006397 "mRNA processing" evidence=TAS

GO:0000375 "RNA splicing, via transesterification reactions" evidence=TAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;TAS

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F1SDG0 SF3B4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 580 (209.2 bits), Expect = 3.7e-97, Sum P(2) = 3.7e-97
 Identities = 107/122 (87%), Positives = 116/122 (95%)

Query:    34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
             DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct:    12 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 71

Query:    94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
             KIMNMIKLYGKPIRVNKAS+H KNLDVGANIFIGNLDPE+DEKLLYDTFSAFGVILQTPK
Sbjct:    72 KIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPK 131

Query:   154 IM 155
             IM
Sbjct:   132 IM 133

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:109580 Sf3b4 "splicing factor 3b, subunit 4" [Mus musculus (taxid:10090)]

 Score = 580 (209.2 bits), Expect = 3.7e-97, Sum P(2) = 3.7e-97
 Identities = 107/122 (87%), Positives = 116/122 (95%)

Query:    34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
             DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct:    12 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 71

Query:    94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
             KIMNMIKLYGKPIRVNKAS+H KNLDVGANIFIGNLDPE+DEKLLYDTFSAFGVILQTPK
Sbjct:    72 KIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPK 131

Query:   154 IM 155
             IM
Sbjct:   132 IM 133

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0005689 "U12-type spliceosomal complex" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

RGD|1309667 Sf3b4 "splicing factor 3b, subunit 4" [Rattus norvegicus (taxid:10116)]

 Score = 580 (209.2 bits), Expect = 3.7e-97, Sum P(2) = 3.7e-97
 Identities = 107/122 (87%), Positives = 116/122 (95%)

Query:    34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
             DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct:    12 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 71

Query:    94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
             KIMNMIKLYGKPIRVNKAS+H KNLDVGANIFIGNLDPE+DEKLLYDTFSAFGVILQTPK
Sbjct:    72 KIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPK 131

Query:   154 IM 155
             IM
Sbjct:   132 IM 133

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0005689 "U12-type spliceosomal complex" evidence=IEA;ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

ZFIN|ZDB-GENE-020419-22 sf3b4 "splicing factor 3b, subunit 4" [Danio rerio (taxid:7955)]

 Score = 575 (207.5 bits), Expect = 1.3e-96, Sum P(2) = 1.3e-96
 Identities = 106/122 (86%), Positives = 115/122 (94%)

Query:    34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
             DA +YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct:    12 DAAVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 71

Query:    94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
             KIMNMIKLYGKPIRVNKAS+H KNLDVGANIFIGNLDPE+DEKLLYDTFSAFGVILQTPK
Sbjct:    72 KIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPK 131

Query:   154 IM 155
             IM
Sbjct:   132 IM 133

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

FB|FBgn0015818 Spx "Spliceosomal protein on the X" [Drosophila melanogaster (taxid:7227)]

 Score = 458 (166.3 bits), Expect = 1.4e-94, Sum P(3) = 1.4e-94
 Identities = 87/94 (92%), Positives = 90/94 (95%)

Query:    62 VNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVG 121
             VNVHMPKDRVTQ HQGYGF+EF+ EEDADY IKIMNMIKLYGKPIRVNKAS+HQKNLDVG
Sbjct:    59 VNVHMPKDRVTQMHQGYGFVEFLSEEDADYGIKIMNMIKLYGKPIRVNKASAHQKNLDVG 118

Query:   122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIM 155
             ANIFIGNLD EVDEKLLYDTFSAFGVILQTPKIM
Sbjct:   119 ANIFIGNLDVEVDEKLLYDTFSAFGVILQTPKIM 152

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;ISS

GO:0005681 "spliceosomal complex" evidence=ISS;NAS

GO:0003729 "mRNA binding" evidence=ISS

GO:0005686 "U2 snRNP" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0022008 "neurogenesis" evidence=IMP

WB|WBGene00004723 sap-49 [Caenorhabditis elegans (taxid:6239)]

 Score = 566 (204.3 bits), Expect = 3.9e-89, Sum P(2) = 3.9e-89
 Identities = 103/122 (84%), Positives = 118/122 (96%)

Query:    34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
             DATIYVGGLD+KVSE+++WEL VQ+GPVV+V+MPKDRVT  HQG+GF+EFMGEEDADYAI
Sbjct:    12 DATIYVGGLDEKVSESILWELMVQAGPVVSVNMPKDRVTANHQGFGFVEFMGEEDADYAI 71

Query:    94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
             KI+NMIKLYGKPI+VNKAS+H+KN+DVGANIF+GNLDPEVDEKLLYDTFSAFGVILQ PK
Sbjct:    72 KILNMIKLYGKPIKVNKASAHEKNMDVGANIFVGNLDPEVDEKLLYDTFSAFGVILQVPK 131

Query:   154 IM 155
             IM
Sbjct:   132 IM 133

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0040022 "feminization of hermaphroditic germ-line" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

---

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)
Q6AYL5	SF3B4_RAT	No assigned EC number	0.7436	0.6557	0.4716	yes	N/A
Q99181	HSH49_YEAST	No assigned EC number	0.3054	0.6098	0.8732	yes	N/A
Q8QZY9	SF3B4_MOUSE	No assigned EC number	0.7436	0.6557	0.4716	yes	N/A
Q15427	SF3B4_HUMAN	No assigned EC number	0.7436	0.6557	0.4716	yes	N/A
Q09442	SF3B4_CAEEL	No assigned EC number	0.6156	0.7606	0.5979	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	305
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	8e-54
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-52
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-32
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	4e-24
smart00360	73	smart00360, RRM, RNA recognition motif	2e-23
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-20
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-20
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-18
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-18
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-17
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-17
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	6e-17
smart00360	73	smart00360, RRM, RNA recognition motif	3e-16
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-16
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-14
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	5e-14
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-14
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-13
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-13
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-13
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	4e-13
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	8e-13
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-12
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-12
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-11
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-11
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-11
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-11
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-11
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-11
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-11
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-11
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-11
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	8e-11
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-10
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-10
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-10
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-10
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-10
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	5e-10
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	7e-10
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	9e-10
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-09
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-09
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-09
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-09
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-09
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-09
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-09
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-09
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-09
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	4e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-09
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	7e-09
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	8e-09
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	9e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	9e-09
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-08
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	1e-08
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-08
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-08
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	1e-08
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-08
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-08
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	3e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-08
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-08
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	4e-08
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	4e-08
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	4e-08
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-08
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-08
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-08
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	6e-08
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	6e-08
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-08
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	8e-08
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	9e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	9e-08
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-07
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	1e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-07
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	1e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-07
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-07
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	2e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-07
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-07
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	2e-07
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-07
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-07
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-07
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-07
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	4e-07
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	5e-07
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-07
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	8e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	9e-07
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	9e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-06
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-06
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-06
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	1e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-06
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	1e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-06
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-06
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	2e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-06
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	2e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-06
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	5e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	5e-06
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	5e-06
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	5e-06
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	5e-06
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	6e-06
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	6e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	7e-06
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	7e-06
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	8e-06
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	9e-06
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	9e-06
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	9e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-05
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	2e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	2e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	2e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	3e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	3e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	3e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-05
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	3e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	4e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-05
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	4e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	5e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	5e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	5e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	5e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	5e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-05
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	6e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	7e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	7e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	7e-05
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	8e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	9e-05
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	9e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-04
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	1e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	1e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-04
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	1e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	1e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-04
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	2e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	2e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	2e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	3e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	3e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	3e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	3e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	3e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	3e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	4e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	4e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	4e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	4e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	6e-04
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	6e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	6e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	7e-04
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	7e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	7e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	7e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	8e-04
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	8e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	0.001
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.001
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	0.001
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.001
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	0.001
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.001
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.001
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.001
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	0.001
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	0.001
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.001
cd12274	71	cd12274, RRM2_NEFsp, RNA recognition motif 2 in ve	0.001
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	0.001
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.002
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.002
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.002
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	0.002
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.002
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.002
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	0.002
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.002
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	0.002
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.003
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.003
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	0.003
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	0.003
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	0.003
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	0.003
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.003
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	0.003
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	0.003
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	0.004
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.004
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	0.004
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	0.004
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	0.004
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.004
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	0.004

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

 Score =  169 bits (431), Expect = 8e-54
 Identities = 61/74 (82%), Positives = 70/74 (94%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVG LD+KV+E L+WELF+Q+GPVVNVH+PKDRVTQ HQGYGF+EF+ EEDADYAIKIM
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 97  NMIKLYGKPIRVNK 110
           NMIKLYGKPIRVNK
Sbjct: 61  NMIKLYGKPIRVNK 74

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

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

 Score =  166 bits (422), Expect = 2e-52
 Identities = 76/121 (62%), Positives = 82/121 (67%), Gaps = 38/121 (31%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           GAN+FIGNLDPEVDEKLLYDTFSAFGVILQTPKIM                         
Sbjct: 1   GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIM------------------------- 35

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                        RDPDTGNSKGFAFI+Y SFEASDA+I+AM+GQYLCNRPI+VSYAFKK
Sbjct: 36  -------------RDPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITVSYAFKK 82

Query: 241 D 241
           D
Sbjct: 83  D 83

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

 Score =  126 bits (317), Expect = 1e-32
 Identities = 78/244 (31%), Positives = 121/244 (49%), Gaps = 57/244 (23%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           A++YVG LD  V+E  +++LF   GPV++V + +D VT+   GYG++ F    DA+ A++
Sbjct: 1   ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALE 60

Query: 95  IMNMIKLYGKPIRV---NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQT 151
            MN  +L GKPIR+    +  S +++  VG NIF+ NLD  VD K L+DTFS FG IL  
Sbjct: 61  TMNFKRLGGKPIRIMWSQRDPSLRRS-GVG-NIFVKNLDKSVDNKALFDTFSKFGNILSC 118

Query: 152 PKIMN---MIKLYG-----------KPI-RVNKASSHQKNLDVG---------------- 180
               +     + YG             I +VN    + K + VG                
Sbjct: 119 KVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKF 178

Query: 181 ANIFIGNLDPEI--------------------MRDPDTGNSKGFAFINYASFEASDASID 220
            N+++ NLDP +                    M+D  +G S+GFAF+N+   E +  +++
Sbjct: 179 TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVE 237

Query: 221 AMHG 224
            M+G
Sbjct: 238 EMNG 241

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

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

 Score = 92.8 bits (231), Expect = 4e-24
 Identities = 29/75 (38%), Positives = 52/75 (69%), Gaps = 1/75 (1%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           D T++VG LD +V+E +++ELF+Q+GP+  V +PKD   +  + + F+ F  E    YAI
Sbjct: 1   DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKP-KSFAFVTFKHEVSVPYAI 59

Query: 94  KIMNMIKLYGKPIRV 108
           +++N I+L+G+ +R+
Sbjct: 60  QLLNGIRLFGRELRI 74

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

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

 Score = 90.7 bits (226), Expect = 2e-23
 Identities = 27/73 (36%), Positives = 47/73 (64%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++VG L    +E  + ELF + G V +V + +D+ T   +G+ F+EF  EEDA+ A++ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 96  MNMIKLYGKPIRV 108
           +N  +L G+P++V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 83.8 bits (208), Expect = 1e-20
 Identities = 31/73 (42%), Positives = 47/73 (64%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVGGL ++V E ++   F+  G + ++ +P D  TQ H+G+ F+EF   EDA  AI  M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 97  NMIKLYGKPIRVN 109
           N  +L+G+ IRVN
Sbjct: 61  NESELFGRTIRVN 73

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

 Score = 89.5 bits (222), Expect = 7e-20
 Identities = 63/305 (20%), Positives = 110/305 (36%), Gaps = 83/305 (27%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YV  LD  V+E  + ELF + G + +  + KD   ++ +G+ F+ F   EDA  A++ M
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRS-RGFAFVNFEKHEDAAKAVEEM 239

Query: 97  NMIKL----YGKPIRVNKASS-----------------HQKNLDVGANIFIGNLDPEVDE 135
           N  K+     GK + V +A                    +K    G N+++ NLD  V +
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTD 299

Query: 136 KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD 195
           + L + FS  G I                                          ++M D
Sbjct: 300 EKLRELFSECGEITSA---------------------------------------KVMLD 320

Query: 196 PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDR--------- 246
              G S+GF F+ +++ E ++ ++  MHG+ L  +P+ V+ A +K+ +            
Sbjct: 321 E-KGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQ 379

Query: 247 ------------HGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPP 294
                        G+  +     Q P  Q +     +           P  P+   GL P
Sbjct: 380 PRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAP 439

Query: 295 PPPSG 299
                
Sbjct: 440 MNAVR 444

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

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

 Score = 84.6 bits (209), Expect = 2e-18
 Identities = 59/218 (27%), Positives = 90/218 (41%), Gaps = 53/218 (24%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           D T++V  L  K  E  ++E F + G V +V   KDR ++  +G  ++EF   E    A+
Sbjct: 89  DRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL 148

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGA------------NIFIGNLDPEVDEKLLYDT 141
            +     L G+PI V ++S  +KN    A             +++GNL   + E+ L   
Sbjct: 149 ALTGQ-MLLGRPIIV-QSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQI 206

Query: 142 FSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS 201
           F  FG I                                        D ++ RDP+TG S
Sbjct: 207 FEPFGDI---------------------------------------EDVQLHRDPETGRS 227

Query: 202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
           KGF FI +   E +  +++ M+G  L  RPI V YA  
Sbjct: 228 KGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD 265

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

 Score = 81.9 bits (201), Expect = 6e-18
 Identities = 45/143 (31%), Positives = 72/143 (50%), Gaps = 23/143 (16%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
           +S + + T++VG L   V+E  + ELF + GPV  V + +DR T   +G+ F+EF  EE 
Sbjct: 110 KSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEES 169

Query: 89  ADYAIKIMNMIKLYGKPIRVNKASSHQK-----------------------NLDVGANIF 125
           A+ AI+ +N  +L G+P+RV KA    +                        L+   N++
Sbjct: 170 AEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLY 229

Query: 126 IGNLDPEVDEKLLYDTFSAFGVI 148
           +GNL  +  E+ L D F + G I
Sbjct: 230 VGNLPLKTAEEELADLFKSRGDI 252

Length = 306

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 74.9 bits (184), Expect = 2e-17
 Identities = 34/75 (45%), Positives = 53/75 (70%), Gaps = 1/75 (1%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           D T++VG LD KV+E L++ELF+Q+GPV+ V +PKD+  +  Q + F+ F  E    YA+
Sbjct: 1   DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQ-FAFVNFKHEVSVPYAM 59

Query: 94  KIMNMIKLYGKPIRV 108
            ++N IKLYG+P+ +
Sbjct: 60  NLLNGIKLYGRPLNI 74

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 74.3 bits (183), Expect = 3e-17
 Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L    +E  + ELF + G + +V + +D+     +G+ F+EF   EDA+ A++ +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 97  NMIKLYGKPIRVN 109
           N  +L G+ ++V+
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 73.8 bits (181), Expect = 6e-17
 Identities = 31/76 (40%), Positives = 53/76 (69%), Gaps = 1/76 (1%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           D T++VG L+ +V E +++ELF+Q+GP+  V + KD+  +  + +GF+ F   E   YAI
Sbjct: 1   DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKP-KSFGFVCFKHSESVPYAI 59

Query: 94  KIMNMIKLYGKPIRVN 109
            ++N I+LYG+PI+V+
Sbjct: 60  ALLNGIRLYGRPIKVH 75

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

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

 Score = 71.5 bits (176), Expect = 3e-16
 Identities = 29/112 (25%), Positives = 49/112 (43%), Gaps = 39/112 (34%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            +F+GNL P+  E+ L + FS FG +                                  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESV------------------------------- 29

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
                    ++RD +TG SKGFAF+ + S E ++ +++A++G+ L  RP+ V
Sbjct: 30  --------RLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 71.8 bits (177), Expect = 4e-16
 Identities = 25/71 (35%), Positives = 45/71 (63%)

Query: 38  YVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN 97
           YVG L   V+E +++E+F  +GPV+++ + +D +T+   GY ++ F    DA+ A+  +N
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 98  MIKLYGKPIRV 108
              + GKPIR+
Sbjct: 63  FDVIKGKPIRI 73

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

 Score = 72.2 bits (177), Expect = 3e-14
 Identities = 61/267 (22%), Positives = 104/267 (38%), Gaps = 60/267 (22%)

Query: 28  GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
                    +YVG L   ++E  + ++F   G + +V + +D  T   +G+GFI+F   E
Sbjct: 180 PGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAE 239

Query: 88  DADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPE-------------VD 134
           +A  A+++MN  +L G+PI+V  A      LD  AN F      +             + 
Sbjct: 240 EAKEALEVMNGFELAGRPIKVGYAQDSTYLLD-AANTFEDIDKQQQMGKNLNTEEREQLM 298

Query: 135 EKLLYDTFSAFGVI------------LQTPKIM------------NMIKLYGKPIRVNKA 170
           EKL  D      +I            LQ   I+              I      +     
Sbjct: 299 EKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNN 358

Query: 171 SSHQKNLDVGANIF---IG---NLDPEIMRD---------------PDTGNSKGFAFINY 209
           +     L V +N+F        N D EI+ D                DT NS G  ++ +
Sbjct: 359 NLATTCL-VLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKF 417

Query: 210 ASFEASDASIDAMHGQYLCNRPISVSY 236
           +S +A+ A+  A++G+Y   + I+ ++
Sbjct: 418 SSVDAALAAFQALNGRYFGGKMITAAF 444

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

 Score = 65.7 bits (161), Expect = 5e-14
 Identities = 34/116 (29%), Positives = 51/116 (43%), Gaps = 41/116 (35%)

Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
            VG NIFI NLD  +D K LYDTFSAFG IL                             
Sbjct: 1   GVG-NIFIKNLDKSIDNKALYDTFSAFGNILSC--------------------------- 32

Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
                       ++  D + G SKG+ F+++ + EA+  +I+ ++G  L ++ + V
Sbjct: 33  ------------KVATD-ENGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFV 75

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|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 = 65.7 bits (161), Expect = 6e-14
 Identities = 29/76 (38%), Positives = 44/76 (57%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            ++V GL  + +E  +  LF + G V  V + KD  T   +G+GF+ F   EDAD AI+ 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 96  MNMIKLYGKPIRVNKA 111
           +N  +L G+ I+V KA
Sbjct: 63  LNGKELEGRVIKVEKA 78

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|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 = 65.7 bits (161), Expect = 6e-14
 Identities = 32/119 (26%), Positives = 47/119 (39%), Gaps = 39/119 (32%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           G  +F+  L     EK L   FS FG                   RV +           
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFG-------------------RVEEV---------- 31

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
                      +M+DP+TG S+GF F+ + S E +DA+I  ++G+ L  R I V  A +
Sbjct: 32  ----------LLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKAKR 80

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

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

 Score = 65.3 bits (160), Expect = 6e-14
 Identities = 23/71 (32%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L    +E  + +LF + GP+ ++ + +D  T   +G+ F+EF  EEDA+ A++ +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 97  NMIKLYGKPIR 107
           N  +L G+ +R
Sbjct: 60  NGKELGGRELR 70

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

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

 Score = 64.2 bits (157), Expect = 2e-13
 Identities = 30/109 (27%), Positives = 47/109 (43%), Gaps = 40/109 (36%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+GNL P+  E+ L D FS FG I                                 +I
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIE--------------------------------SI 28

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPI 232
                   I+RD  TG SKGFAF+ +   E ++ +++A++G+ L  R +
Sbjct: 29  -------RIVRDE-TGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69

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

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

 Score = 64.2 bits (157), Expect = 2e-13
 Identities = 27/76 (35%), Positives = 43/76 (56%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +YVG L   V+E  + +LF Q G V +  +  DR T   +G+GF+E    E+A+ AI+ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 96  MNMIKLYGKPIRVNKA 111
           +N     G+ + VN+A
Sbjct: 61  LNGTDFGGRTLTVNEA 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|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 = 63.4 bits (155), Expect = 3e-13
 Identities = 27/75 (36%), Positives = 43/75 (57%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG +    +E  + E+F + GPVV+  +  DR T   +GYGF EF   E A  AI+ +
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 97  NMIKLYGKPIRVNKA 111
           N  +  G+ +RV+ A
Sbjct: 61  NGYEFNGRALRVDFA 75

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

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

 Score = 63.8 bits (156), Expect = 4e-13
 Identities = 32/117 (27%), Positives = 50/117 (42%), Gaps = 39/117 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+  +  E  E+ ++D F+ FG I                          KNL +    
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEI--------------------------KNLHL---- 38

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
              NLD        TG  KG+A I Y + + + A+I+ ++G+ L  + ISV +AF K
Sbjct: 39  ---NLDRR------TGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTISVDWAFVK 86

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

 Score = 62.7 bits (153), Expect = 8e-13
 Identities = 27/75 (36%), Positives = 40/75 (53%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           IYV  +   +SE  +  +F   G + +  +  D  T  H+GYGFIE+   + A  AI  M
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 97  NMIKLYGKPIRVNKA 111
           N+  L G+ +RV KA
Sbjct: 63  NLFDLGGQQLRVGKA 77

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

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

 Score = 62.2 bits (152), Expect = 1e-12
 Identities = 28/74 (37%), Positives = 44/74 (59%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVG L    +E  ++ELF + G +  + M  DR T+T  G+ F+E+   EDA+ A+K +
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 97  NMIKLYGKPIRVNK 110
           N  KL  + IRV+ 
Sbjct: 61  NGTKLDDRIIRVDW 74

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

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

 Score = 61.2 bits (149), Expect = 2e-12
 Identities = 28/110 (25%), Positives = 47/110 (42%), Gaps = 39/110 (35%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           +IF+G+L PE+D + L   F+ FG I                                  
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEIS--------------------------------- 27

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPI 232
                 D  +++D  TG SKG+ F+++   E ++ +I +M+GQ+L  R I
Sbjct: 28  ------DARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAI 71

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

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

 Score = 61.2 bits (149), Expect = 2e-12
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVG LD  V+E L+ ELF Q GP+ +  + ++     +  Y F+E+     A  A++ M
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE---HGNDPYAFVEYYDHRSAAAALQTM 57

Query: 97  NMIKLYGKPIRVNKA 111
           N   + G+ I+VN A
Sbjct: 58  NGRLILGQEIKVNWA 72

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

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

 Score = 59.2 bits (144), Expect = 1e-11
 Identities = 31/112 (27%), Positives = 48/112 (42%), Gaps = 40/112 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+GNL P+  E+ L + FS FG I                                   
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESV-------------------------------- 28

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS 235
                   I+RD D G SKGFAF+ + S E ++ +++A++G+ L  R + VS
Sbjct: 29  -------RIVRDKD-GKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72

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

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

 Score = 59.5 bits (145), Expect = 1e-11
 Identities = 26/118 (22%), Positives = 52/118 (44%), Gaps = 40/118 (33%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           N+++ NL  ++D++ L + F  +G                      K +S +        
Sbjct: 3   NVYVKNLGEDMDDEKLKELFGKYG----------------------KITSAK-------- 32

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                    +M+D D G SKGF F+N+ + EA+  +++ ++G+ +  + + V  A KK
Sbjct: 33  ---------VMKD-DEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKKLYVGRAQKK 80

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

>gnl|CDD|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 = 59.5 bits (144), Expect = 1e-11
 Identities = 26/77 (33%), Positives = 45/77 (58%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
             +++GGL    +E  + ++F + G +  V + KDR TQ  +G+GF+ F   +DA  A+ 
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 95  IMNMIKLYGKPIRVNKA 111
            MN   + G+ IRV++A
Sbjct: 61  AMNGKSVDGRQIRVDQA 77

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

 Score = 64.7 bits (157), Expect = 1e-11
 Identities = 46/206 (22%), Positives = 84/206 (40%), Gaps = 54/206 (26%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVG +  ++ E  +   F   GP+ +++M  D  T  H+G+ F+E+   E A  A++ M
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 97  NMIKLYGKPIRVNKASSH----------QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFG 146
           N   L G+ I+V + S+           Q+       I++ ++ P++ E  +   F AFG
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFG 229

Query: 147 VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAF 206
            I++                                        ++ R P     KG+ F
Sbjct: 230 EIVKC---------------------------------------QLARAPTGRGHKGYGF 250

Query: 207 INYASFEASDASIDAMH-----GQYL 227
           I Y + ++   +I +M+     GQYL
Sbjct: 251 IEYNNLQSQSEAIASMNLFDLGGQYL 276

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

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

 Score = 59.1 bits (144), Expect = 1e-11
 Identities = 25/72 (34%), Positives = 42/72 (58%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L   V++  + E+F   G V +V +P DR     +GY ++EF   EDA+ AIK M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 97  NMIKLYGKPIRV 108
           +  ++ G+ + V
Sbjct: 61  DGGQIDGQEVTV 72

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

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

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 24/74 (32%), Positives = 45/74 (60%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           A IY+GGL  +++E  +  +F Q G +V++++ +D+ T   +G+ F+ +  +     A+ 
Sbjct: 10  AYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVD 69

Query: 95  IMNMIKLYGKPIRV 108
            +N IKL G+ IRV
Sbjct: 70  NLNGIKLLGRTIRV 83

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

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

 Score = 58.3 bits (142), Expect = 2e-11
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           +++VG L   + E  + + F   G V  V + +DR T   +G+G++ F  ++    A+K 
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK- 59

Query: 96  MNMIKLYGKPIRV 108
           +N IKL G+ IRV
Sbjct: 60  LNGIKLKGRKIRV 72

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

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

 Score = 58.0 bits (141), Expect = 3e-11
 Identities = 28/74 (37%), Positives = 37/74 (50%), Gaps = 28/74 (37%)

Query: 124 IFIGNLDPEVDEKLLYDTF--------------------SAFG-VILQTP-------KIM 155
           +++GNLD +V E+LL++ F                      +G V   +        KIM
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 156 NMIKLYGKPIRVNK 169
           NMIKLYGKPIRVNK
Sbjct: 61  NMIKLYGKPIRVNK 74

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

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

 Score = 58.0 bits (141), Expect = 3e-11
 Identities = 26/73 (35%), Positives = 42/73 (57%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVG L   ++E  +  +F   G +  V + +D  T   +GYGFI+F   EDA  A++ +
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 97  NMIKLYGKPIRVN 109
           N  +L G+PI+V 
Sbjct: 61  NGFELAGRPIKVG 73

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

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

 Score = 62.7 bits (152), Expect = 3e-11
 Identities = 52/225 (23%), Positives = 87/225 (38%), Gaps = 43/225 (19%)

Query: 54  LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
           LF   G + +  + +D+VT    GYGF+ ++  EDA+ A+  +N ++L  K I+V+ A  
Sbjct: 23  LFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP 82

Query: 114 HQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSH 173
              ++  GAN+++  L   + +  L   FS FG I+ +                      
Sbjct: 83  SSDSIK-GANLYVSGLPKTMTQHELESIFSPFGQIITS---------------------- 119

Query: 174 QKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL--CNRP 231
                             I+ D  TG SKG  FI +   + +D +I  ++G     C  P
Sbjct: 120 -----------------RILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEP 162

Query: 232 ISVSYAFKKDSKGDRH-GSAAERLLAAQNPLSQADRPHQLFADAP 275
           I+V +A    S   +   S  E +   Q                P
Sbjct: 163 ITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGP 207

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

 Score = 57.5 bits (140), Expect = 4e-11
 Identities = 23/62 (37%), Positives = 35/62 (56%)

Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
          TI V  L +   E  + ELF   GP+  V++ KD+ T   +G+ F+ F   EDA+ AI+ 
Sbjct: 1  TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 96 MN 97
          +N
Sbjct: 61 LN 62

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

 Score = 61.5 bits (148), Expect = 7e-11
 Identities = 35/178 (19%), Positives = 67/178 (37%), Gaps = 44/178 (24%)

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           +                  S QK+ +    +F+GNL  +V E+ L + F  FG + +   
Sbjct: 88  RGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVR- 146

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                                 ++RD +TG S+GFAF+ + S E
Sbjct: 147 --------------------------------------LVRDRETGKSRGFAFVEFESEE 168

Query: 214 ASDASIDAMHGQYLCNRPISVSYAF-----KKDSKGDRHGSAAERLLAAQNPLSQADR 266
           +++ +I+ ++G+ L  RP+ V  A      + +   +   S A++L   +  L +   
Sbjct: 169 SAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSD 226

Length = 306

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

 Score = 57.0 bits (138), Expect = 8e-11
 Identities = 26/73 (35%), Positives = 40/73 (54%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VG L  ++    +   F   G + +  + KD  T   +GYGF+ F+ +EDA+ AI+ M
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 97  NMIKLYGKPIRVN 109
           N   L G+ IR N
Sbjct: 62  NGQWLGGRAIRTN 74

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

 Score = 61.2 bits (148), Expect = 1e-10
 Identities = 61/279 (21%), Positives = 105/279 (37%), Gaps = 50/279 (17%)

Query: 12  STPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRV 71
           ST  L SL     +    +  G   I V  L   +++  ++ LF   GP+    + +D  
Sbjct: 86  STNSLNSLGSGGSDDNDTNNSGTNLI-VNYLPQDMTDRELYALFRTIGPINTCRIMRDYK 144

Query: 72  TQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDP 131
           T    GY F++F  E D+  AIK +N I +  K ++V+ A    +++    N+++ NL  
Sbjct: 145 TGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESIK-DTNLYVTNLPR 203

Query: 132 EVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPE 191
            + +  L   F  +G I+                        QKN               
Sbjct: 204 TITDDQLDTIFGKYGQIV------------------------QKN--------------- 224

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL--CNRPISVSYAFKKDSKGDRHGS 249
           I+RD  TG  +G AF+ +   E +  +I A++       ++P++V  A       + HG 
Sbjct: 225 ILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLA-------EEHGK 277

Query: 250 AAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPIN 288
           A      +Q                   + + PP PP  
Sbjct: 278 AKAHHYMSQMGHGNMGNMGHGNMGMAGGSGMNPPNPPAF 316

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

 Score = 56.2 bits (136), Expect = 1e-10
 Identities = 26/76 (34%), Positives = 43/76 (56%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++VG L   V +  +   F + G VV   +  DR T   +G+G+++F   EDA  AI+ 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 96  MNMIKLYGKPIRVNKA 111
           M+  +L G+PI V+ +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 29/112 (25%), Positives = 43/112 (38%), Gaps = 39/112 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++G L  EVDEK+L+  F  FG I                                   
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDI----------------------------------- 25

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS 235
                D +I  D +T   +GFAF+ +   E + A+ID M+   L  R I V+
Sbjct: 26  ----KDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGRTIRVN 73

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

 Score = 56.0 bits (135), Expect = 2e-10
 Identities = 28/114 (24%), Positives = 50/114 (43%), Gaps = 39/114 (34%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           NIF+G+L PEV +  L+  FSAF                                     
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFP------------------------------------ 24

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
                 D  +M D  +G S+G+ F+++ S + ++ +I+ M+G++L +RPI  ++
Sbjct: 25  ---SCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPIRCNW 75

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

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 30/119 (25%), Positives = 49/119 (41%), Gaps = 41/119 (34%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           G  IF+ NL P+ DE LL+  FS FG +                                
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAV-------------------------------- 28

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
            N+       +++RD  T   KG+ F+   ++E + ++I +++G  L  R + VS  FK
Sbjct: 29  TNV-------KVIRDLTTNKCKGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQVS--FK 78

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|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 = 54.9 bits (133), Expect = 4e-10
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 6/74 (8%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
            T+YVG L   ++E  +   F   G +  V + KD      +GY F+ F   E A  AI 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIV 54

Query: 95  IMNMIKLYGKPIRV 108
            +N   + G+ ++ 
Sbjct: 55  AVNGTSINGQTVKC 68

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|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 = 54.5 bits (132), Expect = 5e-10
 Identities = 28/113 (24%), Positives = 44/113 (38%), Gaps = 42/113 (37%)

Query: 125 FIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIF 184
           F+G L     E+ +   F  +G I                             +V     
Sbjct: 3   FVGQLPKTATEEDVRALFEEYGNIE----------------------------EVT---- 30

Query: 185 IGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL---CNRPISV 234
                  I+RD DTG SKG AF+ ++S E +  +I+A+HG+      +RP+ V
Sbjct: 31  -------IIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTMPGASRPLQV 76

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

 Score = 54.4 bits (130), Expect = 7e-10
 Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+YVG L   V+E L+ +LF Q GP  +  M  +  +  +  Y F+EF    DA  A+  
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAA 58

Query: 96  MNMIKLYGKPIRVNKASS 113
           MN  K+ GK ++VN A++
Sbjct: 59  MNGRKILGKEVKVNWATT 76

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

 Score = 53.8 bits (130), Expect = 9e-10
 Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++V  L  KV E  ++E F ++G V +V + +DR ++  +G  ++EF  EE    A+ +
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 96  MNMIKLYGKPIRV 108
               +L G+PI V
Sbjct: 61  TGQ-RLLGQPIMV 72

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

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

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 5/71 (7%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+++G L+  + E  ++  F + G V +V + +++ T    GYGF+EF   E A+ A++ 
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 96  MNMIKLYGKPI 106
           +N     GKPI
Sbjct: 61  LN-----GKPI 66

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|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 53.3 bits (128), Expect = 1e-09
 Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVG LD +V+E ++ ++F   GPV NV +  D+       YGF+E+    DA+ A++ +
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 97  NMIKLYGKPIRVNKA 111
           N  ++    IRVN A
Sbjct: 60  NGRQIENNEIRVNWA 74

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

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

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVV-NVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           A +++G LD +V E L+++ F   G ++    + +D  T   +G+ FI +   E +D AI
Sbjct: 2   ANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAI 61

Query: 94  KIMNMIKLYGKPIRVNKA 111
           + MN   L  +PI V+ A
Sbjct: 62  EAMNGQYLCNRPITVSYA 79

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|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 = 53.3 bits (128), Expect = 2e-09
 Identities = 25/75 (33%), Positives = 46/75 (61%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG +  + +E  + ++F + GPVV+  +  DR T   +GYGF E+  +E A  A++ +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 97  NMIKLYGKPIRVNKA 111
           N  +L G+ +RV+ A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            I+VGG+    +E  + + F + G V +V +  DR   + +GYGF+ F  +EDA+  + +
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVS-KGYGFVTFETQEDAEKILAM 62

Query: 96  MNMIKLYGKPIRVNKA 111
            N+    GK + +  A
Sbjct: 63  GNLN-FRGKKLNIGPA 77

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

 Score = 52.8 bits (127), Expect = 2e-09
 Identities = 24/74 (32%), Positives = 43/74 (58%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVG +  ++ E  + + F   GP+ ++ M  D VT  H+G+ F+E+   E A  A++ M
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 97  NMIKLYGKPIRVNK 110
           N + L G+ I+V +
Sbjct: 63  NGVMLGGRNIKVGR 76

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

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

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 24/78 (30%), Positives = 45/78 (57%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
            +T+YV  L   ++   + ++F + G VV V + KD+ T+  +G  FI F+  EDA   +
Sbjct: 1   KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60

Query: 94  KIMNMIKLYGKPIRVNKA 111
           K +N  +L+G+ ++ + A
Sbjct: 61  KALNNKELFGRTLKCSIA 78

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 22/73 (30%), Positives = 39/73 (53%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++V  L+   +E+ +   F + GP+  + + +D+ T   +GY FIEF  E D   A K 
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY 62

Query: 96  MNMIKLYGKPIRV 108
            +  K+ G+ + V
Sbjct: 63  ADGKKIDGRRVLV 75

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|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 = 51.9 bits (125), Expect = 4e-09
 Identities = 24/115 (20%), Positives = 43/115 (37%), Gaps = 45/115 (39%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
             +++GNL   + E+ L  TFS FG I +              +RV K            
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEE--------------VRVFK------------ 34

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
                               KG+AF+ + + EA+  +I A++G  +  + +  S+
Sbjct: 35  -------------------DKGYAFVRFDTHEAAATAIVAVNGTSINGQTVKCSW 70

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

 Score = 52.1 bits (126), Expect = 4e-09
 Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 36  TIYVGGLDDKVSETLM----WELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           T+Y+  L++K+ +  +    + LF Q GPV+++   K   T   +G  F+ F   E A  
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKDVESATN 57

Query: 92  AIKIMNMIKLYGKPIRVNKA 111
           A++ +     Y KP+R+  A
Sbjct: 58  ALRALQGFPFYDKPMRIQYA 77

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

 Score = 52.0 bits (124), Expect = 4e-09
 Identities = 29/76 (38%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+YVG L   V+E L+ +LF Q GP  +  M  D  T  +  Y F+EF     A  ++  
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAA 58

Query: 96  MNMIKLYGKPIRVNKA 111
           MN  K+ GK ++VN A
Sbjct: 59  MNGRKIMGKEVKVNWA 74

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

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

 Score = 51.4 bits (124), Expect = 6e-09
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 37  IYVGGLDDKVSET-LMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           +YV  L   V+E  L  E F   G V  V + ++      +G+ F+EF   EDA+ A+K 
Sbjct: 1   LYVRNLPPSVTEEDLR-EFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKK 57

Query: 96  MNMIKLYGKPIR 107
           +N + L G+ +R
Sbjct: 58  LNGLVLDGRTLR 69

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

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

 Score = 51.2 bits (123), Expect = 7e-09
 Identities = 27/115 (23%), Positives = 48/115 (41%), Gaps = 39/115 (33%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            +F+GNL   VD++ L   F  FG ++                                 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVV--------------------------------- 27

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                    ++ D +TG S+GF ++++ S E +  +I+AM G+ L  RPI+V ++
Sbjct: 28  ------GARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76

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

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

 Score = 51.5 bits (124), Expect = 8e-09
 Identities = 27/117 (23%), Positives = 49/117 (41%), Gaps = 40/117 (34%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           G N+++ NLD  +D++ L + FS FG I                                
Sbjct: 1   GVNLYVKNLDDSIDDERLREEFSPFGTITSA----------------------------- 31

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                     ++M D + G SKGF F+ ++S E +  ++  M+G+ +  +P+ V+ A
Sbjct: 32  ----------KVMTD-EKGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALA 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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 51.2 bits (123), Expect = 9e-09
 Identities = 26/73 (35%), Positives = 40/73 (54%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            I+V  L     E+L+W+LF   G V NV + +D  T   +GYGF+     E+A  AI  
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 96  MNMIKLYGKPIRV 108
           +N  +L G+ ++V
Sbjct: 63  LNGYRLGGRVLQV 75

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

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

 Score = 50.6 bits (122), Expect = 9e-09
 Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 5/60 (8%)

Query: 52  WELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
           ++LF   G V  + + K        G+ F+EF  EE A+ A++ +N +   G+P+RV+ +
Sbjct: 2   YKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 28/114 (24%), Positives = 47/114 (41%), Gaps = 38/114 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+G+L P+V + +L +TF A    ++  K++                            
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVM--------------------------- 36

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                      DP TG SKG+ F+ +   +  D ++  M+G Y  +RP+ VS A
Sbjct: 37  -----------DPVTGRSKGYGFVRFGDEDERDRALTEMNGVYCSSRPMRVSPA 79

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

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

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 7/76 (9%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           TI+VGG+D  +SE  + E F   G V  V +  DR       + F+EF    DA+ A+  
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR--FAFVEF---ADAESALSA 56

Query: 96  MNM--IKLYGKPIRVN 109
           +N+    L G P+RV+
Sbjct: 57  LNLSGTLLGGHPLRVS 72

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

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

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 5/77 (6%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVG L  + ++  + + F + GP+ +V      V +   G+ F+EF    DA+ A++ +
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVW-----VARNPPGFAFVEFEDPRDAEDAVRAL 56

Query: 97  NMIKLYGKPIRVNKASS 113
           +  ++ G  +RV  +  
Sbjct: 57  DGRRICGNRVRVELSRG 73

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

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

 Score = 50.6 bits (121), Expect = 1e-08
 Identities = 27/73 (36%), Positives = 38/73 (52%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            IY+G L     E  + + F Q G V NV + + + T   + YGFI+F+  E A  A K 
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 96  MNMIKLYGKPIRV 108
           MN   L GK ++V
Sbjct: 61  MNNYLLMGKVLQV 73

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

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

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 26/113 (23%), Positives = 46/113 (40%), Gaps = 41/113 (36%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+G L P+V ++ L + FS  G IL+    +N+IK      R N  ++           
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILE----VNLIK------RANHTNA----------- 44

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
                               FAFI +   +A+  ++++ +   L N+ + V Y
Sbjct: 45  --------------------FAFIKFEREQAAARAVESENHSMLKNKTMHVQY 77

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

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

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 4/75 (5%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+Y G        + +  LF   GPV  V M     ++T Q + FI F   E A  AI+ 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIET 56

Query: 96  MNMIKLYGKPIRVNK 110
           +N   + G  I+V +
Sbjct: 57  LNGASVDGNCIKVQR 71

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

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 32/123 (26%), Positives = 47/123 (38%), Gaps = 40/123 (32%)

Query: 112 SSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKAS 171
           S H +  D  A I+IG L  E+ E  +   FS +G I+                      
Sbjct: 1   SWHDQYKD-SAYIYIGGLPYELTEGDILCVFSQYGEIV---------------------- 37

Query: 172 SHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRP 231
                            D  ++RD  TG SKGFAF+ Y    ++  ++D ++G  L  R 
Sbjct: 38  -----------------DINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRT 80

Query: 232 ISV 234
           I V
Sbjct: 81  IRV 83

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

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

 Score = 49.6 bits (119), Expect = 2e-08
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++VGGLD  V+E  +  LF   G +V V +P  +      G GF++F+    A+ AI+ 
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGK------GCGFVQFVHRAAAEAAIQQ 56

Query: 96  MNMIKLYGKPIRVN 109
           +    + G  IR++
Sbjct: 57  LQGTIIGGSRIRLS 70

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

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 49.6 bits (119), Expect = 3e-08
 Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVV-NVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           D +I+VG L   V++ ++ E F    P V    +  D VT   +GYGF+ F  E++ D A
Sbjct: 1   DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60

Query: 93  IKIMNMIKLYGKPIRVNKAS 112
           +  MN +    +P+RV+ A+
Sbjct: 61  LTEMNGVYCSSRPMRVSPAT 80

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

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

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           +I+VG L   V++  + E F + G ++ V++ K         + FI+F  E+ A  A++ 
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKR--ANHTNAFAFIKFEREQAAARAVES 62

Query: 96  MNMIKLYGKPIRVNK 110
            N   L  K + V  
Sbjct: 63  ENHSMLKNKTMHVQY 77

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

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

 Score = 49.7 bits (119), Expect = 3e-08
 Identities = 16/46 (34%), Positives = 28/46 (60%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           I+RD  TG S G+ F++Y     +  +I+ ++G  + N+ + VSYA
Sbjct: 32  IVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKVSYA 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 53.4 bits (128), Expect = 4e-08
 Identities = 56/267 (20%), Positives = 95/267 (35%), Gaps = 57/267 (21%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
            A +YV GL   +++  +  +F   G ++   +  D VT   +G GFI F   ++AD AI
Sbjct: 89  GANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAI 148

Query: 94  KIMNMIKLYG--KPIRV----NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGV 147
           K +N     G  +PI V    N +SS+ K L              V    +        +
Sbjct: 149 KTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPM 208

Query: 148 ILQTPKIMNMIKLYGKPIRVNKASSHQK------------------NLDVGAN------- 182
                +       +   +   +                         L  GA        
Sbjct: 209 HHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGA 268

Query: 183 ---IFIGNLDPE--------------------IMRDPDTGNSKGFAFINYASFEASDASI 219
              IF+ NL P+                    I+RD  T   KG+ F++  +++ +  +I
Sbjct: 269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAI 328

Query: 220 DAMHGQYLCNRPISVSYAFKKDSKGDR 246
            +++G  L NR + VS+   K +K  R
Sbjct: 329 LSLNGYTLGNRVLQVSF---KTNKAYR 352

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

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

 Score = 49.2 bits (118), Expect = 4e-08
 Identities = 21/70 (30%), Positives = 41/70 (58%)

Query: 39  VGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM 98
           V  L  + +   +  +F + G V +V++P+DR T+  +G+ F+ F  + DA+ A+  M+ 
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 99  IKLYGKPIRV 108
            +L G+ +RV
Sbjct: 63  KELDGRELRV 72

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

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

 Score = 49.3 bits (118), Expect = 4e-08
 Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VGGL   V+E    E F Q G VV+  + +D  T   +G+GF+ F   E A   +   
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF-DSESAVERVFSA 60

Query: 97  NMIKLYGKPIRVNKA 111
            M++L GK + V +A
Sbjct: 61  GMLELGGKQVEVKRA 75

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

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

 Score = 49.2 bits (118), Expect = 4e-08
 Identities = 22/76 (28%), Positives = 40/76 (52%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++V  L    ++  + E F + GP+    + KD+ ++  +G+G++ F  EEDA  A++ 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 96  MNMIKLYGKPIRVNKA 111
               K  G+ I V  A
Sbjct: 61  KKKTKFGGRKIHVEFA 76

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|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 = 49.2 bits (118), Expect = 4e-08
 Identities = 18/52 (34%), Positives = 33/52 (63%), Gaps = 1/52 (1%)

Query: 53  ELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK 104
           ELF   G V +V +PK +   +H+G+ F+EF+ +++A  A++ +    LYG+
Sbjct: 19  ELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGR 69

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

 Score = 49.1 bits (118), Expect = 5e-08
 Identities = 19/99 (19%), Positives = 40/99 (40%), Gaps = 39/99 (39%)

Query: 126 IGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFI 185
           + NL  + DE  L + F  FG                    +++             +++
Sbjct: 4   VTNLSEDADEDDLRELFRPFG-------------------PISR-------------VYL 31

Query: 186 GNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHG 224
                   +D +TG S+GFAF+ + + E ++ +I+ ++G
Sbjct: 32  A-------KDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

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

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 49.3 bits (118), Expect = 5e-08
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VGGL   V+ET + + F Q G V  V +  D   +  +G+GFI F  E+  D  +   
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN-E 63

Query: 97  NMIKLYGKPIRVNKA 111
           +   + GK + V +A
Sbjct: 64  HFHDINGKKVEVKRA 78

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

 Score = 48.8 bits (117), Expect = 6e-08
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 20/76 (26%)

Query: 182 NIFIGNL--------------------DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
           N+++GNL                       ++ D +TG S+GF F+   + E ++A+I+ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 222 MHGQYLCNRPISVSYA 237
           ++G     R ++V+ A
Sbjct: 61  LNGTDFGGRTLTVNEA 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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 49.1 bits (118), Expect = 6e-08
 Identities = 23/74 (31%), Positives = 42/74 (56%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++VG + + VS+  + +L  + G V++    KD  T   + +GF EF   E A  A+++
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 96  MNMIKLYGKPIRVN 109
           +N ++L GK + V 
Sbjct: 62  LNGLELGGKKLLVK 75

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

 Score = 48.9 bits (117), Expect = 6e-08
 Identities = 19/58 (32%), Positives = 32/58 (55%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
          I+VGGL  + +E  + E F + G +V + +P D+ T   +G+ FI F  EE     ++
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILE 59

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

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

 Score = 48.4 bits (116), Expect = 7e-08
 Identities = 27/112 (24%), Positives = 42/112 (37%), Gaps = 39/112 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++GNL   + E  L   F  FG I                                   
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFV-------------------------------- 28

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS 235
                  ++ RDP+TG SKG+ FI +A  E +  +++ ++G  L  RPI V 
Sbjct: 29  -------QLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKVG 73

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

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

 Score = 48.4 bits (116), Expect = 8e-08
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++V  LD  V E  + +LF + G + +V + K+      +GY ++EF  EE    A+K 
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALK- 58

Query: 96  MNMIKLYGKPIRV 108
           ++   + G+P+ V
Sbjct: 59  LDRELIKGRPMFV 71

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

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

 Score = 52.8 bits (126), Expect = 9e-08
 Identities = 25/75 (33%), Positives = 39/75 (52%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           IYV  +   +SET +  +F   G +V   + +    + H+GYGFIE+   +    AI  M
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM 266

Query: 97  NMIKLYGKPIRVNKA 111
           N+  L G+ +RV K 
Sbjct: 267 NLFDLGGQYLRVGKC 281

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

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

 Score = 48.4 bits (116), Expect = 9e-08
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 4/77 (5%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ---GYGFIEFMGEEDADYAI 93
           IYV  LD K+ E  +  +F + G V ++ +PK +  +  +   G+ F+ F     A+ A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 94  KIMNMIKLYGKPIRVNK 110
           + +N  +L G+ I V+ 
Sbjct: 63  Q-LNGTELGGRKISVSL 78

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

 Score = 52.2 bits (125), Expect = 1e-07
 Identities = 22/86 (25%), Positives = 33/86 (38%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D    IY+G L   + E  + EL    G +   ++ KD  T   +GY F E+      D 
Sbjct: 293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDV 352

Query: 92  AIKIMNMIKLYGKPIRVNKASSHQKN 117
           AI  +N        + V +A      
Sbjct: 353 AIAALNGKDTGDNKLHVQRACVGANQ 378

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 47.9 bits (114), Expect = 1e-07
 Identities = 27/114 (23%), Positives = 41/114 (35%), Gaps = 38/114 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+G+L PEV+E  L   F                                       + 
Sbjct: 4   IFVGDLSPEVNESDLVSLF--------------------------------------QSR 25

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           F      +IM DP TG S+G+ F+ ++       ++  M G Y   RP+ +S A
Sbjct: 26  FPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIEMQGVYCGGRPMRISTA 79

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

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

 Score = 47.6 bits (114), Expect = 1e-07
 Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 45  KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK 104
           K +E  + +LF   G V  V +P+       +G+ F++F  + DA+ AIK +N  K+ G+
Sbjct: 10  KCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGR 68

Query: 105 PIRVNKA 111
           P+ V+ A
Sbjct: 69  PVAVDWA 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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 48.2 bits (114), Expect = 1e-07
 Identities = 24/79 (30%), Positives = 44/79 (55%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+V  L  +  E+++W+LF   G V NV + +D  T   +G+GF+     ++A  AI  +
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 97  NMIKLYGKPIRVNKASSHQ 115
           N  +L  + ++V+  +S Q
Sbjct: 64  NGYRLGDRVLQVSFKTSKQ 82

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

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 21/81 (25%), Positives = 44/81 (54%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           ++YV  + D      +  LF + GP+V+V++P D  T+  +G+ +++F    DA+ A+  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 96  MNMIKLYGKPIRVNKASSHQK 116
           ++  +  G+ I +  A   +K
Sbjct: 62  LDRTRFLGREIEIQFAQGDRK 82

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 22/114 (19%), Positives = 41/114 (35%), Gaps = 39/114 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+GN+  +  E+ L + FS  G ++                R                 
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVS--------------FR----------------- 29

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                   ++ D DTG  KG+ F  +   E + ++I  ++G     R + V +A
Sbjct: 30  --------LVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALRVDFA 75

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

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 24/75 (32%), Positives = 44/75 (58%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+V G+ ++  E  + + F + G + N+H+  DR T   +GY  IE+  +++A  AI+ +
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 97  NMIKLYGKPIRVNKA 111
           N  +L G+ I V+ A
Sbjct: 69  NGKELLGQTISVDWA 83

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

 Score = 47.1 bits (112), Expect = 2e-07
 Identities = 23/73 (31%), Positives = 38/73 (52%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VG L  +V++  ++  F       +  +  D  +   +GYGF+ F  ++DA+ AI  M
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 97  NMIKLYGKPIRVN 109
           N   L  +PIR N
Sbjct: 62  NGKWLGSRPIRCN 74

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 20/66 (30%), Positives = 39/66 (59%)

Query: 46  VSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP 105
           +++  +  LF   GP+ +  + +DR+T    GYGF++++ E DA  AI  +N  ++  K 
Sbjct: 12  MTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKR 71

Query: 106 IRVNKA 111
           ++V+ A
Sbjct: 72  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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VGGL   V E  + E F Q GPV    +  D+ T   +G+GF+ F   + AD A  ++
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA-VV 60

Query: 97  NMIKLYGKPIRVNKASSHQK 116
               + G  + V KA   ++
Sbjct: 61  KFHPINGHRVEVKKAVPKEE 80

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

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 24/70 (34%), Positives = 40/70 (57%)

Query: 39  VGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM 98
           V GL    +E  + E+F + GP+  V +  D+ T   +G+GF+ F   EDA  A + +N 
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

Query: 99  IKLYGKPIRV 108
           +++ G+ IRV
Sbjct: 64  MEIDGRRIRV 73

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

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

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 21/59 (35%), Positives = 35/59 (59%)

Query: 53  ELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
            LF   G + +  + +D+VT    GYGF+ ++  EDA+ AI  +N ++L  K I+V+ A
Sbjct: 20  SLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSYA 78

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

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

 Score = 47.0 bits (112), Expect = 2e-07
 Identities = 21/73 (28%), Positives = 41/73 (56%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L     E  ++E F + G + +V +P D  +   +G+G++EF  +E A  A+  +
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 97  NMIKLYGKPIRVN 109
               L G+P+R++
Sbjct: 61  GGTDLLGRPVRLD 73

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

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 9/74 (12%)

Query: 37  IYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           ++VG L+ DKVS+  + E+F + G ++ + +        H+GYGF++F  EEDA  A+  
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVAG 54

Query: 96  MNMIKLYGKPIRVN 109
            N  ++ G+ + +N
Sbjct: 55  ENGREIAGQKLDIN 68

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

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 19/73 (26%), Positives = 34/73 (46%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +Y+G L     E  + + F Q G V  + + + + T   +GY F+EF   E A    + 
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET 60

Query: 96  MNMIKLYGKPIRV 108
           MN   L+ + ++ 
Sbjct: 61  MNNYLLFERLLKC 73

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

 Score = 47.0 bits (112), Expect = 3e-07
 Identities = 28/109 (25%), Positives = 45/109 (41%), Gaps = 39/109 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+GNL  + DE  +Y+ F                  YG+   V                
Sbjct: 1   LFVGNLSFDADEDSIYEAFGE----------------YGEISSV---------------- 28

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPI 232
                   +  DPD+G  KGF ++ ++S EA+ A++DA+ G  L  RP+
Sbjct: 29  -------RLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGRPV 70

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

 Score = 47.0 bits (112), Expect = 3e-07
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
          I+VGGL    +E  + + F Q G V +  +  D+ T  H+G+GF+ F  E+  D   +I
Sbjct: 2  IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 46.4 bits (111), Expect = 4e-07
 Identities = 23/98 (23%), Positives = 36/98 (36%), Gaps = 39/98 (39%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FIG L  +  E+ L + FS +G ++                                  
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVV---------------------------------- 26

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
                D  IM+DP TG S+GF F+ +A   + D  + A
Sbjct: 27  -----DCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 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|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 46.5 bits (110), Expect = 4e-07
 Identities = 31/81 (38%), Positives = 45/81 (55%), Gaps = 2/81 (2%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DA +YV GL   +S+  M +LF Q G ++   +  D+VT   +G GFI F    +A+ AI
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60

Query: 94  KIMNMIKLYG--KPIRVNKAS 112
           K +N  K  G  +PI V  A+
Sbjct: 61  KGLNGQKPLGAAEPITVKFAN 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|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 46.1 bits (110), Expect = 5e-07
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L + ++E    ELF + G V  V + K++      G+GFI      +A+ A   +
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK------GFGFIRLDTRTNAEKAKAEL 57

Query: 97  NMIKLYGKPIRV 108
           + I   G+ +RV
Sbjct: 58  DGIMRKGRQLRV 69

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

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

 Score = 45.7 bits (109), Expect = 6e-07
 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
          ++VGGL + V+E  + E F Q G V +V +  D+ T   +G+ F+ F   +D D   KI
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF---DDYDPVDKI 57

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|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 46.0 bits (109), Expect = 8e-07
 Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 3/76 (3%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++VGG+D ++ ET +   F + G V  V +  DR T   +GYGF+ F   +D D    +
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFY--DDVDVQKIV 63

Query: 96  MNMIKLYGKPIRVNKA 111
            + I  +GK +++  A
Sbjct: 64  ESQINFHGKKLKLGPA 79

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

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

 Score = 47.3 bits (112), Expect = 9e-07
 Identities = 26/76 (34%), Positives = 41/76 (53%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL     +  + + F   G VV+  +  DR T   +G+GF+ F  E  A  AI  M
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 97  NMIKLYGKPIRVNKAS 112
           +  +L G+ IRVN A+
Sbjct: 97  DGKELNGRHIRVNPAN 112

Length = 144

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

 Score = 45.5 bits (108), Expect = 9e-07
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+Y+G L   ++E  + E F +   + +V +  D+ T   +G+G ++F  EE  D A+K+
Sbjct: 1   TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59

Query: 96  MNMIKLYGKPIRVN 109
                L G+PIR+ 
Sbjct: 60  DGT-VLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 25/112 (22%), Positives = 44/112 (39%), Gaps = 37/112 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           I++ NLD ++DE  L   FS FG +         I++   P + ++      N       
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEV-------ESIRI---PKKQDEKQGRLNN------- 45

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS 235
                              GFAF+ +    +++ ++  ++G  L  R ISVS
Sbjct: 46  -------------------GFAFVTFKDASSAENAL-QLNGTELGGRKISVS 77

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

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            I+VGGL    ++  + + F Q G +    +  DR T   +GYGF+ F  +E A+ A K 
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 96  MNMIKLYGKPIRVNKA 111
            N I + G+   VN A
Sbjct: 62  PNPI-IDGRKANVNLA 76

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

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

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L D  +   +  LF + G V       D V      YGF+    EEDA+ AIK +
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTEC----DVVKN----YGFVHMEEEEDAEDAIKAL 53

Query: 97  NMIKLYGKPIRV 108
           N  +  GK I V
Sbjct: 54  NGYEFMGKRINV 65

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

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

 Score = 45.2 bits (108), Expect = 1e-06
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 5/82 (6%)

Query: 35  ATIYVGGLDDKVSE-TLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
            T+ + GLD   +E  ++  L   +  P+ +V + +D++T T +G+ F+EF   EDA   
Sbjct: 3   NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQW 62

Query: 93  IKI---MNMIKLYGKPIRVNKA 111
           +     ++   + G+ +RV+ A
Sbjct: 63  MDALNNLDPFVIDGRVVRVSYA 84

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

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VGG+D K +E  + + F Q G V  V +  DR   + +GYGF+ F  +EDA   ++  
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVS-KGYGFVTFETQEDAQKILQEA 63

Query: 97  NMIKLYGKPIRVNKA 111
           N +    K + + +A
Sbjct: 64  NRLCFRDKKLNIGQA 78

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 23/77 (29%), Positives = 41/77 (53%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D   T++VG L  + +E  + E+F + G +  + + +D VT   +GY F+E+  E DA  
Sbjct: 1   DPYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60

Query: 92  AIKIMNMIKLYGKPIRV 108
           A +  + + + G  I V
Sbjct: 61  AYRDAHKLVIDGSEIFV 77

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

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

 Score = 45.1 bits (106), Expect = 1e-06
 Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 2/80 (2%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DA +YV GL   +++  + +LF Q G ++   +  D+VT   +G GFI F    +A+ AI
Sbjct: 2   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61

Query: 94  KIMNMIKLYG--KPIRVNKA 111
           K +N  K  G  +PI V  A
Sbjct: 62  KGLNGQKPSGAAEPITVKFA 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|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 22/115 (19%), Positives = 43/115 (37%), Gaps = 36/115 (31%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            ++IGNLD  + E  L   FS +G      KI     L+                  G  
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYG------KIKKFDFLF---------------HKSG-- 37

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                        P  G  +G+ F+ + + E ++ ++ +++G+    + + V +A
Sbjct: 38  -------------PLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVVRWA 79

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|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 = 45.0 bits (107), Expect = 2e-06
 Identities = 18/56 (32%), Positives = 29/56 (51%)

Query: 53  ELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV 108
           ELF   G +  VH+P D+ T+  +G+ F+ FM  E A  A   ++     G+ + V
Sbjct: 18  ELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLHV 73

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

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

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 21/55 (38%), Positives = 34/55 (61%)

Query: 54  LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV 108
           LF+  GPV N  + +D+ T    G+GF+++   EDA  AI+ +N ++L  K I+V
Sbjct: 20  LFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKV 74

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

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

 Score = 44.5 bits (105), Expect = 2e-06
 Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 2/79 (2%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           A +YV GL   +++  + +LF Q G ++   + +D++T   +G GFI F    +A+ AIK
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 95  IMNMIKLYG--KPIRVNKA 111
            +N  K  G  +PI V  A
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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           ++++G L+  + E  +   F   G  V++V + ++++T    GY F+EF  E  A+    
Sbjct: 1   SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERC-- 58

Query: 95  IMNMIKLYGKPI 106
              + KL GKPI
Sbjct: 59  ---LHKLNGKPI 67

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YV  L    +E  + ELF + G V  V   KD        Y F+ F   +DA  A++ M
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 97  NMIKLYGKPIRV 108
           N  +L G PI V
Sbjct: 56  NGKELEGSPIEV 67

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

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

 Score = 44.0 bits (104), Expect = 2e-06
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+YVG L   + E  + +LF + GP+V++ +   ++     GY FIEF    DA+ AI+ 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRG 57

Query: 96  MNMIKLYGKPIRV 108
            +     G+ +RV
Sbjct: 58  RDGYDFDGQRLRV 70

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

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 23/113 (20%), Positives = 39/113 (34%), Gaps = 39/113 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+G L  +  E+ L + FS +G I              + +R                 
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDI--------------RRLR----------------- 34

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
                   ++RD  TG SKG+AF+ Y     +  +    H   +    I V +
Sbjct: 35  --------LVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDGSEIFVDF 79

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

 Score = 44.3 bits (104), Expect = 3e-06
 Identities = 24/76 (31%), Positives = 40/76 (52%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L  +++   +   F   G + +  + KD  T   +GYGF+ F  + DA+ AI+ M
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 97  NMIKLYGKPIRVNKAS 112
               L G+ IR N A+
Sbjct: 64  GGQWLGGRQIRTNWAT 79

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 44.1 bits (104), Expect = 3e-06
 Identities = 22/76 (28%), Positives = 40/76 (52%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++V  L   V++  + + F    P+ +  +  D  T   +GYGF+ F   EDA  A+  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 96  MNMIKLYGKPIRVNKA 111
           +   KL+G+ +R++ A
Sbjct: 61  LKNKKLHGRILRLDIA 76

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

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 3/49 (6%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDA---MHGQYLCNRPISVSYA 237
           ++RD  TG S+GFAF+ + S E +   +DA   +    +  R + VSYA
Sbjct: 36  LIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 43.9 bits (103), Expect = 4e-06
 Identities = 22/73 (30%), Positives = 39/73 (53%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I++  L     E ++W++F   G V NV + +D  T   +G+GF+     E+A  AI  +
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 97  NMIKLYGKPIRVN 109
           N  +L  K ++V+
Sbjct: 64  NGYRLGDKILQVS 76

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

 Score = 43.5 bits (102), Expect = 5e-06
 Identities = 28/124 (22%), Positives = 47/124 (37%), Gaps = 39/124 (31%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           G  IF+ NL PE DE +L+  F  FG +                                
Sbjct: 1   GWCIFVYNLSPEADESVLWQLFGPFGAVTNV----------------------------- 31

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                     +++RD  T   KGF F+   +++ +  +I +++G  L +R + VS+   K
Sbjct: 32  ----------KVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTSK 81

Query: 241 DSKG 244
             K 
Sbjct: 82  QHKA 85

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

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 20/46 (43%), Positives = 29/46 (63%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           I+RD  TG S GF F++Y S E +  +I  ++G  L N+ I V+YA
Sbjct: 32  IVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYA 77

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

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 17/76 (22%)

Query: 39  VGGLDDKVSETLMWE----LFVQSGPVV--NVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           V GL +  S    W+       Q+G V   +V   +D+     +G G +EF  +ED + A
Sbjct: 5   VSGLPEGAS----WQDLKDFGRQAGDVTYADVD--RDQ-----EGEGVVEFTSQEDMERA 53

Query: 93  IKIMNMIKLYGKPIRV 108
           ++ ++  +  G+ +RV
Sbjct: 54  LRKLDGTEFRGRRVRV 69

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of 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). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 22/80 (27%), Positives = 42/80 (52%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           + D  I+VG L ++V++ ++   F +        + +D+ T   +GYGF+ F    D   
Sbjct: 4   ENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLK 63

Query: 92  AIKIMNMIKLYGKPIRVNKA 111
           A+K MN   +  +PI++ K+
Sbjct: 64  AMKEMNGKYVGNRPIKLRKS 83

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

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 7/81 (8%)

Query: 36  TIYVGGLD-----DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
           TI+V G D     D +  +L  E F   G +  V +P DR T   +G+ +IEF   +  +
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLT-EHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVE 59

Query: 91  YAIKIMNMIKLYGKPIRVNKA 111
            A++ ++   L G  + V++A
Sbjct: 60  KALE-LDGSDLGGGNLVVDEA 79

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 43.2 bits (102), Expect = 6e-06
 Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 1/54 (1%)

Query: 185 IGNLDP-EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           IG ++  +++RD  TG S G+ F+NY   E ++ +I+ ++G  L N+ I VSYA
Sbjct: 25  IGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSYA 78

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

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

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 30/115 (26%), Positives = 47/115 (40%), Gaps = 45/115 (39%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+G+L  EV +++L   FS +                          S QK        
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKY-------------------------PSFQK-------- 35

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDA---MHGQYLCNRPISVS 235
                  +++RD  TG SKG+ F+   SF   +  + A   M+G+Y+ NRPI + 
Sbjct: 36  ------AKVVRDKRTGKSKGYGFV---SFSDPNDYLKAMKEMNGKYVGNRPIKLR 81

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

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 3/80 (3%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNV-HMPKDRVTQTHQ--GYGFIEFMGEEDADYA 92
            +++G LD +++E  + +LF + G +     +         Q  GY F+ F  +E+A+ A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 93  IKIMNMIKLYGKPIRVNKAS 112
           +K +N     GK + V  A 
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

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

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

 Score = 43.2 bits (101), Expect = 7e-06
 Identities = 22/80 (27%), Positives = 43/80 (53%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D    + V  L   +++  +  LF   G + +  + +D++T    GYGF+ ++  +DA+ 
Sbjct: 2   DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61

Query: 92  AIKIMNMIKLYGKPIRVNKA 111
           AI  +N ++L  K I+V+ A
Sbjct: 62  AINTLNGLRLQTKTIKVSYA 81

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

 Score = 43.6 bits (102), Expect = 7e-06
 Identities = 29/82 (35%), Positives = 46/82 (56%), Gaps = 2/82 (2%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DA +YV GL   +++  + +LF Q G ++   +  D+VT   +G GFI F    +A+ AI
Sbjct: 5   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64

Query: 94  KIMNMIKLYG--KPIRVNKASS 113
           K +N  K  G  +PI V  A++
Sbjct: 65  KGLNGQKPPGATEPITVKFANN 86

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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 43.2 bits (102), Expect = 8e-06
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+YV  +D +V+E  +  LF   G VV+  +  D    +   + FIEF  EE A  A+ +
Sbjct: 4   TVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGD--PNSVLRFAFIEFTDEEGARAALSL 61

Query: 96  M-NMIKLYGKPIRV 108
              M+  Y  P+RV
Sbjct: 62  SGTMLGFY--PVRV 73

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

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

 Score = 42.5 bits (101), Expect = 9e-06
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 21/73 (28%)

Query: 183 IFIGNLDPE--------------------IMRDPDTGNSKGFAFINYASFEASDASIDAM 222
           +F+GNL  +                    I+RD  TG  KGF ++ + + ++   ++  +
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 223 HGQYLCNRPISVS 235
           +G  L  R I V 
Sbjct: 61  NGIKLKGRKIRVK 73

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

 Score = 43.2 bits (101), Expect = 9e-06
 Identities = 21/77 (27%), Positives = 42/77 (54%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+V  L     E+++W++F   G V NV + +D  T   +G+GF+     ++A  AI  +
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 97  NMIKLYGKPIRVNKASS 113
           N  +L  + ++V+  ++
Sbjct: 66  NGYRLGDRVLQVSFKTN 82

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 43.0 bits (102), Expect = 9e-06
 Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHM--PKDRVTQTHQGY-GFIEFMGEEDADYAI 93
           +YVG L+ KV+E ++ + F + GP+ +V +  P+    +      GF+ FM   DA+ A+
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 94  KIMNMIKLYGKPIRV 108
             ++   + G  +++
Sbjct: 64  DELDGKDVMGYELKL 78

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YV  LDD + +  + E F   G + +  +  D   ++ +G+GF+ F   E+A  A+  M
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRS-KGFGFVCFSSPEEATKAVTEM 62

Query: 97  NMIKLYGKPIRVNKA 111
           N   + GKP+ V  A
Sbjct: 63  NGRIIGGKPLYVALA 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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 13/42 (30%), Positives = 20/42 (47%)

Query: 194 RDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS 235
           R   TG SKG+AF+ + S E +    + M+   L  R +   
Sbjct: 33  RSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKCK 74

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

 Score = 42.8 bits (100), Expect = 1e-05
 Identities = 27/123 (21%), Positives = 48/123 (39%), Gaps = 39/123 (31%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           G  IF+ NL P+ DE +L+  F  FG +                                
Sbjct: 3   GWCIFVYNLAPDADESILWQMFGPFGAVTNV----------------------------- 33

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                     +++RD +T   KGF F+   +++ +  +I +++G  L +R + VS+   K
Sbjct: 34  ----------KVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK 83

Query: 241 DSK 243
             K
Sbjct: 84  THK 86

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 42.8 bits (100), Expect = 1e-05
 Identities = 24/80 (30%), Positives = 41/80 (51%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D    + V  L   +++     LF   G + +  + +D++T    GYGF+ ++   DAD 
Sbjct: 1   DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADK 60

Query: 92  AIKIMNMIKLYGKPIRVNKA 111
           AI  +N +KL  K I+V+ A
Sbjct: 61  AINTLNGLKLQTKTIKVSYA 80

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

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VG +D   +   + E F   G +  + +  D+ T   +G+ +IEF+ +   + A+  +
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-L 60

Query: 97  NMIKLYGKPIRV 108
           N  +  G+ I+V
Sbjct: 61  NESEFRGRQIKV 72

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

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 27/119 (22%), Positives = 45/119 (37%), Gaps = 44/119 (36%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FI NL  +  E+ L + FS FG +            Y +                    
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVK-----------YAR-------------------- 31

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDA-----MHGQYLCNRPISVSYA 237
                   I++D  TG+SKG AF+ + + E++   ++A       G  L  R + V+ A
Sbjct: 32  --------IVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDGRRLIVTLA 82

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

>gnl|CDD|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 = 20/75 (26%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 38  YVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN 97
           +VG L    +E  +  LF + G +  V + +D+ T   +G  F++F   E+A  AI+ ++
Sbjct: 3   FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALH 62

Query: 98  -MIKLYG--KPIRVN 109
             + + G  +P++V 
Sbjct: 63  GKVTMPGASRPLQVK 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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 20/72 (27%)

Query: 183 IFIGNLDPEIMR-------------------DPDTGNSKGFAFINYASFEASDASIDAMH 223
           ++IGNL  +I                     D +TG  KGF  +++A  E+ DA++  + 
Sbjct: 2   VYIGNLAWDITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KLD 60

Query: 224 GQYLCNRPISVS 235
           G  LC RPI ++
Sbjct: 61  GTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 24/76 (31%), Positives = 39/76 (51%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L  +++   +   F   G + +  + KD  T   +GYGF+ F  + DA+ AI  M
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 97  NMIKLYGKPIRVNKAS 112
               L G+ IR N A+
Sbjct: 64  GGQWLGGRQIRTNWAT 79

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

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRV-----TQTHQGYGFIEFMGEEDA 89
           T++V  L+ K +E  + + F + G V +V + K +           GYGF+EF  +E A
Sbjct: 1  TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 90 DYAIKIMN 97
            A+K + 
Sbjct: 61 QKALKRLQ 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|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 27/119 (22%), Positives = 41/119 (34%), Gaps = 41/119 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVI-----LQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
           +F+ NL P   E+ L + F + G+I        PKI                        
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIW----------------------- 37

Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                        + +D DTG  KG A + Y    A+ A+I+  + +      I VS A
Sbjct: 38  -------------LYKDKDTGEPKGEATVTYDDPHAASAAIEWFNNKDFMGNTIKVSLA 83

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

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

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 19/61 (31%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
          ++VG L+ + +E  + E+F   G V +++M +D + Q+ +G  F+++  +E A  AIK +
Sbjct: 2  LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQS-RGCAFVKYSSKEMAQAAIKAL 60

Query: 97 N 97
          N
Sbjct: 61 N 61

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

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 4/61 (6%)

Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
          ESG     +++  L    +E  + +LF + GP+  VH+P D++T+  +G+ F+ +M  E 
Sbjct: 1  ESG----RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEH 56

Query: 89 A 89
          A
Sbjct: 57 A 57

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

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 22/75 (29%), Positives = 41/75 (54%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           + V  L   +++  +  LF   G V +  + +D+V     GYGF+ ++  +DA+ AI  +
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 97  NMIKLYGKPIRVNKA 111
           N ++L  K I+V+ A
Sbjct: 64  NGLRLQSKTIKVSYA 78

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

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 29/123 (23%), Positives = 50/123 (40%), Gaps = 39/123 (31%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           G  IF+ NL P+ DE +L+  F  FG +       N +K                     
Sbjct: 3   GWCIFVYNLSPDSDESVLWQLFGPFGAV-------NNVK--------------------- 34

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                      ++RD +T   KGF F+   +++ +  +I +++G  L +R + VS+   K
Sbjct: 35  -----------VIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK 83

Query: 241 DSK 243
             K
Sbjct: 84  THK 86

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
          T+YV  L    +   +  +F + G VV V +P+ + T   +G+ FIEF   E+A  A K 
Sbjct: 1  TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 96 MN 97
          +N
Sbjct: 61 LN 62

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

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 10/82 (12%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTH----QGYGFIEFMGEEDADY 91
           T++VG L     +  + E F + G VV+V     R+ Q      +G+G +EF  EE A  
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDV-----RIAQDDDGRSKGFGHVEFATEEGAQK 55

Query: 92  AIKIMNMIKLYGKPIRVNKASS 113
           A++  +  +L G+ IRV+ A+ 
Sbjct: 56  ALE-KSGEELLGREIRVDLATE 76

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

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 29/112 (25%), Positives = 41/112 (36%), Gaps = 42/112 (37%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+ NLD +V  K L + F                KL GK +R                 
Sbjct: 1   IFVANLDYKVGWKKLKEVF----------------KLAGKVVRA---------------- 28

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYA-SFEASDASIDAMHGQYLCNRPISV 234
                  +I  D + G S+G   + +    EA  A I   +GQ L +RP+ V
Sbjct: 29  -------DIKEDKE-GKSRGMGVVQFEHPIEAVQA-ISMFNGQMLFDRPMRV 71

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

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 17/52 (32%), Positives = 27/52 (51%)

Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           ++VG L   V    + E F Q G V + ++P D+ T   +GYGF+ F   +
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRD 52

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

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 24/118 (20%), Positives = 45/118 (38%), Gaps = 39/118 (33%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
             +FIG L  + +E+ L   FS +G I +                               
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEV------------------------------ 30

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
                     +++D +T  S+GF F+ + + + +  ++ AM+G+ +  R I V  A K
Sbjct: 31  ---------VVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQAGK 79

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

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

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 17/46 (36%), Positives = 26/46 (56%)

Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
           D  I RD  T  S+GFAF+ +     ++ ++DAM G+ L  R + V
Sbjct: 27  DVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRV 72

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

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

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 20/52 (38%), Positives = 33/52 (63%), Gaps = 4/52 (7%)

Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL---CNRPISVSYA 237
           D  +MRD +   S+G AF+ Y+S E + A+I A++G Y    C++P+ V +A
Sbjct: 28  DIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKALNGVYTMRGCDQPLIVRFA 78

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

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 22/73 (30%), Positives = 40/73 (54%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+V  L     E+++W+LF   G V NV + +D  T   +G+GF+     ++A  AI  +
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 97  NMIKLYGKPIRVN 109
           N  +L  + ++V+
Sbjct: 66  NGYRLGDRVLQVS 78

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|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 = 41.1 bits (97), Expect = 3e-05
 Identities = 15/44 (34%), Positives = 27/44 (61%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS 235
           +  D +TG SK F F++Y + E++ A+I AM+G  +  + + V 
Sbjct: 30  VFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73

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

>gnl|CDD|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 = 41.1 bits (97), Expect = 3e-05
 Identities = 18/59 (30%), Positives = 33/59 (55%)

Query: 51  MWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN 109
           +++LF   G V++  +  D+ T   + +GF+ +   E A  AIK MN  ++ GK ++V 
Sbjct: 15  LYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73

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

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

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 16/33 (48%), Positives = 24/33 (72%)

Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
           D  +MRDP+T  S+GF F+ Y+S E  DA+++A
Sbjct: 31  DCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 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|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 = 23/78 (29%), Positives = 44/78 (56%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D +  + V GL    +E  + E+F + GP+ +V +  D+ ++  +G+ F+ F   +DA  
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 92  AIKIMNMIKLYGKPIRVN 109
           A +  N ++L G+ IRV+
Sbjct: 67  AKERANGMELDGRRIRVD 84

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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 8/76 (10%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+YV G    ++E ++ + F   G ++N+ M K++        GF+ F   E AD AI  
Sbjct: 6   TLYVHGY--GLTEEILKKAFSPFGNIINISMEKEK------NCGFVTFEKMESADRAIAE 57

Query: 96  MNMIKLYGKPIRVNKA 111
           +N   + G  ++V+ A
Sbjct: 58  LNGTTVQGVQLKVSLA 73

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 24/108 (22%), Positives = 44/108 (40%), Gaps = 39/108 (36%)

Query: 125 FIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIF 184
           ++G+L P+V E +LY+ FS  G +L               IRV                 
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLS--------------IRV----------------- 31

Query: 185 IGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPI 232
                    RD  T  S G+A++N+ +   ++ ++D ++   +  +PI
Sbjct: 32  --------CRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKGKPI 71

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 21/73 (28%)

Query: 183 IFIGNLDPE--------------------IMRDPDTGNSKGFAFINYASFEASDASIDAM 222
           IF+GN+D                      I+ D  TG  KGFA+I +    + + ++  +
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60

Query: 223 HGQYLCNRPISVS 235
           +      R I V+
Sbjct: 61  NESEFRGRQIKVT 73

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

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 6/57 (10%)

Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
          T+YVGGL ++V+E  + + F Q G + ++ +    V +  Q   F+ F   E A+ A
Sbjct: 3  TLYVGGLGERVTEKDLRDHFYQFGEIRSITV----VPR--QQCAFVTFTTREAAEKA 53

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 27/114 (23%), Positives = 42/114 (36%), Gaps = 42/114 (36%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+GNL  E  E  L   F   G I +              +R+                
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRR--------------VRM---------------- 30

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                    M   D+G  KGFAF++   FE  + + +A+ G++L  R + V Y 
Sbjct: 31  ---------MTFEDSGKCKGFAFVD---FEEIEFATNALKGKHLNGRALRVEYG 72

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

 Score = 40.9 bits (95), Expect = 4e-05
 Identities = 19/58 (32%), Positives = 35/58 (60%)

Query: 54  LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
           LF   G + +  + +D++T    GYGF+ ++  +DA+ AI  +N ++L  K I+V+ A
Sbjct: 22  LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA 79

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

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 17/58 (29%), Positives = 30/58 (51%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
          +++GGL    +E  + E F + G VV+  + KD +T   +G+GF+ F      D  + 
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLA 58

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

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 20/72 (27%)

Query: 183 IFIGNL-----DPEIM---------------RDPDTGNSKGFAFINYASFEASDASIDAM 222
           IFIG L     + ++                +D  TG SKG+AF  Y     +D +I  +
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 223 HGQYLCNRPISV 234
           +G  L ++ ++V
Sbjct: 63  NGMQLGDKKLTV 74

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

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 24/75 (32%), Positives = 40/75 (53%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I++GGL + +SE  + EL    G +   ++ KD  T   +GY F E++     D AI  +
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 97  NMIKLYGKPIRVNKA 111
           N ++L  K + V +A
Sbjct: 63  NGMQLGDKKLTVQRA 77

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

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

 Score = 40.6 bits (96), Expect = 5e-05
 Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 1/44 (2%)

Query: 58  SGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL 101
            G +V ++MP D   +T +GY F+EF   E+A  A+K +N  KL
Sbjct: 33  VGKIVGIYMPVDETGKT-KGYAFVEFATPEEAKEAVKALNGYKL 75

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

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

 Score = 40.7 bits (95), Expect = 5e-05
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 3/78 (3%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG +   ++E  +  +F + G V+ V + KD+ T   QG  F+++   ++AD AI+ +
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 97  -NMIKLYG--KPIRVNKA 111
            N   L G   P++V  A
Sbjct: 62  HNQRTLPGGASPVQVRYA 79

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

 Score = 44.0 bits (104), Expect = 6e-05
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
             +YV  LDD V++  + ELF + G + +  +  D    + +G+GF+ F   E+A+ A+ 
Sbjct: 286 VNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVS-RGFGFVCFSNPEEANRAVT 344

Query: 95  IMNMIKLYGKPIRVNKA 111
            M+   L GKP+ V  A
Sbjct: 345 EMHGRMLGGKPLYVALA 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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 40.4 bits (95), Expect = 6e-05
 Identities = 24/112 (21%), Positives = 41/112 (36%), Gaps = 40/112 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+GNLD  V E++LY+ F                 L   P+                  
Sbjct: 4   LFVGNLDARVTEEILYELF-----------------LQAGPLE----------------- 29

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS 235
                  +I +DP+ G  K FAF+ +    +   +I  ++G  L  R + + 
Sbjct: 30  -----GVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLLNGIRLFGRELRIK 75

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

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

 Score = 40.4 bits (95), Expect = 7e-05
 Identities = 29/83 (34%), Positives = 41/83 (49%), Gaps = 9/83 (10%)

Query: 36  TIYVGGLDDKV-SETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           TIYVG LD    ++ L+ E F Q+G V  V M  D    T   Y F+EF  +     A+K
Sbjct: 6   TIYVGNLDPTTTADQLL-EFFSQAGEVKYVRMAGDETQPTR--YAFVEFAEQTSVINALK 62

Query: 95  IMNMIKLYGKPIRVNKASSHQKN 117
           +   +   G+P++VN    H  N
Sbjct: 63  LNGAM-FGGRPLKVN----HSNN 80

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

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

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 12/27 (44%), Positives = 18/27 (66%)

Query: 188 LDPEIMRDPDTGNSKGFAFINYASFEA 214
           L  ++ +DP TG SKGF F+ +A +E 
Sbjct: 27  LMVQVKKDPKTGQSKGFGFVRFADYED 53

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

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 19/62 (30%), Positives = 30/62 (48%)

Query: 39  VGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM 98
           V GL  K +E  + + F   G ++ V + KD  T   +G+GF+ F   ED    +   +M
Sbjct: 4   VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRHM 63

Query: 99  IK 100
           I 
Sbjct: 64  ID 65

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|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 40.1 bits (94), Expect = 8e-05
 Identities = 17/33 (51%), Positives = 25/33 (75%), Gaps = 1/33 (3%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHG 224
           I+R PD GNSKG AF+ ++S   + A+I+A+HG
Sbjct: 33  ILRGPD-GNSKGCAFVKFSSHAEAQAAINALHG 64

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

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

 Score = 40.0 bits (94), Expect = 9e-05
 Identities = 15/46 (32%), Positives = 25/46 (54%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           I++D +T  SKG AFI +   E +   + A++ + L  R +  S A
Sbjct: 33  IVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLKCSIA 78

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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 39.7 bits (93), Expect = 9e-05
 Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 8/78 (10%)

Query: 37  IYVGGLDDKVSETLMWELFV-QSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           +Y+G L   V+E+ + +LF     PV +V + K        GY F++   +  AD AI+ 
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKG-------GYAFVDCPDQSWADKAIEK 53

Query: 96  MNMIKLYGKPIRVNKASS 113
           +N   L GK I V  +  
Sbjct: 54  LNGKILQGKVIEVEHSVP 71

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

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

 Score = 38.6 bits (91), Expect = 1e-04
 Identities = 11/38 (28%), Positives = 23/38 (60%)

Query: 200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
              GFAF+ +++ EA++ ++  ++G     RP+ V Y+
Sbjct: 19  KKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 21/117 (17%), Positives = 41/117 (35%), Gaps = 39/117 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+ NL  +  ++ L + FS  G                 PI+                 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVG-----------------PIK---------------RC 29

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
           F+       ++D  +   +GF ++ +A  E +  +++         R I V +A KK
Sbjct: 30  FV-------VKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAKKK 79

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

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGP-VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           +I+VG L  +V+E+ +  LF    P   +  +  D VT   +GYGF+ F  E D   A+ 
Sbjct: 3   SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 95  IMNMIKLYGKPIRVNKAS 112
            M  +   G+P+R++ A+
Sbjct: 63  EMQGVYCGGRPMRISTAT 80

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

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

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 27/123 (21%), Positives = 47/123 (38%), Gaps = 39/123 (31%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           G  IFI NL  + DE +L+  F  FG +                                
Sbjct: 1   GWCIFIYNLGQDADEGILWQMFGPFGAVTNV----------------------------- 31

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                     +++RD +T   KGF F+   ++E +  +I +++G  L ++ + VS+   K
Sbjct: 32  ----------KVIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSFKTSK 81

Query: 241 DSK 243
             K
Sbjct: 82  SHK 84

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

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

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 1/54 (1%)

Query: 185 IGNLDP-EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           IG ++  +++RD  TG S G+ F+NY     +D +I+ ++G  L  + I VSYA
Sbjct: 27  IGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYA 80

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|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+Y GG+   ++E LM + F   G ++ V +  D+      GY F+ F   E A +AI  
Sbjct: 2   TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDK------GYSFVRFNSHESAAHAIVS 55

Query: 96  MNMIKLYGKPIR 107
           +N   + G  ++
Sbjct: 56  VNGTTIEGHVVK 67

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 2/54 (3%)

Query: 53  ELFVQSGPVVNVHMPKDRV-TQTHQGYGFIEFMGEEDADYAIK-IMNMIKLYGK 104
           ELF   G +  V +PK    T +H+G+GF++F+ ++DA  A K + +   LYG+
Sbjct: 19  ELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALCHSTHLYGR 72

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

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 15/58 (25%), Positives = 31/58 (53%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
          +++GGL  + ++  +   F Q G + +  + KD  T+  +G+GF+ F    + D A+ 
Sbjct: 2  LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMN 59

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 27/108 (25%), Positives = 37/108 (34%), Gaps = 47/108 (43%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FIG L  E  +  L + FS +G I                                   
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEIT---------------------------------- 27

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRP 231
                D  +M+DP+T  S+GF F+ +AS    DA   AM       RP
Sbjct: 28  -----DCVVMKDPNTKRSRGFGFVTFASASEVDA---AM-----NARP 62

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 4/80 (5%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YV  L + + +  + ELF + G + +  + KD   ++ +G+GF+ F   E A  A++ +
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKS-KGFGFVNFENHEAAQKAVEEL 62

Query: 97  NMIKLYGKPIRVNKASSHQK 116
           N  ++ GK + V +A   QK
Sbjct: 63  NGKEVNGKKLYVGRA---QK 79

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 26/114 (22%), Positives = 44/114 (38%), Gaps = 40/114 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+G L P+V E+   + FS FG ++                                  
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVV---------------------------------- 27

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                D ++M+D DTG S+GF F+ + S E++   + +     L  + + V  A
Sbjct: 28  -----DAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSAGMLELGGKQVEVKRA 75

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

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

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 1/34 (2%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIM 155
            N+++GNL+P+V E++L   F  FG +    KIM
Sbjct: 2   TNLYVGNLNPKVTEEVLCQEFGRFGPLASV-KIM 34

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA-DYAIKI 95
           ++VGGL   V+E+ + E F + G V +V + K +     +G+ +I+    E         
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 96  MNMIKLYGKPIRVNKA 111
           +N  K  G  +++ +A
Sbjct: 62  LNGTKWKGSVLKIEEA 77

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+ V  LD  VS   + ++F   G +  +     R T   + + FIEF     A+ A+K 
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEI-----RETPNKRHHKFIEFYDVRSAEAALKA 57

Query: 96  MNMIKLYGKPIRV 108
           +N  ++ GK I++
Sbjct: 58  LNRSEIAGKRIKL 70

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

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 12/34 (35%), Positives = 24/34 (70%)

Query: 191 EIMRDPDTGNSKGFAFINYASFEASDASIDAMHG 224
           ++ RDP TG SKGFA++ Y++  ++  + + ++G
Sbjct: 30  DLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNG 63

This subfamily corresponds to the RRM3 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 = 75

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

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 22/73 (30%), Positives = 42/73 (57%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           + V GL    +E  + E+F + GP+  V++  D+ T   +G+ F+ F   +D+  A++  
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHA 61

Query: 97  NMIKLYGKPIRVN 109
           N ++L G+ IRV+
Sbjct: 62  NGMELDGRRIRVD 74

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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
          T++V GL +  +E  + E F  S   +   +  DR T + +G+GF++F  EEDA  A + 
Sbjct: 2  TLFVKGLSEDTTEETLKESFDGS---IAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEA 58

Query: 96 MN 97
          M 
Sbjct: 59 ME 60

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           A +YV GL   +++  +  LF   G ++   +  D VT   +G GFI F    +A+ AIK
Sbjct: 1   ANLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIK 60

Query: 95  IMNMIKLYG--KPIRV 108
            +N     G  +PI V
Sbjct: 61  ALNGTIPPGATEPITV 76

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

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 22/114 (19%), Positives = 37/114 (32%), Gaps = 40/114 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           I + NL   V E  L + F + G +                                   
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVT---------------------------------- 28

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                D ++MR  D G S+ F F+ + S E +  ++   +  ++    ISV  A
Sbjct: 29  -----DVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVKYFNKTFIDTSKISVELA 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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 20/55 (36%), Positives = 33/55 (60%)

Query: 188 LDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
           +D +++ D +TG S+GF F+N+    A+ A+I  M G+ L  R I V+ A  + S
Sbjct: 62  VDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS 116

Length = 144

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

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 19/57 (33%), Positives = 35/57 (61%)

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
           F G++   I+ D DTG+SKGF F++++S E + A+ +AM    +    +++ +A  K
Sbjct: 21  FDGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNKVTLDFAKPK 77

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

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 8/46 (17%)

Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
           D  +MRDP T  S+GF F+ Y+  E  DA+        +  RP  V
Sbjct: 31  DCVVMRDPQTKRSRGFGFVTYSCVEEVDAA--------MSARPHKV 68

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|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 = 15/47 (31%), Positives = 29/47 (61%), Gaps = 6/47 (12%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDA--SIDAMHGQYL--CNRPISV 234
           +++D  T  SKG A++ +A  +AS A  +++ M+G+ L    +P+ V
Sbjct: 34  VVKDKQTKESKGVAYVKFA--KASSAARAMEEMNGKCLGGDTKPLKV 78

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 18/59 (30%), Positives = 36/59 (61%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
          ++VG +   + E  +  LF ++GP+ ++ +  D ++  ++GY FI F G+E A  A+K+
Sbjct: 4  VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKL 62

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

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

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 43  DDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY 102
           DD  SE L  E F + GP+V+V++P D  T+  +G+ +++F    DA+ A+  ++   + 
Sbjct: 10  DDTRSEDLRRE-FGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNLDRKWIC 68

Query: 103 GKPIRVNKASSHQK 116
           G+ I +  A   +K
Sbjct: 69  GRQIEIQFAQGDRK 82

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

 Score = 38.1 bits (88), Expect = 3e-04
 Identities = 16/51 (31%), Positives = 27/51 (52%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
          ++VGGL    +E  + E F   G + N+ +P D  T   +G+ F+ +  EE
Sbjct: 2  VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEE 52

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

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

 Score = 38.1 bits (88), Expect = 4e-04
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 20/76 (26%)

Query: 182 NIFIGNLDPEI--------------------MRDPDTGNSKGFAFINYASFEASDASIDA 221
           ++F+G+L PEI                    ++D  TG SKG+ F+++ +   ++ +I  
Sbjct: 3   HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 222 MHGQYLCNRPISVSYA 237
           M GQ+L  R I  ++A
Sbjct: 63  MGGQWLGGRQIRTNWA 78

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 38.2 bits (88), Expect = 4e-04
 Identities = 19/54 (35%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 185 IGNLDP-EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           IG ++  +++RD  TG S G+ F+NY   + ++ +I+ ++G  L  + I VSYA
Sbjct: 28  IGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA 81

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 2/48 (4%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL--CNRPISVSYA 237
           I+ D  TG S+G  FI +     ++ +I A++G        PI+V +A
Sbjct: 32  ILCDNVTGLSRGVGFIRFDKRIEAERAIKALNGTIPPGATEPITVKFA 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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 38.2 bits (89), Expect = 4e-04
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 6/71 (8%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VGGL+ K S++ +   F + G +    +  D  T+  +G+GFI F   ++AD A++  
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQ 64

Query: 97  ------NMIKL 101
                 N I+L
Sbjct: 65  PHSIDGNQIEL 75

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

 Score = 38.1 bits (88), Expect = 4e-04
 Identities = 19/61 (31%), Positives = 36/61 (59%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
          I+VG +   + E  +  LF ++GP+ ++ +  D +T  ++GY F+ F  +E A  A+K+ 
Sbjct: 4  IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63

Query: 97 N 97
          N
Sbjct: 64 N 64

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

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

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 22/109 (20%), Positives = 39/109 (35%), Gaps = 44/109 (40%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           I++ ++ P++ E  +   F AFG I                                   
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSC-------------------------------- 30

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMH-----GQYL 227
                   +  DP+TG  KG+ FI Y + +++  +I +M+     GQ L
Sbjct: 31  -------SLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQL 72

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

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 14/47 (29%), Positives = 27/47 (57%)

Query: 191 EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           +++ D  TG S+GF F+ + S E +  + + ++G  +  R I V Y+
Sbjct: 30  QVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRVDYS 76

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

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 37.4 bits (87), Expect = 6e-04
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+V  LD KV    + E+F  +G VV   + +D+  ++ +G G ++F    +A  AI + 
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKS-RGMGVVQFEHPIEAVQAISMF 59

Query: 97  NMIKLYGKPIRV 108
           N   L+ +P+RV
Sbjct: 60  NGQMLFDRPMRV 71

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

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

 Score = 37.4 bits (87), Expect = 6e-04
 Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L  + +E  +   F + G +  V M     +   +G+ F++F   E+ ++A   +
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF---EEIEFATNAL 57

Query: 97  NMIKLYGKPIRVNKAS 112
               L G+ +RV    
Sbjct: 58  KGKHLNGRALRVEYGE 73

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

 Score = 37.8 bits (87), Expect = 6e-04
 Identities = 19/54 (35%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 185 IGNLDP-EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           IG ++  +++RD  TG S G+ F+NY   + ++ +I+ ++G  L  + I VSYA
Sbjct: 26  IGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA 79

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

 Score = 37.4 bits (87), Expect = 7e-04
 Identities = 25/115 (21%), Positives = 41/115 (35%), Gaps = 42/115 (36%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            +F+GNL+  + E+ L   F  +GV+                                  
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVE--------------------------------- 30

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFE-ASDASIDAMHGQYLCNRPISVSY 236
                 D +I R P  G    +AF+ + + + A  A + AM GQY+    I + Y
Sbjct: 31  ------DVDIKR-PPRGQGNAYAFVKFLNLDMAHRAKV-AMSGQYIGRNQIKIGY 77

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

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

 Score = 40.6 bits (95), Expect = 7e-04
 Identities = 64/288 (22%), Positives = 99/288 (34%), Gaps = 43/288 (14%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++V  L   V E  + E  +  GPV  V M         +    +EF  EE A   +   
Sbjct: 5   VHVRNLPQDVVEADLVEALIPFGPVSYVMMLP------GKRQALVEFEDEESAKACVNFA 58

Query: 97  --NMIKLYGKPIRVNKASSHQK-----NLDV---GAN----IFIGNLDPEVDEKLLYDTF 142
               I + G+P   N  S+ Q+     N D    G N    + + N    +   +LY  F
Sbjct: 59  TSVPIYIRGQPAFFN-YSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIF 117

Query: 143 SAFGVILQ--TPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIG--NLDPEIMRDPDT 198
           + +G +L+  T    N+ +   +   VN A   +  L+ GA+I+ G   L  E  + P  
Sbjct: 118 NPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALN-GADIYNGCCTLKIEYAK-PTR 175

Query: 199 -----GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAER 253
                 +     + N       D  +D  H Q           ++  D      G  A  
Sbjct: 176 LNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLA-- 233

Query: 254 LLAAQNPLSQADR---PHQLFADAPPPAPLPPPPPPINIMGLPPPPPS 298
                 PL+  DR   PH   +   P     P  P I+  G     P 
Sbjct: 234 ------PLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPG 275

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067). Length = 481

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

 Score = 37.0 bits (86), Expect = 7e-04
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 9/74 (12%)

Query: 36  TIYVGGLDDKVSETLMWE-LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           T++V G D   +     E LF   GP+V   + K         + F+EF   EDA  A++
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKT--------FAFVEFEDSEDATKALE 52

Query: 95  IMNMIKLYGKPIRV 108
            ++  ++ G  + V
Sbjct: 53  ALHGSRIDGSVLTV 66

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

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

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +Y+G L  +  E  +   F   G +  +++          G+GF+EF    DAD A+  +
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYEL 53

Query: 97  NMIKLYGKPIRVNKA 111
           N  +L G+ + V  A
Sbjct: 54  NGKELCGERVIVEHA 68

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

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

 Score = 37.2 bits (87), Expect = 8e-04
 Identities = 19/118 (16%), Positives = 37/118 (31%), Gaps = 44/118 (37%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+ N++  V+++ L   F  FG I     +    K                        
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDI---RTLYTACK------------------------ 36

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                             +GF  ++Y    A+  +  A+ G  L  R + + ++  KD
Sbjct: 37  -----------------HRGFIMVSYYDIRAARRAKRALQGTELGGRKLDIHFSIPKD 77

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

>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 37.7 bits (87), Expect = 8e-04
 Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 7/82 (8%)

Query: 36  TIYVGGLDDKVS-ETL---MWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           TIY+  L+DK+  E L   ++ LF Q G VV++   K   T   +G  F+ F     A  
Sbjct: 3   TIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELSSATN 59

Query: 92  AIKIMNMIKLYGKPIRVNKASS 113
           A++ +     YGKP+R+  A +
Sbjct: 60  ALRQLQGFPFYGKPMRIQYAKT 81

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 22/109 (20%), Positives = 39/109 (35%), Gaps = 41/109 (37%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++ NL P V E                  +      YGK   V                
Sbjct: 1   LYVRNLPPSVTE----------------EDLREFFSPYGKVEGV---------------- 28

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPI 232
                   ++R+ D    +GFAF+ +AS E ++A++  ++G  L  R +
Sbjct: 29  -------RLVRNKD--RPRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68

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

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 3/48 (6%)

Query: 191 EIMRDPDTGNSKGFAFINYAS-FEASDASIDAMHGQYLCNRPISVSYA 237
            I R PD G  KGFAF+ + S  +A  A I  ++G+ +  RP++V +A
Sbjct: 30  TIPRKPD-GKKKGFAFVQFTSKADAEKA-IKGVNGKKIKGRPVAVDWA 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|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 20/76 (26%)

Query: 182 NIFIGNLDPEI--------------------MRDPDTGNSKGFAFINYASFEASDASIDA 221
           ++F+G+L PEI                    ++D  TG SKG+ F+++ +   ++ +I  
Sbjct: 3   HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 222 MHGQYLCNRPISVSYA 237
           M GQ+L  R I  ++A
Sbjct: 63  MGGQWLGGRQIRTNWA 78

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

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

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 16/47 (34%), Positives = 32/47 (68%)

Query: 191 EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           +++RD   G+S G+ F+NY + + ++ +I+ ++G  L ++ I VSYA
Sbjct: 32  KLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSKTIKVSYA 78

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 10/28 (35%), Positives = 21/28 (75%)

Query: 197 DTGNSKGFAFINYASFEASDASIDAMHG 224
           +TG +KG+AF+ +A+ E +  ++ A++G
Sbjct: 45  ETGKTKGYAFVEFATPEEAKEAVKALNG 72

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

>gnl|CDD|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 = 36.9 bits (86), Expect = 0.001
 Identities = 13/39 (33%), Positives = 22/39 (56%)

Query: 198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
            G SKGFA++ +AS  A+ A  + + G+    +   V+Y
Sbjct: 38  NGKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKCVVTY 76

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           D +++R  D G S+  AFI Y + E +  + D  +  Y+    ISV +A
Sbjct: 30  DVKLLRTED-GKSRRIAFIGYKTEEEAQKAKDYFNNTYINTSKISVEFA 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|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            ++VG L    +   +   F  +G   +V +  D+ T   +G  F+EF   E    A+K 
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK- 60

Query: 96  MNMIKLYGKPIRV 108
           ++   L G+ I V
Sbjct: 61  LHHTLLKGRKINV 73

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

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 19/62 (30%), Positives = 36/62 (58%)

Query: 55  FVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH 114
           F + GP+V+V++P D  T+  +G+ +I+F    DA+ A+  +N   + G+ I +  A   
Sbjct: 21  FGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNLNRKWVCGRQIEIQFAQGD 80

Query: 115 QK 116
           +K
Sbjct: 81  RK 82

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

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+Y GG+   ++E LM + F   G ++ + +  ++      GY FI F   E A +AI  
Sbjct: 2   TVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEK------GYSFIRFSTHESAAHAIVS 55

Query: 96  MNMIKLYGKPIR 107
           +N   + G  ++
Sbjct: 56  VNGTTIEGHVVK 67

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

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

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 17/51 (33%), Positives = 28/51 (54%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
          I+VGGL    +   + + F Q G V +  +  D+ T  H+G+GF+ F  E+
Sbjct: 2  IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52

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|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative RNA exonuclease NEF-sp

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 16/61 (26%), Positives = 29/61 (47%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
          IYV G    ++E  + E F Q   +  + +PKD ++     Y F++F   + A  A+  +
Sbjct: 1  IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60

Query: 97 N 97
           
Sbjct: 61 T 61

This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 14/74 (18%)

Query: 36  TIYVGGLD-----DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
           T+YV G       D + E      F + G V N+ M +D   +  +G  F+EF  EEDA 
Sbjct: 1   TVYVKGFPKDATLDDIQE-----FFEKFGKVNNIRMRRDL-DKKFKGSVFVEFKTEEDAK 54

Query: 91  YAIKIMNMIKLYGK 104
              K +   KL  K
Sbjct: 55  ---KFLEKEKLKYK 65

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

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 26/113 (23%), Positives = 48/113 (42%), Gaps = 39/113 (34%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
           A++++G+LDP+V E  LYD F  FG +L               +RV              
Sbjct: 1   ASLYVGDLDPDVTEAKLYDLFKPFGPVLS--------------VRV-------------- 32

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
                       RD  T  S G+ ++N+ +   ++ +++ M+ + L  +PI +
Sbjct: 33  -----------CRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRI 74

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

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 17/40 (42%), Positives = 23/40 (57%)

Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
           DP T   KGFAF+ Y   EA+  +++ M+G  L  R I V
Sbjct: 35  DPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 74

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

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 18/111 (16%), Positives = 40/111 (36%), Gaps = 44/111 (39%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++GNL P   ++ L D F  +G +                                 ++
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPL--------------------------------RSV 29

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
           ++        R+P      GFAF+ +     ++ ++ A+ G+ +C   + V
Sbjct: 30  WVA-------RNP-----PGFAFVEFEDPRDAEDAVRALDGRRICGNRVRV 68

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

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

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 3/53 (5%)

Query: 188 LDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC---NRPISVSYA 237
           L+  I++D  TG+ +G  F+ Y++ + +D +I A+H Q        P+ V YA
Sbjct: 27  LEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRALHNQRTLPGGASPVQVRYA 79

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 22/96 (22%), Positives = 33/96 (34%), Gaps = 42/96 (43%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+G L P V E  L + FS FG +                                   
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTV----------------------------------- 26

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASI 219
                D EI++  D G  +GFA+I+      S+A +
Sbjct: 27  ----SDVEIIKKKDAGPDRGFAYID---LRTSEAQL 55

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            ++V GL   V++  + +LF + G V +V +  +R  +  +G  ++E+  E  A  A+  
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKP-KGLAYVEYENESSASQAVLK 62

Query: 96  MNMIKLYGKPIRV 108
           M+  ++  K I V
Sbjct: 63  MDGTEIKEKTISV 75

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

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

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VGGL    ++  + E F + G VV+  +  D VT   +G+GF+ F   +DA    K++
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLF---KDAASVEKVL 57

Query: 97  NMI--KLYGKPIRVNKA 111
           +    KL G+ I   +A
Sbjct: 58  DQKEHKLDGRVIDPKRA 74

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

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 13/35 (37%), Positives = 23/35 (65%)

Query: 202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
             FAF+ + S E++  + D++HG+ L N P+ V+Y
Sbjct: 33  SNFAFVEFESLESAIRAKDSVHGKVLNNNPLYVTY 67

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVV--NVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           I+V  L   V+   + +LF + G V+  +V    D  ++   G+G + F   EDA  AI+
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSK---GFGTVLFESPEDAQRAIE 57

Query: 95  IMNMIKLYGKPIRV 108
           + N   L G+ + V
Sbjct: 58  MFNGYDLEGRELEV 71

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

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 26/114 (22%), Positives = 46/114 (40%), Gaps = 42/114 (36%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++GNLD  V E LL + FS  G                 PI+  K              
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIG-----------------PIKSCK-------------- 29

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                   ++R+   GN   +AF+ Y    ++ A++  M+G+ +  + I V++A
Sbjct: 30  --------LIREH--GNDP-YAFVEYYDHRSAAAALQTMNGRLILGQEIKVNWA 72

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

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 13/66 (19%), Positives = 32/66 (48%), Gaps = 13/66 (19%)

Query: 183 IFIGNLDPEIMRDPD-----------TGNS--KGFAFINYASFEASDASIDAMHGQYLCN 229
           +F+GNL+ + +   D            G S  KG+ F+ + + E + A++   +G+ +  
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKGYGFVQFDNEEDARAAVAGENGREIAG 62

Query: 230 RPISVS 235
           + + ++
Sbjct: 63  QKLDIN 68

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

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

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 16/49 (32%), Positives = 27/49 (55%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
           ++ D  TG S+GFAF+ +   + S  +++  +G  L  R I V Y+  K
Sbjct: 31  VVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRVDYSITK 79

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

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 17/51 (33%), Positives = 27/51 (52%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
          I+VGGL        + + F Q G V +  +  D+ T  H+G+GF+ F  E+
Sbjct: 6  IFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENED 56

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 13/43 (30%), Positives = 22/43 (51%)

Query: 55 FVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN 97
          F + G + +  + +D+ T     Y FIEF  +ED + A   M+
Sbjct: 24 FSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMD 66

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|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 7/61 (11%)

Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
          G  T++VGGL +  +E ++ E+F Q G ++ + M K       + +  I F  E   D A
Sbjct: 5  GCKTVFVGGLPENATEEIIREVFEQCGEIIAIRMSK-------KNFCHIRFAEEFAVDKA 57

Query: 93 I 93
          I
Sbjct: 58 I 58

This subgroup corresponds to the conserved RNA recognition motif (RRM) in ECTO-NOX proteins (also termed ENOX), comprising a family of plant and animal NAD(P)H oxidases exhibiting both, oxidative and protein disulfide isomerase-like, activities. They are growth-related and drive cell enlargement, and may play roles in aging and neurodegenerative diseases. ENOX proteins function as terminal oxidases of plasma membrane electron transport (PMET) through catalyzing electron transport from plasma membrane quinones to extracellular oxygen, forming water as a product. They are also hydroquinone oxidases that oxidize externally supplied NADH, hence NOX. ENOX proteins harbor a di-copper center that lack flavin. ENOX proteins display protein disulfide interchange activity that is also possessed by protein disulfide isomerase. In contrast to the classic protein disulfide isomerases, ENOX proteins lack the double CXXC motif. This family includes two ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed candidate growth-related and time keeping constitutive hydroquinone [NADH] oxidase (cCNOX), or cell proliferation-inducing gene 38 protein, or Constitutive Ecto-NOX (cNOX), is the constitutively expressed cell surface NADH (ubiquinone) oxidase that is ubiquitous and refractory to drugs. ENOX2, also termed APK1 antigen, or cytosolic ovarian carcinoma antigen 1, or tumor-associated hydroquinone oxidase (tNOX), is a cancer-specific variant of ENOX1 and plays a key role in cell proliferation and tumor progression. In contrast to ENOX1, ENOX2 is drug-responsive and harbors a drug binding site to which the cancer-specific S-peptide tagged pan-ENOX2 recombinant (scFv) is directed. Moreover, ENOX2 is specifically inhibited by a variety of quinone site inhibitors that have anticancer activity and is unique to the surface of cancer cells. ENOX proteins contain many functional motifs. Length = 84

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 16/47 (34%), Positives = 29/47 (61%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEF 83
          ++VGGL  + ++  +   F Q G VV+  + KD+ T   +G+GF++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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 19/51 (37%), Positives = 26/51 (50%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
          I+VGGL     E  + E F   G V ++ +P D  T   +G+ FI F  EE
Sbjct: 2  IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEE 52

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

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 4/58 (6%)

Query: 156 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
           N I L G P+ V +       +  G    +   D  +MR   TG S+GFAF+ + S E
Sbjct: 3   NTIMLRGLPLSVTEEDIRNALVSHG----VEPKDVRLMRRKTTGASRGFAFVEFMSLE 56

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 11/36 (30%), Positives = 22/36 (61%)

Query: 202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           K +AF+++   + +  +++ M+G+ L   PI VS A
Sbjct: 35  KDYAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLA 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|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 = 35.8 bits (83), Expect = 0.004
 Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL---CNRPISVSYA 237
           +++D  TG  KG AF+ Y + E++  +  A+H Q      NRPI V  A
Sbjct: 37  VLKDKYTGMHKGCAFLTYCARESALKAQSALHEQKTLPGMNRPIQVKPA 85

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

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 20/103 (19%), Positives = 36/103 (34%), Gaps = 39/103 (37%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           N++I  L P   ++ L      FG I+ T  I+                           
Sbjct: 2   NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAIL--------------------------- 34

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQ 225
                       D  T   KG+ F+++ S EA+  +I+ ++G+
Sbjct: 35  ------------DKKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65

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

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

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPV-VNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           T+++G L+  + E  + +++   G   VNV + + R +  + GY F+EF     A  A+ 
Sbjct: 1   TLWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALS 60

Query: 95  IMNM-IKLYGKPIRVNKASS 113
           +    I    +  ++N AS 
Sbjct: 61  LNGTPIPNSNRTFKLNWASG 80

This subgroup corresponds to the RRM1 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 81

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

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 26/118 (22%), Positives = 44/118 (37%), Gaps = 40/118 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+G+L P+VD+  LY+ FS                         +  S +         
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSK------------------------RYPSCK--------- 30

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYAS-FEASDASIDAMHGQYLCNRPISVSYAFKK 240
                  +++ D   GNS+G+ F+ ++   E   A  +      L  +PI VS A  K
Sbjct: 31  -----GAKVVLDQ-NGNSRGYGFVRFSDESEQKRALTEMQGASGLGGKPIRVSLAIPK 82

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

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

 Score = 35.3 bits (81), Expect = 0.004
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 3/60 (5%)

Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
          I+VGG+ +   E  + + F Q G +  + +  DR +   +G+ F+ F   +D D   KI+
Sbjct: 3  IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF---DDHDSVDKIV 59

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

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

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 8/75 (10%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +Y+G L   V E  +   F   G ++ + +          GYGF+EF    DAD A+  +
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYEL 53

Query: 97  NMIKLYGKPIRVNKA 111
           N   L G+ + V  A
Sbjct: 54  NGKDLCGERVIVEHA 68

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	305
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0148|consensus	321		100.0
KOG0131|consensus	203		100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
KOG0144|consensus	510		99.98
KOG0117|consensus	506		99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.96
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.96
KOG0145|consensus	360		99.96
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
KOG0145|consensus	360		99.94
KOG0124|consensus	544		99.93
KOG0109|consensus	346		99.93
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.92
KOG0127|consensus	678		99.91
KOG0127|consensus	678		99.9
KOG0123|consensus	369		99.9
KOG0146|consensus	371		99.89
KOG0123|consensus	369		99.89
KOG0148|consensus	321		99.88
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.86
KOG0110|consensus	725		99.86
KOG0144|consensus	510		99.86
KOG0147|consensus	549		99.85
KOG4205|consensus	311		99.84
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.82
KOG0147|consensus	549		99.8
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.77
KOG0117|consensus	506		99.76
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.74
KOG0105|consensus	241		99.74
KOG4212|consensus	608		99.72
KOG1457|consensus	284		99.68
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.67
KOG1548|consensus	382		99.67
KOG4206|consensus	221		99.67
KOG0124|consensus	544		99.65
KOG0106|consensus	216		99.64
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.64
KOG0122|consensus	270		99.62
KOG0125|consensus	376		99.6
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.59
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.58
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.57
KOG0121|consensus	153		99.57
KOG1190|consensus	492		99.57
KOG0149|consensus	247		99.56
KOG0120|consensus	500		99.55
KOG0110|consensus	725		99.54
PLN03120	260	nucleic acid binding protein; Provisional	99.54
KOG0113|consensus	335		99.52
KOG0132|consensus	894		99.5
PLN03213	759	repressor of silencing 3; Provisional	99.5
KOG4211|consensus	510		99.49
KOG0126|consensus	219		99.49
smart00362	72	RRM_2 RNA recognition motif.	99.48
KOG0107|consensus	195		99.48
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.47
PLN03121	243	nucleic acid binding protein; Provisional	99.46
KOG0111|consensus	298		99.45
smart00360	71	RRM RNA recognition motif.	99.45
KOG4207|consensus	256		99.44
KOG1456|consensus	494		99.42
KOG0122|consensus	270		99.42
KOG0108|consensus	435		99.41
KOG1190|consensus	492		99.41
KOG4212|consensus	608		99.4
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.39
KOG0130|consensus	170		99.38
KOG0114|consensus	124		99.38
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.38
KOG0107|consensus	195		99.36
KOG1456|consensus	494		99.33
KOG0111|consensus	298		99.33
KOG0149|consensus	247		99.33
KOG4207|consensus	256		99.33
KOG0121|consensus	153		99.32
KOG1365|consensus	508		99.32
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.3
smart00361	70	RRM_1 RNA recognition motif.	99.29
KOG0125|consensus	376		99.28
PLN03120	260	nucleic acid binding protein; Provisional	99.28
KOG0130|consensus	170		99.26
KOG0120|consensus	500		99.24
smart00362	72	RRM_2 RNA recognition motif.	99.24
KOG0126|consensus	219		99.24
KOG0108|consensus	435		99.23
PLN03213	759	repressor of silencing 3; Provisional	99.23
KOG0113|consensus	335		99.22
KOG0131|consensus	203		99.21
smart00360	71	RRM RNA recognition motif.	99.21
KOG4454|consensus	267		99.18
KOG0114|consensus	124		99.16
KOG0129|consensus	520		99.13
KOG4661|consensus	940		99.12
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.12
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.12
KOG0109|consensus	346		99.11
smart00361	70	RRM_1 RNA recognition motif.	99.1
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.1
KOG0146|consensus	371		99.09
PLN03121	243	nucleic acid binding protein; Provisional	99.07
KOG0415|consensus	479		99.07
KOG0226|consensus	290		99.06
KOG0132|consensus	894		99.03
KOG0112|consensus	975		99.03
KOG0105|consensus	241		99.0
KOG4660|consensus	549		98.99
KOG0153|consensus	377		98.98
KOG4210|consensus	285		98.97
KOG0415|consensus	479		98.96
KOG4208|consensus	214		98.94
KOG4205|consensus	311		98.83
KOG4206|consensus	221		98.81
KOG0533|consensus	243		98.78
KOG0226|consensus	290		98.76
KOG4211|consensus	510		98.74
KOG4208|consensus	214		98.73
KOG0128|consensus	881		98.68
KOG0116|consensus	419		98.64
KOG2193|consensus	584		98.62
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.6
KOG4209|consensus	231		98.59
KOG4676|consensus	479		98.57
KOG0151|consensus	877		98.45
KOG1457|consensus	284		98.38
KOG4849|consensus	498		98.37
KOG0153|consensus	377		98.35
KOG4661|consensus	940		98.31
KOG4660|consensus	549		98.24
KOG0151|consensus	877		98.23
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.2
KOG4849|consensus	498		98.13
KOG0533|consensus	243		98.13
KOG4307|consensus	944		98.11
KOG4209|consensus	231		98.04
KOG0116|consensus	419		98.03
KOG0106|consensus	216		98.02
KOG1365|consensus	508		97.97
KOG4454|consensus	267		97.97
KOG1548|consensus	382		97.92
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.91
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.9
KOG1995|consensus	351		97.81
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.77
KOG0128|consensus	881		97.73
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.7
KOG4210|consensus	285		97.6
KOG2416|consensus	718		97.57
KOG3152|consensus	278		97.5
KOG2314|consensus	698		97.5
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.47
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.41
KOG1995|consensus	351		97.35
KOG4307|consensus	944		97.29
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.03
KOG0115|consensus	275		97.02
KOG2202|consensus	260		97.01
KOG2314|consensus	698		97.01
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.92
KOG1855|consensus	484		96.88
KOG1924|consensus	1102		96.79
KOG0129|consensus	520		96.77
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.71
KOG1996|consensus	378		96.68
KOG2202|consensus	260		96.67
KOG4676|consensus	479		96.59
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.4
KOG0112|consensus	975		96.31
KOG2416|consensus	718		95.92
KOG1996|consensus	378		95.74
KOG3152|consensus	278		95.68
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.68
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	95.3
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.26
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.22
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	94.81
KOG2193|consensus	584		94.66
KOG0115|consensus	275		94.63
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.62
KOG2068|consensus	327		94.45
KOG1855|consensus	484		94.27
KOG2591|consensus	684		93.99
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.8
KOG2253|consensus	668		93.78
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.64
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.48
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	93.2
KOG4285|consensus	350		92.72
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	92.53
KOG0804|consensus	493		91.09
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	89.78
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	89.74
KOG2135|consensus	526		89.55
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	89.4
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	88.83
KOG4574|consensus	1007		88.02
KOG2591|consensus	684		85.26
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	85.26
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	84.73
KOG4285|consensus	350		84.23
KOG4574|consensus	1007		83.2
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	82.74
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	80.93

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=2.9e-34  Score=266.44  Aligned_cols=208  Identities=29%  Similarity=0.517  Sum_probs=175.2

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (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            46799999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             CccccccccccccccCCCchhcHHHHHHHHhhcCcccchh----------------------------hhhhhhhhcC--
Q psy3016         113 SHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP----------------------------KIMNMIKLYG--  162 (305)
Q Consensus       113 ~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~----------------------------~~~~~~~~~~--  162 (305)
                      +..... ..++|||+||+..+++++|+++|+.||.|..+.                            ..+|+..+.|  
T Consensus        82 ~~~~~~-~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~  160 (352)
T TIGR01661        82 PSSDSI-KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCT  160 (352)
T ss_pred             cccccc-ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCc
Confidence            654322 356899999999999999999999999886542                            1255555555  


Q ss_pred             cceeeecCcccccc------------------------------------------------------------------
Q psy3016         163 KPIRVNKASSHQKN------------------------------------------------------------------  176 (305)
Q Consensus       163 ~~~~~~~~~~~~~~------------------------------------------------------------------  176 (305)
                      ..+.+.++......                                                                  
T Consensus       161 ~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (352)
T TIGR01661       161 EPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHA  240 (352)
T ss_pred             eeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccc
Confidence            34556555322100                                                                  


Q ss_pred             -------------------------CCCcceeEeccCCCC--------------------cccCCCCCCccceEEEEeCC
Q psy3016         177 -------------------------LDVGANIFIGNLDPE--------------------IMRDPDTGNSKGFAFINYAS  211 (305)
Q Consensus       177 -------------------------~~~~~~~~~~~l~~~--------------------i~~d~~~~~~~g~afV~f~~  211 (305)
                                               ...+.+||++||+..                    +++|..++.++|||||+|.+
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~  320 (352)
T TIGR01661       241 AQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTN  320 (352)
T ss_pred             cccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECC
Confidence                                     011236999999976                    57787889999999999999


Q ss_pred             hHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         212 FEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       212 ~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .++|.+|+.+|||.+|+||.|+|.|+..+.
T Consensus       321 ~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       321 YDEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             HHHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence            999999999999999999999999987664

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=1e-33  Score=259.94  Aligned_cols=173  Identities=25%  Similarity=0.464  Sum_probs=157.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||.++|+++|+++|+.||+|.+|+|+.|..+++++|||||+|.+.++|++|++.|++..+.++.|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            44567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             eCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCC
Q psy3016         110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLD  189 (305)
Q Consensus       110 ~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  189 (305)
                      ++.+..... ...+|||+||+..+|+++|+++|++||.|..+                                      
T Consensus       183 ~a~p~~~~~-~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v--------------------------------------  223 (346)
T TIGR01659       183 YARPGGESI-KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQK--------------------------------------  223 (346)
T ss_pred             ccccccccc-ccceeEEeCCCCcccHHHHHHHHHhcCCEEEE--------------------------------------
Confidence            987644322 35689999999999999999999999999877                                      


Q ss_pred             CCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecC--eeeEEEEeeecCC
Q psy3016         190 PEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN--RPISVSYAFKKDS  242 (305)
Q Consensus       190 ~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g--~~l~v~~a~~~~~  242 (305)
                       +++.|..+++++|||||+|.+.++|.+||+.||+..+.+  +.|+|.++.....
T Consensus       224 -~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       224 -NILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             -EEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcccc
Confidence             678888899999999999999999999999999998865  7899999876543

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).

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

Probab=100.00  E-value=3.1e-33  Score=274.76  Aligned_cols=212  Identities=30%  Similarity=0.552  Sum_probs=181.7

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ...+..+|||+|||.++|+++|+++|+.||.|.+|+++.+. +|+++|||||+|.+.++|.+|++.+||..+.|+.|.|.
T Consensus        84 ~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~  162 (562)
T TIGR01628        84 RRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVG  162 (562)
T ss_pred             cccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEe
Confidence            44456789999999999999999999999999999999885 77899999999999999999999999999999999998


Q ss_pred             eCCCcccc----ccccccccccCCCchhcHHHHHHHHhhcCcccchh---------------------------hhhhhh
Q psy3016         110 KASSHQKN----LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP---------------------------KIMNMI  158 (305)
Q Consensus       110 ~~~~~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~---------------------------~~~~~~  158 (305)
                      ....+...    .....+|||+||+.++|+++|+++|+.||.|..+.                           ..+++.
T Consensus       163 ~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~  242 (562)
T TIGR01628       163 RFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGK  242 (562)
T ss_pred             ccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCc
Confidence            76654333    23457899999999999999999999999987752                           225667


Q ss_pred             hhc----CcceeeecCcccccc-----------------CCCcceeEeccCCCC--------------------cccCCC
Q psy3016         159 KLY----GKPIRVNKASSHQKN-----------------LDVGANIFIGNLDPE--------------------IMRDPD  197 (305)
Q Consensus       159 ~~~----~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~l~~~--------------------i~~d~~  197 (305)
                      .+.    |+.+.+.+++...+.                 ...+.+||++||+..                    ++.| .
T Consensus       243 ~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~  321 (562)
T TIGR01628       243 KIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-E  321 (562)
T ss_pred             EecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-C
Confidence            777    888888887765332                 345688999999876                    4566 5


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.++..+..+
T Consensus       322 ~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~  367 (562)
T TIGR01628       322 KGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQR  367 (562)
T ss_pred             CCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHHH
Confidence            6899999999999999999999999999999999999999876543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0148|consensus

Probab=100.00  E-value=2.6e-33  Score=238.14  Aligned_cols=167  Identities=28%  Similarity=0.483  Sum_probs=154.0

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..-.||||.|...++.++|++.|.+||+|.+++|++|..++++||||||.|.+.++|++||..|||.-|.+|.|+.+|+.
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            35589999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             Cccccc---------------cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccC
Q psy3016         113 SHQKNL---------------DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNL  177 (305)
Q Consensus       113 ~~~~~~---------------~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  177 (305)
                      .+..+.               ...++|||+|++..+||++|++.|.+||.|.++                          
T Consensus       141 RKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EV--------------------------  194 (321)
T KOG0148|consen  141 RKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEV--------------------------  194 (321)
T ss_pred             cCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEE--------------------------
Confidence            765322               235889999999999999999999999999987                          


Q ss_pred             CCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcC
Q psy3016         178 DVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKG  244 (305)
Q Consensus       178 ~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~  244 (305)
                                   +++.|      +||+||+|++.|+|.+||..+|++++.|..++|.|.++..+..
T Consensus       195 -------------RvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~~  242 (321)
T KOG0148|consen  195 -------------RVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDGI  242 (321)
T ss_pred             -------------EEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCCC
Confidence                         56666      8999999999999999999999999999999999998876543

>KOG0131|consensus

Probab=100.00  E-value=1.2e-32  Score=221.83  Aligned_cols=194  Identities=78%  Similarity=1.265  Sum_probs=183.2

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      ..+.++..|||||||+..++++.|+++|-+.|+|.++.+.+|+.+...+|||||+|.++|+|+-|++-||+..+.|+.|+
T Consensus         3 ~~~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIr   82 (203)
T KOG0131|consen    3 IIERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIR   82 (203)
T ss_pred             ccccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeE
Confidence            45667788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEecc
Q psy3016         108 VNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGN  187 (305)
Q Consensus       108 v~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  187 (305)
                      |..+.....+.+...+|||+||++.+++..|+++|+.||.+....                                   
T Consensus        83 v~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P-----------------------------------  127 (203)
T KOG0131|consen   83 VNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPP-----------------------------------  127 (203)
T ss_pred             EEecccccccccccccccccccCcchhHHHHHHHHHhccccccCC-----------------------------------
Confidence            999997777788889999999999999999999999999998643                                   


Q ss_pred             CCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcCCCCCchHHhhhhhcC
Q psy3016         188 LDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQN  259 (305)
Q Consensus       188 l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~  259 (305)
                         +||+|+.+|+++||+||.|++.+.+.+|+..+||+.+++++++|++++.++.++.+++....++.+.+.
T Consensus       128 ---~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg~~~g~~~~rllaa~~  196 (203)
T KOG0131|consen  128 ---KIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKGERHGTAAERLLAAQD  196 (203)
T ss_pred             ---cccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCCcccCCCHHHHHhhccC
Confidence               679999999999999999999999999999999999999999999999999999999999999888873

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=100.00  E-value=5.5e-32  Score=261.05  Aligned_cols=174  Identities=25%  Similarity=0.433  Sum_probs=157.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++||||||+..+++++|+++|+.||+|.+|+++.|+.+++++|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus       103 a~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~  182 (612)
T TIGR01645       103 ALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  182 (612)
T ss_pred             hhcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeec
Confidence            34467899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eCCCccc----------cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCC
Q psy3016         110 KASSHQK----------NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDV  179 (305)
Q Consensus       110 ~~~~~~~----------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  179 (305)
                      +......          .....++|||+||+.++++++|+++|+.||.|..+                            
T Consensus       183 rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~sv----------------------------  234 (612)
T TIGR01645       183 RPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKC----------------------------  234 (612)
T ss_pred             ccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEE----------------------------
Confidence            7553211          11234789999999999999999999999999987                            


Q ss_pred             cceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       180 ~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                                 .+++|..+++++|||||+|++.++|.+|+..||+..++|+.|+|.++.....
T Consensus       235 -----------rl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~  286 (612)
T TIGR01645       235 -----------QLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPD  286 (612)
T ss_pred             -----------EEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCcc
Confidence                       7788888899999999999999999999999999999999999999886543

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.

>KOG0144|consensus

Probab=99.98  E-value=1.1e-31  Score=241.10  Aligned_cols=183  Identities=29%  Similarity=0.531  Sum_probs=164.1

Q ss_pred             cccCCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCc-e
Q psy3016          22 TKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMI-K  100 (305)
Q Consensus        22 ~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~-~  100 (305)
                      ..+...+..+.+.-++|||-||+.++|.||+++|++||.|.+|.|++|+.++.++|||||+|.+.++|.+|+..|+++ .
T Consensus        22 ~~~~~~d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~kt  101 (510)
T KOG0144|consen   22 GSLDHTDNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKT  101 (510)
T ss_pred             CCCCCCCCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccc
Confidence            334455556677789999999999999999999999999999999999999999999999999999999999999875 5


Q ss_pred             eCC--eeeEEeeCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCC
Q psy3016         101 LYG--KPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD  178 (305)
Q Consensus       101 ~~g--~~l~v~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  178 (305)
                      +.|  +.|.|+++....++...+++|||+-|+..+||.+++++|.+||.|+.|                           
T Consensus       102 lpG~~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~---------------------------  154 (510)
T KOG0144|consen  102 LPGMHHPVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDC---------------------------  154 (510)
T ss_pred             cCCCCcceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchh---------------------------
Confidence            555  689999999888887778999999999999999999999999999987                           


Q ss_pred             CcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCee-e--cCeeeEEEEeeecCCcC
Q psy3016         179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY-L--CNRPISVSYAFKKDSKG  244 (305)
Q Consensus       179 ~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~-~--~g~~l~v~~a~~~~~~~  244 (305)
                                  .|++|.. +.+||||||+|++.+.|..||++|||.. +  +..+|.|.||..+.++.
T Consensus       155 ------------~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~  210 (510)
T KOG0144|consen  155 ------------YILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKD  210 (510)
T ss_pred             ------------hheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCch
Confidence                        7899965 9999999999999999999999999975 3  56799999998876654

>KOG0117|consensus

Probab=99.97  E-value=4e-31  Score=238.38  Aligned_cols=209  Identities=23%  Similarity=0.370  Sum_probs=177.6

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC-CeeeEEe
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY-GKPIRVN  109 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~-g~~l~v~  109 (305)
                      ....+.||||.||.++.|++|..+|++.|+|.+++||.|+.+|.++|||||+|.+.+.|++||+.||+.+|. |+.|.|.
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE
Confidence            355689999999999999999999999999999999999999999999999999999999999999999885 8999998


Q ss_pred             eCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchh-------------------------------hhhhh-
Q psy3016         110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP-------------------------------KIMNM-  157 (305)
Q Consensus       110 ~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~-------------------------------~~~~~-  157 (305)
                      .+...       ++|||+|+|.++++++|.+.+++.++-....                               +++++ 
T Consensus       160 ~Svan-------~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~  232 (506)
T KOG0117|consen  160 VSVAN-------CRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGK  232 (506)
T ss_pred             Eeeec-------ceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCc
Confidence            77653       6799999999999999999999877544321                               22222 


Q ss_pred             hhhcCcceeeecCccccccCCC----cceeEeccCCCCcccCCC------------CCCccceEEEEeCChHHHHHHHHH
Q psy3016         158 IKLYGKPIRVNKASSHQKNLDV----GANIFIGNLDPEIMRDPD------------TGNSKGFAFINYASFEASDASIDA  221 (305)
Q Consensus       158 ~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~l~~~i~~d~~------------~~~~~g~afV~f~~~~~A~~Al~~  221 (305)
                      +++.|+-+.|+|++...+..+.    ..-||++||...+..+..            -.+.+.||||+|.+.++|.+|++.
T Consensus       233 ~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rDYaFVHf~eR~davkAm~~  312 (506)
T KOG0117|consen  233 IKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRDYAFVHFAEREDAVKAMKE  312 (506)
T ss_pred             eeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccceeEEeecchHHHHHHHHH
Confidence            7899999999999997554443    367899999987533220            034578999999999999999999


Q ss_pred             hcCeeecCeeeEEEEeeecCCcCCC
Q psy3016         222 MHGQYLCNRPISVSYAFKKDSKGDR  246 (305)
Q Consensus       222 l~~~~~~g~~l~v~~a~~~~~~~~~  246 (305)
                      +||++++|..|.|.+|++.+.++..
T Consensus       313 ~ngkeldG~~iEvtLAKP~~k~k~~  337 (506)
T KOG0117|consen  313 TNGKELDGSPIEVTLAKPVDKKKKE  337 (506)
T ss_pred             hcCceecCceEEEEecCChhhhccc
Confidence            9999999999999999988765443

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

Probab=99.97  E-value=1.5e-29  Score=248.70  Aligned_cols=206  Identities=36%  Similarity=0.626  Sum_probs=175.4

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCcc
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQ  115 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~~  115 (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            79999999999999999999999999999999999889999999999999999999999999999999999999986433


Q ss_pred             -ccccccccccccCCCchhcHHHHHHHHhhcCcccchhh---------------------------hhhhhhhcCcceee
Q psy3016         116 -KNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK---------------------------IMNMIKLYGKPIRV  167 (305)
Q Consensus       116 -~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~---------------------------~~~~~~~~~~~~~~  167 (305)
                       .......+|||+||+.++++++|+++|+.||.|..|..                           .+|+..++|+.+.+
T Consensus        82 ~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v  161 (562)
T TIGR01628        82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYV  161 (562)
T ss_pred             cccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEE
Confidence             22334568999999999999999999999999987632                           25556677888887


Q ss_pred             ecCccccc----cCCCcceeEeccCCCCc--------------------ccCCCCCCccceEEEEeCChHHHHHHHHHhc
Q psy3016         168 NKASSHQK----NLDVGANIFIGNLDPEI--------------------MRDPDTGNSKGFAFINYASFEASDASIDAMH  223 (305)
Q Consensus       168 ~~~~~~~~----~~~~~~~~~~~~l~~~i--------------------~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~  223 (305)
                      ........    ......+||++||+..+                    +.| .++.++|||||+|.+.++|.+|++.||
T Consensus       162 ~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~-~~g~~~G~afV~F~~~e~A~~Av~~l~  240 (562)
T TIGR01628       162 GRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMN  240 (562)
T ss_pred             eccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEEC-CCCCcccEEEEEECCHHHHHHHHHHhC
Confidence            66554322    23345789999998763                    344 458899999999999999999999999


Q ss_pred             Ceeec----CeeeEEEEeeecCC
Q psy3016         224 GQYLC----NRPISVSYAFKKDS  242 (305)
Q Consensus       224 ~~~~~----g~~l~v~~a~~~~~  242 (305)
                      |..+.    |+.|.|.++..+..
T Consensus       241 g~~i~~~~~g~~l~v~~a~~k~e  263 (562)
T TIGR01628       241 GKKIGLAKEGKKLYVGRAQKRAE  263 (562)
T ss_pred             CcEecccccceeeEeecccChhh
Confidence            99999    99999998865543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.96  E-value=3.3e-29  Score=240.43  Aligned_cols=168  Identities=32%  Similarity=0.550  Sum_probs=152.8

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||..+++++|+++|+.||.|..|+++.++.++.++|||||+|.+.++|.+|+. |+|..+.|+.|.|.++
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeec
Confidence            456799999999999999999999999999999999999899999999999999999999998 8999999999999876


Q ss_pred             CCcccc-----------ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCc
Q psy3016         112 SSHQKN-----------LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG  180 (305)
Q Consensus       112 ~~~~~~-----------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  180 (305)
                      ......           .....+|||+||+..+|+++|.++|+.||.|..+                             
T Consensus       166 ~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v-----------------------------  216 (457)
T TIGR01622       166 QAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDV-----------------------------  216 (457)
T ss_pred             chhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEE-----------------------------
Confidence            532211           1124789999999999999999999999999877                             


Q ss_pred             ceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       181 ~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                                .++.|..+|.++|||||+|.+.++|.+|+..|||..+.|+.|.|.|+..
T Consensus       217 ----------~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       217 ----------QLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             ----------EEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence                      6788888889999999999999999999999999999999999999863

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.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.96  E-value=1.3e-28  Score=237.39  Aligned_cols=205  Identities=22%  Similarity=0.418  Sum_probs=167.1

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC-CeeeEEe
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY-GKPIRVN  109 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~-g~~l~v~  109 (305)
                      ....++|||+|||.+++|++|+++|++||.|.+|+|+.| .++.++|||||+|.+.++|++||+.||+..+. |+.|.|.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            445689999999999999999999999999999999999 68999999999999999999999999998885 7888887


Q ss_pred             eCCCccccccccccccccCCCchhcHHHHHHHHhhcCcc-cchh------------------------------hhhh-h
Q psy3016         110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVI-LQTP------------------------------KIMN-M  157 (305)
Q Consensus       110 ~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v-~~~~------------------------------~~~~-~  157 (305)
                      ++..       .++|||+|||.++++++|.+.|+.++.. ..+.                              ++++ .
T Consensus       134 ~S~~-------~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gk  206 (578)
T TIGR01648       134 ISVD-------NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGR  206 (578)
T ss_pred             cccc-------CceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccc
Confidence            6542       4689999999999999999999998641 1110                              1111 1


Q ss_pred             hhhcCcceeeecCcccccc----CCCcceeEeccCCCCcccCC------CC--------CCccceEEEEeCChHHHHHHH
Q psy3016         158 IKLYGKPIRVNKASSHQKN----LDVGANIFIGNLDPEIMRDP------DT--------GNSKGFAFINYASFEASDASI  219 (305)
Q Consensus       158 ~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~l~~~i~~d~------~~--------~~~~g~afV~f~~~~~A~~Al  219 (305)
                      ..+.|+.+.|.|+..+...    .....+||++||+..+-.+.      ..        ...++||||+|++.++|.+|+
T Consensus       207 i~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rgfAFVeF~s~e~A~kAi  286 (578)
T TIGR01648       207 IQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDREDAVKAM  286 (578)
T ss_pred             eEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecCeEEEEeCCHHHHHHHH
Confidence            3467888999998875332    22357899999998742111      01        245789999999999999999


Q ss_pred             HHhcCeeecCeeeEEEEeeecCCc
Q psy3016         220 DAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       220 ~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      +.||+.+|+|+.|+|+|+++.+..
T Consensus       287 ~~lnG~~i~Gr~I~V~~Akp~~~~  310 (578)
T TIGR01648       287 DELNGKELEGSEIEVTLAKPVDKK  310 (578)
T ss_pred             HHhCCCEECCEEEEEEEccCCCcc
Confidence            999999999999999999876544

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0145|consensus

Probab=99.96  E-value=1.3e-28  Score=208.52  Aligned_cols=173  Identities=27%  Similarity=0.526  Sum_probs=158.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ..+...+|.|.-||..+|++||+.+|...|+|++|++++|+.+|.+.||+||.|.+++||++|+..|||..+..+.|+|+
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            45566789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCC
Q psy3016         110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLD  189 (305)
Q Consensus       110 ~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  189 (305)
                      ++.+...... ..+|||.+||..+|..+|.++|.+||.|...                                      
T Consensus       117 yARPSs~~Ik-~aNLYvSGlPktMtqkelE~iFs~fGrIItS--------------------------------------  157 (360)
T KOG0145|consen  117 YARPSSDSIK-DANLYVSGLPKTMTQKELEQIFSPFGRIITS--------------------------------------  157 (360)
T ss_pred             eccCChhhhc-ccceEEecCCccchHHHHHHHHHHhhhhhhh--------------------------------------
Confidence            9988765443 5789999999999999999999999999765                                      


Q ss_pred             CCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeee--cCeeeEEEEeeecCC
Q psy3016         190 PEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL--CNRPISVSYAFKKDS  242 (305)
Q Consensus       190 ~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~--~g~~l~v~~a~~~~~  242 (305)
                       +|..|.-+|.++|.+||+|+..++|+.||..|||..-  +..+|+|.|+.....
T Consensus       158 -RiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq  211 (360)
T KOG0145|consen  158 -RILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQ  211 (360)
T ss_pred             -hhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCccc
Confidence             6788889999999999999999999999999999986  446899999976643

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.94  E-value=7.5e-26  Score=218.08  Aligned_cols=162  Identities=23%  Similarity=0.396  Sum_probs=137.6

Q ss_pred             CCceEEEcCCCc-cccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          33 GDATIYVGGLDD-KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        33 ~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ..++|||+||+. .+|+++|+++|+.||.|.+|+++.++     +|||||+|.+.++|..|++.|||..+.|+.|+|.++
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s  348 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPS  348 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            567999999997 69999999999999999999998863     599999999999999999999999999999999987


Q ss_pred             CCccc----c--------------------------------ccccccccccCCCchhcHHHHHHHHhhcCc--ccchhh
Q psy3016         112 SSHQK----N--------------------------------LDVGANIFIGNLDPEVDEKLLYDTFSAFGV--ILQTPK  153 (305)
Q Consensus       112 ~~~~~----~--------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~--v~~~~~  153 (305)
                      .....    .                                .....+|||+|||.++|+++|+++|+.||.  +..+  
T Consensus       349 ~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~i--  426 (481)
T TIGR01649       349 KQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKF--  426 (481)
T ss_pred             ccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEE--
Confidence            53210    0                                012458999999999999999999999998  5443  


Q ss_pred             hhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCee--
Q psy3016         154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRP--  231 (305)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~--  231 (305)
                                                           +++.+ . +..+++|||+|++.++|.+|+..||++.+.++.  
T Consensus       427 -------------------------------------k~~~~-~-~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~  467 (481)
T TIGR01649       427 -------------------------------------KFFPK-D-NERSKMGLLEWESVEDAVEALIALNHHQLNEPNGS  467 (481)
T ss_pred             -------------------------------------EEecC-C-CCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCC
Confidence                                                 22222 2 335889999999999999999999999999985  


Q ss_pred             ----eEEEEeeec
Q psy3016         232 ----ISVSYAFKK  240 (305)
Q Consensus       232 ----l~v~~a~~~  240 (305)
                          |+|+|++.+
T Consensus       468 ~~~~lkv~fs~~~  480 (481)
T TIGR01649       468 APYHLKVSFSTSR  480 (481)
T ss_pred             ccceEEEEeccCC
Confidence                999998653

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).

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.94  E-value=1.2e-25  Score=218.63  Aligned_cols=172  Identities=21%  Similarity=0.294  Sum_probs=145.1

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      .+..++|||+|||..+|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|..|++.|+|..+.|+.|.|.+
T Consensus       292 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~  371 (509)
T TIGR01642       292 LDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQR  371 (509)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             CCCcccc---------------------------ccccccccccCCCch----------hcHHHHHHHHhhcCcccchhh
Q psy3016         111 ASSHQKN---------------------------LDVGANIFIGNLDPE----------VDEKLLYDTFSAFGVILQTPK  153 (305)
Q Consensus       111 ~~~~~~~---------------------------~~~~~~l~v~nl~~~----------~t~~~l~~~f~~~g~v~~~~~  153 (305)
                      +......                           .....+|+|.|+...          ...++|++.|+.||.|..+  
T Consensus       372 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v--  449 (509)
T TIGR01642       372 ACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINI--  449 (509)
T ss_pred             CccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEE--
Confidence            7532110                           012466888888532          1236799999999999876  


Q ss_pred             hhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC---CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCe
Q psy3016         154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD---PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR  230 (305)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d---~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~  230 (305)
                                                           .|+++   ..++.+.|+|||+|++.++|.+|+.+|||.+|.|+
T Consensus       450 -------------------------------------~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr  492 (509)
T TIGR01642       450 -------------------------------------VIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDR  492 (509)
T ss_pred             -------------------------------------EeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCe
Confidence                                                 34433   23456789999999999999999999999999999


Q ss_pred             eeEEEEeeecC
Q psy3016         231 PISVSYAFKKD  241 (305)
Q Consensus       231 ~l~v~~a~~~~  241 (305)
                      .|.|.|.....
T Consensus       493 ~v~~~~~~~~~  503 (509)
T TIGR01642       493 VVVAAFYGEDC  503 (509)
T ss_pred             EEEEEEeCHHH
Confidence            99999986543

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.94  E-value=6.6e-26  Score=220.38  Aligned_cols=165  Identities=24%  Similarity=0.426  Sum_probs=140.3

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccC------------CCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQS------------GPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN   97 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~------------G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~   97 (305)
                      .....++|||||||..+|+++|+++|+.+            +.|..+.+      +..+|||||+|.+.++|..||. |+
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~-l~  243 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMA-LD  243 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhc-CC
Confidence            34467899999999999999999999974            34555554      2356999999999999999995 99


Q ss_pred             CceeCCeeeEEeeCCCccc----------------------------cccccccccccCCCchhcHHHHHHHHhhcCccc
Q psy3016          98 MIKLYGKPIRVNKASSHQK----------------------------NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVIL  149 (305)
Q Consensus        98 g~~~~g~~l~v~~~~~~~~----------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~  149 (305)
                      |..+.|+.|.|.+......                            ..+...+|||+||+..+|+++|.++|+.||.|.
T Consensus       244 g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~  323 (509)
T TIGR01642       244 SIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLK  323 (509)
T ss_pred             CeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCee
Confidence            9999999999975432210                            012246899999999999999999999999998


Q ss_pred             chhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecC
Q psy3016         150 QTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN  229 (305)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g  229 (305)
                      .+                                       .++.|..+|.++|||||+|.+.++|..|+..|||..|.|
T Consensus       324 ~~---------------------------------------~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~  364 (509)
T TIGR01642       324 AF---------------------------------------NLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGD  364 (509)
T ss_pred             EE---------------------------------------EEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            76                                       667888889999999999999999999999999999999


Q ss_pred             eeeEEEEeeec
Q psy3016         230 RPISVSYAFKK  240 (305)
Q Consensus       230 ~~l~v~~a~~~  240 (305)
                      +.|.|.++...
T Consensus       365 ~~l~v~~a~~~  375 (509)
T TIGR01642       365 NKLHVQRACVG  375 (509)
T ss_pred             eEEEEEECccC
Confidence            99999998654

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.94  E-value=1.2e-25  Score=216.66  Aligned_cols=159  Identities=21%  Similarity=0.316  Sum_probs=136.1

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHh--cCceeCCeeeEEeeC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM--NMIKLYGKPIRVNKA  111 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l--~g~~~~g~~l~v~~~  111 (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            679999999999999999999999999999999864      489999999999999999975  678999999999998


Q ss_pred             CCccccc-----------cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCc
Q psy3016         112 SSHQKNL-----------DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG  180 (305)
Q Consensus       112 ~~~~~~~-----------~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  180 (305)
                      .......           ....+|||+||+..+|+++|+++|+.||.|..+                             
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v-----------------------------  126 (481)
T TIGR01649        76 TSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRI-----------------------------  126 (481)
T ss_pred             CCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEE-----------------------------
Confidence            6532111           112378999999999999999999999999876                             


Q ss_pred             ceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecC--eeeEEEEeeecC
Q psy3016         181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN--RPISVSYAFKKD  241 (305)
Q Consensus       181 ~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g--~~l~v~~a~~~~  241 (305)
                                .++++.    ..++|||+|.+.++|.+|++.|||..+.+  ++|+|.|++...
T Consensus       127 ----------~i~~~~----~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~  175 (481)
T TIGR01649       127 ----------VTFTKN----NVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTR  175 (481)
T ss_pred             ----------EEEecC----CceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCC
Confidence                      445442    24689999999999999999999999954  589999987543

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).

>KOG0145|consensus

Probab=99.94  E-value=4.7e-26  Score=192.98  Aligned_cols=176  Identities=30%  Similarity=0.516  Sum_probs=155.1

Q ss_pred             CCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC--
Q psy3016          26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG--  103 (305)
Q Consensus        26 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g--  103 (305)
                      +|....-...+|||.+||+.+|..||..+|++||.|..-+|..|..+|-++|.|||.|+..++|+.||+.|||..-.|  
T Consensus       119 RPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~t  198 (360)
T KOG0145|consen  119 RPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCT  198 (360)
T ss_pred             cCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCC
Confidence            444445556699999999999999999999999999999999999999999999999999999999999999987766  


Q ss_pred             eeeEEeeCCCcccc--------------------------------------------------------------cccc
Q psy3016         104 KPIRVNKASSHQKN--------------------------------------------------------------LDVG  121 (305)
Q Consensus       104 ~~l~v~~~~~~~~~--------------------------------------------------------------~~~~  121 (305)
                      ..|.|.++.....+                                                              ....
T Consensus       199 epItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g  278 (360)
T KOG0145|consen  199 EPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGG  278 (360)
T ss_pred             CCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCe
Confidence            47888776532110                                                              0013


Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      .||||.||.++.+|..|+++|.+||.|..+                                       +|++|..++++
T Consensus       279 ~ciFvYNLspd~de~~LWQlFgpFGAv~nV---------------------------------------KvirD~ttnkC  319 (360)
T KOG0145|consen  279 WCIFVYNLSPDADESILWQLFGPFGAVTNV---------------------------------------KVIRDFTTNKC  319 (360)
T ss_pred             eEEEEEecCCCchHhHHHHHhCcccceeeE---------------------------------------EEEecCCcccc
Confidence            689999999999999999999999999987                                       88999999999


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +||+||.+.+.++|..|+..|||..+++|.|.|+|...+
T Consensus       320 KGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  320 KGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             cceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            999999999999999999999999999999999997544

>KOG0124|consensus

Probab=99.93  E-value=2.9e-25  Score=196.02  Aligned_cols=169  Identities=25%  Similarity=0.461  Sum_probs=155.6

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (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            37999999999999999999999999999999999999999999999999999999999999999999999999997665


Q ss_pred             ccc----------cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCccee
Q psy3016         114 HQK----------NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI  183 (305)
Q Consensus       114 ~~~----------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  183 (305)
                      ...          +....++|||..+..++++++|+.+|+.||+|..|                                
T Consensus       193 mpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C--------------------------------  240 (544)
T KOG0124|consen  193 MPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKC--------------------------------  240 (544)
T ss_pred             CcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeE--------------------------------
Confidence            322          22346889999999999999999999999999999                                


Q ss_pred             EeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       184 ~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                             ++.+++..+.++||+|++|.+..+-..|+..||-..++|.-|+|--+-...
T Consensus       241 -------~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP  291 (544)
T KOG0124|consen  241 -------QLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  291 (544)
T ss_pred             -------EeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCCC
Confidence                   778888888999999999999999999999999999999999998776544

>KOG0109|consensus

Probab=99.93  E-value=1.8e-25  Score=192.17  Aligned_cols=152  Identities=22%  Similarity=0.451  Sum_probs=139.1

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (305)
                      ..|||||||..+++.+|+.+|++||.|.+|+|++        .||||+.++...|+.||.+|++..|+|..|.|+.++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK--------NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK--------NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec--------ccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            4799999999999999999999999999999966        69999999999999999999999999999999998877


Q ss_pred             cccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc
Q psy3016         115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR  194 (305)
Q Consensus       115 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  194 (305)
                      .   ....+|+|+|+.+.++.++|+..|++||.|.+|                                       +|+ 
T Consensus        75 s---k~stkl~vgNis~tctn~ElRa~fe~ygpviec---------------------------------------div-  111 (346)
T KOG0109|consen   75 S---KASTKLHVGNISPTCTNQELRAKFEKYGPVIEC---------------------------------------DIV-  111 (346)
T ss_pred             C---CCccccccCCCCccccCHHHhhhhcccCCceee---------------------------------------eee-
Confidence            3   345789999999999999999999999999988                                       333 


Q ss_pred             CCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcC
Q psy3016         195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKG  244 (305)
Q Consensus       195 d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~  244 (305)
                             ++|+||+|+-.++|..|++.|+|++|.|++++|..+..+-.-.
T Consensus       112 -------kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrta  154 (346)
T KOG0109|consen  112 -------KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTA  154 (346)
T ss_pred             -------cceeEEEEeeccchHHHHhcccccccccceeeeeeeccccccC
Confidence                   6699999999999999999999999999999999987655443

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.92  E-value=5.3e-24  Score=204.42  Aligned_cols=166  Identities=25%  Similarity=0.434  Sum_probs=139.0

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (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            68999999999999999999999999999999999988889999999999999999999999999999999999999532


Q ss_pred             ccc-----------------------------------------------------------------------------
Q psy3016         114 HQK-----------------------------------------------------------------------------  116 (305)
Q Consensus       114 ~~~-----------------------------------------------------------------------------  116 (305)
                      ...                                                                             
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (457)
T TIGR01622       266 STYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALA  345 (457)
T ss_pred             CCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccc
Confidence            100                                                                             


Q ss_pred             ------------cccccccccccCCCchhc----------HHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCcccc
Q psy3016         117 ------------NLDVGANIFIGNLDPEVD----------EKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQ  174 (305)
Q Consensus       117 ------------~~~~~~~l~v~nl~~~~t----------~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~  174 (305)
                                  ......+|+|.|+-...+          .++|.+.|++||.|..+                       
T Consensus       346 ~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v-----------------------  402 (457)
T TIGR01622       346 IMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHI-----------------------  402 (457)
T ss_pred             cccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEE-----------------------
Confidence                        001234567777743322          36799999999999865                       


Q ss_pred             ccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         175 KNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       175 ~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                                      .+.    .....|++||+|.+.++|.+|++.|||++|+|+.|.+.|......
T Consensus       403 ----------------~v~----~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~~  450 (457)
T TIGR01622       403 ----------------YVD----TKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVY  450 (457)
T ss_pred             ----------------EEe----CCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHHH
Confidence                            111    234679999999999999999999999999999999999866543

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.

>KOG0127|consensus

Probab=99.91  E-value=3e-24  Score=198.10  Aligned_cols=167  Identities=26%  Similarity=0.448  Sum_probs=150.5

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (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            79999999999999999999999999999999999999999999999999999999999999999999999999987653


Q ss_pred             cccc-------------------------cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeec
Q psy3016         115 QKNL-------------------------DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK  169 (305)
Q Consensus       115 ~~~~-------------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~  169 (305)
                      .+..                         .....|.|.|||+.+...+|..+|+.||.|..+                  
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei------------------  147 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEI------------------  147 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEE------------------
Confidence            3211                         014579999999999999999999999999876                  


Q ss_pred             CccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       170 ~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                                           .|.+..+ |+-.|||||.|....+|.+|++.+|+..|+||+|-|.||-.++
T Consensus       148 ---------------------~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  148 ---------------------VIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             ---------------------EcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence                                 5565544 5556999999999999999999999999999999999997765

>KOG0127|consensus

Probab=99.90  E-value=4.9e-23  Score=190.15  Aligned_cols=199  Identities=26%  Similarity=0.417  Sum_probs=161.0

Q ss_pred             CCccceeecCccccccC---------cccccCCCCCcCC----CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEccc
Q psy3016           3 LGREIQAGISTPCLQSL---------SQTKLEGGGESGD----GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKD   69 (305)
Q Consensus         3 ~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~----~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~   69 (305)
                      +||.|.+.....+..+.         ......++.+...    ..-+|+|.|||..+.+.+|..+|+.||.|.+|.|.+.
T Consensus        73 ~Gr~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k  152 (678)
T KOG0127|consen   73 EGRILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRK  152 (678)
T ss_pred             cceecccccccccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccC
Confidence            57777777776444333         1122222222222    2458999999999999999999999999999999977


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCccc---------------------------------
Q psy3016          70 RVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQK---------------------------------  116 (305)
Q Consensus        70 ~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~~~---------------------------------  116 (305)
                      .. |.-.|||||+|....+|..|++.+|+..|.||.|-|.|+.++..                                 
T Consensus       153 ~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~  231 (678)
T KOG0127|consen  153 KD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFD  231 (678)
T ss_pred             CC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccc
Confidence            64 45559999999999999999999999999999999999864210                                 


Q ss_pred             --------------c------------------------------------------ccccccccccCCCchhcHHHHHH
Q psy3016         117 --------------N------------------------------------------LDVGANIFIGNLDPEVDEKLLYD  140 (305)
Q Consensus       117 --------------~------------------------------------------~~~~~~l~v~nl~~~~t~~~l~~  140 (305)
                                    .                                          .....+|||.||++++|+++|.+
T Consensus       232 ~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~  311 (678)
T KOG0127|consen  232 EEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKE  311 (678)
T ss_pred             hhcccccccccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHH
Confidence                          0                                          00026899999999999999999


Q ss_pred             HHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHH
Q psy3016         141 TFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASID  220 (305)
Q Consensus       141 ~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~  220 (305)
                      .|..||.|.+.                                       .++.|+.|+.++|.|||.|.+..+|.+||.
T Consensus       312 ~fskFG~v~ya---------------------------------------~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~  352 (678)
T KOG0127|consen  312 HFSKFGEVKYA---------------------------------------IIVKDKDTGHSKGTAFVKFKTQIAAQNCIE  352 (678)
T ss_pred             HHHhhccceeE---------------------------------------EEEeccCCCCcccceEEEeccHHHHHHHHH
Confidence            99999999987                                       689999999999999999999999999998


Q ss_pred             Hh-----cC-eeecCeeeEEEEeeecC
Q psy3016         221 AM-----HG-QYLCNRPISVSYAFKKD  241 (305)
Q Consensus       221 ~l-----~~-~~~~g~~l~v~~a~~~~  241 (305)
                      +-     .| ..++||.|.|..+-.+.
T Consensus       353 ~Aspa~e~g~~ll~GR~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  353 AASPASEDGSVLLDGRLLKVTLAVTRK  379 (678)
T ss_pred             hcCccCCCceEEEeccEEeeeeccchH
Confidence            76     33 56799999999987654

>KOG0123|consensus

Probab=99.90  E-value=4.1e-23  Score=190.91  Aligned_cols=157  Identities=36%  Similarity=0.667  Sum_probs=144.7

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCcc
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQ  115 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~~  115 (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            68999   999999999999999999999999997 5  99999999999999999999999999999999999988665


Q ss_pred             ccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         116 KNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       116 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      ..      |||.||+++++...|+++|+.||.|.+|                                       +++.|
T Consensus        77 ~~------~~i~nl~~~~~~~~~~d~f~~~g~ilS~---------------------------------------kv~~~  111 (369)
T KOG0123|consen   77 SL------VFIKNLDESIDNKSLYDTFSEFGNILSC---------------------------------------KVATD  111 (369)
T ss_pred             ce------eeecCCCcccCcHHHHHHHHhhcCeeEE---------------------------------------EEEEc
Confidence            43      9999999999999999999999999999                                       67777


Q ss_pred             CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcCCC
Q psy3016         196 PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDR  246 (305)
Q Consensus       196 ~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~~~  246 (305)
                      .. | ++|| ||+|++.++|.+|+..+||..+.++.|.|.....+..+...
T Consensus       112 ~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~  159 (369)
T KOG0123|consen  112 EN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAP  159 (369)
T ss_pred             CC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhccc
Confidence            44 5 8999 99999999999999999999999999999988777665433

>KOG0146|consensus

Probab=99.89  E-value=5.7e-23  Score=174.90  Aligned_cols=171  Identities=25%  Similarity=0.415  Sum_probs=150.8

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCce-eCC--eeeEEe
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIK-LYG--KPIRVN  109 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~-~~g--~~l~v~  109 (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            67899999999999999999999999999999999885 78999999999999999999999999853 333  567777


Q ss_pred             eCCCccc-------------------------------------------------------------------------
Q psy3016         110 KASSHQK-------------------------------------------------------------------------  116 (305)
Q Consensus       110 ~~~~~~~-------------------------------------------------------------------------  116 (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            7654110                                                                         


Q ss_pred             --------------------------------------------------------------------------------
Q psy3016         117 --------------------------------------------------------------------------------  116 (305)
Q Consensus       117 --------------------------------------------------------------------------------  116 (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             ------------------------cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCcc
Q psy3016         117 ------------------------NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASS  172 (305)
Q Consensus       117 ------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~  172 (305)
                                              .....|+|||..||.+.++.+|.++|-+||.|.+.                     
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSa---------------------  315 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSA---------------------  315 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeee---------------------
Confidence                                    00113899999999999999999999999999876                     


Q ss_pred             ccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         173 HQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       173 ~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                                        +++.|..|+.+|.|+||.|++..+|..||.+|||..|+-++|+|.+.++++.+
T Consensus       316 ------------------KVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkdan  368 (371)
T KOG0146|consen  316 ------------------KVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDAN  368 (371)
T ss_pred             ------------------eeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCccccC
Confidence                              78999999999999999999999999999999999999999999998887654

>KOG0123|consensus

Probab=99.89  E-value=1.1e-22  Score=188.04  Aligned_cols=214  Identities=28%  Similarity=0.485  Sum_probs=179.2

Q ss_pred             cccccCcccccCCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHH
Q psy3016          14 PCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI   93 (305)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai   93 (305)
                      +.+.||+++..+-          |||.||++++|.++|.++|+.||+|.+|++..+. .| ++|| ||+|.+++.|.+|+
T Consensus        66 ~~rim~s~rd~~~----------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai  132 (369)
T KOG0123|consen   66 PIRIMWSQRDPSL----------VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAI  132 (369)
T ss_pred             EEEeehhccCCce----------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHH
Confidence            5556666654222          9999999999999999999999999999999997 44 8999 99999999999999


Q ss_pred             HHhcCceeCCeeeEEeeCCCccccc-------cccccccccCCCchhcHHHHHHHHhhcCcccchh--------------
Q psy3016          94 KIMNMIKLYGKPIRVNKASSHQKNL-------DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP--------------  152 (305)
Q Consensus        94 ~~l~g~~~~g~~l~v~~~~~~~~~~-------~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~--------------  152 (305)
                      +.+||..+.|++|.|.....+..+.       ....+++|.+++..++++.|.+.|..+|.|..+.              
T Consensus       133 ~~~ng~ll~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gf  212 (369)
T KOG0123|consen  133 EKLNGMLLNGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGF  212 (369)
T ss_pred             HHhcCcccCCCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccc
Confidence            9999999999999998877654322       2356799999999999999999999999998853              


Q ss_pred             -------------hhhhhhhhcCcceeeecCccccc-----------------cCCCcceeEeccCCCC-----------
Q psy3016         153 -------------KIMNMIKLYGKPIRVNKASSHQK-----------------NLDVGANIFIGNLDPE-----------  191 (305)
Q Consensus       153 -------------~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~l~~~-----------  191 (305)
                                   +-+++..++++.+.|..+++..+                 ..-..+++|++|++..           
T Consensus       213 v~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~  292 (369)
T KOG0123|consen  213 VNFENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFS  292 (369)
T ss_pred             eeecChhHHHHHHHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHh
Confidence                         22677777888888888887422                 1335789999998854           


Q ss_pred             ---------cccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         192 ---------IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       192 ---------i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                               ++.+ ..|.++||+||.|++.++|.+|+..+|+..+.++.|.|.++....
T Consensus       293 ~~GeI~s~kv~~~-~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~  350 (369)
T KOG0123|consen  293 SFGEITSAKVMVD-ENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKE  350 (369)
T ss_pred             cccceeeEEEEec-cCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhc
Confidence                     3444 448999999999999999999999999999999999999986443

>KOG0148|consensus

Probab=99.88  E-value=1.5e-22  Score=172.74  Aligned_cols=141  Identities=33%  Similarity=0.620  Sum_probs=121.4

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      .+..+|||||||...+||+-|..||+..|.|.+|+++.+                                   .++|.|
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~-----------------------------------e~~v~w   47 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD-----------------------------------ELKVNW   47 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh-----------------------------------hhcccc
Confidence            467899999999999999999999999999999999876                                   244444


Q ss_pred             CCCcccc----ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEec
Q psy3016         111 ASSHQKN----LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIG  186 (305)
Q Consensus       111 ~~~~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  186 (305)
                      +......    .....-+||+.|...++.++|++.|.+||+|+.+                                   
T Consensus        48 a~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~a-----------------------------------   92 (321)
T KOG0148|consen   48 ATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDA-----------------------------------   92 (321)
T ss_pred             ccCcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccc-----------------------------------
Confidence            4432211    1123458899999999999999999999999976                                   


Q ss_pred             cCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcCC
Q psy3016         187 NLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGD  245 (305)
Q Consensus       187 ~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~~  245 (305)
                          +|++|..|++++||+||.|-+.++|++||..|||.||++|.|+..|+..+.....
T Consensus        93 ----kvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n  147 (321)
T KOG0148|consen   93 ----KVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMN  147 (321)
T ss_pred             ----eEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccC
Confidence                8999999999999999999999999999999999999999999999988765433

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.86  E-value=1.1e-20  Score=183.02  Aligned_cols=109  Identities=28%  Similarity=0.424  Sum_probs=88.8

Q ss_pred             CCccceeecCccccccCcccccCCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEE
Q psy3016           3 LGREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIE   82 (305)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~   82 (305)
                      .||.|.+.+.....+..  .......+.....++|||+||+.++++++|+++|+.||.|.+|+|.++..+++++|||||+
T Consensus       175 ~GR~IkV~rp~~~p~a~--~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVe  252 (612)
T TIGR01645       175 GGRNIKVGRPSNMPQAQ--PIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIE  252 (612)
T ss_pred             ecceeeecccccccccc--cccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEE
Confidence            57777777554332211  1111112233456799999999999999999999999999999999999889999999999


Q ss_pred             EcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          83 FMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        83 f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (305)
                      |.+.++|.+|++.||+..+.|+.|+|.++..
T Consensus       253 Fe~~e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       253 YNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             ECCHHHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            9999999999999999999999999988653

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=99.86  E-value=1.4e-21  Score=185.75  Aligned_cols=171  Identities=20%  Similarity=0.422  Sum_probs=145.8

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCC---CCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVT---QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~---~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (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            3344999999999999999999999999999988654411   1345999999999999999999999999999999999


Q ss_pred             eCCC--------ccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcc
Q psy3016         110 KASS--------HQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA  181 (305)
Q Consensus       110 ~~~~--------~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (305)
                      ++..        ..........|+|.|||...+..+++.+|..||.+..+                              
T Consensus       594 ~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksv------------------------------  643 (725)
T KOG0110|consen  594 ISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSV------------------------------  643 (725)
T ss_pred             eccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeee------------------------------
Confidence            9882        22222335789999999999999999999999999876                              


Q ss_pred             eeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       182 ~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                               ++......+.++|||||+|-+..+|.+|+.+|.++.+.||.|.+.|+.....
T Consensus       644 ---------RlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  644 ---------RLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             ---------ccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccchH
Confidence                     3443334467899999999999999999999999999999999999977654

>KOG0144|consensus

Probab=99.86  E-value=1e-21  Score=177.10  Aligned_cols=170  Identities=26%  Similarity=0.430  Sum_probs=149.6

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCc-eeC--CeeeEE
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMI-KLY--GKPIRV  108 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~-~~~--g~~l~v  108 (305)
                      ...++||||.|++.+||.|++++|++||.|++|.|++|. .+.++|||||+|.+.|.|..||+.|||. .+.  ...|.|
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVV  200 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVV  200 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEE
Confidence            347899999999999999999999999999999999996 7899999999999999999999999984 333  468899


Q ss_pred             eeCCCccccc----------------------------------------------------------------------
Q psy3016         109 NKASSHQKNL----------------------------------------------------------------------  118 (305)
Q Consensus       109 ~~~~~~~~~~----------------------------------------------------------------------  118 (305)
                      +|+..++++.                                                                      
T Consensus       201 kFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~  280 (510)
T KOG0144|consen  201 KFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAAL  280 (510)
T ss_pred             EecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHh
Confidence            9887521100                                                                      


Q ss_pred             --------------------------------------------------------------------------------
Q psy3016         119 --------------------------------------------------------------------------------  118 (305)
Q Consensus       119 --------------------------------------------------------------------------------  118 (305)
                                                                                                      
T Consensus       281 ~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~  360 (510)
T KOG0144|consen  281 AAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPV  360 (510)
T ss_pred             hhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCcc
Confidence                                                                                            


Q ss_pred             -------------------------------------------------------------cccccccccCCCchhcHHH
Q psy3016         119 -------------------------------------------------------------DVGANIFIGNLDPEVDEKL  137 (305)
Q Consensus       119 -------------------------------------------------------------~~~~~l~v~nl~~~~t~~~  137 (305)
                                                                                   ....++||++||.+..+.+
T Consensus       361 aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~  440 (510)
T KOG0144|consen  361 AASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQD  440 (510)
T ss_pred             cccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHH
Confidence                                                                         0015799999999999999


Q ss_pred             HHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHH
Q psy3016         138 LYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDA  217 (305)
Q Consensus       138 l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~  217 (305)
                      |...|..||.|.+.                                       ++..|..++-++.|+||.|++..+|.+
T Consensus       441 l~~~f~pfG~Vlsa---------------------------------------kvfidk~tnlskcfgfvSyen~~sa~~  481 (510)
T KOG0144|consen  441 LIATFQPFGGVLSA---------------------------------------KVFIDKVTNLSKCFGFVSYENAQSAQN  481 (510)
T ss_pred             HHHHhccccceeEE---------------------------------------EEEEecccCHhhhcCcccccchhhhHH
Confidence            99999999999876                                       678888999999999999999999999


Q ss_pred             HHHHhcCeeecCeeeEEEEeeecC
Q psy3016         218 SIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       218 Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      ||.+|||..++.++++|....++.
T Consensus       482 aI~amngfQig~KrlkVQlk~~~~  505 (510)
T KOG0144|consen  482 AISAMNGFQIGSKRLKVQLKRDRN  505 (510)
T ss_pred             HHHHhcchhhccccceEEeeeccC
Confidence            999999999999999999876654

>KOG0147|consensus

Probab=99.85  E-value=6e-22  Score=183.66  Aligned_cols=173  Identities=25%  Similarity=0.454  Sum_probs=153.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....+|||+--|....+..+|.++|+.+|.|..|.++.|..+++++|.|||+|.+.+....||. |.|..+.|..|.|.
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEec
Confidence            44566899999999999999999999999999999999999999999999999999999999996 89999999999998


Q ss_pred             eCCCccccc-------------cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCcccccc
Q psy3016         110 KASSHQKNL-------------DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKN  176 (305)
Q Consensus       110 ~~~~~~~~~-------------~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~  176 (305)
                      .........             -+-..|||+||..++++++|+.+|++||.|..+                         
T Consensus       254 ~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v-------------------------  308 (549)
T KOG0147|consen  254 LSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENV-------------------------  308 (549)
T ss_pred             ccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceee-------------------------
Confidence            765432110             011238999999999999999999999999987                         


Q ss_pred             CCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         177 LDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       177 ~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                                    ..+.|..+|.++||+||+|.+.++|.+|+..|||.++.|+.|+|.....+..
T Consensus       309 --------------~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  309 --------------QLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             --------------eeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecc
Confidence                          7788988999999999999999999999999999999999999988766543

>KOG4205|consensus

Probab=99.84  E-value=5e-21  Score=171.54  Aligned_cols=171  Identities=26%  Similarity=0.457  Sum_probs=153.4

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++||||+|+..++++.|++.|..||+|.+|.+++|..+++++||+||+|.+.+...+++. .....+.|+.|....+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            68899999999999999999999999999999999999999999999999999999998887 35678899999999988


Q ss_pred             Cccccccc-----cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEecc
Q psy3016         113 SHQKNLDV-----GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGN  187 (305)
Q Consensus       113 ~~~~~~~~-----~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  187 (305)
                      +.......     ...|||+.|+.+++++++++.|+.||.|..+                                    
T Consensus        84 ~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~------------------------------------  127 (311)
T KOG4205|consen   84 SREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADV------------------------------------  127 (311)
T ss_pred             CcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEee------------------------------------
Confidence            76644332     4589999999999999999999999988754                                    


Q ss_pred             CCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcC
Q psy3016         188 LDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKG  244 (305)
Q Consensus       188 l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~  244 (305)
                         .+|.|..+...+||+||.|.+.++..+++. .+-+.|+++.+.|..|.+++...
T Consensus       128 ---~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  128 ---VIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             ---EEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhcc
Confidence               789999999999999999998887777776 78889999999999998887654

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.82  E-value=1.5e-19  Score=167.88  Aligned_cols=141  Identities=29%  Similarity=0.477  Sum_probs=117.2

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC--eeeEEee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG--KPIRVNK  110 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g--~~l~v~~  110 (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            35689999999999999999999999999999999988788899999999999999999999999998877  5678877


Q ss_pred             CCCcccc-------------------------------------------------------------------------
Q psy3016         111 ASSHQKN-------------------------------------------------------------------------  117 (305)
Q Consensus       111 ~~~~~~~-------------------------------------------------------------------------  117 (305)
                      +......                                                                         
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            6432100                                                                         


Q ss_pred             ------------------ccccccccccCCCchhcHHHHHHHHhhcCcccchh---------------------------
Q psy3016         118 ------------------LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP---------------------------  152 (305)
Q Consensus       118 ------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~---------------------------  152 (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                              00112599999999999999999999999998863                           


Q ss_pred             -hhhhhhhhcCcceeeecCccc
Q psy3016         153 -KIMNMIKLYGKPIRVNKASSH  173 (305)
Q Consensus       153 -~~~~~~~~~~~~~~~~~~~~~  173 (305)
                       ..||+..++|+.+.|.+...+
T Consensus       328 i~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       328 ILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             HHHhCCCEECCeEEEEEEccCC
Confidence             226777777777777776653

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0147|consensus

Probab=99.80  E-value=2.8e-19  Score=165.98  Aligned_cols=203  Identities=25%  Similarity=0.354  Sum_probs=133.5

Q ss_pred             EEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCccc
Q psy3016          37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQK  116 (305)
Q Consensus        37 l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~~~  116 (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            99999999999999999999999999999999988999999999999999999999999999999999999987654433


Q ss_pred             cccccccc------cccCCCch-hcHHHHHHHHhhcCcccchh-hh--------hhh-hhhcCcceeeecCccccccCCC
Q psy3016         117 NLDVGANI------FIGNLDPE-VDEKLLYDTFSAFGVILQTP-KI--------MNM-IKLYGKPIRVNKASSHQKNLDV  179 (305)
Q Consensus       117 ~~~~~~~l------~v~nl~~~-~t~~~l~~~f~~~g~v~~~~-~~--------~~~-~~~~~~~~~~~~~~~~~~~~~~  179 (305)
                      ......+.      --+.|+.. ....+++..|.+.-.+..+. .+        +.. .-+++.. .+....+.+.  -+
T Consensus       361 ~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~-~~~~~~p~~~--~p  437 (549)
T KOG0147|consen  361 TKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVV-RVRSVDPADA--SP  437 (549)
T ss_pred             cccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCc-CccccCcccc--cc
Confidence            22211111      11233332 23466666665533332211 00        000 1111100 0111111100  00


Q ss_pred             cceeEeccCCCCcccCCCC------------------------------CCccceEEEEeCChHHHHHHHHHhcCeeecC
Q psy3016         180 GANIFIGNLDPEIMRDPDT------------------------------GNSKGFAFINYASFEASDASIDAMHGQYLCN  229 (305)
Q Consensus       180 ~~~~~~~~l~~~i~~d~~~------------------------------~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g  229 (305)
                      +-.|-..|+-..-|.|+.+                              ..+-|+.||+|.+.+.|..|+++|||.||.|
T Consensus       438 ~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrWF~g  517 (549)
T KOG0147|consen  438 AFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRWFAG  517 (549)
T ss_pred             ccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhhhcc
Confidence            0012222222222333321                              2345999999999999999999999999999


Q ss_pred             eeeEEEEeeecCC
Q psy3016         230 RPISVSYAFKKDS  242 (305)
Q Consensus       230 ~~l~v~~a~~~~~  242 (305)
                      +.|+++|-.....
T Consensus       518 r~Ita~~~~~~~Y  530 (549)
T KOG0147|consen  518 RMITAKYLPLERY  530 (549)
T ss_pred             ceeEEEEeehhhh
Confidence            9999999765544

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.77  E-value=4.2e-18  Score=137.99  Aligned_cols=91  Identities=30%  Similarity=0.434  Sum_probs=83.9

Q ss_pred             CCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe
Q psy3016          25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK  104 (305)
Q Consensus        25 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~  104 (305)
                      +.-+......++|||+|||..+|+++|+++|++||.|.+|+++.+..+++++|||||+|.+.++|++|++.||+..+.|+
T Consensus        25 ~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr  104 (144)
T PLN03134         25 SMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGR  104 (144)
T ss_pred             cccccccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            34445566788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEeeCCCcc
Q psy3016         105 PIRVNKASSHQ  115 (305)
Q Consensus       105 ~l~v~~~~~~~  115 (305)
                      .|+|.++..+.
T Consensus       105 ~l~V~~a~~~~  115 (144)
T PLN03134        105 HIRVNPANDRP  115 (144)
T ss_pred             EEEEEeCCcCC
Confidence            99999987654

>KOG0117|consensus

Probab=99.76  E-value=2.9e-18  Score=155.54  Aligned_cols=146  Identities=23%  Similarity=0.358  Sum_probs=125.0

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCC-eEEEEEcccCC-CCCcceEEEEEEcCHHHHHHHHHHhc--CceeCCeeeEE
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGP-VVNVHMPKDRV-TQTHQGYGFIEFMGEEDADYAIKIMN--MIKLYGKPIRV  108 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~-i~~i~~~~~~~-~~~~~g~afV~f~~~e~A~~Ai~~l~--g~~~~g~~l~v  108 (305)
                      .+++|||||||+.+++++|.+-|++.++ |..|.|..+.. ..+++|||||+|.++..|..|.++|-  .+.++|+.+.|
T Consensus       163 an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tV  242 (506)
T KOG0117|consen  163 ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITV  242 (506)
T ss_pred             ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCccee
Confidence            4679999999999999999999999884 67777776653 46889999999999999999998875  46889999999


Q ss_pred             eeCCCcccc----ccccccccccCCCchhcHHHHHHHHhhcCcccchh--------------------hhhhhhhhcCcc
Q psy3016         109 NKASSHQKN----LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP--------------------KIMNMIKLYGKP  164 (305)
Q Consensus       109 ~~~~~~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~--------------------~~~~~~~~~~~~  164 (305)
                      .|+.+....    ....+.|||.||+.++|+|.|.++|+.||.|+.++                    +.+|+..++|..
T Consensus       243 dWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rDYaFVHf~eR~davkAm~~~ngkeldG~~  322 (506)
T KOG0117|consen  243 DWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRDYAFVHFAEREDAVKAMKETNGKELDGSP  322 (506)
T ss_pred             eccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccceeEEeecchHHHHHHHHHhcCceecCce
Confidence            999986533    33457899999999999999999999999999975                    338999999999


Q ss_pred             eeeecCccccccCC
Q psy3016         165 IRVNKASSHQKNLD  178 (305)
Q Consensus       165 ~~~~~~~~~~~~~~  178 (305)
                      +.+.-+++.++.++
T Consensus       323 iEvtLAKP~~k~k~  336 (506)
T KOG0117|consen  323 IEVTLAKPVDKKKK  336 (506)
T ss_pred             EEEEecCChhhhcc
Confidence            99999998655433

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.74  E-value=9.5e-18  Score=162.32  Aligned_cols=143  Identities=23%  Similarity=0.380  Sum_probs=118.1

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCC-eEEEEEc-ccCCCCCcceEEEEEEcCHHHHHHHHHHhcC--ceeCCeeeEE
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGP-VVNVHMP-KDRVTQTHQGYGFIEFMGEEDADYAIKIMNM--IKLYGKPIRV  108 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~-i~~i~~~-~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g--~~~~g~~l~v  108 (305)
                      ..++|||+|||.++|+++|.+.|++++. +.++.++ .....++++|||||+|.++++|..|++.|+.  ..++|+.|.|
T Consensus       137 ~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~V  216 (578)
T TIGR01648       137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV  216 (578)
T ss_pred             cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEE
Confidence            4689999999999999999999999864 4444443 3333567899999999999999999998863  5688999999


Q ss_pred             eeCCCcccc----ccccccccccCCCchhcHHHHHHHHhhc--Ccccchh--------------------hhhhhhhhcC
Q psy3016         109 NKASSHQKN----LDVGANIFIGNLDPEVDEKLLYDTFSAF--GVILQTP--------------------KIMNMIKLYG  162 (305)
Q Consensus       109 ~~~~~~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~~~--g~v~~~~--------------------~~~~~~~~~~  162 (305)
                      .|+.+....    ....++|||+||+.++|+++|+++|+.|  |.|..+.                    +.||+..++|
T Consensus       217 dwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rgfAFVeF~s~e~A~kAi~~lnG~~i~G  296 (578)
T TIGR01648       217 DWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDREDAVKAMDELNGKELEG  296 (578)
T ss_pred             EeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecCeEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            998865432    2235789999999999999999999999  9998873                    2388899999


Q ss_pred             cceeeecCccccc
Q psy3016         163 KPIRVNKASSHQK  175 (305)
Q Consensus       163 ~~~~~~~~~~~~~  175 (305)
                      +.+.|.++...+.
T Consensus       297 r~I~V~~Akp~~~  309 (578)
T TIGR01648       297 SEIEVTLAKPVDK  309 (578)
T ss_pred             EEEEEEEccCCCc
Confidence            9999999987543

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.

>KOG0105|consensus

Probab=99.74  E-value=2e-17  Score=134.15  Aligned_cols=148  Identities=21%  Similarity=0.324  Sum_probs=125.5

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ...+++|||||||.++.+.||.++|-+||.|..|.|..-.   ..-.||||+|++..+|+.||..-+|..+.|..|+|++
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEf   79 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEF   79 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEe
Confidence            3567899999999999999999999999999999984432   2458999999999999999999999999999999998


Q ss_pred             CCCccc-------------------------cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcce
Q psy3016         111 ASSHQK-------------------------NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPI  165 (305)
Q Consensus       111 ~~~~~~-------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~  165 (305)
                      +..-..                         .......+.|.+||.+-++++|++.+.+.|+|-..              
T Consensus        80 prggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfa--------------  145 (241)
T KOG0105|consen   80 PRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFA--------------  145 (241)
T ss_pred             ccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeee--------------
Confidence            764311                         11124679999999999999999999999999754              


Q ss_pred             eeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeee
Q psy3016         166 RVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL  227 (305)
Q Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~  227 (305)
                                               ++.+|       |++.|+|...++.+-|++.|..+.+
T Consensus       146 -------------------------dv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  146 -------------------------DVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             -------------------------eeecc-------cceeeeeeehhhHHHHHHhhccccc
Confidence                                     33444       4789999999999999999998876

>KOG4212|consensus

Probab=99.72  E-value=1.7e-16  Score=143.63  Aligned_cols=175  Identities=23%  Similarity=0.362  Sum_probs=146.2

Q ss_pred             ccCCCCCcCCCCceEEEcCCCccccHHHHHHHhc-cCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee
Q psy3016          23 KLEGGGESGDGDATIYVGGLDDKVSETLMWELFV-QSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL  101 (305)
Q Consensus        23 ~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~  101 (305)
                      ..+..+......+.+||.|||+++.+.+|+++|. +-|+|+.|.+..|. .|+++|+|.|+|.++|.+++|++.||...+
T Consensus        33 ~gs~~gn~~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~  111 (608)
T KOG4212|consen   33 AGSQGGNVAARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEV  111 (608)
T ss_pred             ccCCCCCcccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccc
Confidence            3344455556667799999999999999999997 68899999999996 789999999999999999999999999999


Q ss_pred             CCeeeEEeeCCCccc-----------------------------------------------------------------
Q psy3016         102 YGKPIRVNKASSHQK-----------------------------------------------------------------  116 (305)
Q Consensus       102 ~g~~l~v~~~~~~~~-----------------------------------------------------------------  116 (305)
                      .||.|.|.--...+.                                                                 
T Consensus       112 ~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~  191 (608)
T KOG4212|consen  112 NGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNS  191 (608)
T ss_pred             cCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccc
Confidence            999999974332000                                                                 


Q ss_pred             -------------------cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccC
Q psy3016         117 -------------------NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNL  177 (305)
Q Consensus       117 -------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  177 (305)
                                         ..+...++||.||...+..+.|++.|.-.|.|..+                          
T Consensus       192 ~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~v--------------------------  245 (608)
T KOG4212|consen  192 SNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSV--------------------------  245 (608)
T ss_pred             hhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeee--------------------------
Confidence                               00012568999999999999999999999998876                          


Q ss_pred             CCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         178 DVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       178 ~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                                   .+-.|.. |.++|+|.++|+..-+|..||..+++.-+..++.++.+..
T Consensus       246 -------------df~idKe-G~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl~~  292 (608)
T KOG4212|consen  246 -------------DFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRLDR  292 (608)
T ss_pred             -------------ceeeccc-cccCCeeEEEecchHHHHHHHHhhccCCCccccceeeccc
Confidence                         5666644 7999999999999999999999999877788888887743

>KOG1457|consensus

Probab=99.68  E-value=6.5e-16  Score=128.91  Aligned_cols=157  Identities=19%  Similarity=0.296  Sum_probs=121.0

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcc-cCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC---C
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPK-DRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY---G  103 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~-~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~---g  103 (305)
                      .+.....+||||.+||.++...||+.+|..|---+.+.+.. ++.....+-+||++|.+.+.|.+|+..|||..|+   +
T Consensus        28 ~~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~  107 (284)
T KOG1457|consen   28 ADEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETG  107 (284)
T ss_pred             cccccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccC
Confidence            33455689999999999999999999999986555555533 2222344579999999999999999999999997   7


Q ss_pred             eeeEEeeCCCcccccc----------------------------------------------------------------
Q psy3016         104 KPIRVNKASSHQKNLD----------------------------------------------------------------  119 (305)
Q Consensus       104 ~~l~v~~~~~~~~~~~----------------------------------------------------------------  119 (305)
                      ..|+++.++...+.+.                                                                
T Consensus       108 stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~  187 (284)
T KOG1457|consen  108 STLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPD  187 (284)
T ss_pred             ceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhh
Confidence            8899988764211000                                                                


Q ss_pred             ---------------------ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCC
Q psy3016         120 ---------------------VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD  178 (305)
Q Consensus       120 ---------------------~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  178 (305)
                                           ...+|||.||..++||++|+.+|+.|.--...                           
T Consensus       188 ~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l---------------------------  240 (284)
T KOG1457|consen  188 SKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHIL---------------------------  240 (284)
T ss_pred             hcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEE---------------------------
Confidence                                 02579999999999999999999998655432                           


Q ss_pred             CcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeee
Q psy3016         179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL  227 (305)
Q Consensus       179 ~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~  227 (305)
                                    ... . ...-..||++|++++.|..|+..|.|..+
T Consensus       241 --------------~~~-~-~~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  241 --------------KIR-A-RGGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             --------------EEe-c-CCCcceEeecHHHHHHHHHHHHHhhccee
Confidence                          111 1 22345799999999999999999999765

>PF00076 RRM_1: RNA recognition motif

Probab=99.67  E-value=3.8e-16  Score=110.33  Aligned_cols=70  Identities=34%  Similarity=0.638  Sum_probs=67.3

Q ss_pred             EEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        37 l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (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 5788999999999999999999999999999999985

(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 ....

>KOG1548|consensus

Probab=99.67  E-value=2.3e-15  Score=132.92  Aligned_cols=166  Identities=21%  Similarity=0.372  Sum_probs=134.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEE--------EEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN--------VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL  101 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~--------i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~  101 (305)
                      ....+..|||.|||.++|-+++.++|++||-|..        |+|.++. .|..+|-|+|.|--.+++..|++.|++..+
T Consensus       130 ~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~  208 (382)
T KOG1548|consen  130 EPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDEL  208 (382)
T ss_pred             ccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccc
Confidence            4556678999999999999999999999997754        8998886 599999999999999999999999999999


Q ss_pred             CCeeeEEeeCCCccc-------------------------------------cccccccccccCCCc----hhc------
Q psy3016         102 YGKPIRVNKASSHQK-------------------------------------NLDVGANIFIGNLDP----EVD------  134 (305)
Q Consensus       102 ~g~~l~v~~~~~~~~-------------------------------------~~~~~~~l~v~nl~~----~~t------  134 (305)
                      .|++|+|+.|.-..+                                     +....++|.+.|+=.    ..+      
T Consensus       209 rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~d  288 (382)
T KOG1548|consen  209 RGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLND  288 (382)
T ss_pred             cCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHH
Confidence            999999998753110                                     001135566666521    122      


Q ss_pred             -HHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChH
Q psy3016         135 -EKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE  213 (305)
Q Consensus       135 -~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~  213 (305)
                       .++|.+-+.+||.|..+                                        ++.|   .++.|.+-|.|.+.+
T Consensus       289 lkedl~eec~K~G~v~~v----------------------------------------vv~d---~hPdGvvtV~f~n~e  325 (382)
T KOG1548|consen  289 LKEDLTEECEKFGQVRKV----------------------------------------VVYD---RHPDGVVTVSFRNNE  325 (382)
T ss_pred             HHHHHHHHHHHhCCcceE----------------------------------------EEec---cCCCceeEEEeCChH
Confidence             45567778899999875                                        3555   567899999999999


Q ss_pred             HHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         214 ASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       214 ~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      +|..|++.|+|+||+||.|..+.-..
T Consensus       326 eA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  326 EADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             HHHHHHHHhcCeeecceEEEEEEeCC
Confidence            99999999999999999999887543

>KOG4206|consensus

Probab=99.67  E-value=1.2e-15  Score=128.15  Aligned_cols=158  Identities=24%  Similarity=0.450  Sum_probs=132.5

Q ss_pred             CceEEEcCCCccccHHHHHH----HhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          34 DATIYVGGLDDKVSETLMWE----LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~----~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ..||||.||...+..++|++    +|+.||.|..|...+   +.+.+|-|||.|.+.+.|..|+..|+|..+.|+.+++.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            44999999999999999988    999999999998865   35788999999999999999999999999999999999


Q ss_pred             eCCCcccc-------------------------------------------------ccccccccccCCCchhcHHHHHH
Q psy3016         110 KASSHQKN-------------------------------------------------LDVGANIFIGNLDPEVDEKLLYD  140 (305)
Q Consensus       110 ~~~~~~~~-------------------------------------------------~~~~~~l~v~nl~~~~t~~~l~~  140 (305)
                      |+..+...                                                 ......+++.|||..++.+.+..
T Consensus        86 yA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~  165 (221)
T KOG4206|consen   86 YAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSD  165 (221)
T ss_pred             cccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHH
Confidence            98753211                                                 11235689999999999999999


Q ss_pred             HHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHH
Q psy3016         141 TFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASID  220 (305)
Q Consensus       141 ~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~  220 (305)
                      +|..|..-.+++                                        +.+    ..++.|||+|.+...|..|..
T Consensus       166 lf~qf~g~keir----------------------------------------~i~----~~~~iAfve~~~d~~a~~a~~  201 (221)
T KOG4206|consen  166 LFEQFPGFKEIR----------------------------------------LIP----PRSGIAFVEFLSDRQASAAQQ  201 (221)
T ss_pred             HHhhCcccceeE----------------------------------------ecc----CCCceeEEecchhhhhHHHhh
Confidence            999887666542                                        222    237799999999999999999


Q ss_pred             HhcCeeec-CeeeEEEEee
Q psy3016         221 AMHGQYLC-NRPISVSYAF  238 (305)
Q Consensus       221 ~l~~~~~~-g~~l~v~~a~  238 (305)
                      ++.+..+- ...+++.|++
T Consensus       202 ~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  202 ALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             hhccceeccCceEEecccC
Confidence            99998884 7888888763

>KOG0124|consensus

Probab=99.65  E-value=4.8e-16  Score=137.95  Aligned_cols=110  Identities=29%  Similarity=0.423  Sum_probs=94.8

Q ss_pred             CCCCccceeecCccccccCcccccCCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEE
Q psy3016           1 MSLGREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGF   80 (305)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~af   80 (305)
                      |-+||-|++.+.+++.+.-.  ....-.+....-.+|||..+.++.+|+||+..|+.||+|..|++-++..++..+||+|
T Consensus       179 mlGGRNiKVgrPsNmpQAQp--iID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGf  256 (544)
T KOG0124|consen  179 MLGGRNIKVGRPSNMPQAQP--IIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGF  256 (544)
T ss_pred             cccCccccccCCCCCcccch--HHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceee
Confidence            45899999999888776432  2222233455677999999999999999999999999999999999998889999999


Q ss_pred             EEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          81 IEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        81 V~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      |+|.+...-..|+..+|-+.+.|.-|+|..+.
T Consensus       257 iEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  257 IEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             EEeccccchHHHhhhcchhhcccceEeccccc
Confidence            99999999999999999999999999998653

>KOG0106|consensus

Probab=99.64  E-value=3.7e-16  Score=132.33  Aligned_cols=148  Identities=25%  Similarity=0.435  Sum_probs=128.3

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (305)
                      ..||||+||..+.+.+|..+|..||.+.++.+        ..||+||+|.+..+|..|+..||+..+.|..+.++++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~m--------k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADM--------KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhcccccccee--------ecccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            36999999999999999999999999999988        3489999999999999999999999999988999988742


Q ss_pred             ccc-------------------ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccc
Q psy3016         115 QKN-------------------LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQK  175 (305)
Q Consensus       115 ~~~-------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~  175 (305)
                      ...                   ....+.+.|.++...+.+.+|.+.|..+|.+.+.                        
T Consensus        74 ~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~------------------------  129 (216)
T KOG0106|consen   74 RRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYV------------------------  129 (216)
T ss_pred             ccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchh------------------------
Confidence            100                   1124678899999999999999999999999543                        


Q ss_pred             cCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         176 NLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       176 ~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                                             -..++++||+|++.++|.+|+..|++..+.++.|++...
T Consensus       130 -----------------------~~~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  130 -----------------------DARRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             -----------------------hhhccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence                                   114789999999999999999999999999999999443

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.64  E-value=7.6e-16  Score=124.77  Aligned_cols=83  Identities=34%  Similarity=0.597  Sum_probs=77.5

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+..+|+++|+++|++||.|..+                                       .++.|..++
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v---------------------------------------~i~~d~~tg   73 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDA---------------------------------------KVIVDRETG   73 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEE---------------------------------------EEEecCCCC
Confidence            46789999999999999999999999999887                                       678898899


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +++|||||+|++.++|.+|++.||+..|+|+.|+|+++..+.
T Consensus        74 ~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~  115 (144)
T PLN03134         74 RSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRP  115 (144)
T ss_pred             CcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCC
Confidence            999999999999999999999999999999999999987653

>KOG0122|consensus

Probab=99.62  E-value=1.9e-15  Score=127.80  Aligned_cols=85  Identities=28%  Similarity=0.416  Sum_probs=81.2

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ..+...+|-|.||+.+++|++|+++|.+||.|..|.|.+|+.+|.++|||||+|.+.++|.+||+.|||.-+..--|+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            45577899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCc
Q psy3016         110 KASSH  114 (305)
Q Consensus       110 ~~~~~  114 (305)
                      |+.++
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99864

>KOG0125|consensus

Probab=99.60  E-value=2.9e-15  Score=131.42  Aligned_cols=93  Identities=23%  Similarity=0.341  Sum_probs=84.5

Q ss_pred             ccccCCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCce
Q psy3016          21 QTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIK  100 (305)
Q Consensus        21 ~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~  100 (305)
                      +...+...++++..++|+|.|||+...|-||+.+|++||.|.+|.|+.+.  .-+||||||+|++.++|++|.++|||..
T Consensus        83 ~~~~st~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~  160 (376)
T KOG0125|consen   83 QTQPSTNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTV  160 (376)
T ss_pred             ccCCCCcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcce
Confidence            44455677788899999999999999999999999999999999999986  3488999999999999999999999999


Q ss_pred             eCCeeeEEeeCCCcc
Q psy3016         101 LYGKPIRVNKASSHQ  115 (305)
Q Consensus       101 ~~g~~l~v~~~~~~~  115 (305)
                      +.||+|.|+.+...-
T Consensus       161 VEGRkIEVn~ATarV  175 (376)
T KOG0125|consen  161 VEGRKIEVNNATARV  175 (376)
T ss_pred             eeceEEEEeccchhh
Confidence            999999999988653

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.59  E-value=8.8e-15  Score=134.80  Aligned_cols=83  Identities=28%  Similarity=0.488  Sum_probs=76.9

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC--eeeEEee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG--KPIRVNK  110 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g--~~l~v~~  110 (305)
                      ..++|||+|||..+|+++|+++|++||.|..|+|+.++.+++++|||||+|.+.++|++||+.||+..+.+  +.|+|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            45689999999999999999999999999999999999899999999999999999999999999998876  6899988


Q ss_pred             CCCcc
Q psy3016         111 ASSHQ  115 (305)
Q Consensus       111 ~~~~~  115 (305)
                      +....
T Consensus       272 a~~~~  276 (346)
T TIGR01659       272 AEEHG  276 (346)
T ss_pred             CCccc
Confidence            87643

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).

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.58  E-value=1.3e-14  Score=102.82  Aligned_cols=70  Identities=30%  Similarity=0.601  Sum_probs=64.9

Q ss_pred             EEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        37 l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (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 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999876 88999999999999999999999999999999874

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 ....

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.57  E-value=2.3e-14  Score=126.64  Aligned_cols=117  Identities=37%  Similarity=0.595  Sum_probs=104.5

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC-
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS-  112 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~-  112 (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            6999999999999999999999999999999999998889999999999999999999999999999999999999953 


Q ss_pred             ---Cccccc-------------------cccccccccCCCchhcHHHHHHHHhhcCcccc
Q psy3016         113 ---SHQKNL-------------------DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQ  150 (305)
Q Consensus       113 ---~~~~~~-------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~  150 (305)
                         ......                   .....+++.+++..++..++...|..+|.+..
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  254 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVR  254 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhcccccccee
Confidence               221111                   12467899999999999999999999998854

>KOG0121|consensus

Probab=99.57  E-value=5.3e-15  Score=113.25  Aligned_cols=84  Identities=29%  Similarity=0.530  Sum_probs=79.2

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ....++|||||||+..++|++|+++|+++|+|..|.+--|+.+...-|||||+|.+.++|..|++.+++..+..+.|++.
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            55678999999999999999999999999999999999998888899999999999999999999999999999999999


Q ss_pred             eCCC
Q psy3016         110 KASS  113 (305)
Q Consensus       110 ~~~~  113 (305)
                      |-..
T Consensus       112 ~D~G  115 (153)
T KOG0121|consen  112 WDAG  115 (153)
T ss_pred             cccc
Confidence            8654

>KOG1190|consensus

Probab=99.57  E-value=3.5e-14  Score=127.87  Aligned_cols=158  Identities=22%  Similarity=0.365  Sum_probs=133.0

Q ss_pred             CceEEEcCCC-ccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          34 DATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        34 ~~~l~V~nLp-~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      +..|.|.||- ..+|.+-|..+|.-||.|.+|+|..++     +-.|+|+|.+...|+.|++.|+|..|.|+.|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            6789999995 579999999999999999999998875     2569999999999999999999999999999999886


Q ss_pred             Cccc------------------------c----------ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhh
Q psy3016         113 SHQK------------------------N----------LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMI  158 (305)
Q Consensus       113 ~~~~------------------------~----------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~  158 (305)
                      ...-                        +          ...+.+|+..|+|.++++|+++..|...|.....       
T Consensus       372 H~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vka-------  444 (492)
T KOG1190|consen  372 HTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKA-------  444 (492)
T ss_pred             CccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEe-------
Confidence            4210                        0          0124589999999999999999999998877542       


Q ss_pred             hhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCe-eeEEEEe
Q psy3016         159 KLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR-PISVSYA  237 (305)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~-~l~v~~a  237 (305)
                                                       .+.   .++.+.+|++.+++.|+|..|+..+|++.+++. .|+|+|+
T Consensus       445 ---------------------------------fkf---f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFS  488 (492)
T KOG1190|consen  445 ---------------------------------FKF---FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFS  488 (492)
T ss_pred             ---------------------------------eee---cCCCcceeecccCChhHhhhhccccccccCCCCceEEEEee
Confidence                                             111   244577999999999999999999999999655 9999998


Q ss_pred             ee
Q psy3016         238 FK  239 (305)
Q Consensus       238 ~~  239 (305)
                      +.
T Consensus       489 ks  490 (492)
T KOG1190|consen  489 KS  490 (492)
T ss_pred             cc
Confidence            64

>KOG0149|consensus

Probab=99.56  E-value=4.9e-15  Score=124.83  Aligned_cols=83  Identities=29%  Similarity=0.368  Sum_probs=75.7

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .+..-++||||+|+..++.++|++.|++||+|.+..|+.|+.+|++||||||+|.+.+.|++|++. -+-.|+||+..++
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcn   86 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCN   86 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccc
Confidence            344567899999999999999999999999999999999999999999999999999999999995 3567899999998


Q ss_pred             eCCC
Q psy3016         110 KASS  113 (305)
Q Consensus       110 ~~~~  113 (305)
                      .+.-
T Consensus        87 lA~l   90 (247)
T KOG0149|consen   87 LASL   90 (247)
T ss_pred             hhhh
Confidence            8764

>KOG0120|consensus

Probab=99.55  E-value=1.7e-14  Score=135.80  Aligned_cols=175  Identities=25%  Similarity=0.376  Sum_probs=133.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .......+||++||..++++++.++...||++...+++.+..+|-++||||.+|.+......|+..|||+.+.+++|.+.
T Consensus       285 ~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq  364 (500)
T KOG0120|consen  285 VPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQ  364 (500)
T ss_pred             cccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEee
Confidence            44556789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             eCCCcccccc-----------------------ccccccccCC--Cch-hcH-------HHHHHHHhhcCcccchhhhhh
Q psy3016         110 KASSHQKNLD-----------------------VGANIFIGNL--DPE-VDE-------KLLYDTFSAFGVILQTPKIMN  156 (305)
Q Consensus       110 ~~~~~~~~~~-----------------------~~~~l~v~nl--~~~-~t~-------~~l~~~f~~~g~v~~~~~~~~  156 (305)
                      .+........                       ....|...|+  +.+ ..+       |+++.-+.+||.|..|     
T Consensus       365 ~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v-----  439 (500)
T KOG0120|consen  365 RAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSV-----  439 (500)
T ss_pred             hhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEE-----
Confidence            8765322111                       0112222222  111 112       2244445668877765     


Q ss_pred             hhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC---CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeE
Q psy3016         157 MIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD---PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPIS  233 (305)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d---~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~  233 (305)
                                                        .|.++   ..-.-+.|..||+|.+.++|.+|+.+|+|+.|.|++|.
T Consensus       440 ----------------------------------~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVv  485 (500)
T KOG0120|consen  440 ----------------------------------EIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVV  485 (500)
T ss_pred             ----------------------------------ecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEE
Confidence                                              22222   12234567789999999999999999999999999999


Q ss_pred             EEEeeecCCc
Q psy3016         234 VSYAFKKDSK  243 (305)
Q Consensus       234 v~~a~~~~~~  243 (305)
                      ++|..+...+
T Consensus       486 tsYydeDkY~  495 (500)
T KOG0120|consen  486 ASYYDEDKYH  495 (500)
T ss_pred             EEecCHHHhh
Confidence            9998766554

>KOG0110|consensus

Probab=99.54  E-value=3.9e-14  Score=135.44  Aligned_cols=164  Identities=23%  Similarity=0.357  Sum_probs=132.1

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (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 AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPG---G---TGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLE  454 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccccceeecCcc---c---ceeeeeecCccchHHHHHHhchhhhccCccccc
Confidence            4556778999999999999999999999999999965422   1   248999999999999999999888887777777


Q ss_pred             eCCCccc------------------------------------c-------------ccccccccccCCCchhcHHHHHH
Q psy3016         110 KASSHQK------------------------------------N-------------LDVGANIFIGNLDPEVDEKLLYD  140 (305)
Q Consensus       110 ~~~~~~~------------------------------------~-------------~~~~~~l~v~nl~~~~t~~~l~~  140 (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            6532000                                    0             00113499999999999999999


Q ss_pred             HHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcc--cCCC-CCCccceEEEEeCChHHHHH
Q psy3016         141 TFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIM--RDPD-TGNSKGFAFINYASFEASDA  217 (305)
Q Consensus       141 ~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~--~d~~-~~~~~g~afV~f~~~~~A~~  217 (305)
                      .|...|.|..+                                       .|.  .|+. .-.+.|||||+|.+.++|.+
T Consensus       535 ~F~k~G~VlS~---------------------------------------~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~  575 (725)
T KOG0110|consen  535 LFSKQGTVLSI---------------------------------------EISKKKDPANKYLSMGFGFVEFAKPESAQA  575 (725)
T ss_pred             HHHhcCeEEEE---------------------------------------EEeccccccccccccceeEEEecCHHHHHH
Confidence            99999999875                                       222  2221 12356999999999999999


Q ss_pred             HHHHhcCeeecCeeeEEEEee
Q psy3016         218 SIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       218 Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      |+++|+|+.++|+.|.|.++.
T Consensus       576 a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  576 ALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             HHHHhcCceecCceEEEEecc
Confidence            999999999999999999987

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.54  E-value=3.6e-14  Score=123.38  Aligned_cols=78  Identities=18%  Similarity=0.265  Sum_probs=71.8

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||+||++.+|+++|+++|+.||.|.+|.|+.+..   ++|||||+|.+.++|..|+. |+|..|.|+.|.|.++.
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            357999999999999999999999999999999988753   56999999999999999996 99999999999999987


Q ss_pred             Cc
Q psy3016         113 SH  114 (305)
Q Consensus       113 ~~  114 (305)
                      ..
T Consensus        79 ~~   80 (260)
T PLN03120         79 DY   80 (260)
T ss_pred             CC
Confidence            54

>KOG0113|consensus

Probab=99.52  E-value=4.9e-14  Score=122.36  Aligned_cols=88  Identities=31%  Similarity=0.473  Sum_probs=82.4

Q ss_pred             CCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        26 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      ++....+.-+||||+.|++.++|.+|++.|+.||+|..|.|+.++.+|+++|||||+|.++.+...|.+..+|+.|+|+.
T Consensus        93 dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrr  172 (335)
T KOG0113|consen   93 DPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRR  172 (335)
T ss_pred             CCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcE
Confidence            45556688899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEeeCCC
Q psy3016         106 IRVNKASS  113 (305)
Q Consensus       106 l~v~~~~~  113 (305)
                      |.|.+...
T Consensus       173 i~VDvERg  180 (335)
T KOG0113|consen  173 ILVDVERG  180 (335)
T ss_pred             EEEEeccc
Confidence            99987554

>KOG0132|consensus

Probab=99.50  E-value=1.8e-13  Score=131.88  Aligned_cols=103  Identities=20%  Similarity=0.301  Sum_probs=83.5

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (305)
                      ++|||||+|+..++|.||.++|+.||+|.+|+++..      +|||||.+...++|.+|+.+|++..+.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            469999999999999999999999999999999664      59999999999999999999999999999999999998


Q ss_pred             ccccccc----cccccccCCCchhcHHHHHHHH
Q psy3016         114 HQKNLDV----GANIFIGNLDPEVDEKLLYDTF  142 (305)
Q Consensus       114 ~~~~~~~----~~~l~v~nl~~~~t~~~l~~~f  142 (305)
                      +..+.+-    ...+=|.-||+..-.+++..++
T Consensus       495 ~G~kse~k~~wD~~lGVt~IP~~kLt~dl~~~~  527 (894)
T KOG0132|consen  495 KGPKSEYKDYWDVELGVTYIPWEKLTDDLEAWC  527 (894)
T ss_pred             CCcchhhhhhhhcccCeeEeehHhcCHHHHHhh
Confidence            7765521    1123345566653333344444

>PLN03213 repressor of silencing 3; Provisional

Probab=99.50  E-value=8.6e-14  Score=128.02  Aligned_cols=81  Identities=23%  Similarity=0.408  Sum_probs=73.4

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCH--HHHHHHHHHhcCceeCCeee
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE--EDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~--e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      +......+||||||++.+|+++|+..|+.||.|..|.|++.  +|  +|||||+|.+.  ..+.+||..|||..|.|+.|
T Consensus         5 es~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~L   80 (759)
T PLN03213          5 SSGGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRL   80 (759)
T ss_pred             ccCCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCcee
Confidence            34455689999999999999999999999999999999954  55  89999999987  67999999999999999999


Q ss_pred             EEeeCCC
Q psy3016         107 RVNKASS  113 (305)
Q Consensus       107 ~v~~~~~  113 (305)
                      +|+.+.+
T Consensus        81 KVNKAKP   87 (759)
T PLN03213         81 RLEKAKE   87 (759)
T ss_pred             EEeeccH
Confidence            9998875

>KOG4211|consensus

Probab=99.49  E-value=4.8e-13  Score=123.41  Aligned_cols=166  Identities=18%  Similarity=0.300  Sum_probs=128.3

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      +...-|-+.+||.++|++||.++|+.+ .|+++.+.+.  +|+..|-|||+|.+.|++++|++ .+...+.-|-|.|-.+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRR--NGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEecc--CCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            445678899999999999999999998 5788766554  68899999999999999999999 4777777787887655


Q ss_pred             CCcccc----------ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcc
Q psy3016         112 SSHQKN----------LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA  181 (305)
Q Consensus       112 ~~~~~~----------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (305)
                      .....+          ......|.+..||+.+|+++|.++|...-.|...                              
T Consensus        84 ~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~g------------------------------  133 (510)
T KOG4211|consen   84 GGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDG------------------------------  133 (510)
T ss_pred             CCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccc------------------------------
Confidence            433211          1245678899999999999999999875544320                              


Q ss_pred             eeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       182 ~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                               -.+.....+++.|-|||+|++.+.|++|+. -|...|.-|-|.|-.+...+
T Consensus       134 ---------i~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~Ss~~e  183 (510)
T KOG4211|consen  134 ---------ILLPMDQRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRSSRAE  183 (510)
T ss_pred             ---------eeeeccCCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehhHHHH
Confidence                     113333457889999999999999999998 46667777777776655443

>KOG0126|consensus

Probab=99.49  E-value=5.1e-15  Score=119.92  Aligned_cols=83  Identities=29%  Similarity=0.544  Sum_probs=78.0

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      .+--|||||||+..||.||--.|++||+|..|++++|+.||+++||||+.|.+-.....|+.+|||..|.||.|+|....
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            35589999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             Ccc
Q psy3016         113 SHQ  115 (305)
Q Consensus       113 ~~~  115 (305)
                      ...
T Consensus       114 ~Yk  116 (219)
T KOG0126|consen  114 NYK  116 (219)
T ss_pred             ccc
Confidence            443

>smart00362 RRM_2 RNA recognition motif

Probab=99.48  E-value=2.6e-13  Score=95.10  Aligned_cols=72  Identities=44%  Similarity=0.768  Sum_probs=67.4

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      +|||+|||..+++++|+++|+.||.|..+.+..+.  +.++|+|||+|.+.++|++|++.+++..+.|+.+.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999998876  6788999999999999999999999999999998873

>KOG0107|consensus

Probab=99.48  E-value=9.3e-14  Score=112.09  Aligned_cols=80  Identities=25%  Similarity=0.571  Sum_probs=73.1

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++||||||+..+++.||...|..||+|.+|-|-..     ..|||||+|.+..+|+.|+..|+|..|.|..|+|+.+
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            45789999999999999999999999999999988554     5699999999999999999999999999999999998


Q ss_pred             CCccc
Q psy3016         112 SSHQK  116 (305)
Q Consensus       112 ~~~~~  116 (305)
                      .....
T Consensus        83 ~G~~r   87 (195)
T KOG0107|consen   83 TGRPR   87 (195)
T ss_pred             cCCcc
Confidence            86543

>PF00076 RRM_1: RNA recognition motif

Probab=99.47  E-value=8.5e-14  Score=98.12  Aligned_cols=70  Identities=37%  Similarity=0.753  Sum_probs=64.5

Q ss_pred             ccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccc
Q psy3016         124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKG  203 (305)
Q Consensus       124 l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g  203 (305)
                      |||+|||.++|+++|+++|+.||.+..+                                       .++.+ .++..++
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~---------------------------------------~~~~~-~~~~~~~   40 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESI---------------------------------------KVMRN-SSGKSKG   40 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEE---------------------------------------EEEEE-TTSSEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccc---------------------------------------ccccc-ccccccc
Confidence            7999999999999999999999999876                                       55665 5688999


Q ss_pred             eEEEEeCChHHHHHHHHHhcCeeecCeeeE
Q psy3016         204 FAFINYASFEASDASIDAMHGQYLCNRPIS  233 (305)
Q Consensus       204 ~afV~f~~~~~A~~Al~~l~~~~~~g~~l~  233 (305)
                      +|||+|++.++|.+|+..|+|..+.|+.|+
T Consensus        41 ~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   41 YAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             eEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            999999999999999999999999999885

(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 ....

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.46  E-value=4.2e-13  Score=114.96  Aligned_cols=77  Identities=14%  Similarity=0.267  Sum_probs=70.7

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ...+|||+||+..+|+++|+++|+.||.|.+|+|+.+.   ..++||||+|.+.++|+.|+. |+|..|.++.|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            35799999999999999999999999999999999884   456899999999999999996 99999999999998865


Q ss_pred             C
Q psy3016         113 S  113 (305)
Q Consensus       113 ~  113 (305)
                      .
T Consensus        80 ~   80 (243)
T PLN03121         80 Q   80 (243)
T ss_pred             c
Confidence            4

>KOG0111|consensus

Probab=99.45  E-value=7.5e-14  Score=116.36  Aligned_cols=88  Identities=39%  Similarity=0.684  Sum_probs=82.5

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++||||+|...|||.-|...|-+||.|..|++..|-.+++.+|||||+|...|+|.+||.+||+.++.||.|+|+++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccccc
Q psy3016         112 SSHQKNLD  119 (305)
Q Consensus       112 ~~~~~~~~  119 (305)
                      .+..-+..
T Consensus        88 kP~kikeg   95 (298)
T KOG0111|consen   88 KPEKIKEG   95 (298)
T ss_pred             CCccccCC
Confidence            98765444

>smart00360 RRM RNA recognition motif

Probab=99.45  E-value=4.6e-13  Score=93.50  Aligned_cols=71  Identities=37%  Similarity=0.646  Sum_probs=66.8

Q ss_pred             EcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          39 VGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        39 V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      |+|||..+++++|+++|+.||.|..+.+..+..++.++|+|||+|.+.++|.+|++.+++..+.|+.|.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            68999999999999999999999999999987778899999999999999999999999999999998873

>KOG4207|consensus

Probab=99.44  E-value=2e-13  Score=112.93  Aligned_cols=84  Identities=29%  Similarity=0.477  Sum_probs=79.5

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ..-++-.+|.|-||.+.++.++|+.+|++||.|-+|.|..|.-++.++|||||-|....+|+.|++.|+|.+++|+.|+|
T Consensus         8 Pdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrV   87 (256)
T KOG4207|consen    8 PDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRV   87 (256)
T ss_pred             CCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeee
Confidence            35566779999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCC
Q psy3016         109 NKAS  112 (305)
Q Consensus       109 ~~~~  112 (305)
                      +.+.
T Consensus        88 q~ar   91 (256)
T KOG4207|consen   88 QMAR   91 (256)
T ss_pred             hhhh
Confidence            8765

>KOG1456|consensus

Probab=99.42  E-value=5.3e-12  Score=112.75  Aligned_cols=164  Identities=17%  Similarity=0.229  Sum_probs=127.4

Q ss_pred             cCCCCceEEEcCCCc-cccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          30 SGDGDATIYVGGLDD-KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      .....+.+.|.+|.. .+..+.|.++|..||+|+.|++++.+     .|.|.|++.+..+.++|+..||+..+.|.+|.|
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v  357 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNV  357 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEE
Confidence            444567899999976 57788999999999999999999986     378999999999999999999999999999999


Q ss_pred             eeCCCc------------------------------------cccccccccccccCCCchhcHHHHHHHHhhcCcccchh
Q psy3016         109 NKASSH------------------------------------QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP  152 (305)
Q Consensus       109 ~~~~~~------------------------------------~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~  152 (305)
                      ..++..                                    .+....++.|+.-|.|..+||+.|.++|...+.- .++
T Consensus       358 ~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~-~~s  436 (494)
T KOG1456|consen  358 CVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVP-PTS  436 (494)
T ss_pred             eeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCC-cce
Confidence            876531                                    1112346889999999999999999999875544 220


Q ss_pred             hhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCe--
Q psy3016         153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR--  230 (305)
Q Consensus       153 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~--  230 (305)
                                                           .+ +.+.+ .+....+.++|++.++|..||.++|...+.+.  
T Consensus       437 -------------------------------------vk-vFp~k-serSssGllEfe~~s~Aveal~~~NH~pi~~p~g  477 (494)
T KOG1456|consen  437 -------------------------------------VK-VFPLK-SERSSSGLLEFENKSDAVEALMKLNHYPIEGPNG  477 (494)
T ss_pred             -------------------------------------EE-eeccc-ccccccceeeeehHHHHHHHHHHhccccccCCCC
Confidence                                                 01 12222 33344689999999999999999999988543  


Q ss_pred             --eeEEEEee
Q psy3016         231 --PISVSYAF  238 (305)
Q Consensus       231 --~l~v~~a~  238 (305)
                        +.++.|+.
T Consensus       478 s~PfilKlcf  487 (494)
T KOG1456|consen  478 SFPFILKLCF  487 (494)
T ss_pred             CCCeeeeeee
Confidence              34444443

>KOG0122|consensus

Probab=99.42  E-value=3.1e-13  Score=114.44  Aligned_cols=82  Identities=29%  Similarity=0.437  Sum_probs=77.8

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|.|.||+.++++++|.++|.+||.|..+                                       .+.+|..||
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rv---------------------------------------ylardK~TG  228 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRV---------------------------------------YLARDKETG  228 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCcccee---------------------------------------EEEEccccC
Confidence            46789999999999999999999999999987                                       789999999


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      .++|||||.|.+.++|.+||+.|||.-++.-.|.|.|++++
T Consensus       229 ~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  229 LSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSKPS  269 (270)
T ss_pred             cccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecCCC
Confidence            99999999999999999999999999999999999999765

>KOG0108|consensus

Probab=99.41  E-value=4.5e-13  Score=125.46  Aligned_cols=81  Identities=35%  Similarity=0.598  Sum_probs=78.5

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (305)
                      +.|||||||+++++++|.++|+..|.|.+++++.|+.+|+.+||||++|.+.++|..|++.|||.++.||+|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999998764


Q ss_pred             c
Q psy3016         115 Q  115 (305)
Q Consensus       115 ~  115 (305)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            3

>KOG1190|consensus

Probab=99.41  E-value=3e-12  Score=115.58  Aligned_cols=168  Identities=15%  Similarity=0.312  Sum_probs=131.0

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceE-EEEEEcCHHHHHHHHHHhcCceeCCe--eeEE
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGY-GFIEFMGEEDADYAIKIMNMIKLYGK--PIRV  108 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~-afV~f~~~e~A~~Ai~~l~g~~~~g~--~l~v  108 (305)
                      ..--+++|+|+-+-+|-|-|..+|++||.|..|.-...     +.+| |+|+|.+.+.|..|...|+|..|..-  .|+|
T Consensus       148 n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~K-----nn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrI  222 (492)
T KOG1190|consen  148 NPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTK-----NNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRI  222 (492)
T ss_pred             ceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEec-----ccchhhhhhccchhhHHHHHHhccCCcccCceeEEEe
Confidence            34457899999999999999999999999998865332     3355 99999999999999999999877654  4455


Q ss_pred             eeCCC----------cccc--------c------------------------------------------c--ccccccc
Q psy3016         109 NKASS----------HQKN--------L------------------------------------------D--VGANIFI  126 (305)
Q Consensus       109 ~~~~~----------~~~~--------~------------------------------------------~--~~~~l~v  126 (305)
                      .++.-          ++++        .                                          .  ....|.|
T Consensus       223 d~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllv  302 (492)
T KOG1190|consen  223 DFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLV  302 (492)
T ss_pred             ehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEE
Confidence            44321          1000        0                                          0  0256778


Q ss_pred             cCCCc-hhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceE
Q psy3016         127 GNLDP-EVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFA  205 (305)
Q Consensus       127 ~nl~~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~a  205 (305)
                      .||.. .+|.+.|..+|+-||+|.++                                       +|++..     +..|
T Consensus       303 snln~~~VT~d~LftlFgvYGdVqRV---------------------------------------kil~nk-----kd~A  338 (492)
T KOG1190|consen  303 SNLNEEAVTPDVLFTLFGVYGDVQRV---------------------------------------KILYNK-----KDNA  338 (492)
T ss_pred             ecCchhccchhHHHHHHhhhcceEEE---------------------------------------EeeecC-----Ccce
Confidence            88875 49999999999999999987                                       455442     3579


Q ss_pred             EEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcCCCCC
Q psy3016         206 FINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHG  248 (305)
Q Consensus       206 fV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~~~~~  248 (305)
                      +|+|.+...|.-|++.|+|..+.|+.|+|++++.....-.+.+
T Consensus       339 LIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~eg  381 (492)
T KOG1190|consen  339 LIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREG  381 (492)
T ss_pred             eeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCC
Confidence            9999999999999999999999999999999987765544433

>KOG4212|consensus

Probab=99.40  E-value=5.5e-12  Score=114.71  Aligned_cols=76  Identities=24%  Similarity=0.398  Sum_probs=65.1

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ...++||+||...+..+.|++.|.-.|.|+.+.+--|+. |.++|||.|+|..+-.|..||..|++..+.++...++
T Consensus       214 l~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~R  289 (608)
T KOG4212|consen  214 LHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVR  289 (608)
T ss_pred             ccceeeeeccccccchHHHHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhhccCCCccccceee
Confidence            345899999999999999999999999999999988885 4889999999999999999999998665555544443

>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=99.39  E-value=3.6e-12  Score=89.76  Aligned_cols=74  Identities=39%  Similarity=0.654  Sum_probs=68.4

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      +|+|+|||..+++++|+++|+.||.|..+.+..+..+ ..+++|||+|.+.++|..|++.+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            5899999999999999999999999999999887644 6689999999999999999999999999999998864

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).

>KOG0130|consensus

Probab=99.38  E-value=8.5e-13  Score=102.11  Aligned_cols=84  Identities=25%  Similarity=0.417  Sum_probs=78.6

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..-.|||.++...+||++|.+.|..||+|..|.+--|..+|-.+|||+|+|.+.+.|++|+..+||..+.|..|.|.|+.
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            44589999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             Cccc
Q psy3016         113 SHQK  116 (305)
Q Consensus       113 ~~~~  116 (305)
                      .+..
T Consensus       151 v~gp  154 (170)
T KOG0130|consen  151 VKGP  154 (170)
T ss_pred             ecCC
Confidence            5443

>KOG0114|consensus

Probab=99.38  E-value=3.1e-12  Score=94.64  Aligned_cols=87  Identities=15%  Similarity=0.216  Sum_probs=77.3

Q ss_pred             CCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        26 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      +..-..+..+.|||.|||+++|.+++.++|.+||.|..|+|-..+.   .+|-|||.|.+..+|.+|++.|+|..+.++-
T Consensus        10 ~~rlppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ry   86 (124)
T KOG0114|consen   10 NIRLPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRY   86 (124)
T ss_pred             CCCCChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCce
Confidence            3444566788999999999999999999999999999999977653   5699999999999999999999999999999


Q ss_pred             eEEeeCCCcc
Q psy3016         106 IRVNKASSHQ  115 (305)
Q Consensus       106 l~v~~~~~~~  115 (305)
                      +.|-+..+..
T Consensus        87 l~vlyyq~~~   96 (124)
T KOG0114|consen   87 LVVLYYQPED   96 (124)
T ss_pred             EEEEecCHHH
Confidence            9999877643

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.38  E-value=1.2e-12  Score=92.62  Aligned_cols=70  Identities=30%  Similarity=0.652  Sum_probs=62.1

Q ss_pred             ccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccc
Q psy3016         124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKG  203 (305)
Q Consensus       124 l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g  203 (305)
                      |||+|||.++++++|.++|+.||.|..+                                       .+..+.. +..++
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v---------------------------------------~~~~~~~-~~~~~   40 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKV---------------------------------------RLIKNKD-GQSRG   40 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEE---------------------------------------EEEESTT-SSEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceE---------------------------------------EEEeeec-cccCC
Confidence            6899999999999999999999998766                                       5666655 88999


Q ss_pred             eEEEEeCChHHHHHHHHHhcCeeecCeeeE
Q psy3016         204 FAFINYASFEASDASIDAMHGQYLCNRPIS  233 (305)
Q Consensus       204 ~afV~f~~~~~A~~Al~~l~~~~~~g~~l~  233 (305)
                      +|||+|.+.++|.+|+..+++.+++|+.|+
T Consensus        41 ~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   41 FAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             EEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            999999999999999999999999999885

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 ....

>KOG0107|consensus

Probab=99.36  E-value=6.6e-13  Score=107.22  Aligned_cols=79  Identities=20%  Similarity=0.447  Sum_probs=70.8

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..+.|||+||+..+++.+|...|..||.+..+|+.                                            .
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvA--------------------------------------------r   44 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVA--------------------------------------------R   44 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEe--------------------------------------------e
Confidence            46789999999999999999999999999887533                                            3


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      ...|||||+|++..||.+|+..|+|+.|+|..|+|.++.-...
T Consensus        45 nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen   45 NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            5689999999999999999999999999999999999865543

>KOG1456|consensus

Probab=99.33  E-value=2.6e-11  Score=108.46  Aligned_cols=164  Identities=19%  Similarity=0.261  Sum_probs=128.2

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHh--cCceeCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM--NMIKLYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l--~g~~~~g~~l~  107 (305)
                      ....+-.|.|.+|-..++|.||-+.++.||+|..+..+..+      .-|.|+|++.+.|..|+.--  +...+.|+.-.
T Consensus        27 k~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~------r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al  100 (494)
T KOG1456|consen   27 KPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHK------RQALVEFEDIEGAKNCVNFAADNQIYIAGQQAL  100 (494)
T ss_pred             CCCCCceEEEeccccccchhHHHHHHhcCCceEEEEecccc------ceeeeeeccccchhhheehhccCcccccCchhh
Confidence            34456689999999999999999999999999999887654      67999999999999998632  34677788888


Q ss_pred             EeeCCCcccc------ccccccccc--cCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCC
Q psy3016         108 VNKASSHQKN------LDVGANIFI--GNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDV  179 (305)
Q Consensus       108 v~~~~~~~~~------~~~~~~l~v--~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  179 (305)
                      ++++..+.-.      ......|.+  -|--+.+|.+.|+.++.+.|.|.++                            
T Consensus       101 ~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRI----------------------------  152 (494)
T KOG1456|consen  101 FNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRI----------------------------  152 (494)
T ss_pred             cccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEE----------------------------
Confidence            8888543211      112233443  4444579999999999999999976                            


Q ss_pred             cceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeee--cCeeeEEEEeeecCCc
Q psy3016         180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL--CNRPISVSYAFKKDSK  243 (305)
Q Consensus       180 ~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~--~g~~l~v~~a~~~~~~  243 (305)
                                 .|++.     .--.|.|+|++.+.|.+|..+|||..|  +.++|+|.||++..-+
T Consensus       153 -----------vIfkk-----ngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rln  202 (494)
T KOG1456|consen  153 -----------VIFKK-----NGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLN  202 (494)
T ss_pred             -----------EEEec-----cceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceee
Confidence                       22222     234799999999999999999999987  5689999999876544

>KOG0111|consensus

Probab=99.33  E-value=1.1e-12  Score=109.42  Aligned_cols=84  Identities=32%  Similarity=0.515  Sum_probs=78.9

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||++|...+|+..|...|-+||+|.-+                                       ++..|.++++
T Consensus        10 KrtlYVGGladeVtekvLhaAFIPFGDI~dI---------------------------------------qiPlDyesqk   50 (298)
T KOG0111|consen   10 KRTLYVGGLADEVTEKVLHAAFIPFGDIKDI---------------------------------------QIPLDYESQK   50 (298)
T ss_pred             ceeEEeccchHHHHHHHHHhccccccchhhc---------------------------------------ccccchhccc
Confidence            5789999999999999999999999999855                                       8899999999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .|||+||+|+..|||..||..||+.++.||+|+|.|+++...+
T Consensus        51 HRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~kik   93 (298)
T KOG0111|consen   51 HRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEKIK   93 (298)
T ss_pred             ccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCcccc
Confidence            9999999999999999999999999999999999999886654

>KOG0149|consensus

Probab=99.33  E-value=3.9e-12  Score=107.45  Aligned_cols=79  Identities=27%  Similarity=0.447  Sum_probs=71.6

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ..+|||++|++.+..+.|++.|+.||+|++.                                       .|+.|..+|+
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~ea---------------------------------------vvitd~~t~r   52 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEA---------------------------------------VVITDKNTGR   52 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEE---------------------------------------EEEeccCCcc
Confidence            4689999999999999999999999999876                                       7889999999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      +|||+||.|.+.++|.+|.+- -+-.|+||+.-|++|..
T Consensus        53 skGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   53 SKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             ccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhh
Confidence            999999999999999999983 34578999999999865

>KOG4207|consensus

Probab=99.33  E-value=1.5e-12  Score=107.73  Aligned_cols=83  Identities=27%  Similarity=0.380  Sum_probs=76.3

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      .+.-..|.|.||...++.++|+.+|++||.|-.|                                       .|.+|..
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDV---------------------------------------yIPrdr~   50 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDV---------------------------------------YIPRDRY   50 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccce---------------------------------------ecccccc
Confidence            3345679999999999999999999999999744                                       8899999


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      |+.++|||||.|....+|++|+.+|+|..++|+-|+|++|+-
T Consensus        51 Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   51 TRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             cccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            999999999999999999999999999999999999999863

>KOG0121|consensus

Probab=99.32  E-value=2.4e-12  Score=98.81  Aligned_cols=80  Identities=25%  Similarity=0.450  Sum_probs=70.9

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      .+++|||+||+..++||+|+++|++.|+|..+                                       -+=.|..+.
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irri---------------------------------------iMGLdr~kk   75 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRI---------------------------------------IMGLDRFKK   75 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchhee---------------------------------------EeccccCCc
Confidence            46899999999999999999999999999875                                       123455556


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      ..-|||||+|-+.++|..|++-++|+.++.+.|++.|-.
T Consensus        76 tpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   76 TPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             CccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            788999999999999999999999999999999999853

>KOG1365|consensus

Probab=99.32  E-value=3.8e-12  Score=114.00  Aligned_cols=175  Identities=18%  Similarity=0.207  Sum_probs=128.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccC----CCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQS----GPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~----G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      ++...-.|-+.+||+++|+.|+.++|..-    |-.+.|.++... +|+..|-|||.|..+++|+.|+.+ |...+.-|-
T Consensus       157 sk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRY  234 (508)
T KOG1365|consen  157 SKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRY  234 (508)
T ss_pred             CcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHH
Confidence            44556688899999999999999999632    244566666653 688899999999999999999975 433333332


Q ss_pred             eEEeeCCC----------------------------c--cccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhh
Q psy3016         106 IRVNKASS----------------------------H--QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIM  155 (305)
Q Consensus       106 l~v~~~~~----------------------------~--~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~  155 (305)
                      |.+-++..                            .  -.......||.+.+||+..+.|+|.++|+.|..-...    
T Consensus       235 IElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f----  310 (508)
T KOG1365|consen  235 IELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRF----  310 (508)
T ss_pred             HHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhccc----
Confidence            22221110                            0  0011235789999999999999999999998754432    


Q ss_pred             hhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEE
Q psy3016         156 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS  235 (305)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~  235 (305)
                                                      ..+.+..+. .|+..|-|||+|.+.++|..|....|++....|-|.|-
T Consensus       311 --------------------------------~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  311 --------------------------------QGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             --------------------------------ceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence                                            111334443 38899999999999999999999999999999999998


Q ss_pred             EeeecCCc
Q psy3016         236 YAFKKDSK  243 (305)
Q Consensus       236 ~a~~~~~~  243 (305)
                      -+...+..
T Consensus       358 p~S~eeln  365 (508)
T KOG1365|consen  358 PCSVEELN  365 (508)
T ss_pred             eccHHHHH
Confidence            77666554

>PF13893 RRM_5: RNA recognition motif

Probab=99.30  E-value=1.5e-11  Score=83.16  Aligned_cols=56  Identities=34%  Similarity=0.663  Sum_probs=51.0

Q ss_pred             HHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          51 MWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        51 L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (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-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999997653     589999999999999999999999999999999885

(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=99.29  E-value=1.5e-11  Score=87.17  Aligned_cols=62  Identities=24%  Similarity=0.281  Sum_probs=55.4

Q ss_pred             HHHHHHHhc----cCCCeEEEE-EcccCCC--CCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          48 ETLMWELFV----QSGPVVNVH-MPKDRVT--QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        48 e~~L~~~F~----~~G~i~~i~-~~~~~~~--~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      +++|+++|+    .||.|.+|. ++.++.+  +.++|||||+|.+.++|.+|++.|||..+.|+.|++.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578888888    999999995 6666655  8899999999999999999999999999999999863

>KOG0125|consensus

Probab=99.28  E-value=4.4e-12  Score=111.61  Aligned_cols=100  Identities=24%  Similarity=0.415  Sum_probs=80.8

Q ss_pred             ceeCCeeeEEeeCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCC
Q psy3016          99 IKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD  178 (305)
Q Consensus        99 ~~~~g~~l~v~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  178 (305)
                      -...|..+....+... ...+..++|||.|||...-+.||+.+|++||.|..|                           
T Consensus        75 ~~t~g~~~~~~~st~s-~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldV---------------------------  126 (376)
T KOG0125|consen   75 APTDGQPIQTQPSTNS-SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDV---------------------------  126 (376)
T ss_pred             CCCCCCccccCCCCcC-CCCCCCceeEeecCCccccCccHHHHHHhhCceeeE---------------------------
Confidence            3444555555443332 233446789999999999999999999999999765                           


Q ss_pred             CcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       179 ~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                                  .|+.. + ..+|||+||.|++.+||++|-.+|||+.+.||+|.|+.+..+
T Consensus       127 ------------EIIfN-E-RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  127 ------------EIIFN-E-RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             ------------EEEec-c-CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchh
Confidence                        55655 2 558999999999999999999999999999999999998765

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.28  E-value=7.2e-12  Score=109.07  Aligned_cols=75  Identities=13%  Similarity=0.272  Sum_probs=67.5

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+||++.+|+++|+++|+.||.|..+                                       .+..|.   .
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V---------------------------------------~I~~d~---~   41 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYV---------------------------------------EMQSEN---E   41 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEeecC---C
Confidence            4689999999999999999999999999987                                       555663   3


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      .+|||||+|++.++|..|+. |||..+.|+.|+|.++.
T Consensus        42 ~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120         42 RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            57999999999999999996 99999999999999974

>KOG0130|consensus

Probab=99.26  E-value=9.2e-12  Score=96.41  Aligned_cols=84  Identities=31%  Similarity=0.549  Sum_probs=77.0

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ....|||+++....|+++|.+.|..||+|..+                                       .+-.|..+|
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNi---------------------------------------hLNLDRRtG  111 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNI---------------------------------------HLNLDRRTG  111 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccce---------------------------------------eeccccccc
Confidence            35679999999999999999999999999866                                       556777889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      -.+|||+|+|++.++|..|+.++||..+-|..|.|.||..+..
T Consensus       112 y~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~gp  154 (170)
T KOG0130|consen  112 YVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVKGP  154 (170)
T ss_pred             cccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEecCC
Confidence            9999999999999999999999999999999999999987754

>KOG0120|consensus

Probab=99.24  E-value=2.5e-11  Score=114.59  Aligned_cols=167  Identities=27%  Similarity=0.471  Sum_probs=138.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccC-----------C-CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQS-----------G-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN   97 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~-----------G-~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~   97 (305)
                      .....+.++|++++..++++.+-.+|..-           | .+..+.+-      ..++|||++|.+.+.|..|+. ++
T Consensus       171 ~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n------~~~nfa~ie~~s~~~at~~~~-~~  243 (500)
T KOG0120|consen  171 ATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLN------LEKNFAFIEFRSISEATEAMA-LD  243 (500)
T ss_pred             hhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeec------ccccceeEEecCCCchhhhhc-cc
Confidence            34456799999999999999999998763           2 36666663      345899999999999999988 78


Q ss_pred             CceeCCeeeEEeeCCCccc----------------------cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhh
Q psy3016          98 MIKLYGKPIRVNKASSHQK----------------------NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIM  155 (305)
Q Consensus        98 g~~~~g~~l~v~~~~~~~~----------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~  155 (305)
                      +..+.|..+++........                      .....+.|||++|+..++++++.++++.||.+...    
T Consensus       244 ~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f----  319 (500)
T KOG0120|consen  244 GIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAF----  319 (500)
T ss_pred             chhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhh----
Confidence            8888898888875443211                      11234679999999999999999999999999765    


Q ss_pred             hhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEE
Q psy3016         156 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS  235 (305)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~  235 (305)
                                                         .+..|..+|.++||||.+|.+...+..|+..|||..+.++.|+|.
T Consensus       320 -----------------------------------~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq  364 (500)
T KOG0120|consen  320 -----------------------------------RLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQ  364 (500)
T ss_pred             -----------------------------------eeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEee
Confidence                                               567777889999999999999999999999999999999999999


Q ss_pred             EeeecCC
Q psy3016         236 YAFKKDS  242 (305)
Q Consensus       236 ~a~~~~~  242 (305)
                      .+.....
T Consensus       365 ~A~~g~~  371 (500)
T KOG0120|consen  365 RAIVGAS  371 (500)
T ss_pred             hhhccch
Confidence            9876544

>smart00362 RRM_2 RNA recognition motif

Probab=99.24  E-value=2.5e-11  Score=84.88  Aligned_cols=72  Identities=43%  Similarity=0.772  Sum_probs=64.1

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      +|||+||+..+++++|.++|..||.+..+                                       .+..+.  +.++
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~---------------------------------------~~~~~~--~~~~   39 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESV---------------------------------------KIPKDT--GKSK   39 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEE---------------------------------------EEecCC--CCCC
Confidence            58999999999999999999999999865                                       445443  6788


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeeecCeeeEEE
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYLCNRPISVS  235 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~  235 (305)
                      |+|||+|.+.++|.+|+..+++..+.|+.|+|+
T Consensus        40 ~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362       40 GFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             ceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            999999999999999999999999999998873

>KOG0126|consensus

Probab=99.24  E-value=4.7e-13  Score=108.61  Aligned_cols=80  Identities=34%  Similarity=0.559  Sum_probs=75.1

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      +.-|||+|||..+|+.+|.-+|+.||+|..+                                       .+++|..||+
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdi---------------------------------------nLiRDk~TGK   75 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDI---------------------------------------NLIRDKKTGK   75 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEE---------------------------------------EEEecCCCCc
Confidence            5679999999999999999999999999865                                       7899999999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      ++||||+.|++..+..-|+..|||..|.||.|+|.....
T Consensus        76 SKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   76 SKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             ccceEEEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence            999999999999999999999999999999999998644

>KOG0108|consensus

Probab=99.23  E-value=1e-11  Score=116.44  Aligned_cols=82  Identities=29%  Similarity=0.577  Sum_probs=77.6

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      +.+||||+++++++++|.++|+..|.|...                                       +++.|+.+|+.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~---------------------------------------~~v~D~~tG~~   59 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSF---------------------------------------RLVYDRETGKP   59 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCcccee---------------------------------------eecccccCCCc
Confidence            789999999999999999999999999876                                       88999999999


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +||||++|.+.++|..|++.|||.++.|++|+|.|+.....
T Consensus        60 ~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~~~  100 (435)
T KOG0108|consen   60 KGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNRKN  100 (435)
T ss_pred             CceeeEecCchhhHHHHHHhcCCcccCCceEEeecccccch
Confidence            99999999999999999999999999999999999866554

>PLN03213 repressor of silencing 3; Provisional

Probab=99.23  E-value=1.4e-11  Score=113.56  Aligned_cols=79  Identities=19%  Similarity=0.339  Sum_probs=70.3

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..-+||||||.+.+++++|...|..||.|..+                                       .|+  ..+|
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdV---------------------------------------EIp--RETG   47 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAV---------------------------------------EFV--RTKG   47 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEE---------------------------------------EEe--cccC
Confidence            34689999999999999999999999999987                                       556  3456


Q ss_pred             CccceEEEEeCCh--HHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASF--EASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~--~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                        ||||||+|.+.  .++.+||..|||..|.|+.|+|.-|++.-
T Consensus        48 --RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP~Y   89 (759)
T PLN03213         48 --RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKEHY   89 (759)
T ss_pred             --CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccHHH
Confidence              99999999987  78999999999999999999999997654

>KOG0113|consensus

Probab=99.22  E-value=2.9e-11  Score=105.26  Aligned_cols=89  Identities=28%  Similarity=0.389  Sum_probs=81.5

Q ss_pred             ccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         116 KNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       116 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      ...++-++|||+.|+.+++|..|...|+.||.|..+                                       .++.|
T Consensus        96 a~gDPy~TLFv~RLnydT~EskLrreF~~YG~Ikri---------------------------------------rlV~d  136 (335)
T KOG0113|consen   96 AIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRI---------------------------------------RLVRD  136 (335)
T ss_pred             ccCCccceeeeeeccccccHHHHHHHHHhcCcceeE---------------------------------------EEeee
Confidence            344567999999999999999999999999999987                                       78999


Q ss_pred             CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         196 PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       196 ~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ..+|+++|||||+|++..+...|.+..+|..|+|+.|.|.+-.....+
T Consensus       137 ~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvERgRTvk  184 (335)
T KOG0113|consen  137 KVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERGRTVK  184 (335)
T ss_pred             cccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEeccccccc
Confidence            999999999999999999999999999999999999999997666554

>KOG0131|consensus

Probab=99.21  E-value=2.7e-11  Score=98.55  Aligned_cols=86  Identities=31%  Similarity=0.488  Sum_probs=78.1

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEE-EEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~-i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...+|||+||.+.++|..|+++|+.||.+.. -+++++..+|.++|||||.|.+.+.+.+|++.+||+.+..+.++|.++
T Consensus        95 vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya  174 (203)
T KOG0131|consen   95 VGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYA  174 (203)
T ss_pred             ccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEE
Confidence            3479999999999999999999999998766 488899888999999999999999999999999999999999999998


Q ss_pred             CCccccc
Q psy3016         112 SSHQKNL  118 (305)
Q Consensus       112 ~~~~~~~  118 (305)
                      ..+..+.
T Consensus       175 ~k~~~kg  181 (203)
T KOG0131|consen  175 FKKDTKG  181 (203)
T ss_pred             EecCCCc
Confidence            8665443

>smart00360 RRM RNA recognition motif

Probab=99.21  E-value=4.2e-11  Score=83.39  Aligned_cols=71  Identities=44%  Similarity=0.785  Sum_probs=63.6

Q ss_pred             ccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceE
Q psy3016         126 IGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFA  205 (305)
Q Consensus       126 v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~a  205 (305)
                      |+||+..+++++|+++|+.||.|..+                                       .+..+..++.++|+|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~---------------------------------------~i~~~~~~~~~~~~a   41 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESV---------------------------------------RLVRDKDTGKSKGFA   41 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEE---------------------------------------EEEeCCCCCCCCceE
Confidence            57999999999999999999999876                                       456665578899999


Q ss_pred             EEEeCChHHHHHHHHHhcCeeecCeeeEEE
Q psy3016         206 FINYASFEASDASIDAMHGQYLCNRPISVS  235 (305)
Q Consensus       206 fV~f~~~~~A~~Al~~l~~~~~~g~~l~v~  235 (305)
                      ||+|.+.++|.+|+..+++..+.|+.|+|+
T Consensus        42 ~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360       42 FVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             EEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            999999999999999999999999998873

>KOG4454|consensus

Probab=99.18  E-value=8.9e-12  Score=104.05  Aligned_cols=149  Identities=30%  Similarity=0.477  Sum_probs=120.7

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      ....+..+||||+|+...|+|+-|.++|-.-|+|..+.|..++ .+..+ ||||.|.++-.+..|++.+||..+.++.+.
T Consensus         3 aaaae~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    3 AAAAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQ   80 (267)
T ss_pred             CCCcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhh
Confidence            3456778999999999999999999999999999999998886 44555 999999999999999999999999998887


Q ss_pred             EeeCCCccccccccccccccC----CCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCccee
Q psy3016         108 VNKASSHQKNLDVGANIFIGN----LDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI  183 (305)
Q Consensus       108 v~~~~~~~~~~~~~~~l~v~n----l~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  183 (305)
                      +..              +.|+    |+..++++.++..|...|.++.+                                
T Consensus        81 ~~~--------------r~G~shapld~r~~~ei~~~v~s~a~p~~~~--------------------------------  114 (267)
T KOG4454|consen   81 RTL--------------RCGNSHAPLDERVTEEILYEVFSQAGPIEGV--------------------------------  114 (267)
T ss_pred             ccc--------------ccCCCcchhhhhcchhhheeeecccCCCCCc--------------------------------
Confidence            753              3344    77789999999999988888754                                


Q ss_pred             EeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeee
Q psy3016         184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPI  232 (305)
Q Consensus       184 ~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l  232 (305)
                             .+-.+.+ |..+.+.|+.+....+.-.++....+....-+++
T Consensus       115 -------R~~~~~d-~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~~  155 (267)
T KOG4454|consen  115 -------RIPTDND-GRNRNFGFVTYQRLCAVPFALDLYQGLELFQKKV  155 (267)
T ss_pred             -------ccccccc-CCccCccchhhhhhhcCcHHhhhhcccCcCCCCc
Confidence                   4444433 7788899999887777777777666655444433

>KOG0114|consensus

Probab=99.16  E-value=7.3e-11  Score=87.38  Aligned_cols=79  Identities=28%  Similarity=0.448  Sum_probs=69.2

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..+-|||.|||..+|.|+++++|.+||.|..++                                       |   ..+.
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIR---------------------------------------i---G~~k   54 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIR---------------------------------------I---GNTK   54 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEE---------------------------------------e---cCcc
Confidence            457799999999999999999999999998751                                       1   1345


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      ..+|-|||.|+++.+|++|+..|+|..++++.|.|-+-...
T Consensus        55 ~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   55 ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            67999999999999999999999999999999999886543

>KOG0129|consensus

Probab=99.13  E-value=9.1e-10  Score=102.61  Aligned_cols=152  Identities=23%  Similarity=0.321  Sum_probs=112.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccC---CCCCcce---EEEEEEcCHHHHHHHHHHhcC---c-
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDR---VTQTHQG---YGFIEFMGEEDADYAIKIMNM---I-   99 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~---~~~~~~g---~afV~f~~~e~A~~Ai~~l~g---~-   99 (305)
                      ...-++.||||+||.+++|+.|...|..||.+. +......   ..-..+|   |+|+-|+++..+..-+.....   . 
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~  333 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNY  333 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccce
Confidence            445678999999999999999999999999854 4544211   1123456   999999999998866554321   1 


Q ss_pred             ee-------CCeeeEEeeC--------CCccccccccccccccCCCchhcHHHHHHHHh-hcCcccchhhhhhhhhhcCc
Q psy3016         100 KL-------YGKPIRVNKA--------SSHQKNLDVGANIFIGNLDPEVDEKLLYDTFS-AFGVILQTPKIMNMIKLYGK  163 (305)
Q Consensus       100 ~~-------~g~~l~v~~~--------~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~-~~g~v~~~~~~~~~~~~~~~  163 (305)
                      .|       ..+.+.|..-        .......+..++||||+||.-++.++|..+|+ -||.|..+            
T Consensus       334 yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~ya------------  401 (520)
T KOG0129|consen  334 YFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYV------------  401 (520)
T ss_pred             EEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEE------------
Confidence            11       1222333211        11223445679999999999999999999999 69999887            


Q ss_pred             ceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHH
Q psy3016         164 PIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDA  221 (305)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~  221 (305)
                                                 .|-.|++.+-.+|-|=|.|++..+=.+||.+
T Consensus       402 ---------------------------GIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  402 ---------------------------GIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ---------------------------EeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence                                       6778888888999999999999999999974

>KOG4661|consensus

Probab=99.12  E-value=1.7e-10  Score=108.10  Aligned_cols=83  Identities=24%  Similarity=0.384  Sum_probs=76.2

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ..-.++|||.+|...+...+|++||++||.|...+|+.+..+.-.+.|+||+|.+.++|.+||+.|+..+++|+.|.|+.
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            34567999999999999999999999999999999999887666778999999999999999999999999999999998


Q ss_pred             CCC
Q psy3016         111 ASS  113 (305)
Q Consensus       111 ~~~  113 (305)
                      ++.
T Consensus       482 aKN  484 (940)
T KOG4661|consen  482 AKN  484 (940)
T ss_pred             ccc
Confidence            764

>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=99.12  E-value=2.2e-10  Score=80.49  Aligned_cols=74  Identities=39%  Similarity=0.769  Sum_probs=65.2

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      +|+|++||..+++++|.++|..+|.|..+                                       .+..+.. +..+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~---------------------------------------~~~~~~~-~~~~   40 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESV---------------------------------------RIVRDKD-TKSK   40 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEE---------------------------------------EEeeCCC-CCcc
Confidence            48899999999999999999999998765                                       4455543 3678


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEE
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYLCNRPISVSY  236 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~  236 (305)
                      ++|||+|.+.++|..|++.+++..+.|+.+.|.+
T Consensus        41 ~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590          41 GFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             eEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            9999999999999999999999999999999874

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).

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.12  E-value=1.2e-10  Score=102.83  Aligned_cols=80  Identities=35%  Similarity=0.663  Sum_probs=74.5

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ..+|||+||+..+|+++|.++|..||.+..+                                       .+..|..++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~---------------------------------------~~~~d~~~~~  155 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRV---------------------------------------RLVRDRETGK  155 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEE---------------------------------------EeeeccccCc
Confidence            5899999999999999999999999999766                                       6677777899


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      ++|||||+|.+.++|..|+..+++..|.|+.|.|.++..
T Consensus       156 ~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         156 SRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             cCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            999999999999999999999999999999999999653

>KOG0109|consensus

Probab=99.11  E-value=9.2e-11  Score=101.87  Aligned_cols=77  Identities=25%  Similarity=0.438  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      .-+.+|+||||.+.++.+||+..|++||+|.+|+|++        +|+||+|+..++|..|++.|++.++.|+.++|..+
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeec--------ceeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            3466899999999999999999999999999999965        68999999999999999999999999999999988


Q ss_pred             CCccc
Q psy3016         112 SSHQK  116 (305)
Q Consensus       112 ~~~~~  116 (305)
                      ..+-+
T Consensus       148 tsrlr  152 (346)
T KOG0109|consen  148 TSRLR  152 (346)
T ss_pred             ccccc
Confidence            76544

>smart00361 RRM_1 RNA recognition motif

Probab=99.10  E-value=1.9e-10  Score=81.55  Aligned_cols=63  Identities=21%  Similarity=0.377  Sum_probs=53.3

Q ss_pred             HHHHHHHHh----hcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC--CCccceEEEE
Q psy3016         135 EKLLYDTFS----AFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT--GNSKGFAFIN  208 (305)
Q Consensus       135 ~~~l~~~f~----~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~--~~~~g~afV~  208 (305)
                      +++|++.|.    .||.|..+.                                      ++..+..+  +.++|||||+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~--------------------------------------~v~~~~~~~~~~~rG~~fV~   43 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKIN--------------------------------------KIYIDNVGYENHKRGNVYIT   43 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEE--------------------------------------EEEeCCCCCCCCCcEEEEEE
Confidence            567888888    999998752                                      13555555  8899999999


Q ss_pred             eCChHHHHHHHHHhcCeeecCeeeEEE
Q psy3016         209 YASFEASDASIDAMHGQYLCNRPISVS  235 (305)
Q Consensus       209 f~~~~~A~~Al~~l~~~~~~g~~l~v~  235 (305)
                      |.+.++|.+|+..|||.++.|+.|+++
T Consensus        44 f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361       44 FERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             ECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            999999999999999999999999873

>PF13893 RRM_5: RNA recognition motif

Probab=99.10  E-value=2.9e-10  Score=76.83  Aligned_cols=36  Identities=42%  Similarity=0.870  Sum_probs=34.8

Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      +++|||+|.+.++|.+|++.|||..++|++|+|.|+
T Consensus        21 ~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen   21 RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            689999999999999999999999999999999986

(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 ....

>KOG0146|consensus

Probab=99.09  E-value=1.3e-10  Score=99.84  Aligned_cols=87  Identities=21%  Similarity=0.381  Sum_probs=80.3

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ...+.|+|||-.||....+.||...|-.||.|.+.++..|+.++.+|.|+||.|++...|+.||..|||..|.-++|+|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            45568999999999999999999999999999999999999999999999999999999999999999999999989888


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      .-.+++.
T Consensus       361 LKRPkda  367 (371)
T KOG0146|consen  361 LKRPKDA  367 (371)
T ss_pred             hcCcccc
Confidence            7665543

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.07  E-value=2.5e-10  Score=98.03  Aligned_cols=75  Identities=25%  Similarity=0.411  Sum_probs=67.2

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ..+|||+||++.+|+++|+++|+.||.|..+                                       .+.+|   ++
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V---------------------------------------~I~~D---~e   42 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHV---------------------------------------EIIRS---GE   42 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEecC---CC
Confidence            4689999999999999999999999999987                                       56666   45


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      .+++|||+|++.++|..|+. |+|..|.+++|.|....
T Consensus        43 t~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121         43 YACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             cceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            56899999999999999995 99999999999998754

>KOG0415|consensus

Probab=99.07  E-value=2e-10  Score=102.19  Aligned_cols=84  Identities=23%  Similarity=0.332  Sum_probs=78.8

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ......|||..|.+-+|+++|.-+|+.||.|.+|.|++|..+|.+..||||+|.+.+++++|.-+|++..|.++.|+|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            34456899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCc
Q psy3016         111 ASSH  114 (305)
Q Consensus       111 ~~~~  114 (305)
                      +.+-
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            7653

>KOG0226|consensus

Probab=99.06  E-value=1.2e-10  Score=99.42  Aligned_cols=165  Identities=22%  Similarity=0.348  Sum_probs=131.0

Q ss_pred             CCceEEEcCCCccccHHH-H--HHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          33 GDATIYVGGLDDKVSETL-M--WELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~-L--~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....+++++-..+..+- |  ...|+.|-.+...+++++. -+...+++|+.|.....-.++-..-++..+..+.+++.
T Consensus        95 ~vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a  173 (290)
T KOG0226|consen   95 AVFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLA  173 (290)
T ss_pred             ccccccccccccccCCCCCCcchhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceeec
Confidence            344677777766665554 3  6778888888888888875 46678999999998888888877767777777777665


Q ss_pred             eCCCccc-----cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeE
Q psy3016         110 KASSHQK-----NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIF  184 (305)
Q Consensus       110 ~~~~~~~-----~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  184 (305)
                      ......+     -.+...+||++.|..+++++.|...|.+|-.-...                                 
T Consensus       174 ~gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~a---------------------------------  220 (290)
T KOG0226|consen  174 AGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKA---------------------------------  220 (290)
T ss_pred             cccccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhc---------------------------------
Confidence            4443221     12246789999999999999999999998755432                                 


Q ss_pred             eccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         185 IGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       185 ~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                            ++++|.-+|+++||+||.|.+.+++..|++.|+|.+++.+.|++.-+
T Consensus       221 ------kviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  221 ------KVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             ------cccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence                  67899999999999999999999999999999999999999987654

>KOG0132|consensus

Probab=99.03  E-value=1.5e-09  Score=105.22  Aligned_cols=78  Identities=21%  Similarity=0.399  Sum_probs=70.3

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      +++|||+.|+..+++.+|.++|++||+|.++                                             ....
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi---------------------------------------------~li~  455 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSI---------------------------------------------ILIP  455 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeE---------------------------------------------eecc
Confidence            4799999999999999999999999999987                                             2244


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .+|+|||.+....+|.+|+.+|++..+.++.|++.|+..+..+
T Consensus       456 ~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~k  498 (894)
T KOG0132|consen  456 PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPK  498 (894)
T ss_pred             CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcc
Confidence            6999999999999999999999999999999999999765544

>KOG0112|consensus

Probab=99.03  E-value=3.2e-10  Score=111.38  Aligned_cols=162  Identities=23%  Similarity=0.299  Sum_probs=135.6

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....+|||+|||+..+++.+|+..|..+|.|.+|.|-.-. -+....||||.|.+.+.+-.|+..+.+..|..-.+++.
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            45567899999999999999999999999999999885542 23445799999999999999999999987776666666


Q ss_pred             eCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCC
Q psy3016         110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLD  189 (305)
Q Consensus       110 ~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  189 (305)
                      +...   .......+++++|...+....+...|..||.|..+                                      
T Consensus       447 lG~~---kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~I--------------------------------------  485 (975)
T KOG0112|consen  447 LGQP---KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRII--------------------------------------  485 (975)
T ss_pred             cccc---ccccceeeccCCCCCCChHHHHHHHhhccCcceee--------------------------------------
Confidence            6544   23345679999999999999999999999999854                                      


Q ss_pred             CCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecC--eeeEEEEeeec
Q psy3016         190 PEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN--RPISVSYAFKK  240 (305)
Q Consensus       190 ~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g--~~l~v~~a~~~  240 (305)
                             +..+..-||||.|++...|..|+..|-|..|++  +.+.|.|+.+.
T Consensus       486 -------dy~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  486 -------DYRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPP  531 (975)
T ss_pred             -------ecccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCC
Confidence                   234557799999999999999999999999955  77889998654

>KOG0105|consensus

Probab=99.00  E-value=4.4e-10  Score=91.70  Aligned_cols=79  Identities=20%  Similarity=0.323  Sum_probs=67.8

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..+.|||+|||.++-+.+|.++|-+||.|..+                                     +.++.     -
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~i-------------------------------------eLK~r-----~   42 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREI-------------------------------------ELKNR-----P   42 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEE-------------------------------------EeccC-----C
Confidence            35789999999999999999999999999865                                     11111     2


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      ....||||+|++..+|..||..-+|..++|+.|+|.|+..-
T Consensus        43 g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen   43 GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             CCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            34779999999999999999999999999999999998654

>KOG4660|consensus

Probab=98.99  E-value=1e-09  Score=103.05  Aligned_cols=163  Identities=22%  Similarity=0.262  Sum_probs=113.0

Q ss_pred             CCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe
Q psy3016          25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK  104 (305)
Q Consensus        25 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~  104 (305)
                      ..|.+.....++|||-|||..|++++|+++|+.||+|..|+.     +....|..||+|-|..+|+.|+++|++.++.|+
T Consensus        66 ~np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~  140 (549)
T KOG4660|consen   66 DNPSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGK  140 (549)
T ss_pred             CCCCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhh
Confidence            467777888999999999999999999999999999999765     344669999999999999999999999999999


Q ss_pred             eeEEeeCCCccccc-------------------cc--cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCc
Q psy3016         105 PIRVNKASSHQKNL-------------------DV--GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGK  163 (305)
Q Consensus       105 ~l~v~~~~~~~~~~-------------------~~--~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~  163 (305)
                      .|............                   ..  ...++ +.|++..+...+..++.-+|.+..             
T Consensus       141 ~~k~~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~-g~l~P~~s~~~~~~~~~~~~~~~~-------------  206 (549)
T KOG4660|consen  141 RIKRPGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLF-GMLSPTRSSILLEHISSVDGSSPG-------------  206 (549)
T ss_pred             hhcCCCcccccchhcccchhhhhccchhhcCCCCCCcCCcce-eeeccchhhhhhhcchhccCcccc-------------
Confidence            88832221110000                   00  11122 225555555444444544454431             


Q ss_pred             ceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         164 PIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                                                      .+++.-...-|+.|.+..++..+...+ |..+.+.....+|+..
T Consensus       207 --------------------------------~~~~~~~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  207 --------------------------------RETPLLNHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             --------------------------------ccccchhhhhhhhhccccchhhcccCC-ceecCCCCceEEecCC
Confidence                                            122333335677888888886666633 7778888888888765

>KOG0153|consensus

Probab=98.98  E-value=1.9e-09  Score=95.91  Aligned_cols=80  Identities=25%  Similarity=0.444  Sum_probs=70.7

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHh-cCceeCCeeeEE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM-NMIKLYGKPIRV  108 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l-~g~~~~g~~l~v  108 (305)
                      .+....+||||+|-..++|.+|++.|.+||+|.+|.++..+      ++|||+|.+.+.|+.|.+++ +...+.|++|.|
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            44567799999999999999999999999999999997654      79999999999999998764 567889999999


Q ss_pred             eeCCCcc
Q psy3016         109 NKASSHQ  115 (305)
Q Consensus       109 ~~~~~~~  115 (305)
                      .|..+.+
T Consensus       298 ~Wg~~~~  304 (377)
T KOG0153|consen  298 KWGRPKQ  304 (377)
T ss_pred             EeCCCcc
Confidence            9998843

>KOG4210|consensus

Probab=98.97  E-value=6.9e-10  Score=99.55  Aligned_cols=170  Identities=18%  Similarity=0.286  Sum_probs=139.7

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++.|+|++...+.+.+...++..+|......+........++|++++.|...+.+..|+.......+.++.+.....
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            46789999999999999999999999998888888877777889999999999999999999854334555555544433


Q ss_pred             CCccc---------ccccccccc-ccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcc
Q psy3016         112 SSHQK---------NLDVGANIF-IGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA  181 (305)
Q Consensus       112 ~~~~~---------~~~~~~~l~-v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (305)
                      .....         ......++| |++++.++++++|+..|..+|.|..+                              
T Consensus       166 ~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~------------------------------  215 (285)
T KOG4210|consen  166 TRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSV------------------------------  215 (285)
T ss_pred             ccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceee------------------------------
Confidence            32221         112345666 99999999999999999999999876                              


Q ss_pred             eeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       182 ~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                               ++..+..++..+|++||+|.+..++..++.. ....+.++++.+.+.....
T Consensus       216 ---------r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  216 ---------RLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             ---------ccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCc
Confidence                     6788888999999999999999999999998 8888999999999876653

>KOG0415|consensus

Probab=98.96  E-value=5e-10  Score=99.69  Aligned_cols=85  Identities=27%  Similarity=0.438  Sum_probs=79.8

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      .++.+.|||.-|.+-+|+++|.-+|+.||.|..|                                       .|++|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sc---------------------------------------eVIRD~k  276 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSC---------------------------------------EVIRDRK  276 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceee---------------------------------------eEEeccc
Confidence            4467899999999999999999999999999998                                       8899999


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +|.+..||||+|++.+++.+|.-+|++..|+++.|.|.|+..-.
T Consensus       277 tgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQSVs  320 (479)
T KOG0415|consen  277 TGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQSVS  320 (479)
T ss_pred             ccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhhhh
Confidence            99999999999999999999999999999999999999986543

>KOG4208|consensus

Probab=98.94  E-value=2.5e-09  Score=88.95  Aligned_cols=84  Identities=25%  Similarity=0.384  Sum_probs=76.3

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccC-CCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQS-GPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~-G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....-++|..+|..+.+.++..+|.+| |.|..+++-+++.||.++|||||+|.+.+.|.-|-+.||+..+.|+.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3345579999999999999999999988 788999998999999999999999999999999999999999999999998


Q ss_pred             eCCCc
Q psy3016         110 KASSH  114 (305)
Q Consensus       110 ~~~~~  114 (305)
                      .-.+.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            76554

>KOG4205|consensus

Probab=98.83  E-value=4.4e-09  Score=94.81  Aligned_cols=116  Identities=24%  Similarity=0.347  Sum_probs=92.4

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ....||||+||..+++++|+++|++||.|..+.++.|..+.+++||+||+|.+++.+.+++. .....|+|+.+.|..+.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            35689999999999999999999999999999999999999999999999999999999988 47889999999999999


Q ss_pred             Ccccccccc----ccccccCCCchhcHHHHHHHHhhcCccc
Q psy3016         113 SHQKNLDVG----ANIFIGNLDPEVDEKLLYDTFSAFGVIL  149 (305)
Q Consensus       113 ~~~~~~~~~----~~l~v~nl~~~~t~~~l~~~f~~~g~v~  149 (305)
                      ++.......    ...+..++....+.-.|...|..|+.+.
T Consensus       175 pk~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~~~g~~~~~  215 (311)
T KOG4205|consen  175 PKEVMQSTKSSVSTRGKGNNLGNGRTGFFLKKYFKGYGPVG  215 (311)
T ss_pred             chhhccccccccccccccccccccccccccchhccccCccc
Confidence            876544321    1122223444444445566666666653

>KOG4206|consensus

Probab=98.81  E-value=5.7e-09  Score=88.11  Aligned_cols=84  Identities=26%  Similarity=0.446  Sum_probs=73.0

Q ss_pred             cccccccCCCchhcHHHHHH----HHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYD----TFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~----~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      ..+|||.||+..+..++|+.    +|+.||.|..+                                         +-- 
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI-----------------------------------------~a~-   46 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDI-----------------------------------------SAF-   46 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEE-----------------------------------------Eec-
Confidence            34899999999999999877    99999999854                                         222 


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcCCC
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDR  246 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~~~  246 (305)
                      .+.+.+|.|||.|.+.+.|..|+++|+|..|.|+.+++.||+.+.+...+
T Consensus        47 kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~sdii~~   96 (221)
T KOG4206|consen   47 KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDSDIIAQ   96 (221)
T ss_pred             CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCccchhhc
Confidence            45788999999999999999999999999999999999999988765444

>KOG0533|consensus

Probab=98.78  E-value=2.2e-08  Score=87.00  Aligned_cols=84  Identities=26%  Similarity=0.358  Sum_probs=76.6

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (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            45566889999999999999999999999999999998886 78999999999999999999999999999999999888


Q ss_pred             eCCCc
Q psy3016         110 KASSH  114 (305)
Q Consensus       110 ~~~~~  114 (305)
                      .....
T Consensus       158 ~i~~~  162 (243)
T KOG0533|consen  158 IISSP  162 (243)
T ss_pred             EecCc
Confidence            76643

>KOG0226|consensus

Probab=98.76  E-value=7.7e-09  Score=88.49  Aligned_cols=86  Identities=23%  Similarity=0.409  Sum_probs=79.2

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      -++...+||.|.|-..++++-|...|.+|-.....++++|+.+|+++||+||.|.+..++..|+.+++|..++.+.|.++
T Consensus       186 w~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  186 WDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             CccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhh
Confidence            45567899999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      -+.-+.
T Consensus       266 kS~wke  271 (290)
T KOG0226|consen  266 KSEWKE  271 (290)
T ss_pred             hhhHHh
Confidence            655443

>KOG4211|consensus

Probab=98.74  E-value=5e-07  Score=84.08  Aligned_cols=99  Identities=18%  Similarity=0.196  Sum_probs=69.1

Q ss_pred             CccceeecCccccccCcccccCCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEE-EEEcccCCCCCcceEEEEE
Q psy3016           4 GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIE   82 (305)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~-i~~~~~~~~~~~~g~afV~   82 (305)
                      -|+|-+.-..+....|.-+.....+  ......|-+.+||..||++||.++|+..-.+.. |.+..+. .+++.|-|||+
T Consensus        75 ~RYIEVf~~~~~e~d~~~~~~g~~s--~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVq  151 (510)
T KOG4211|consen   75 HRYIEVFTAGGAEADWVMRPGGPNS--SANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQ  151 (510)
T ss_pred             CceEEEEccCCccccccccCCCCCC--CCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEE
Confidence            3566666666555555444332222  256778999999999999999999998754444 5555664 56788999999


Q ss_pred             EcCHHHHHHHHHHhcCceeCCeee
Q psy3016          83 FMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        83 f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      |.+.+.|++|+.. |...|.-|-|
T Consensus       152 F~sqe~ae~Al~r-hre~iGhRYI  174 (510)
T KOG4211|consen  152 FESQESAEIALGR-HRENIGHRYI  174 (510)
T ss_pred             ecCHHHHHHHHHH-HHHhhccceE
Confidence            9999999999984 4433333333

>KOG4208|consensus

Probab=98.73  E-value=2.8e-08  Score=82.76  Aligned_cols=82  Identities=21%  Similarity=0.413  Sum_probs=72.6

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhc-CcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAF-GVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~-g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ....+|+..++.-+.+.++...|..| |.+...                                       ...+...|
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~---------------------------------------rlsRnkrT   88 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRF---------------------------------------RLSRNKRT   88 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEE---------------------------------------Eeeccccc
Confidence            45679999999999999999999998 666554                                       44578899


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      |+++|||||+|++.+.|.-|.+.||++.+.++-|.|.+-.+.
T Consensus        89 GNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   89 GNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             CCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            999999999999999999999999999999999999997554

>KOG0128|consensus

Probab=98.68  E-value=2.7e-09  Score=104.58  Aligned_cols=147  Identities=19%  Similarity=0.226  Sum_probs=123.2

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (305)
                      .++||.||+..+.+.+|...|..+|.+..+++..-...++-+|+||+.|...+++.+|+...+.+.+ |           
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~-g-----------  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF-G-----------  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh-h-----------
Confidence            4789999999999999999999999988887775556788999999999999999999995444433 3           


Q ss_pred             cccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc
Q psy3016         115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR  194 (305)
Q Consensus       115 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  194 (305)
                            ...++|.|.+..-|.++++.++..+|.+...                                       .+..
T Consensus       736 ------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~---------------------------------------~~vt  770 (881)
T KOG0128|consen  736 ------KISVAISGPPFQGTKEELKSLASKTGNVTSL---------------------------------------RLVT  770 (881)
T ss_pred             ------hhhhheeCCCCCCchHHHHhhccccCCcccc---------------------------------------chhh
Confidence                  2358999999999999999999999998764                                       2223


Q ss_pred             CCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       195 d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      . ..|+.+|.|||.|.+..++.+++......-+....+.|..+.+
T Consensus       771 ~-r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  771 V-RAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             h-hccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            3 3489999999999999999999998888877777777777655

>KOG0116|consensus

Probab=98.64  E-value=8.5e-08  Score=89.76  Aligned_cols=82  Identities=20%  Similarity=0.334  Sum_probs=69.3

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ......+|||+|||.+++.++|+++|..||+|....|......+.+..||||+|.+.+.+..||++ +-..+.+++|.|+
T Consensus       284 ~~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Ve  362 (419)
T KOG0116|consen  284 PRADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVE  362 (419)
T ss_pred             eeecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEE
Confidence            344455699999999999999999999999999988766543455559999999999999999995 6889999999998


Q ss_pred             eCC
Q psy3016         110 KAS  112 (305)
Q Consensus       110 ~~~  112 (305)
                      --.
T Consensus       363 ek~  365 (419)
T KOG0116|consen  363 EKR  365 (419)
T ss_pred             ecc
Confidence            543

>KOG2193|consensus

Probab=98.62  E-value=1.2e-08  Score=92.99  Aligned_cols=151  Identities=20%  Similarity=0.382  Sum_probs=122.6

Q ss_pred             ceEEEcCCCccccHHHHHHHhccC--CCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcC-ceeCCeeeEEeeC
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQS--GPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM-IKLYGKPIRVNKA  111 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~--G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g-~~~~g~~l~v~~~  111 (305)
                      ..+|+|||.+.++.++|..+|...  |--..+ ++       ..|||||.+.+...|.+|++.++| .++.|..+.+..+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~f-l~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~s   73 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQF-LV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcce-ee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccch
Confidence            368999999999999999999753  111111 11       238999999999999999999998 4788999999988


Q ss_pred             CCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCC
Q psy3016         112 SSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPE  191 (305)
Q Consensus       112 ~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  191 (305)
                      .++...   ++.+-|.|++..+.++.+..++..||.++.|.                                      .
T Consensus        74 v~kkqr---srk~Qirnippql~wevld~Ll~qyg~ve~~e--------------------------------------q  112 (584)
T KOG2193|consen   74 VPKKQR---SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCE--------------------------------------Q  112 (584)
T ss_pred             hhHHHH---hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhh--------------------------------------h
Confidence            765433   45699999999999999999999999999873                                      3


Q ss_pred             cccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       192 i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      ++.|.++-    ..-|.|.+.+.+..|+..++|..+.+..+++.|--
T Consensus       113 vnt~~eta----vvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen  113 VNTDSETA----VVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             hccchHHH----HHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            45555432    23468899999999999999999999999999853

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.60  E-value=3.2e-07  Score=68.67  Aligned_cols=80  Identities=19%  Similarity=0.274  Sum_probs=68.6

Q ss_pred             ceEEEcCCCccccHHHHHHHhcc--CCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC----CeeeEE
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQ--SGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY----GKPIRV  108 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~--~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~----g~~l~v  108 (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            58999999999999999988875  457777888888888899999999999999999999999998886    456677


Q ss_pred             eeCCCc
Q psy3016         109 NKASSH  114 (305)
Q Consensus       109 ~~~~~~  114 (305)
                      .+|.-+
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            776544

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4209|consensus

Probab=98.59  E-value=7.6e-08  Score=83.74  Aligned_cols=83  Identities=24%  Similarity=0.366  Sum_probs=77.0

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .......+||||+...+|.+++...|+.||.|..+.+..+...+.++|||||+|.+.+.+..++. |++..+.|+.+.+.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            44567799999999999999999999999999999999999999999999999999999999999 99999999999998


Q ss_pred             eCCC
Q psy3016         110 KASS  113 (305)
Q Consensus       110 ~~~~  113 (305)
                      +..-
T Consensus       176 ~~r~  179 (231)
T KOG4209|consen  176 LKRT  179 (231)
T ss_pred             eeee
Confidence            7554

>KOG4676|consensus

Probab=98.57  E-value=1.1e-07  Score=85.95  Aligned_cols=156  Identities=10%  Similarity=0.085  Sum_probs=119.5

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCC---CCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVT---QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~---~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ....|-|.||.+.+|.++++.+|...|.|.++.|+.+..+   ......|||.|.+...+..|.. |.+.++-|+.|.|.
T Consensus         6 ~~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~   84 (479)
T KOG4676|consen    6 SLGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVR   84 (479)
T ss_pred             CCceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEE
Confidence            3448999999999999999999999999999999875422   3445789999999999998877 77788888888776


Q ss_pred             eCCCcc-c------------------------------------------------------cccccccccccCCCchhc
Q psy3016         110 KASSHQ-K------------------------------------------------------NLDVGANIFIGNLDPEVD  134 (305)
Q Consensus       110 ~~~~~~-~------------------------------------------------------~~~~~~~l~v~nl~~~~t  134 (305)
                      .+.... .                                                      -.+...+++|.+|...+.
T Consensus        85 p~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~  164 (479)
T KOG4676|consen   85 PYGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAI  164 (479)
T ss_pred             ecCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhc
Confidence            543200 0                                                      000126799999999999


Q ss_pred             HHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHH
Q psy3016         135 EKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEA  214 (305)
Q Consensus       135 ~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~  214 (305)
                      ..++.+.|..+|+|.+.+.                                           ..+...-+|-+.|....+
T Consensus       165 l~e~~e~f~r~Gev~ya~~-------------------------------------------ask~~s~~c~~sf~~qts  201 (479)
T KOG4676|consen  165 LPESGESFERKGEVSYAHT-------------------------------------------ASKSRSSSCSHSFRKQTS  201 (479)
T ss_pred             chhhhhhhhhcchhhhhhh-------------------------------------------hccCCCcchhhhHhhhhh
Confidence            9999999999999987521                                           123345578899998888


Q ss_pred             HHHHHHHhcCeeecCeeeE
Q psy3016         215 SDASIDAMHGQYLCNRPIS  233 (305)
Q Consensus       215 A~~Al~~l~~~~~~g~~l~  233 (305)
                      ...|+. ++|.++.-...+
T Consensus       202 ~~halr-~~gre~k~qhsr  219 (479)
T KOG4676|consen  202 SKHALR-SHGRERKRQHSR  219 (479)
T ss_pred             HHHHHH-hcchhhhhhhhh
Confidence            888988 678777643333

>KOG0151|consensus

Probab=98.45  E-value=5.3e-07  Score=87.10  Aligned_cols=82  Identities=24%  Similarity=0.451  Sum_probs=73.2

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccC---CCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDR---VTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~---~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ...++|||+||++.++++.|...|..||+|.+++++.-.   ...+.+.+|||-|-+..+|++|++.|+|+.+.+..+++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~  251 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKL  251 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeee
Confidence            345789999999999999999999999999999998643   23456689999999999999999999999999999999


Q ss_pred             eeCCC
Q psy3016         109 NKASS  113 (305)
Q Consensus       109 ~~~~~  113 (305)
                      .|+..
T Consensus       252 gWgk~  256 (877)
T KOG0151|consen  252 GWGKA  256 (877)
T ss_pred             ccccc
Confidence            99853

>KOG1457|consensus

Probab=98.38  E-value=1.2e-06  Score=73.86  Aligned_cols=91  Identities=18%  Similarity=0.294  Sum_probs=70.9

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||.+||.++---+|+.+|.+|.--+.+...                                      +.+....
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK--------------------------------------~Tsk~~~   74 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLK--------------------------------------YTSKGDQ   74 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeee--------------------------------------eccCCCc
Confidence            36899999999999999999999998655543100                                      2222223


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeee---cCeeeEEEEeeecCCcCCCCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYL---CNRPISVSYAFKKDSKGDRHG  248 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~---~g~~l~v~~a~~~~~~~~~~~  248 (305)
                      ..+-+|||.|.+..+|..|+++|||..|   .+.+|++.+++.......+..
T Consensus        75 ~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNtK~kr~k~  126 (284)
T KOG1457|consen   75 VCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNTKRKRRKG  126 (284)
T ss_pred             cccceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcCcccccCCC
Confidence            4567999999999999999999999998   688999999987765443333

>KOG4849|consensus

Probab=98.37  E-value=1.6e-06  Score=77.42  Aligned_cols=80  Identities=18%  Similarity=0.229  Sum_probs=66.9

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .-|+||+||-+.+|+++|.+.+...|.-. +                                    ++++++....+|.
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~-~------------------------------------~dmKFFENR~NGQ  122 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQ-F------------------------------------ADMKFFENRTNGQ  122 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHH-H------------------------------------hhhhhhhcccCCc
Confidence            35899999999999999999888777543 2                                    3457888889999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      ++|||+|-..+....++.++.|-.++|.|..-+|.-+
T Consensus       123 SKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen  123 SKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             ccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            9999999999999999999999999998876665443

>KOG0153|consensus

Probab=98.35  E-value=5.7e-07  Score=80.35  Aligned_cols=75  Identities=23%  Similarity=0.396  Sum_probs=64.2

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...+|||++|...+++.+|++.|..||+|..+                                       .++.     
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi---------------------------------------~~~~-----  262 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSI---------------------------------------RILP-----  262 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeE---------------------------------------Eeec-----
Confidence            35789999999999999999999999999986                                       2222     


Q ss_pred             CccceEEEEeCChHHHHHHHHHh-cCeeecCeeeEEEEeee
Q psy3016         200 NSKGFAFINYASFEASDASIDAM-HGQYLCNRPISVSYAFK  239 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l-~~~~~~g~~l~v~~a~~  239 (305)
                       .+++|||+|.+.+.|+.|..++ |...|+|.+|+|.|...
T Consensus       263 -~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  263 -RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             -ccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence             2569999999999999998764 55567999999999987

>KOG4661|consensus

Probab=98.31  E-value=1e-06  Score=83.20  Aligned_cols=81  Identities=20%  Similarity=0.407  Sum_probs=71.1

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||.+|...+-..+|+.+|++||+|.-.                                       +++....+-.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGA---------------------------------------KVVTNaRsPG  445 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGA---------------------------------------KVVTNARSPG  445 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceece---------------------------------------eeeecCCCCC
Confidence            5789999999999999999999999999754                                       4555555555


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      .+.|+||++++.++|.++|..||.+++.|+-|.|.-++..
T Consensus       446 aRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNE  485 (940)
T KOG4661|consen  446 ARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNE  485 (940)
T ss_pred             cceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccC
Confidence            7889999999999999999999999999999999987643

>KOG4660|consensus

Probab=98.24  E-value=1e-06  Score=83.28  Aligned_cols=70  Identities=20%  Similarity=0.418  Sum_probs=63.8

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...+|+|.|||..+++++|..+|+.||+|..+.                                            .+-
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir--------------------------------------------~t~  109 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIR--------------------------------------------ETP  109 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhh--------------------------------------------ccc
Confidence            467899999999999999999999999998752                                            345


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeE
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPIS  233 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~  233 (305)
                      ..+|.+||+|-++.+|+.|+++|+++++.|+.|+
T Consensus       110 ~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen  110 NKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            6789999999999999999999999999999998

>KOG0151|consensus

Probab=98.23  E-value=3.6e-06  Score=81.48  Aligned_cols=81  Identities=21%  Similarity=0.502  Sum_probs=71.3

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC---C
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP---D  197 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~---~  197 (305)
                      ..++||+||++.++++.|...|+.||.|..+                                       +||+..   +
T Consensus       174 TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasv---------------------------------------KimwpRtEeE  214 (877)
T KOG0151|consen  174 TTNLYVGNLNPSVDENFLLRTFGRFGPLASV---------------------------------------KIMWPRTEEE  214 (877)
T ss_pred             ccceeeecCCccccHHHHHHHhcccCcccce---------------------------------------eeecccchhh
Confidence            4789999999999999999999999999987                                       555544   2


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      ....+.++||-|-+..||.+|+..|+|..+.+..+++-|++.-
T Consensus       215 k~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWgk~V  257 (877)
T KOG0151|consen  215 KRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWGKAV  257 (877)
T ss_pred             hccccccceeeehhhhhHHHHHHHhcceeeeeeeeeecccccc
Confidence            3456889999999999999999999999999999999998543

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.20  E-value=6.1e-06  Score=59.22  Aligned_cols=69  Identities=25%  Similarity=0.350  Sum_probs=48.3

Q ss_pred             ceEEEcCCCccccHHH----HHHHhccCC-CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          35 ATIYVGGLDDKVSETL----MWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~----L~~~F~~~G-~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ..|+|.|||...+...    |++++..+| .|.+|.          .+.|+|.|.+.+.|.+|.+.|+|..+.|++|.|+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            4799999999888665    567777887 666652          2679999999999999999999999999999999


Q ss_pred             eCCC
Q psy3016         110 KASS  113 (305)
Q Consensus       110 ~~~~  113 (305)
                      +...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            8743

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4849|consensus

Probab=98.13  E-value=1e-05  Score=72.42  Aligned_cols=76  Identities=14%  Similarity=0.282  Sum_probs=68.2

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCC--CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSG--PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G--~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ..++|||||-.++|++||.+.+...|  .+.++++..++.+|.+||||+|...+.....+-|+.|-...|+|..-.|-
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            34799999999999999999999888  67888999999999999999999999999999999999999998765553

>KOG0533|consensus

Probab=98.13  E-value=5.6e-06  Score=72.11  Aligned_cols=82  Identities=20%  Similarity=0.320  Sum_probs=70.6

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ....|+|.||+..+++++|.++|..||.+..+                                       .+-+| ..|
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~---------------------------------------~vhy~-~~G  121 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRV---------------------------------------AVHYD-RAG  121 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEE---------------------------------------eeccC-CCC
Confidence            34679999999999999999999999977654                                       34555 459


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .+.|.|=|.|...+||.+|++.+||..++|+.+++.......
T Consensus       122 ~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~~  163 (243)
T KOG0533|consen  122 RSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSPS  163 (243)
T ss_pred             CCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCcc
Confidence            999999999999999999999999999999999888765443

>KOG4307|consensus

Probab=98.11  E-value=2.5e-06  Score=82.38  Aligned_cols=169  Identities=14%  Similarity=0.099  Sum_probs=127.5

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      +.+.+-+.+.+.+.++.|++++|... .|.+..|..+...+...|-++|+|....++.+|++. |...+-.|.+.+..+.
T Consensus       310 d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g  387 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPG  387 (944)
T ss_pred             hhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCC
Confidence            45667778899999999999999754 566777766665555579999999999999999884 5566667777776543


Q ss_pred             Ccccc--------------------------------------ccccccccccCCCchhcHHHHHHHHhhcCcccchhhh
Q psy3016         113 SHQKN--------------------------------------LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI  154 (305)
Q Consensus       113 ~~~~~--------------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~  154 (305)
                      .....                                      .....+|||..||..+++..+.++|...-.|+..   
T Consensus       388 ~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~---  464 (944)
T KOG4307|consen  388 NLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDF---  464 (944)
T ss_pred             ccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhhe---
Confidence            21110                                      0124789999999999999999999987666531   


Q ss_pred             hhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEE
Q psy3016         155 MNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV  234 (305)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v  234 (305)
                                                  |       .+.+- -+++.++.|||.|...+++..|...-+.++++.+.|+|
T Consensus       465 ----------------------------I-------~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv  508 (944)
T KOG4307|consen  465 ----------------------------I-------ELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRV  508 (944)
T ss_pred             ----------------------------e-------EeccC-CcccccchhhheeccccccchhhhcccccccCceEEEe
Confidence                                        0       12222 34677889999999999999999988888899999999


Q ss_pred             EEeeecCC
Q psy3016         235 SYAFKKDS  242 (305)
Q Consensus       235 ~~a~~~~~  242 (305)
                      .-..+..+
T Consensus       509 ~si~~~~m  516 (944)
T KOG4307|consen  509 DSIADYAM  516 (944)
T ss_pred             echhhHHH
Confidence            87655544

>KOG4209|consensus

Probab=98.04  E-value=4.2e-06  Score=72.86  Aligned_cols=81  Identities=22%  Similarity=0.402  Sum_probs=73.8

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ....+||+|++..+|.+++...|+.+|.+..+                                       .+..|..++
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~---------------------------------------ti~~d~~~~  140 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRV---------------------------------------TVPKDKFRG  140 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccce---------------------------------------eeeccccCC
Confidence            45789999999999999999999999999765                                       567787888


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      .++||+||+|.+.+.+.+|+. |++..|.|+.+.|++...+
T Consensus       141 ~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r~~  180 (231)
T KOG4209|consen  141 HPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKRTN  180 (231)
T ss_pred             CcceeEEEecccHhhhHHHhh-cCCcccccccceeeeeeee
Confidence            899999999999999999999 9999999999999998766

>KOG0116|consensus

Probab=98.03  E-value=1.5e-05  Score=74.92  Aligned_cols=79  Identities=24%  Similarity=0.369  Sum_probs=63.5

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ..|||+|||.+++..+|.++|+.||.|...                                       .|....-.++.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~---------------------------------------~I~vr~~~~~~  329 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEG---------------------------------------GIQVRSPGGKN  329 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhccccccc---------------------------------------ceEEeccCCCc
Confidence            459999999999999999999999999875                                       23222112333


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      ..||||+|.+.+++..|+.+- -..+++++|.|.-.+..
T Consensus       330 ~~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  330 PCFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             CceEEEEEeecchhhhhhhcC-ccccCCeeEEEEecccc
Confidence            499999999999999999964 66789999999876553

>KOG0106|consensus

Probab=98.02  E-value=4.2e-06  Score=71.38  Aligned_cols=71  Identities=24%  Similarity=0.487  Sum_probs=63.6

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      .+||++|++.+.+.+|..+|..||.+..+                                               -...
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~-----------------------------------------------~mk~   35 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDA-----------------------------------------------DMKN   35 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccc-----------------------------------------------eeec
Confidence            58999999999999999999999999765                                               1236


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      ||+||+|++..+|..|+..||+..+.+-.+.|.|+...
T Consensus        36 gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen   36 GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            78899999999999999999999999988999998754

>KOG1365|consensus

Probab=97.97  E-value=5.4e-05  Score=68.74  Aligned_cols=155  Identities=16%  Similarity=0.152  Sum_probs=108.2

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ..+...-|-..+||...++.+|..+|.-.--..-...+.....|+..|.|.|.|.+.|.-+.|++. +...+.++-|.|.
T Consensus        56 ~~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievY  134 (508)
T KOG1365|consen   56 SADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVY  134 (508)
T ss_pred             ccCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeee
Confidence            445556678899999999999999998643322233333334567789999999999999999984 6677778888886


Q ss_pred             eCCCccc---------------cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCcccc
Q psy3016         110 KASSHQK---------------NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQ  174 (305)
Q Consensus       110 ~~~~~~~---------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~  174 (305)
                      .+...+-               .+...-.|...+||.+.++.++.++|...-.|..                        
T Consensus       135 ka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~------------------------  190 (508)
T KOG1365|consen  135 KATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTG------------------------  190 (508)
T ss_pred             ccCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccC------------------------
Confidence            6554221               0112335677999999999999999974333321                        


Q ss_pred             ccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHH
Q psy3016         175 KNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDA  221 (305)
Q Consensus       175 ~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~  221 (305)
                                 .+.++-++.. -+|+..|-|||.|...++|..|+.+
T Consensus       191 -----------g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  191 -----------GTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             -----------CccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH
Confidence                       0001112222 2488899999999999999999864

>KOG4454|consensus

Probab=97.97  E-value=1.1e-05  Score=67.95  Aligned_cols=78  Identities=17%  Similarity=0.256  Sum_probs=67.2

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|+-..++++.|.++|-..|.|..+                                       .|..+ ..+
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv---------------------------------------~ip~~-~d~   47 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKV---------------------------------------GIPSG-QDQ   47 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEE---------------------------------------eCCCC-ccC
Confidence            45899999999999999999999999999865                                       33333 446


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      +.+ ||||.|++.-+..-|++.+||-.+.++.+++++-.
T Consensus        48 ~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen   48 EQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             CCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            667 99999999999999999999999999988888743

>KOG1548|consensus

Probab=97.92  E-value=1.8e-05  Score=70.83  Aligned_cols=89  Identities=20%  Similarity=0.350  Sum_probs=71.5

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ...|||.|||.++|.+++.++|+.+|.|....                               =....-.++.++ ..|.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~-------------------------------~t~epk~KlYrd-~~G~  181 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDP-------------------------------QTGEPKVKLYRD-NQGK  181 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccC-------------------------------CCCCeeEEEEec-CCCC
Confidence            45699999999999999999999999886530                               000011133444 3488


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .+|=|++.|.-.++..-|+..|++..+.|+.|+|..|+-..
T Consensus       182 lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq~  222 (382)
T KOG1548|consen  182 LKGDALCCYIKRESVELAIKILDEDELRGKKLRVERAKFQM  222 (382)
T ss_pred             ccCceEEEeecccHHHHHHHHhCcccccCcEEEEehhhhhh
Confidence            99999999999999999999999999999999999987543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.91  E-value=2.4e-05  Score=69.84  Aligned_cols=108  Identities=18%  Similarity=0.291  Sum_probs=77.1

Q ss_pred             ceEEEcCCCccccHHHH------HHHhccCCCeEEEEEcccCCC-CCcceEE--EEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          35 ATIYVGGLDDKVSETLM------WELFVQSGPVVNVHMPKDRVT-QTHQGYG--FIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L------~~~F~~~G~i~~i~~~~~~~~-~~~~g~a--fV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      .-|||-+|++.+..+++      .++|.+||.|..|.|-+...+ ....+.+  ||+|.+.|+|.+||...+|..++||.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            36899999998887773      478999999999988654421 1222334  99999999999999999999999999


Q ss_pred             eEEeeCCCc-------cccccccccccccCCCc---hhcHHHHHHHH
Q psy3016         106 IRVNKASSH-------QKNLDVGANIFIGNLDP---EVDEKLLYDTF  142 (305)
Q Consensus       106 l~v~~~~~~-------~~~~~~~~~l~v~nl~~---~~t~~~l~~~f  142 (305)
                      |+..+...+       ...-....|.|+..-..   ..|.++|...-
T Consensus       195 lkatYGTTKYCtsYLRn~~CpNp~CMyLHEpg~e~Ds~tK~el~n~q  241 (480)
T COG5175         195 LKATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNSQ  241 (480)
T ss_pred             EeeecCchHHHHHHHcCCCCCCCCeeeecCCCcccccccHHHHhhhh
Confidence            999876542       12222344566543322   46777776654

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.90  E-value=3.7e-05  Score=57.58  Aligned_cols=82  Identities=18%  Similarity=0.185  Sum_probs=64.0

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      .+|=|.|+|...|.++|.+++.....-..-                                     -.-+..|..++..
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yD-------------------------------------F~YLPiDf~~~~N   44 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYD-------------------------------------FFYLPIDFKNKCN   44 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcce-------------------------------------EEEeeeeccCCCc
Confidence            467899999999999999999774221110                                     0134666677889


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeec----CeeeEEEEeeec
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLC----NRPISVSYAFKK  240 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~----g~~l~v~~a~~~  240 (305)
                      .|||||.|.+.+.|.+-.+.++|..+.    .+...|.||+-.
T Consensus        45 ~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAriQ   87 (97)
T PF04059_consen   45 LGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYARIQ   87 (97)
T ss_pred             eEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhHhh
Confidence            999999999999999999999999873    567788888543

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG1995|consensus

Probab=97.81  E-value=1.9e-05  Score=71.14  Aligned_cols=85  Identities=24%  Similarity=0.337  Sum_probs=76.3

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeE--------EEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVV--------NVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL  101 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~--------~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~  101 (305)
                      ......+|||-+|+.++++++|.++|..+|.|.        .|.|.+++.|++.|+-|.|+|.+...|+.|+..+++..+
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            456677999999999999999999999999773        478888999999999999999999999999999999999


Q ss_pred             CCeeeEEeeCCCc
Q psy3016         102 YGKPIRVNKASSH  114 (305)
Q Consensus       102 ~g~~l~v~~~~~~  114 (305)
                      .+..|+|..+...
T Consensus       142 ~gn~ikvs~a~~r  154 (351)
T KOG1995|consen  142 CGNTIKVSLAERR  154 (351)
T ss_pred             cCCCchhhhhhhc
Confidence            9988888776643

>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=97.77  E-value=6.8e-05  Score=53.91  Aligned_cols=38  Identities=26%  Similarity=0.403  Sum_probs=29.8

Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      .+.|+|+|.+.+.|.+|.+.|+|..+.|..|.|+|...
T Consensus        39 ~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen   39 GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            57899999999999999999999999999999999843

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0128|consensus

Probab=97.73  E-value=5.5e-06  Score=81.86  Aligned_cols=158  Identities=18%  Similarity=0.172  Sum_probs=120.6

Q ss_pred             cCCCCceEEEcCCCccccHH-HHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          30 SGDGDATIYVGGLDDKVSET-LMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~-~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ..-......+.++.+..-.. ..++.|..+|.|+.|++.......+...++++.+..+.+++.|.. ..+.-+.++...+
T Consensus       567 ~~~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av  645 (881)
T KOG0128|consen  567 APLERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAV  645 (881)
T ss_pred             hhhhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccC
Confidence            33445566777887766555 678899999999999997744444455589999999999998877 4677778888888


Q ss_pred             eeCCCcccccc---------ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCC
Q psy3016         109 NKASSHQKNLD---------VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDV  179 (305)
Q Consensus       109 ~~~~~~~~~~~---------~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  179 (305)
                      ..+.+......         ...++||.||+....+++|...|..+|.+..+                            
T Consensus       646 ~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~v----------------------------  697 (881)
T KOG0128|consen  646 GLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVV----------------------------  697 (881)
T ss_pred             CCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhH----------------------------
Confidence            77665432211         13579999999999999999999999998876                            


Q ss_pred             cceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeee
Q psy3016         180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL  227 (305)
Q Consensus       180 ~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~  227 (305)
                                 ++.....++..+|+||+.|...+++.+|+....+..+
T Consensus       698 -----------qi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~  734 (881)
T KOG0128|consen  698 -----------QIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF  734 (881)
T ss_pred             -----------HHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh
Confidence                       3344445688899999999999999999975554433

>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=97.70  E-value=9.6e-05  Score=56.46  Aligned_cols=58  Identities=24%  Similarity=0.358  Sum_probs=38.9

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcC
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM   98 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g   98 (305)
                      +.|+|.++...++-++|++.|+.||.|..|.+....      .-|||-|.+.++|+.|++.+..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~   59 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKE   59 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHh
Confidence            468899999999999999999999999999985543      5699999999999999997653

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4210|consensus

Probab=97.60  E-value=4.6e-05  Score=68.55  Aligned_cols=83  Identities=24%  Similarity=0.501  Sum_probs=74.9

Q ss_pred             CCCceEE-EcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          32 DGDATIY-VGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        32 ~~~~~l~-V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ....++| |++|+..+++++|+..|..+|.|..+++..+..++..+|||||.|.+...+..++.. +...+.++.+.+..
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  260 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEE  260 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccccc
Confidence            3445666 999999999999999999999999999999999999999999999999999999987 88889999999988


Q ss_pred             CCCcc
Q psy3016         111 ASSHQ  115 (305)
Q Consensus       111 ~~~~~  115 (305)
                      ..+..
T Consensus       261 ~~~~~  265 (285)
T KOG4210|consen  261 DEPRP  265 (285)
T ss_pred             CCCCc
Confidence            77654

>KOG2416|consensus

Probab=97.57  E-value=0.00028  Score=67.47  Aligned_cols=80  Identities=18%  Similarity=0.244  Sum_probs=64.5

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhc-CcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAF-GVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~-g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ..++.|||.||-...|.-+|+.++.+- |.|...|                                        | |  
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~W----------------------------------------m-D--  478 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFW----------------------------------------M-D--  478 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHH----------------------------------------H-H--
Confidence            346889999999999999999999964 4554432                                        1 1  


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeee---cCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYL---CNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~---~g~~l~v~~a~~~~~~  243 (305)
                        +-+..|||.|.+.++|.....+|||-.|   +.++|.+.|.......
T Consensus       479 --kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~~deld  525 (718)
T KOG2416|consen  479 --KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVRADELD  525 (718)
T ss_pred             --HhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecchhHHH
Confidence              1255699999999999999999999877   7799999998766543

>KOG3152|consensus

Probab=97.50  E-value=6e-05  Score=65.01  Aligned_cols=73  Identities=18%  Similarity=0.301  Sum_probs=62.6

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCC--------CCcce----EEEEEEcCHHHHHHHHHHhcCce
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVT--------QTHQG----YGFIEFMGEEDADYAIKIMNMIK  100 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~--------~~~~g----~afV~f~~~e~A~~Ai~~l~g~~  100 (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            5568999999999999999999999999999999775544        22222    27899999999999999999999


Q ss_pred             eCCee
Q psy3016         101 LYGKP  105 (305)
Q Consensus       101 ~~g~~  105 (305)
                      |.|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99874

>KOG2314|consensus

Probab=97.50  E-value=0.0004  Score=66.11  Aligned_cols=81  Identities=25%  Similarity=0.338  Sum_probs=65.1

Q ss_pred             CCCCceEEEcCCCccc--c----HHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC-C
Q psy3016          31 GDGDATIYVGGLDDKV--S----ETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY-G  103 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~--t----e~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~-g  103 (305)
                      .--...|+|.|+|---  .    ..-|..+|+++|+|..+.+..+..+| .+||.|++|.+..+|..|++.|||..+. .
T Consensus        55 eg~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldkn  133 (698)
T KOG2314|consen   55 EGFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKN  133 (698)
T ss_pred             CCcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceeccc
Confidence            3345678999998621  1    23356789999999999998887655 9999999999999999999999998776 6


Q ss_pred             eeeEEeeCC
Q psy3016         104 KPIRVNKAS  112 (305)
Q Consensus       104 ~~l~v~~~~  112 (305)
                      +.+.|+...
T Consensus       134 Htf~v~~f~  142 (698)
T KOG2314|consen  134 HTFFVRLFK  142 (698)
T ss_pred             ceEEeehhh
Confidence            788887544

>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=97.47  E-value=0.00011  Score=56.03  Aligned_cols=70  Identities=10%  Similarity=0.267  Sum_probs=43.0

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      +.|+|.+++..++.++|++.|+.||.|.++                                       +      ....
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yV---------------------------------------D------~~~G   36 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYV---------------------------------------D------FSRG   36 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEE---------------------------------------E--------TT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceE---------------------------------------E------ecCC
Confidence            457888899999999999999999999876                                       2      2233


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCe-----eecCeeeEEEE
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQ-----YLCNRPISVSY  236 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~-----~~~g~~l~v~~  236 (305)
                      ...|||+|.+.+.|..|+.++...     .+.+..++++.
T Consensus        37 ~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen   37 DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            457999999999999999887544     45666665554

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.41  E-value=0.00041  Score=46.03  Aligned_cols=52  Identities=23%  Similarity=0.498  Sum_probs=42.5

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHH
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI   93 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai   93 (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            578899999877654 55588899999999984      23478999999999999985

>KOG1995|consensus

Probab=97.35  E-value=0.00017  Score=65.19  Aligned_cols=90  Identities=29%  Similarity=0.366  Sum_probs=75.2

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ..+|||..++..+++++|.++|...|.|..-+.                       + ...       -+.+-+|.+|+.
T Consensus        66 ~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~-----------------------t-~kP-------ki~~y~dkeT~~  114 (351)
T KOG1995|consen   66 NETIFVWGCPDSVCENDNADFFLQCGVIKRNKR-----------------------T-GKP-------KIKIYTDKETGA  114 (351)
T ss_pred             cccceeeccCccchHHHHHHHHhhcceeccCCC-----------------------C-CCc-------chhccccccccC
Confidence            468999999999999999999999998864210                       0 001       114677778999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .++-|.|.|++...|+.|+.-++++.|.+.+|+|.+|..+.
T Consensus       115 ~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  115 PKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERRT  155 (351)
T ss_pred             cCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhcc
Confidence            99999999999999999999999999999999999997665

>KOG4307|consensus

Probab=97.29  E-value=0.00074  Score=65.80  Aligned_cols=78  Identities=15%  Similarity=0.136  Sum_probs=66.6

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      +.+.|-+.|+|++++-+||.++|..|-.+-.-.+++....|...|-|.|-|++.+.|..|...|++..|..|++.+..
T Consensus       866 Gp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  866 GPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            344789999999999999999999997664433344445788999999999999999999999999999999998864

>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=97.03  E-value=0.0031  Score=47.60  Aligned_cols=79  Identities=14%  Similarity=0.169  Sum_probs=53.2

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEc-ccC------CCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMP-KDR------VTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK  104 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~-~~~------~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~  104 (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            34567889999998 456788899999999877511 110      001234688999999999999999 599999885


Q ss_pred             -eeEEeeCC
Q psy3016         105 -PIRVNKAS  112 (305)
Q Consensus       105 -~l~v~~~~  112 (305)
                       .+-|.+.+
T Consensus        82 ~mvGV~~~~   90 (100)
T PF05172_consen   82 LMVGVKPCD   90 (100)
T ss_dssp             EEEEEEE-H
T ss_pred             EEEEEEEcH
Confidence             55566664

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG0115|consensus

Probab=97.02  E-value=0.0012  Score=57.19  Aligned_cols=103  Identities=21%  Similarity=0.250  Sum_probs=81.2

Q ss_pred             HHHHHHHHHhcCceeCCeeeEEeeCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCccee
Q psy3016          87 EDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIR  166 (305)
Q Consensus        87 e~A~~Ai~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~  166 (305)
                      .-|..|..+|++....|+.|+|.++..        ..|||.||...++-+.+.+-|..||.|+..               
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~--------a~l~V~nl~~~~sndll~~~f~~fg~~e~a---------------   61 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH--------AELYVVNLMQGASNDLLEQAFRRFGPIERA---------------   61 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc--------ceEEEEecchhhhhHHHHHhhhhcCccchh---------------
Confidence            346677788999999999999999875        249999999999999999999999999874               


Q ss_pred             eecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCee----ecCeeeEEEEe
Q psy3016         167 VNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY----LCNRPISVSYA  237 (305)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~----~~g~~l~v~~a  237 (305)
                                              .+..| ..++..+-++|.|...-.|.+|++.+...-    ..++...|.-+
T Consensus        62 ------------------------v~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   62 ------------------------VAKVD-DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             ------------------------eeeec-ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence                                    22333 457888889999999999999999874332    24455555433

>KOG2202|consensus

Probab=97.01  E-value=0.00049  Score=59.58  Aligned_cols=44  Identities=18%  Similarity=0.410  Sum_probs=38.9

Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      +-+|-+||.|...++|.+|+..||+.|+.|++|.+.|+.....+
T Consensus       108 hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~~r  151 (260)
T KOG2202|consen  108 HLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTDFR  151 (260)
T ss_pred             hhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCchh
Confidence            45788999999999999999999999999999999998655433

>KOG2314|consensus

Probab=97.01  E-value=0.0016  Score=62.19  Aligned_cols=76  Identities=24%  Similarity=0.400  Sum_probs=58.8

Q ss_pred             cccccccCCCch------hcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc
Q psy3016         121 GANIFIGNLDPE------VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR  194 (305)
Q Consensus       121 ~~~l~v~nl~~~------~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  194 (305)
                      ..+|+|.|+|.-      .-...|..+|+++|++...                                       .+..
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~---------------------------------------~~P~   98 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNM---------------------------------------YYPI   98 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccce---------------------------------------eecc
Confidence            467888888862      2334578889999988754                                       4455


Q ss_pred             CCCCCCccceEEEEeCChHHHHHHHHHhcCeee-cCeeeEEEE
Q psy3016         195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYL-CNRPISVSY  236 (305)
Q Consensus       195 d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~-~g~~l~v~~  236 (305)
                      +.+ |.++||.|++|.+..+|..|++.|||+.+ .+.++.|..
T Consensus        99 ~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~~  140 (698)
T KOG2314|consen   99 DEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVRL  140 (698)
T ss_pred             Ccc-CCeeeEEEEEecChhhHHHHHHhcccceecccceEEeeh
Confidence            655 55999999999999999999999999988 556666654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.92  E-value=0.0011  Score=59.41  Aligned_cols=78  Identities=21%  Similarity=0.391  Sum_probs=58.3

Q ss_pred             ccccccCCCchhcHHHH------HHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         122 ANIFIGNLDPEVDEKLL------YDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l------~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      +-+||-+|+..+..|++      .+.|+.||.|..+                                         +..
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KI-----------------------------------------vvN  153 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKI-----------------------------------------VVN  153 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEE-----------------------------------------Eec
Confidence            45888999988777763      5678889998743                                         211


Q ss_pred             CCC-----CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         196 PDT-----GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       196 ~~~-----~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      .++     ..+..-.||.|.+.+||.+||.+.+|..++||.|+++|...+
T Consensus       154 kkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~lkatYGTTK  203 (480)
T COG5175         154 KKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVLKATYGTTK  203 (480)
T ss_pred             ccccccccccccceEEEEecchHHHHHHHHHhccccccCceEeeecCchH
Confidence            111     111122499999999999999999999999999999997643

>KOG1855|consensus

Probab=96.88  E-value=0.0014  Score=60.57  Aligned_cols=77  Identities=17%  Similarity=0.131  Sum_probs=60.7

Q ss_pred             CCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEccc---CCC--C-Cc-------ceEEEEEEcCHHHHHHH
Q psy3016          26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKD---RVT--Q-TH-------QGYGFIEFMGEEDADYA   92 (305)
Q Consensus        26 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~---~~~--~-~~-------~g~afV~f~~~e~A~~A   92 (305)
                      .-.+..-.+++|.+.|||.+-..+-|.++|..+|.|..|+|.+-   ..+  + .+       +-+|+|+|...+.|.+|
T Consensus       223 ~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA  302 (484)
T KOG1855|consen  223 EFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKA  302 (484)
T ss_pred             CccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHH
Confidence            33444457899999999999999999999999999999999654   111  1 22       46899999999999999


Q ss_pred             HHHhcCceeC
Q psy3016          93 IKIMNMIKLY  102 (305)
Q Consensus        93 i~~l~g~~~~  102 (305)
                      .+.++....+
T Consensus       303 ~e~~~~e~~w  312 (484)
T KOG1855|consen  303 RELLNPEQNW  312 (484)
T ss_pred             HHhhchhhhh
Confidence            9988654333

>KOG1924|consensus

Probab=96.79  E-value=0.0021  Score=63.64  Aligned_cols=6  Identities=17%  Similarity=0.008  Sum_probs=2.3

Q ss_pred             HHHHHH
Q psy3016          89 ADYAIK   94 (305)
Q Consensus        89 A~~Ai~   94 (305)
                      +.+|++
T Consensus       212 iIrClk  217 (1102)
T KOG1924|consen  212 IIRCLK  217 (1102)
T ss_pred             HHHHHH
Confidence            333433

>KOG0129|consensus

Probab=96.77  E-value=0.0036  Score=59.32  Aligned_cols=69  Identities=22%  Similarity=0.268  Sum_probs=61.5

Q ss_pred             CCCcCCCCceEEEcCCCccccHHHHHHHhc-cCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHH
Q psy3016          27 GGESGDGDATIYVGGLDDKVSETLMWELFV-QSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI   95 (305)
Q Consensus        27 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~   95 (305)
                      ....-+..+|||||+||.-++..+|..+|+ .||-|.-+-|=.|..-+-.+|-|=|+|.+.+.-.+||+.
T Consensus       363 ~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  363 HNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            455667789999999999999999999999 799999998877765677889999999999999999984

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.71  E-value=0.0087  Score=43.13  Aligned_cols=57  Identities=14%  Similarity=0.297  Sum_probs=42.7

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN   97 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~   97 (305)
                      ......+|+ .|..+...||.++|+.||.|. |..+.|       .-|||...+.+.|..++..+.
T Consensus         7 ~RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    7 SRDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             SGCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHT
T ss_pred             CcceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhc
Confidence            334455555 999999999999999999965 666666       359999999999999998775

; 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.

>KOG1996|consensus

Probab=96.68  E-value=0.002  Score=56.80  Aligned_cols=39  Identities=15%  Similarity=0.342  Sum_probs=35.3

Q ss_pred             eEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         204 FAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       204 ~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      ..||+|+..++|.+|+--|||++|+||.+...|......
T Consensus       331 RiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~ekf  369 (378)
T KOG1996|consen  331 RIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLEKF  369 (378)
T ss_pred             eeeeeeccHHHHHHHHHhcCCceecceeeeheeccHHhh
Confidence            479999999999999999999999999999999766543

>KOG2202|consensus

Probab=96.67  E-value=0.0008  Score=58.32  Aligned_cols=64  Identities=19%  Similarity=0.296  Sum_probs=52.4

Q ss_pred             HHHHHHhc-cCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          49 TLMWELFV-QSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        49 ~~L~~~F~-~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (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 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            34444455 89999999875553 345678999999999999999999999999999999987654

>KOG4676|consensus

Probab=96.59  E-value=0.015  Score=53.30  Aligned_cols=79  Identities=13%  Similarity=0.221  Sum_probs=57.5

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ..|.|.||.++.|.++++.+|.-.|+|..+..+                              - |     ..|..-...
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrly------------------------------p-~-----~~d~~~pv~   51 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLY------------------------------P-N-----VDDSKIPVI   51 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhcccccccccc------------------------------C-C-----CCCccCcce
Confidence            379999999999999999999999999876322                              0 0     011111223


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      .-.|||.|.+..++..|-. |.++.|-++.|.|-.+
T Consensus        52 sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen   52 SRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             eeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            4579999999877776666 7888887787777654

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.40  E-value=0.015  Score=46.58  Aligned_cols=55  Identities=22%  Similarity=0.367  Sum_probs=45.1

Q ss_pred             HHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          50 LMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        50 ~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (305)
                      +|-+.|..||++.=++++.+.        -+|+|.+.+.|.+|+. ++|..+.|+.|+|+.-.+
T Consensus        52 ~ll~~~~~~GevvLvRfv~~~--------mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGDT--------MWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETTC--------EEEEESSCHHHHHHHH-GCCSEETTEEEEEEE---
T ss_pred             HHHHHHHhCCceEEEEEeCCe--------EEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCc
Confidence            677789999998888886643        6999999999999999 899999999999986543

; PDB: 1UFW_A 2DNR_A.

>KOG0112|consensus

Probab=96.31  E-value=0.0042  Score=62.38  Aligned_cols=78  Identities=23%  Similarity=0.297  Sum_probs=67.6

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC--eeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG--KPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g--~~l~  107 (305)
                      .....+.+|+|+|..++....|...|..||.|..|.+-.      ..-||||+|.+...|+.|++.+-|.-+.|  +.++
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h------gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH------GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc------CCcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            344567899999999999999999999999999998843      33799999999999999999999988875  6788


Q ss_pred             EeeCCC
Q psy3016         108 VNKASS  113 (305)
Q Consensus       108 v~~~~~  113 (305)
                      |.++..
T Consensus       525 vdla~~  530 (975)
T KOG0112|consen  525 VDLASP  530 (975)
T ss_pred             cccccC
Confidence            887764

>KOG2416|consensus

Probab=95.92  E-value=0.012  Score=56.72  Aligned_cols=78  Identities=12%  Similarity=0.150  Sum_probs=63.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhcc-CCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC---Cee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQ-SGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY---GKP  105 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~-~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~---g~~  105 (305)
                      ....+..|+|.||-.-.|.-+|+.++.. .|.|.+. +| |+    -|..|||.|.+.++|.+.+.+|||..|.   ++.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH-HH-HH----hhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            5566778999999999999999999994 5566666 33 32    5678999999999999999999999884   577


Q ss_pred             eEEeeCCC
Q psy3016         106 IRVNKASS  113 (305)
Q Consensus       106 l~v~~~~~  113 (305)
                      |.+.|...
T Consensus       514 L~adf~~~  521 (718)
T KOG2416|consen  514 LIADFVRA  521 (718)
T ss_pred             eEeeecch
Confidence            88777653

>KOG1996|consensus

Probab=95.74  E-value=0.03  Score=49.56  Aligned_cols=65  Identities=22%  Similarity=0.039  Sum_probs=52.3

Q ss_pred             HHHHHHHhccCCCeEEEEEcccCCCCC-cceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          48 ETLMWELFVQSGPVVNVHMPKDRVTQT-HQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        48 e~~L~~~F~~~G~i~~i~~~~~~~~~~-~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ++++++-+++||.|..|.|......-. ..---||+|...+.|.+|+-.|||..|.||.+...+..
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            467888999999999998876642211 12346999999999999999999999999999887643

>KOG3152|consensus

Probab=95.68  E-value=0.0042  Score=53.88  Aligned_cols=80  Identities=10%  Similarity=0.200  Sum_probs=57.6

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC----
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD----  195 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d----  195 (305)
                      ....||+++||+......|+++|..||.|-.+                                |+..-+......    
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRv--------------------------------ylqpE~~s~~~~r~~~  120 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRV--------------------------------YLQPEDDSKRAARKRK  120 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceE--------------------------------EecchhhHHHHHHhhc
Confidence            45689999999999999999999999999754                                222211111000    


Q ss_pred             -CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCee
Q psy3016         196 -PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRP  231 (305)
Q Consensus       196 -~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~  231 (305)
                       ..++....-|.|+|.+...|......|||..|+|+.
T Consensus       121 ~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Iggkk  157 (278)
T KOG3152|consen  121 GGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIGGKK  157 (278)
T ss_pred             CCCccccchhHHHHHHHHHHHHHHHHHhCCCccCCCC
Confidence             011111222789999999999999999999998874

>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=95.68  E-value=0.12  Score=39.66  Aligned_cols=68  Identities=10%  Similarity=0.047  Sum_probs=50.4

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCC-CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG  103 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g  103 (305)
                      ...+.+...|..++.++|..+.+.+- .|..++|+++.  ..++=-+++.|.+.++|....+.+||..++.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            34455555556666677777766654 67789999875  2344568999999999999999999987763

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>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=95.30  E-value=0.06  Score=40.62  Aligned_cols=79  Identities=15%  Similarity=0.277  Sum_probs=51.1

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC----
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP----  196 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~----  196 (305)
                      ...|.|-+.|.. ....|.+.|+.||.|.+...+                                      ..+.    
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~--------------------------------------~~~~~~~~   46 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEV--------------------------------------LRSSSGIN   46 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGG--------------------------------------G-------
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecc--------------------------------------cccccccc
Confidence            355788888887 455678889999999764111                                      1110    


Q ss_pred             --CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeee-EEEEeee
Q psy3016         197 --DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPI-SVSYAFK  239 (305)
Q Consensus       197 --~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l-~v~~a~~  239 (305)
                        ..-...+...|+|++..+|.+||. -||..+.|..+ -|.+++.
T Consensus        47 ~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mvGV~~~~~   91 (100)
T PF05172_consen   47 PYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMVGVKPCDP   91 (100)
T ss_dssp             ---E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEEEEEE-HH
T ss_pred             cccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEEEEEEcHH
Confidence              001245678999999999999999 79999988655 4777743

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.

>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=95.26  E-value=0.031  Score=46.81  Aligned_cols=72  Identities=11%  Similarity=0.102  Sum_probs=46.9

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhcc-CCCe---EEEEEcccC--CCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQ-SGPV---VNVHMPKDR--VTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG  103 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~-~G~i---~~i~~~~~~--~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g  103 (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            34558999999999999999998887 7655   333311111  111233569999999999999999999987754

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.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.22  E-value=0.048  Score=43.76  Aligned_cols=37  Identities=8%  Similarity=0.183  Sum_probs=30.1

Q ss_pred             eEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         204 FAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       204 ~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .-+|.|.+-++|.+|+. ++|.+++|+.|+|+...+.=
T Consensus        72 ~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpdW  108 (146)
T PF08952_consen   72 TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPDW  108 (146)
T ss_dssp             CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE-----
T ss_pred             eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCccH
Confidence            46999999999999999 99999999999999876553

; PDB: 1UFW_A 2DNR_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=94.81  E-value=0.039  Score=36.46  Aligned_cols=51  Identities=20%  Similarity=0.475  Sum_probs=36.9

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      .|-|.+.+....+ .+...|..||+|...                                         -.    ....
T Consensus         3 wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~-----------------------------------------~~----~~~~   36 (53)
T PF14605_consen    3 WISVSGFPPDLAE-EVLEHFASFGEIVDI-----------------------------------------YV----PEST   36 (53)
T ss_pred             EEEEEeECchHHH-HHHHHHHhcCCEEEE-----------------------------------------Ec----CCCC
Confidence            4666777766554 455588889999853                                         11    1346


Q ss_pred             ceEEEEeCChHHHHHHH
Q psy3016         203 GFAFINYASFEASDASI  219 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al  219 (305)
                      ...||+|.+..+|++|+
T Consensus        37 ~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen   37 NWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEECCHHHHHhhC
Confidence            68999999999999985

>KOG2193|consensus

Probab=94.66  E-value=0.025  Score=52.47  Aligned_cols=77  Identities=22%  Similarity=0.368  Sum_probs=59.9

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      +.+|++||.+.++-.++..+|... .+-                                            .....-..
T Consensus         2 nklyignL~p~~~psdl~svfg~a-k~~--------------------------------------------~~g~fl~k   36 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDA-KIP--------------------------------------------GSGQFLVK   36 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccc-cCC--------------------------------------------CCcceeee
Confidence            368999999999999999999763 111                                            11111123


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCe-eecCeeeEEEEeeecCCc
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQ-YLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~-~~~g~~l~v~~a~~~~~~  243 (305)
                      .||+||.+.+...|.+|++.++|. ++.|+++.+.++-.+..+
T Consensus        37 ~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqr   79 (584)
T KOG2193|consen   37 SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQR   79 (584)
T ss_pred             cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHH
Confidence            689999999999999999999997 579999999987665543

>KOG0115|consensus

Probab=94.63  E-value=0.034  Score=48.42  Aligned_cols=75  Identities=24%  Similarity=0.304  Sum_probs=60.6

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCc----eeCCeeeEEee
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMI----KLYGKPIRVNK  110 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~----~~~g~~l~v~~  110 (305)
                      ..|+|.||...++.+.|.+-|+.||+|..-.++.|- .++..+-++|.|...-.|.+|.+.++.-    ...++...|..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            579999999999999999999999999987776663 5777888999999999999999877432    33345555543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.62  E-value=0.15  Score=34.75  Aligned_cols=54  Identities=19%  Similarity=0.237  Sum_probs=44.4

Q ss_pred             ceEEEcCCCccccHHHHHHHhccC---CCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHh
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQS---GPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM   96 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~---G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l   96 (305)
                      ..|+|.++.. ++.++|+.+|..|   .....|..+-|.       -|=|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            4789999854 7889999999998   135688888885       3789999999999999764

>KOG2068|consensus

Probab=94.45  E-value=0.02  Score=51.75  Aligned_cols=79  Identities=23%  Similarity=0.315  Sum_probs=60.4

Q ss_pred             ceEEEcCCCccccHHHHH---HHhccCCCeEEEEEcccCC--CCCcc-eEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          35 ATIYVGGLDDKVSETLMW---ELFVQSGPVVNVHMPKDRV--TQTHQ-GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~---~~F~~~G~i~~i~~~~~~~--~~~~~-g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      .-+||-+|+..+..+++.   +.|..||.|..|.+-.+..  .+..- --+||+|...++|..||...+|..+.|+.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            357888998876655543   5788999999999877652  11111 12899999999999999999999999999777


Q ss_pred             eeCCC
Q psy3016         109 NKASS  113 (305)
Q Consensus       109 ~~~~~  113 (305)
                      .+...
T Consensus       158 ~~gtt  162 (327)
T KOG2068|consen  158 SLGTT  162 (327)
T ss_pred             hhCCC
Confidence            66554

>KOG1855|consensus

Probab=94.27  E-value=0.12  Score=48.23  Aligned_cols=77  Identities=19%  Similarity=0.262  Sum_probs=53.0

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC--
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD--  197 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~--  197 (305)
                      ..++|.+.|||.+-.-+-|.++|+.+|.|..++..              ..               +.++..+..-+.  
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIc--------------kP---------------gaip~d~r~~~~~~  280 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRIC--------------KP---------------GAIPEDVRGFPKKY  280 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeec--------------CC---------------CCCCcccccCCccc
Confidence            57899999999998889999999999999875211              10               001111111100  


Q ss_pred             -CCCccceEEEEeCChHHHHHHHHHhcCe
Q psy3016         198 -TGNSKGFAFINYASFEASDASIDAMHGQ  225 (305)
Q Consensus       198 -~~~~~g~afV~f~~~~~A~~Al~~l~~~  225 (305)
                       --..+-+|+|+|++.+.|.+|.+.|+..
T Consensus       281 ~~~~tk~~AlvEye~~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  281 FELQTKECALVEYEEVEAARKARELLNPE  309 (484)
T ss_pred             hhhhhhhhhhhhhhhhHHHHHHHHhhchh
Confidence             0113567999999999999999988543

>KOG2591|consensus

Probab=93.99  E-value=0.073  Score=51.12  Aligned_cols=70  Identities=19%  Similarity=0.311  Sum_probs=55.6

Q ss_pred             CCceEEEcCCCccccHHHHHHHhcc--CCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcC--ceeCCeeeEE
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQ--SGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM--IKLYGKPIRV  108 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~--~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g--~~~~g~~l~v  108 (305)
                      .-|.|.+..||..+-.++++-||..  +-.+.+|.+-.+.      + =||+|++..||+.|.+.|..  ..|.|+.|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------n-WyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------N-WYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------c-eEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            3467889999999999999999975  6688889885442      3 38999999999999987763  4667776655


Q ss_pred             e
Q psy3016         109 N  109 (305)
Q Consensus       109 ~  109 (305)
                      +
T Consensus       247 R  247 (684)
T KOG2591|consen  247 R  247 (684)
T ss_pred             h
Confidence            4

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.80  E-value=0.2  Score=39.93  Aligned_cols=71  Identities=15%  Similarity=0.137  Sum_probs=53.4

Q ss_pred             CceEEEcCCCccc----cHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          34 DATIYVGGLDDKV----SETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        34 ~~~l~V~nLp~~~----te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      -.||.|.=|..++    +...+...++.||+|.++.+.     |  +.-|.|.|.+...|=+|+.+++. ...|..+.+.
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCs  157 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCS  157 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcC-CCCCceEEee
Confidence            4577776665554    334455667889999999872     2  25699999999999999998765 6678888888


Q ss_pred             eCC
Q psy3016         110 KAS  112 (305)
Q Consensus       110 ~~~  112 (305)
                      |-.
T Consensus       158 Wqq  160 (166)
T PF15023_consen  158 WQQ  160 (166)
T ss_pred             ccc
Confidence            754

>KOG2253|consensus

Probab=93.78  E-value=0.041  Score=53.80  Aligned_cols=108  Identities=19%  Similarity=0.226  Sum_probs=79.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ......+|||||+...+.++-++.+...+|.|.+++...         |||+.|..+..+..|+..++...++|..+.+.
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhcc
Confidence            344567999999999999999999999999999887633         89999999999999999998888888877776


Q ss_pred             eCCCccccc-----------------cccccccccCCCchhcHHHHHHHHhhcC
Q psy3016         110 KASSHQKNL-----------------DVGANIFIGNLDPEVDEKLLYDTFSAFG  146 (305)
Q Consensus       110 ~~~~~~~~~-----------------~~~~~l~v~nl~~~~t~~~l~~~f~~~g  146 (305)
                      .-.....+.                 ...+..+|.+++..+.+......+.-.+
T Consensus       107 ~d~q~~~n~~k~~~~~~~~~~~f~p~~srr~e~i~~k~~~l~~~~~~~~~~is~  160 (668)
T KOG2253|consen  107 VDEQTIENADKEKSIANKESHKFVPSSSRRQESIQNKPLSLDEQIHKKSLQISS  160 (668)
T ss_pred             chhhhhcCccccccchhhhhcccCCchhHHHHHhhccccchhHHHHHHHHhccc
Confidence            422110000                 0124466777777766666655554433

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.64  E-value=0.2  Score=39.93  Aligned_cols=37  Identities=8%  Similarity=0.129  Sum_probs=31.8

Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      ++-.|.|.|.+..+|-+|+.+++. ...|.-+.++|..
T Consensus       124 GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWqq  160 (166)
T PF15023_consen  124 GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQQ  160 (166)
T ss_pred             CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeeccc
Confidence            355799999999999999999987 6788888999864

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=93.48  E-value=0.19  Score=42.32  Aligned_cols=61  Identities=23%  Similarity=0.188  Sum_probs=45.8

Q ss_pred             cHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc--CceeCCeeeEEeeCCC
Q psy3016          47 SETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN--MIKLYGKPIRVNKASS  113 (305)
Q Consensus        47 te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~--g~~~~g~~l~v~~~~~  113 (305)
                      ..+.|+++|..|+.+..+...+.-      +-..|.|.+.++|.+|...|+  +..+.|..+++.++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            347899999999998888776643      558999999999999999999  8999999999988743

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.

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=93.20  E-value=0.55  Score=32.51  Aligned_cols=55  Identities=13%  Similarity=0.203  Sum_probs=43.6

Q ss_pred             cccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          45 KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        45 ~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      .++-.+++..+..|+- ..|..  ++     .|| ||.|.+..+|++|....+|..+.+..+.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~I~~--d~-----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DRIRD--DR-----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ceEEe--cC-----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4677899999999964 44443  32     266 99999999999999999999988877765

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4285|consensus

Probab=92.72  E-value=0.75  Score=41.18  Aligned_cols=75  Identities=21%  Similarity=0.304  Sum_probs=57.5

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe-eeEEeeC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK-PIRVNKA  111 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~-~l~v~~~  111 (305)
                      ....|-|-++|+.-+ ..|.+.|++||+|.+....      .+-.+-+|.|.+.-+|.+|+.. ||..|.|. .|-|..+
T Consensus       196 ~D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpC  267 (350)
T KOG4285|consen  196 ADTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPC  267 (350)
T ss_pred             ccceEEEeccCccch-hHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeec
Confidence            367788889988644 5677899999999877653      2336889999999999999994 88888874 5566665


Q ss_pred             CCcc
Q psy3016         112 SSHQ  115 (305)
Q Consensus       112 ~~~~  115 (305)
                      ..+.
T Consensus       268 tDks  271 (350)
T KOG4285|consen  268 TDKS  271 (350)
T ss_pred             CCHH
Confidence            5544

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=92.53  E-value=0.23  Score=35.93  Aligned_cols=56  Identities=16%  Similarity=0.306  Sum_probs=40.7

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ....||+ .|..+-..+|.++|++||.|...                                        ++-      
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~Vs----------------------------------------Wi~------   41 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYVS----------------------------------------WIN------   41 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEEE----------------------------------------EEC------
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEEE----------------------------------------EEc------
Confidence            3445555 89999999999999999998642                                        222      


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHG  224 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~  224 (305)
                       ...|||...+.+.|..|+..+.-
T Consensus        42 -dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   42 -DTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             -TTEEEEEECCCHHHHHHHHHHTT
T ss_pred             -CCcEEEEeecHHHHHHHHHHhcc
Confidence             23699999999999999998864

; 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.

>KOG0804|consensus

Probab=91.09  E-value=0.64  Score=43.82  Aligned_cols=68  Identities=10%  Similarity=0.150  Sum_probs=57.6

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCC-CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG  103 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g  103 (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            77899999999999999999988655 688999999642  233448999999999999999999987763

>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=89.78  E-value=0.35  Score=40.46  Aligned_cols=86  Identities=19%  Similarity=0.281  Sum_probs=48.4

Q ss_pred             cccccccCCCchhcHHHHHHHHhh-cCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSA-FGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~-~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...|.|.+||+.+|++++.+.+.. ++.-..             |-.+.                 +..+.....    -
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~-------------w~y~~-----------------g~~~~~~~~----~   52 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWD-------------WYYFQ-----------------GKYGKKSFK----P   52 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE----------------EEEE-----------------EEES-SSST----T
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccc-------------eEEEe-----------------cCCCCccCC----C
Confidence            457999999999999999987665 443311             00000                 000001111    1


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecC-----eeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCN-----RPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g-----~~l~v~~a~~~  240 (305)
                      .....|||.|.+.++...-...++|..|-+     ....|.||--.
T Consensus        53 ~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~~~~~~VE~Apyq   98 (176)
T PF03467_consen   53 PTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGNEYPAVVEFAPYQ   98 (176)
T ss_dssp             S--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-EEEEEEEE-SS-
T ss_pred             CcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCCCcceeEEEcchh
Confidence            124469999999999999999999987722     34567776543

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.

>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=89.74  E-value=1.3  Score=31.23  Aligned_cols=59  Identities=20%  Similarity=0.337  Sum_probs=36.7

Q ss_pred             ccccHHHHHHHhccCC-----CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          44 DKVSETLMWELFVQSG-----PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        44 ~~~te~~L~~~F~~~G-----~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ..++..+|-.++...+     .|-.|++..        .|+||+-.. +.|..+++.|++..+.|+.+.|+.+
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3578888988888764     566788733        578998765 4788999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>KOG2135|consensus

Probab=89.55  E-value=0.22  Score=47.12  Aligned_cols=82  Identities=12%  Similarity=0.054  Sum_probs=63.9

Q ss_pred             CCCcCCCCceEEEcCCCcccc-HHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          27 GGESGDGDATIYVGGLDDKVS-ETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        27 ~~~~~~~~~~l~V~nLp~~~t-e~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      ++.-....+.|-+.-.+.... -.+|..-|..||.|..|.+-..      --.|.|+|.+..+|-.|.. ..+..|++|-
T Consensus       365 ~g~~~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~  437 (526)
T KOG2135|consen  365 PGHAVVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRF  437 (526)
T ss_pred             CcchhcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCce
Confidence            333444566777777777654 4789999999999999998433      2468999999999977776 5899999999


Q ss_pred             eEEeeCCCcc
Q psy3016         106 IRVNKASSHQ  115 (305)
Q Consensus       106 l~v~~~~~~~  115 (305)
                      |+|-|..+..
T Consensus       438 iKl~whnps~  447 (526)
T KOG2135|consen  438 IKLFWHNPSP  447 (526)
T ss_pred             eEEEEecCCc
Confidence            9999987643

>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=89.40  E-value=0.43  Score=35.04  Aligned_cols=65  Identities=18%  Similarity=0.200  Sum_probs=44.9

Q ss_pred             EEEEEcCHHHHHHHHHHhc-CceeCCeeeEEeeCC--Ccc-c-----cccccccccccCCCchhcHHHHHHHHh
Q psy3016          79 GFIEFMGEEDADYAIKIMN-MIKLYGKPIRVNKAS--SHQ-K-----NLDVGANIFIGNLDPEVDEKLLYDTFS  143 (305)
Q Consensus        79 afV~f~~~e~A~~Ai~~l~-g~~~~g~~l~v~~~~--~~~-~-----~~~~~~~l~v~nl~~~~t~~~l~~~f~  143 (305)
                      |+|+|.+..-|++-++.-. ...+.+..+.|...-  ... .     ..-..++|-|.|||..+.+++|.+.++
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeEE
Confidence            6899999999999988422 245556665554322  111 1     112357899999999999999998875

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=88.83  E-value=1.1  Score=30.66  Aligned_cols=23  Identities=22%  Similarity=0.403  Sum_probs=19.6

Q ss_pred             ccccccCCCchhcHHHHHHHHhhc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAF  145 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~  145 (305)
                      ..|+|.+++ +++.++|+..|..|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y   28 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEY   28 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHh
Confidence            468999986 48889999999998

>KOG4574|consensus

Probab=88.02  E-value=0.47  Score=48.01  Aligned_cols=77  Identities=21%  Similarity=0.295  Sum_probs=62.7

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      .+.++.|....++..-|..+|..||.|...|                                       ..+|      
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~w---------------------------------------tlr~------  333 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAW---------------------------------------TLRD------  333 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhhe---------------------------------------eccc------
Confidence            3455677777889999999999999998753                                       1233      


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeee--cCeeeEEEEeeecCCc
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYL--CNRPISVSYAFKKDSK  243 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~--~g~~l~v~~a~~~~~~  243 (305)
                      ..-|.|+|.+.+.|..|+.+++|+++  -|-+.+|.|++.....
T Consensus       334 ~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~~~  377 (1007)
T KOG4574|consen  334 LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLPMY  377 (1007)
T ss_pred             ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccccc
Confidence            45689999999999999999999986  7888999999876653

>KOG2591|consensus

Probab=85.26  E-value=11  Score=36.93  Aligned_cols=94  Identities=7%  Similarity=0.080  Sum_probs=56.8

Q ss_pred             HHHHHHhcCceeCCeeeEEeeCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeec
Q psy3016          90 DYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK  169 (305)
Q Consensus        90 ~~Ai~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~  169 (305)
                      ..++++.-+..++.+-.+|+...       ..|.|.+.-|+..+-.|+++.+|+.-..-..+                  
T Consensus       151 ~Evlresp~VqvDekgekVrp~~-------kRcIvilREIpettp~e~Vk~lf~~encPk~i------------------  205 (684)
T KOG2591|consen  151 VEVLRESPNVQVDEKGEKVRPNH-------KRCIVILREIPETTPIEVVKALFKGENCPKVI------------------  205 (684)
T ss_pred             HHHHhcCCCceeccCccccccCc-------ceeEEEEeecCCCChHHHHHHHhccCCCCCce------------------
Confidence            33444444555555555554322       24667789999999999999999863322211                  


Q ss_pred             CccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcC--eeecCeeeEE
Q psy3016         170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHG--QYLCNRPISV  234 (305)
Q Consensus       170 ~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~--~~~~g~~l~v  234 (305)
                                           .+    +.+... -=||.|++..||..|.+.|..  .+|-|+.|..
T Consensus       206 ---------------------sc----efa~N~-nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  206 ---------------------SC----EFAHND-NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ---------------------ee----eeeecC-ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence                                 00    111111 239999999999999877643  2455555443

>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=85.26  E-value=1.4  Score=37.04  Aligned_cols=39  Identities=13%  Similarity=0.172  Sum_probs=29.9

Q ss_pred             cceEEEEeCChHHHHHHHHHhc--CeeecCeeeEEEEeeec
Q psy3016         202 KGFAFINYASFEASDASIDAMH--GQYLCNRPISVSYAFKK  240 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~--~~~~~g~~l~v~~a~~~  240 (305)
                      -+-..|.|.+.++|..|...|+  +..+.|..+++-|+...
T Consensus        31 FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen   31 FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            4468999999999999999999  99999999999998443

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.

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=84.73  E-value=1.6  Score=35.05  Aligned_cols=107  Identities=17%  Similarity=0.131  Sum_probs=70.0

Q ss_pred             eEEEcCCC--ccccHHHHHHHhc----cCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          36 TIYVGGLD--DKVSETLMWELFV----QSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        36 ~l~V~nLp--~~~te~~L~~~F~----~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ...||.+.  ...+-..|.+.+.    ..|.+.-..+        ..++..++|.+.+++.++++. ....+.|..+.+.
T Consensus        17 ~~lVg~~l~~~~~~~~~l~~~l~~~W~~~~~~~i~~l--------~~~~fl~~F~~~~d~~~vl~~-~p~~~~~~~~~l~   87 (153)
T PF14111_consen   17 LCLVGRVLSPKPISLSALEQELAKIWKLKGGVKIRDL--------GDNLFLFQFESEEDRQRVLKG-GPWNFNGHFLILQ   87 (153)
T ss_pred             eEEEEEECCCCCCCHHHHHHHHHHHhCCCCcEEEEEe--------CCCeEEEEEEeccceeEEEec-ccccccccchhhh
Confidence            44555553  2344555555444    3444443333        237899999999999999883 4556777778777


Q ss_pred             eCCCcccccc-----ccccccccCCCch-hcHHHHHHHHhhcCcccch
Q psy3016         110 KASSHQKNLD-----VGANIFIGNLDPE-VDEKLLYDTFSAFGVILQT  151 (305)
Q Consensus       110 ~~~~~~~~~~-----~~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~~  151 (305)
                      .-.+......     ..-=|.|.+||.. .+++-+..+.+..|.+..+
T Consensus        88 ~W~~~~~~~~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~v  135 (153)
T PF14111_consen   88 RWSPDFNPSEVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEV  135 (153)
T ss_pred             hhcccccccccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEE
Confidence            6553322111     1233778999987 7888899999999999865

>KOG4285|consensus

Probab=84.23  E-value=3  Score=37.50  Aligned_cols=44  Identities=14%  Similarity=0.197  Sum_probs=34.9

Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeE-EEEeeecCCcC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPIS-VSYAFKKDSKG  244 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~-v~~a~~~~~~~  244 (305)
                      ..-.+-+|+|.+..+|.+||. -||+.|+|..+. |.-|.++....
T Consensus       230 ~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtDksvi~  274 (350)
T KOG4285|consen  230 SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTDKSVIN  274 (350)
T ss_pred             CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCCHHHhc
Confidence            345688999999999999999 689999887654 88777776543

>KOG4574|consensus

Probab=83.20  E-value=0.72  Score=46.75  Aligned_cols=70  Identities=19%  Similarity=0.234  Sum_probs=56.6

Q ss_pred             EEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC--CeeeEEeeCCC
Q psy3016          38 YVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY--GKPIRVNKASS  113 (305)
Q Consensus        38 ~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~--g~~l~v~~~~~  113 (305)
                      .+.|.+-..+-.-|..+|+.||.|.+....++-      ..|.|+|.+.+.|..|.++|+|+++.  |...+|..++.
T Consensus       302 ~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  302 SLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            344444567778899999999999999887764      67999999999999999999997654  77777777654

>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=82.74  E-value=5.1  Score=27.71  Aligned_cols=30  Identities=10%  Similarity=0.257  Sum_probs=26.6

Q ss_pred             EEEEeCChHHHHHHHHHhcCeeecCeeeEE
Q psy3016         205 AFINYASFEASDASIDAMHGQYLCNRPISV  234 (305)
Q Consensus       205 afV~f~~~~~A~~Al~~l~~~~~~g~~l~v  234 (305)
                      -||-|.+.++|+++....+|+.+.+..+.+
T Consensus        36 fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   36 FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            499999999999999999999988777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=80.93  E-value=2.4  Score=29.82  Aligned_cols=35  Identities=20%  Similarity=0.506  Sum_probs=21.6

Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      ..|+||+-.. +.|..++.+|++..+.|+.|+|+.|
T Consensus        40 ~~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   40 DNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             SS-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             eeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            4488999964 4899999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	305
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		6e-39
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		8e-09
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		8e-35
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-21
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		1e-21
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		9e-16
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		1e-13
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-12
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		4e-12
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		3e-11
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		5e-11
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		9e-11
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		1e-10
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		1e-10
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		4e-10
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		4e-10
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-09
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-09
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		6e-09
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		8e-09
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		1e-08
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-08
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-08
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-08
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		7e-08
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		1e-07
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		5e-04
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-07
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		2e-07
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		6e-07
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		8e-07
2cqi_A	103	Solution Structure Of The Rna Binding Domain Of Nuc		1e-06
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-06
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		4e-06
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		8e-06
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		9e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		9e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-04
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		1e-05
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		8e-04
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		1e-05
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		1e-05
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		7e-04
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-05
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		7e-04
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		1e-05
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		7e-04
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		7e-04
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-05
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		8e-04
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-05
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-05
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-05
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		3e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		4e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		5e-04
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-05
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		4e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		5e-05
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		6e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		6e-05
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		6e-05
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		7e-05
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		2e-04
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		7e-05
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		8e-05
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		8e-05
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		1e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		1e-04
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		1e-04
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		1e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-04
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		2e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		2e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		3e-04
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		3e-04
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		4e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		4e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		4e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		4e-04
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		5e-04
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		6e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		6e-04
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		7e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		9e-04

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score =  157 bits (397), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 70/85 (82%), Positives = 79/85 (92%)
Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 94  KIMNMIKLYGKPIRVNKASSHQKNL 118
           KIM+MIKLYGKPIRVNKAS+H KNL
Sbjct: 75  KIMDMIKLYGKPIRVNKASAHNKNL 99

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 57.8 bits (138), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 35/91 (38%), Positives = 47/91 (51%), Gaps = 30/91 (32%)
Query: 115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP---------------------- 152
           ++N D  A +++G LD +V E LL++ F   G ++ T                       
Sbjct: 11  ERNQD--ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68
Query: 153 ------KIMNMIKLYGKPIRVNKASSHQKNL 177
                 KIM+MIKLYGKPIRVNKAS+H KNL
Sbjct: 69  DADYAIKIMDMIKLYGKPIRVNKASAHNKNL 99

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score =  144 bits (362), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 74/123 (60%), Positives = 84/123 (68%), Gaps = 38/123 (30%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
           + IFIGNLDPE+DEKLLYDTFSAFGVILQT                              
Sbjct: 6   SGIFIGNLDPEIDEKLLYDTFSAFGVILQT------------------------------ 35
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                   P+IMRDPDTGNSKG+AFIN+ASF+ASDA+I+AM+GQYLCNRPI+VSYAFKKD
Sbjct: 36  --------PKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD 87
Query: 242 SKG 244
           SKG
Sbjct: 88  SKG 90

>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 =  100 bits (249), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 63/221 (28%), Positives = 107/221 (48%), Gaps = 45/221 (20%)
Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           A++YVG L   V+E +++E F  +GP++++ + +D +T+   GY ++ F    DA+ A+ 
Sbjct: 11  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 95  IMNMIKLYGKPIRV--NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
            MN   + GKP+R+  ++     +   VG NIFI NLD  +D K LYDTFSAFG IL   
Sbjct: 71  TMNFDVIKGKPVRIMWSQRDPSLRKSGVG-NIFIKNLDKSIDNKALYDTFSAFGNILSCK 129
Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
            +                                          D   SKG+ F+++ + 
Sbjct: 130 VVC-----------------------------------------DENGSKGYGFVHFETQ 148
Query: 213 EASDASIDAMHGQYLCNRPISV-SYAFKKDSKGDRHGSAAE 252
           EA++ +I+ M+G  L +R + V  +  +K+ + +    A E
Sbjct: 149 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKE 189

>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 =  100 bits (248), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 63/221 (28%), Positives = 107/221 (48%), Gaps = 45/221 (20%)
Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           A++YVG L   V+E +++E F  +GP++++ + +D +T+   GY ++ F    DA+ A+ 
Sbjct: 16  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 95  IMNMIKLYGKPIRV--NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
            MN   + GKP+R+  ++     +   VG NIFI NLD  +D K LYDTFSAFG IL   
Sbjct: 76  TMNFDVIKGKPVRIMWSQRDPSLRKSGVG-NIFIKNLDKSIDNKALYDTFSAFGNILSCK 134
Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
            +                                          D   SKG+ F+++ + 
Sbjct: 135 VVC-----------------------------------------DENGSKGYGFVHFETQ 153
Query: 213 EASDASIDAMHGQYLCNRPISV-SYAFKKDSKGDRHGSAAE 252
           EA++ +I+ M+G  L +R + V  +  +K+ + +    A E
Sbjct: 154 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKE 194

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 80.9 bits (198), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 52/205 (25%), Positives = 98/205 (47%), Gaps = 41/205 (20%)
Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +YVG LD  ++E ++ + F   GP+ N+ +  D+    +  Y F+E+    DA+ A++ 
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT 60
Query: 96  MNMIKLYGKPIRVNKA-SSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI 154
           +N  ++    +++N A  S Q + D   N+F+G+L+  VD++ L + F  F   L     
Sbjct: 61  LNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYL----- 115
Query: 155 MNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEA 214
                           S H                  +M D  TG+S+G+ F+++ S + 
Sbjct: 116 ----------------SGH------------------VMWDMQTGSSRGYGFVSFTSQDD 141
Query: 215 SDASIDAMHGQYLCNRPISVSYAFK 239
           +  ++D+M GQ L  RP+ +++A K
Sbjct: 142 AQNAMDSMQGQDLNGRPLRINWAAK 166

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 73.9 bits (180), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 34/82 (41%), Positives = 55/82 (67%), Gaps = 1/82 (1%)
Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           + D T++VG L+ +V E +++ELF+Q+GP+  V + KDR  +  + +GF+ F   E   Y
Sbjct: 14  EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKP-KSFGFVCFKHPESVSY 72
Query: 92  AIKIMNMIKLYGKPIRVNKASS 113
           AI ++N I+LYG+PI V+  SS
Sbjct: 73  AIALLNGIRLYGRPINVSGPSS 94

>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 = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 99/224 (44%), Gaps = 53/224 (23%)
Query: 24  LEGGGESGDGDAT-----------IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVT 72
           + GG + G G A            +YVG +  ++ E  + + F   GP+ ++ M  D VT
Sbjct: 7   MTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVT 66
Query: 73  QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPE 132
             H+G+ F+E+   E A  A++ MN + L G+ I+V + S+            IG   P 
Sbjct: 67  MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN------------IGQAQPI 114
Query: 133 VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQK-NLDVGANIF--IGNLD 189
           +D+  L +   AF                    R+  AS HQ  + D   ++F   G + 
Sbjct: 115 IDQ--LAEEARAFN-------------------RIYVASVHQDLSDDDIKSVFEAFGKIK 153
Query: 190 PEIM-RDPDTGNSKGFAFINYASFEASDASIDAMH-----GQYL 227
              + RDP TG  KG+ FI Y   ++S  ++ +M+     GQYL
Sbjct: 154 SATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 68.9 bits (167), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 56/200 (28%), Positives = 92/200 (46%), Gaps = 42/200 (21%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVG +  ++ E  + + F   GP+ ++ M  D VT  H+G+ F+E+   E A  A++ M
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN 156
           N + L G+ I+V + S+            IG   P +D+  L +   AF           
Sbjct: 76  NSVMLGGRNIKVGRPSN------------IGQAQPIIDQ--LAEEARAFN---------- 111
Query: 157 MIKLYGKPIRVNKASSHQK-NLDVGANIF--IGNLDP-EIMRDPDTGNSKGFAFINYASF 212
                    R+  AS HQ  + D   ++F   G +    + RDP TG  KG+ FI Y   
Sbjct: 112 ---------RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKA 162
Query: 213 EASDASIDAMH-----GQYL 227
           ++S  ++ +M+     GQYL
Sbjct: 163 QSSQDAVSSMNLFDLGGQYL 182

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 65.5 bits (158), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 48/76 (63%)
Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +YVGGL ++V + ++   F+  G + ++ +P D  T+ H+G+ F+EF   EDA  AI  
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 96  MNMIKLYGKPIRVNKA 111
           MN  +L+G+ IRVN A
Sbjct: 74  MNESELFGRTIRVNLA 89

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 65.1 bits (157), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 48/76 (63%)
Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +YVGGL ++V + ++   F+  G + ++ +P D  T+ H+G+ F+EF   EDA  AI  
Sbjct: 65  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 96  MNMIKLYGKPIRVNKA 111
           MN  +L+G+ IRVN A
Sbjct: 125 MNESELFGRTIRVNLA 140

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 63.9 bits (154), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVGGL ++V + ++   F+  G + ++ +P D  T+ H+G+ F+EF   EDA  AI  M
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 97  NMIKLYGKPIRVNKA 111
           N  +L+G+ IRVN A
Sbjct: 65  NESELFGRTIRVNLA 79

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 63.9 bits (154), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVGGL ++V + ++   F+  G + ++ +P D  T+ H+G+ F+EF   EDA  AI  M
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 97  NMIKLYGKPIRVNKA 111
           N  +L+G+ IRVN A
Sbjct: 68  NESELFGRTIRVNLA 82

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 63.9 bits (154), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVGGL ++V + ++   F+  G + ++ +P D  T+ H+G+ F+EF   EDA  AI  M
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 97  NMIKLYGKPIRVNKA 111
           N  +L+G+ IRVN A
Sbjct: 70  NESELFGRTIRVNLA 84

>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 = 47/182 (25%), Positives = 76/182 (41%), Gaps = 42/182 (23%)
Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
             +++GGL+   +E  + E F + G V ++ + KD  T   +G+GF+ F      D  +K
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 95  IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI 154
             ++  L GK I   +A    +  D    IF+G + P+V  K   + FS +G I      
Sbjct: 64  TQHI--LDGKVIDPKRAIPRDEQ-DKTGKIFVGGIGPDVRPKEFEEFFSQWGTI------ 114
Query: 155 MNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEA 214
                                            +D ++M D DTG S+GF F+ Y S +A
Sbjct: 115 ---------------------------------IDAQLMLDKDTGQSRGFGFVTYDSADA 141
Query: 215 SD 216
            D
Sbjct: 142 VD 143

>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 = 62.0 bits (149), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 53/200 (26%), Positives = 89/200 (44%), Gaps = 42/200 (21%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVG +  ++ E  + + F   GP+ ++    D VT  H+G+ F+E+   E A  A++  
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN 156
           N + L G+ I+V + S+            IG   P +D+  L +   AF           
Sbjct: 75  NSVXLGGRNIKVGRPSN------------IGQAQPIIDQ--LAEEARAFN---------- 110
Query: 157 MIKLYGKPIRVNKASSHQK-NLDVGANIF--IGNLDP-EIMRDPDTGNSKGFAFINYASF 212
                    R+  AS HQ  + D   ++F   G +    + RDP TG  KG+ FI Y   
Sbjct: 111 ---------RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKA 161
Query: 213 EASDASIDA-----MHGQYL 227
           ++S  ++ +     + GQYL
Sbjct: 162 QSSQDAVSSXNLFDLGGQYL 181

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 60.1 bits (144), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 48/207 (23%), Positives = 88/207 (42%), Gaps = 42/207 (20%)
Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           G   + V  L   +++  +  LF   G V +  + +D+V     GYGF+ ++  +DA+ A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 93  IKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
           I  +N ++L  K I+V+ A    + +   AN++I  L   + +K + D FS FG I+ + 
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVIK-DANLYISGLPRTMTQKDVEDMFSRFGRIINS- 118
Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
                                                  ++ D  TG S+G AFI +   
Sbjct: 119 --------------------------------------RVLVDQTTGLSRGVAFIRFDKR 140
Query: 213 EASDASIDAMHGQYL--CNRPISVSYA 237
             ++ +I + +G      + PI+V +A
Sbjct: 141 SEAEEAITSFNGHKPPGSSEPITVKFA 167

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 48/207 (23%), Positives = 88/207 (42%), Gaps = 42/207 (20%)
Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           G   + V  L   +++  +  LF   G V +  + +D+V     GYGF+ ++  +DA+ A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 93  IKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
           I  +N ++L  K I+V+ A    + +   AN++I  L   + +K + D FS FG I+ + 
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVIK-DANLYISGLPRTMTQKDVEDMFSRFGRIINS- 118
Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
                                                  ++ D  TG S+G AFI +   
Sbjct: 119 --------------------------------------RVLVDQTTGLSRGVAFIRFDKR 140
Query: 213 EASDASIDAMHGQYL--CNRPISVSYA 237
             ++ +I + +G      + PI+V +A
Sbjct: 141 SEAEEAITSFNGHKPPGSSEPITVXFA 167

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 58.2 bits (139), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 44/190 (23%), Positives = 80/190 (42%), Gaps = 40/190 (21%)
Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           +  + V  L   +++  ++ LF   GP+    + +D  T    GY F++F  E D+  AI
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           K++N I +  K ++V+ A    +++    N+++ NL   + +  L   F  +G I+    
Sbjct: 63  KVLNGITVRNKRLKVSYARPGGESIK-DTNLYVTNLPRTITDDQLDTIFGKYGSIV---- 117
Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                               QKN               I+RD  TG  +G AF+ Y   E
Sbjct: 118 --------------------QKN---------------ILRDKLTGRPRGVAFVRYNKRE 142
Query: 214 ASDASIDAMH 223
            +  +I A++
Sbjct: 143 EAQEAISALN 152

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 57.8 bits (138), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 39/156 (25%), Positives = 74/156 (47%), Gaps = 8/156 (5%)
Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           +  + V  L    ++  ++ LF   GP+    + +D  T    GY F++F  E D+  AI
Sbjct: 14  NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI 73
Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           K++N I +  K ++V+ A    +++    N+++ NL   + +  L   F  +G I+Q   
Sbjct: 74  KVLNGITVRNKRLKVSYARPGGESIK-DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 154 IMNMIKLYGKP-----IRVNKASSHQKNLDVGANIF 184
           + +  KL G+P     +R NK    Q+ +    N+ 
Sbjct: 133 LRD--KLTGRPRGVAFVRYNKREEAQEAISALNNVI 166

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D    +++GGL+ + +E ++  +F + GP+  V + KDR +++ +G+ FI F    DA  
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKS-RGFAFITFENPADAKN 63
Query: 92  AIKIMNMIKLYGKPIRVNKA 111
           A K MN   L+GK I+V +A
Sbjct: 64  AAKDMNGKSLHGKAIKVEQA 83

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 47/208 (22%), Positives = 84/208 (40%), Gaps = 42/208 (20%)
Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D    + V  L   +++     LF   G + +  + +D++T    GYGF+ +    DAD 
Sbjct: 2   DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 92  AIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQT 151
           AI  +N +KL  K I+V+ A     ++   AN+++  L   + +K +   FS +G I+ +
Sbjct: 62  AINTLNGLKLQTKTIKVSYARPSSASIR-DANLYVSGLPKTMSQKEMEQLFSQYGRIITS 120
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
                                                   I+ D  TG S+G  FI +  
Sbjct: 121 ---------------------------------------RILLDQATGVSRGVGFIRFDK 141
Query: 212 FEASDASIDAMHGQYLCN--RPISVSYA 237
              ++ +I  ++GQ       PI+V +A
Sbjct: 142 RIEAEEAIKGLNGQKPLGAAEPITVKFA 169

>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 = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 55/94 (58%), Gaps = 5/94 (5%)
Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           +++VG +  + +E  + ++F + GPVV+  +  DR T   +GYGF E+  +E A  A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 96  MNMIKLYGKPIRVNKASSHQ-----KNLDVGANI 124
           +N  +  G+ +RV+ A+S +     K+L  GA +
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKSLGTGAPV 103

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 45/203 (22%), Positives = 85/203 (41%), Gaps = 42/203 (20%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           + V  L   +++     LF   G + +  + +D++T    GYGF+ ++  +DA+ AI  +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN 156
           N ++L  K I+V+ A     ++   AN+++  L   + +K L   FS +G I+ +     
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIR-DANLYVSGLPKTMTQKELEQLFSQYGRIITS----- 118
Query: 157 MIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASD 216
                                              I+ D  TG S+G  FI +     ++
Sbjct: 119 ----------------------------------RILVDQVTGVSRGVGFIRFDKRIEAE 144
Query: 217 ASIDAMHGQYL--CNRPISVSYA 237
            +I  ++GQ       PI+V +A
Sbjct: 145 EAIKGLNGQKPSGATEPITVKFA 167

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 54.3 bits (129), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 47/84 (55%)
Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           +  ++VGGL    +E  + ++F + G +  V + KDR TQ  +G+GF+ F   +DA  A+
Sbjct: 12  EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 94  KIMNMIKLYGKPIRVNKASSHQKN 117
             MN   + G+ IRV++A     N
Sbjct: 72  MAMNGKSVDGRQIRVDQAGKSSDN 95

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 50/90 (55%), Gaps = 3/90 (3%)
Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           G + +YVG L   ++E ++  +F   G + N+ + KD  T   +GYGFI F   E A  A
Sbjct: 4   GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 93  IKIMNMIKLYGKPIRVNKASSHQKNLDVGA 122
           ++ +N  +L G+P+RV   +   + LD G+
Sbjct: 64  LEQLNGFELAGRPMRVGHVT---ERLDGGS 90

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 31/49 (63%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
           +M+D DTG SKG+ FI ++  E +  +++ ++G  L  RP+ V +  ++
Sbjct: 37  LMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTER 85

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 51/209 (24%), Positives = 85/209 (40%), Gaps = 48/209 (22%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ--GYGFIEFMGEE---DADY 91
           ++VG +    SE  + ELF Q G V  +++ +DR     Q  G  F+ F   +   +A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 92  AIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQT 151
           A+  M ++     PI++  A S + N      +FIG +  +  E  +   FS+FG I + 
Sbjct: 66  ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 125
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
                                                   I+R PD G S+G AF+ + +
Sbjct: 126 ---------------------------------------RILRGPD-GLSRGCAFVTFTT 145
Query: 212 FEASDASIDAMH-GQYL--CNRPISVSYA 237
              +  +I AMH  Q +  C+ P+ V +A
Sbjct: 146 RAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>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 = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 51/209 (24%), Positives = 85/209 (40%), Gaps = 48/209 (22%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ--GYGFIEFMGEE---DADY 91
           ++VG +    SE  + ELF Q G V  +++ +DR     Q  G  F+ F   +   +A  
Sbjct: 18  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 92  AIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQT 151
           A+  M ++     PI++  A S + N      +FIG +  +  E  +   FS+FG I + 
Sbjct: 78  ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 137
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
                                                   I+R PD G S+G AF+ + +
Sbjct: 138 ---------------------------------------RILRGPD-GLSRGCAFVTFTT 157
Query: 212 FEASDASIDAMH-GQYL--CNRPISVSYA 237
              +  +I AMH  Q +  C+ P+ V +A
Sbjct: 158 RAMAQTAIKAMHQAQTMEGCSSPMVVKFA 186

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 51.6 bits (122), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 44/75 (58%)
Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
            T+YVG L    +E  ++ELF +SG +  + M  D++ +T  G+ F+E+    DA+ A++
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 95  IMNMIKLYGKPIRVN 109
            +N  +L  + IR +
Sbjct: 100 YINGTRLDDRIIRTD 114

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 33/112 (29%), Positives = 47/112 (41%), Gaps = 41/112 (36%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           NIFI NLD  +D K LYDTFSAFG IL    +                            
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--------------------------- 39
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
                         D   SKG+ F+++ + EA++ +I+ M+G  L +R + V
Sbjct: 40  --------------DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 77

>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of Nucleolysin Tiar Length = 103

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+YVG L   V+E L+ +LF Q GP  +  M  +  +  +  Y F+EF    DA  A+  
Sbjct: 17  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAA 74
Query: 96  MNMIKLYGKPIRVNKASS 113
           MN  K+ GK ++VN A++
Sbjct: 75  MNGRKILGKEVKVNWATT 92

>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 = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           IYVG L    +   + ELF Q G V NV +  DR T+  +G+GF+E M EE    AI  +
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKL 62
Query: 97  NMIKLYGKPIRVNKAS 112
           +     G+ IRV +A+
Sbjct: 63  DNTDFMGRTIRVTEAN 78

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 48.9 bits (115), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 33/113 (29%), Positives = 47/113 (41%), Gaps = 41/113 (36%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
            NIFI NLD  +D K LYDTFSAFG IL    +                           
Sbjct: 12  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC-------------------------- 45
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
                          D   SKG+ F+++ + EA++ +I+ M+G  L +R + V
Sbjct: 46  ---------------DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 83

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DA +YV GL   +S+  M +LF Q G ++   +  D+ T   +G GFI F    +A+ AI
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 94  KIMNMIKLYG--KPIRVNKASS 113
           K +N  K  G  +PI V  A++
Sbjct: 61  KGLNGQKPLGAAEPITVKFANN 82

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 34/62 (54%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
          D +ATI V  L +   ET + ELF   G +  +++ KD+ T   +G+ FI F   EDA  
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
Query: 92 AI 93
          AI
Sbjct: 73 AI 74

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 43/80 (53%)
Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           G   +YVG L   ++E ++  +F   G + ++ +  D  T   +GYGFI F   E A  A
Sbjct: 25  GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 93  IKIMNMIKLYGKPIRVNKAS 112
           ++ +N  +L G+P++V   +
Sbjct: 85  LEQLNGFELAGRPMKVGHVT 104

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/92 (25%), Positives = 47/92 (51%), Gaps = 10/92 (10%)
Query: 156 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDP-------EIMRDPDTGNSKGFAFIN 208
           N+ K    P+R+   S H    ++  ++  G  +P       ++M D +TG SKG+ FI 
Sbjct: 18  NLQKGSAGPMRLYVGSLH---FNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74
Query: 209 YASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
           ++  E +  +++ ++G  L  RP+ V +  ++
Sbjct: 75  FSDSECAKKALEQLNGFELAGRPMKVGHVTER 106

>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 = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 40/185 (21%), Positives = 77/185 (41%), Gaps = 45/185 (24%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL  + ++  +   F Q G + +  + +D  T+  +G+GF+ +   E+ D A+   
Sbjct: 17  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
              K+ G+ +   +A S + +   GA+     IF+G +  + +E  L D F  +G I   
Sbjct: 77  PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 132
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
                +I                                EIM D  +G  +GFAF+ +  
Sbjct: 133 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 156
Query: 212 FEASD 216
            ++ D
Sbjct: 157 HDSVD 161

>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 = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
           D  +MRDP+T  S+GF F+ YA+ E  DA+++A
Sbjct: 43  DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 49/208 (23%), Positives = 78/208 (37%), Gaps = 48/208 (23%)
Query: 38  YVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYG--FIEFMGEEDADYAIKI 95
           +VG +    SE  + ELF Q G V  +++ +DR     Q  G  F+ F   + A  A   
Sbjct: 7   FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 96  MNMIKLY---GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
           ++  K+      PI+   A S + N      +FIG +  +  E  +   FS+FG I +  
Sbjct: 67  LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEEC- 125
Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
                                                  I+R PD G S+G AF+ + + 
Sbjct: 126 --------------------------------------RILRGPD-GLSRGCAFVTFTTR 146
Query: 213 EASDASIDAMHGQYL---CNRPISVSYA 237
             +  +I A H       C+ P  V +A
Sbjct: 147 AXAQTAIKAXHQAQTXEGCSSPXVVKFA 174

>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 = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 40/185 (21%), Positives = 77/185 (41%), Gaps = 45/185 (24%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL  + ++  +   F Q G + +  + +D  T+  +G+GF+ +   E+ D A+   
Sbjct: 15  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
              K+ G+ +   +A S + +   GA+     IF+G +  + +E  L D F  +G I   
Sbjct: 75  PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 130
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
                +I                                EIM D  +G  +GFAF+ +  
Sbjct: 131 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 154
Query: 212 FEASD 216
            ++ D
Sbjct: 155 HDSVD 159

>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 = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
           D  +MRDP+T  S+GF F+ YA+ E  DA+++A
Sbjct: 41  DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 40/185 (21%), Positives = 77/185 (41%), Gaps = 45/185 (24%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL  + ++  +   F Q G + +  + +D  T+  +G+GF+ +   E+ D A+   
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
              K+ G+ +   +A S + +   GA+     IF+G +  + +E  L D F  +G I   
Sbjct: 76  PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 131
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
                +I                                EIM D  +G  +GFAF+ +  
Sbjct: 132 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 155
Query: 212 FEASD 216
            ++ D
Sbjct: 156 HDSVD 160

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
           D  +MRDP+T  S+GF F+ YA+ E  DA+++A
Sbjct: 42  DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 45/80 (56%)
Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           +G  ++ V  L  + S   +  +F + G V +V++P+DR T+  +G+ F+ F  + DA+ 
Sbjct: 45  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104
Query: 92  AIKIMNMIKLYGKPIRVNKA 111
           A+  M+   L G+ +RV  A
Sbjct: 105 AMDAMDGAVLDGRELRVQMA 124

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 34/125 (27%), Positives = 56/125 (44%), Gaps = 13/125 (10%)
Query: 24  LEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEF 83
           L+ G ++      ++VG L   ++E     LF + G    V + +DR      G+GFI  
Sbjct: 12  LKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRL 65
Query: 84  MGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFS 143
                A+ A   ++   L  +P+R+  A+        GA + + NL P V  +LL   FS
Sbjct: 66  ESRTLAEIAKAELDGTILKSRPLRIRFATH-------GAALTVKNLSPVVSNELLEQAFS 118
Query: 144 AFGVI 148
            FG +
Sbjct: 119 QFGPV 123

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 40/188 (21%), Positives = 78/188 (41%), Gaps = 45/188 (23%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL  + ++  +   F Q G + +  + +D  T+  +G+GF+ +   E+ D A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
              K+ G+ +   +A S + +   GA+     IF+G +  + +E  L D F  +G I   
Sbjct: 69  PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 124
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
                +I                                EIM D  +G  +GFAF+ +  
Sbjct: 125 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 148
Query: 212 FEASDASI 219
            ++ D  +
Sbjct: 149 HDSVDKIV 156

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
           D  +MRDP+T  S+GF F+ YA+ E  DA+++A
Sbjct: 35  DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 45/80 (56%)
Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           +G  ++ V  L  + S   +  +F + G V +V++P+DR T+  +G+ F+ F  + DA+ 
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 92  AIKIMNMIKLYGKPIRVNKA 111
           A+  M+   L G+ +RV  A
Sbjct: 128 AMDAMDGAVLDGRELRVQMA 147

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 40/188 (21%), Positives = 78/188 (41%), Gaps = 45/188 (23%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL  + ++  +   F Q G + +  + +D  T+  +G+GF+ +   E+ D A+   
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
              K+ G+ +   +A S + +   GA+     IF+G +  + +E  L D F  +G I   
Sbjct: 76  PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 131
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
                +I                                EIM D  +G  +GFAF+ +  
Sbjct: 132 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 155
Query: 212 FEASDASI 219
            ++ D  +
Sbjct: 156 HDSVDKIV 163

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
           D  +MRDP+T  S+GF F+ YA+ E  DA+++A
Sbjct: 42  DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 40/188 (21%), Positives = 78/188 (41%), Gaps = 45/188 (23%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL  + ++  +   F Q G + +  + +D  T+  +G+GF+ +   E+ D A+   
Sbjct: 14  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
              K+ G+ +   +A S + +   GA+     IF+G +  + +E  L D F  +G I   
Sbjct: 74  PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 129
Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
                +I                                EIM D  +G  +GFAF+ +  
Sbjct: 130 ----EVI--------------------------------EIMTDRGSGKKRGFAFVTFDD 153
Query: 212 FEASDASI 219
            ++ D  +
Sbjct: 154 HDSVDKIV 161

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
           D  +MRDP+T  S+GF F+ YA+ E  DA+++A
Sbjct: 40  DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 44/81 (54%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL + +++  + EL    GP+   ++ KD  T   +GY F E++     D AI  +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 97  NMIKLYGKPIRVNKASSHQKN 117
           N ++L  K + V +AS   KN
Sbjct: 64  NGMQLGDKKLLVQRASVGAKN 84

>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 = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 43/81 (53%)
Query: 31  GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
           G G   + V  L   +++  +  LF   G V +  + +D+V     GYGF+ ++  +DA+
Sbjct: 1   GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 91  YAIKIMNMIKLYGKPIRVNKA 111
            AI  +N ++L  K I+V+ A
Sbjct: 61  RAINTLNGLRLQSKTIKVSYA 81

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           + V  +   V E  + +LF + GP+ +V +  DR T+  +GYGF++F     A  AI  +
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 97  NMIKLYGKPIRVNKASS-HQKNLDVGA 122
           N   +  K ++V  A+S HQ+    GA
Sbjct: 105 NGFNILNKRLKVALAASGHQRPGIAGA 131

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 45/86 (52%)
Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D    +++GGL + +++  + EL    GP+   ++ KD  T   +GY F E++     D 
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 92  AIKIMNMIKLYGKPIRVNKASSHQKN 117
           AI  +N ++L  K + V +AS   KN
Sbjct: 172 AIAGLNGMQLGDKKLLVQRASVGAKN 197

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 40/76 (52%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L  +++   +   F   G + +  + KD  T   +GYGF+ F  + DA+ AI+ M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 97  NMIKLYGKPIRVNKAS 112
               L G+ IR N A+
Sbjct: 78  GGQWLGGRQIRTNWAT 93

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 28/130 (21%), Positives = 54/130 (41%), Gaps = 39/130 (30%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
           +S  +K+     ++F+G+L PE+  + +   F+ FG I                      
Sbjct: 5   SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRIS--------------------- 43
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
                             D  +++D  TG SKG+ F+++ +   ++ +I  M GQ+L  R
Sbjct: 44  ------------------DARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGR 85
Query: 231 PISVSYAFKK 240
            I  ++A +K
Sbjct: 86  QIRTNWATRK 95

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++VGG+D ++ ET +   F + G V  V +  DR T   +GYGF+ F    D D    +
Sbjct: 12  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY--NDVDVQKIV 68
Query: 96  MNMIKLYGKPIRVNKASSHQ 115
            + I  +GK +++  A   Q
Sbjct: 69  ESQINFHGKKLKLGPAIRKQ 88

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+YVG L    +E  ++ELF +SG +  + M  D++ +T  G+ F+E+    DA+ A++ 
Sbjct: 20  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYSRADAENAMRY 78
Query: 96  MNMIKLYGKPIRVN 109
           +N  +L  + IR +
Sbjct: 79  INGTRLDDRIIRTD 92

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++VGG+D ++ ET +   F + G V  V +  DR T   +GYGF+ F    D D    +
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY--NDVDVQKIV 67
Query: 96  MNMIKLYGKPIRVNKASSHQ 115
            + I  +GK +++  A   Q
Sbjct: 68  ESQINFHGKKLKLGPAIRKQ 87

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VGG+     ET + E F + G V  V M  D   Q  +G+GFI F  E+  D A+  M
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 97  NMIKLYGKPIRVNKA 111
           +   + GK + V +A
Sbjct: 72  HFHDIMGKKVEVKRA 86

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 40/80 (50%)
Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D    + V  L   +++     LF   G + +  + +D++T    GYGF+ +    DAD 
Sbjct: 2   DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 92  AIKIMNMIKLYGKPIRVNKA 111
           AI  +N +KL  K I+V+ A
Sbjct: 62  AINTLNGLKLQTKTIKVSYA 81

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 3/80 (3%)
Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++VGG+D ++ ET +   F + G V  V +  DR T   +GYGF+ F  + D    ++ 
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE- 68
Query: 96  MNMIKLYGKPIRVNKASSHQ 115
            + I  +GK +++  A   Q
Sbjct: 69  -SQINFHGKKLKLGPAIRKQ 87

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 41/76 (53%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L+  V +  +   F      ++ H+  D  T + +GYGF+ F  ++DA  A+  M
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 97  NMIKLYGKPIRVNKAS 112
               L G+P+R+N A+
Sbjct: 64  QGQDLNGRPLRINWAA 79

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 35/56 (62%)
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
           F   L   +M D  TG+S+G+ F+++ S + +  ++D+M GQ L  RP+ +++A K
Sbjct: 25  FPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 80

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 49/94 (52%), Gaps = 3/94 (3%)
Query: 28  GESG---DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
           G SG   DG  T+ V  L  + S   +  +F + G V +V++P++  T+  +G+ F+ F 
Sbjct: 4   GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63
Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNL 118
              DA  A   M+  +L G+ +RV  A   +++L
Sbjct: 64  DRRDAQDAEAAMDGAELDGRELRVQVARYGRRDL 97

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 36/130 (27%), Positives = 61/130 (46%), Gaps = 16/130 (12%)
Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           + ++VG L   ++E  M +LF + G    V + KD+      G+GFI       A+ A  
Sbjct: 23  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKV 76
Query: 95  IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI 154
            ++ + L GK +RV  A          A++ + NL   V  +LL + FS FG   Q  + 
Sbjct: 77  ELDNMPLRGKQLRVRFACH-------SASLTVRNLPQYVSNELLEEAFSVFG---QVERA 126
Query: 155 MNMIKLYGKP 164
           + ++   G+P
Sbjct: 127 VVIVDDRGRP 136

>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 = 44.3 bits (103), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 22/77 (28%), Positives = 44/77 (57%)
Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           +T+YV  L   ++   ++ +F + G VV V + KD+ T+  +G  FI F+ ++ A    +
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 95  IMNMIKLYGKPIRVNKA 111
            +N  +L+G+ I+ + A
Sbjct: 77  AINNKQLFGRVIKASIA 93

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++V G+ ++ +E  + + F + G + N+H+  DR T   +GY  +E+   ++A  A++ +
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 97  NMIKLYGKPIRVN 109
           N   L G+PI V+
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++V G+ ++ +E  + + F + G + N+H+  DR T   +GY  +E+   ++A  A++ +
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 97  NMIKLYGKPIRVN 109
           N   L G+PI V+
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++V G+ ++ +E  + + F + G + N+H+  DR T   +GY  +E+   ++A  A++ +
Sbjct: 12  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 97  NMIKLYGKPIRVN 109
           N   L G+PI V+
Sbjct: 72  NGQDLMGQPISVD 84

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 43/80 (53%)
Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           G   +++GGL + +++  + EL    GP+   ++ KD  T   +GY F E++     D A
Sbjct: 95  GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 154
Query: 93  IKIMNMIKLYGKPIRVNKAS 112
           I  +N ++L  K + V +AS
Sbjct: 155 IAGLNGMQLGDKKLLVQRAS 174

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 43/80 (53%)
Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           G   +++GGL + +++  + EL    GP+   ++ KD  T   +GY F E++     D A
Sbjct: 93  GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152
Query: 93  IKIMNMIKLYGKPIRVNKAS 112
           I  +N ++L  K + V +AS
Sbjct: 153 IAGLNGMQLGDKKLLVQRAS 172

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 39/76 (51%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG L  +++   +   F   G + +  + KD  T   +GYGF+ F  + DA+ AI  M
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 97  NMIKLYGKPIRVNKAS 112
               L G+ IR N A+
Sbjct: 78  GGQWLGGRQIRTNWAT 93

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++V GL +  +E  + E F  S   V   +  DR T + +G+GF++F  EEDA  A + 
Sbjct: 17  TLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 96  MNMIKLYGKPIRVNKA 111
           M   ++ G  + ++ A
Sbjct: 74  MEDGEIDGNKVTLDWA 89

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 41/78 (52%)
Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           +  + V  L   +++  ++ LF   GP+    + +D  T    GY F++F  E D+  AI
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 94  KIMNMIKLYGKPIRVNKA 111
           K++N I +  K ++V+ A
Sbjct: 63  KVLNGITVRNKRLKVSYA 80

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 44/78 (56%)
Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D +  + V GL    +E  + E+F + GP+ +V +  D+ ++  +G+ F+ F   +DA  
Sbjct: 44  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 92  AIKIMNMIKLYGKPIRVN 109
           A +  N ++L G+ IRV+
Sbjct: 104 AKERANGMELDGRRIRVD 121

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 35/61 (57%)
Query: 51  MWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK 110
           +  LF   G V +  + +D+V     GYGF+ ++  +DA+ AI  +N ++L  K I+V+ 
Sbjct: 36  LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 95
Query: 111 A 111
           A
Sbjct: 96  A 96

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 3/74 (4%)
Query: 172 SHQKNLDVGANIF-IGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
           + ++ LD+ +N+  + NL  ++M DP TG SKG+AFI +   E+S +++  ++G  L +R
Sbjct: 15  TEEQILDLCSNVGPVINL--KMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 72
Query: 231 PISVSYAFKKDSKG 244
            +   Y+   D  G
Sbjct: 73  FLKCGYSSNSDISG 86

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++V G+ ++ +E  + + F + G + N+H+  DR T   +GY  +E+   ++A  A++ +
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 97  NMIKLYGKPIRVN 109
           N   L G+PI V+
Sbjct: 85  NGQDLMGQPISVD 97

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/88 (29%), Positives = 48/88 (54%)
Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G   + D +  + V GL    +E  + E+F + GP+ +V +  D+ ++  +G+ F+ F  
Sbjct: 7   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASS 113
            +DA  A +  N ++L G+ IRV+  SS
Sbjct: 67  VDDAKEAKERANGMELDGRRIRVSGPSS 94

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++V G+ ++ +E  + + F + G + N+H+  DR T   +GY  +E+   ++A  A++ +
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 97  NMIKLYGKPIRVN 109
           N   L G+PI V+
Sbjct: 86  NGQDLMGQPISVD 98

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 3/74 (4%)
Query: 172 SHQKNLDVGANIF-IGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
           + ++ LD+ +N+  + NL  ++M DP TG SKG+AFI +   E+S +++  ++G  L +R
Sbjct: 16  TEEQILDLCSNVGPVINL--KMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 73
Query: 231 PISVSYAFKKDSKG 244
            +   Y+   D  G
Sbjct: 74  FLKCGYSSNSDISG 87

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 26/121 (21%), Positives = 49/121 (40%), Gaps = 41/121 (33%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           N+++ NLD  +D++ L   FS FG I     +M                           
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--------------------------- 49
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
                         + G SKGF F+ ++S E +  ++  M+G+ +  +P+ V+ A +K+ 
Sbjct: 50  --------------EGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE 95
Query: 243 K 243
           +
Sbjct: 96  R 96

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++V G+ ++ +E  + + F + G + N+H+  DR T   +GY  +E+   ++A  A++ +
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 97  NMIKLYGKPIRVN 109
           N   L G+PI V+
Sbjct: 70  NGQDLMGQPISVD 82

>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 = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 41/78 (52%)
Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +Y+G +    +E  + +L    GPV+N+ M  D  T   +GY FIEF   E +  A++ 
Sbjct: 6   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 96  MNMIKLYGKPIRVNKASS 113
           +N  +L  + ++   +S+
Sbjct: 66  LNGYQLGSRFLKCGYSSN 83

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 24/84 (28%), Positives = 46/84 (54%)
Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G   + D +  + V GL    +E  + E+F + GP+ +V +  D+ ++  +G+ F+ F  
Sbjct: 4   GSRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
Query: 86  EEDADYAIKIMNMIKLYGKPIRVN 109
            +DA  A +  N ++L G+ IRV+
Sbjct: 64  VDDAKEAKERANGMELDGRRIRVD 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	305
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-83
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-80
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-71
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-24
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-22
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-71
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-19
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-14
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-70
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-20
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-67
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-16
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-61
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	8e-23
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-59
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-16
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-59
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-49
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-57
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-18
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-48
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-17
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-48
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-24
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-48
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-44
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-16
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-44
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-20
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	5e-39
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-17
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-38
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-16
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-37
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	7e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	8e-37
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-18
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-36
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-14
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-33
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-21
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-31
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-14
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-31
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-21
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-30
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-26
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	6e-17
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-26
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-19
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	7e-25
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	9e-15
2div_A	99	TRNA selenocysteine associated protein; structural	7e-25
2div_A	99	TRNA selenocysteine associated protein; structural	2e-20
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-24
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-15
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	9e-24
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-12
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-23
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-16
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-23
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-17
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-23
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	8e-15
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-23
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	8e-19
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-23
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	7e-23
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-13
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-22
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-18
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	6e-22
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	6e-11
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-21
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-17
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-21
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	9e-21
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-21
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-09
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-21
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	6e-14
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-21
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	4e-21
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	4e-17
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-21
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-15
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-21
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-20
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	7e-21
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-18
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	9e-21
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	7e-18
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-20
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-19
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-20
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	8e-16
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-20
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-18
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-20
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-14
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-20
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-16
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-19
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-19
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-19
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-17
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-19
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-14
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-19
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-15
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-19
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-13
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-19
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	8e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-19
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-16
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-19
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-17
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	8e-19
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-18
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-18
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	5e-16
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-18
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-18
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-12
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-18
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-13
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-18
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-17
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-18
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-14
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-18
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-14
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-18
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-18
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-15
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-18
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-15
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-18
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-17
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	7e-18
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-17
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-17
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	7e-14
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-17
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-12
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-17
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-14
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-17
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-16
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-17
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-17
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-16
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-17
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-14
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-17
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-12
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-17
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	5e-17
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-08
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-17
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-16
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-17
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-14
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-17
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	9e-17
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-14
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-16
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-16
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-06
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-16
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-14
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-16
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-16
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-16
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-15
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	4e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	5e-16
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-15
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	6e-16
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-16
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	8e-16
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-06
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	8e-16
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-08
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-15
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	6e-08
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-15
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	7e-12
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-15
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	7e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	8e-13
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-15
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-09
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-15
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-14
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-15
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	7e-15
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-04
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-15
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-14
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	7e-10
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-14
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	7e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-13
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-14
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-11
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	6e-14
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-11
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-14
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	8e-14
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-08
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-08
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-13
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	7e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-13
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-05
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	4e-13
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-12
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-13
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-12
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-13
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-06
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-13
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-07
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-12
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-12
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-12
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-12
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	7e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	4e-12
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-07
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	5e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	4e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	5e-12
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	5e-12
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-05
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	7e-12
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	5e-11
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	9e-12
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-10
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	9e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-11
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	6e-11
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	6e-11
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	7e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	7e-11
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-10
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	8e-10
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	8e-10
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-05
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	9e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	9e-09
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	4e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	5e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	8e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	9e-08
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-07
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	4e-07
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	5e-07
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	9e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	7e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-05
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	1e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	7e-04

>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 =  247 bits (634), Expect = 8e-83
 Identities = 63/230 (27%), Positives = 105/230 (45%), Gaps = 42/230 (18%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
              A++YVG L   V+E +++E F  +GP++++ + +D +T+   GY ++ F    DA+ 
Sbjct: 13  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72

Query: 92  AIKIMNMIKLYGKPIRVNKASSHQKNLDVG-ANIFIGNLDPEVDEKLLYDTFSAFGVILQ 150
           A+  MN   + GKP+R+  +         G  NIFI NLD  +D K LYDTFSAFG IL 
Sbjct: 73  ALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 132

Query: 151 TPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYA 210
             K++                                         D   SKG+ F+++ 
Sbjct: 133 -CKVV----------------------------------------CDENGSKGYGFVHFE 151

Query: 211 SFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNP 260
           + EA++ +I+ M+G  L +R + V     +  +    G+ A+       P
Sbjct: 152 TQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVP 201

>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 =  240 bits (615), Expect = 1e-80
 Identities = 50/205 (24%), Positives = 96/205 (46%), Gaps = 41/205 (20%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +YVG LD  ++E ++ + F   GP+ N+ +  D+    +  Y F+E+    DA+ A++ 
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT 60

Query: 96  MNMIKLYGKPIRVNKAS-SHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI 154
           +N  ++    +++N A  S Q + D   N+F+G+L+  VD++ L + F  F         
Sbjct: 61  LNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSY------ 114

Query: 155 MNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEA 214
                                            L   +M D  TG+S+G+ F+++ S + 
Sbjct: 115 ---------------------------------LSGHVMWDMQTGSSRGYGFVSFTSQDD 141

Query: 215 SDASIDAMHGQYLCNRPISVSYAFK 239
           +  ++D+M GQ L  RP+ +++A K
Sbjct: 142 AQNAMDSMQGQDLNGRPLRINWAAK 166

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 79.5 bits (197), Expect = 3e-18
 Identities = 29/108 (26%), Positives = 51/108 (47%), Gaps = 11/108 (10%)

Query: 16  LQSLSQTKLEG-----------GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNV 64
           LQ+L+  ++E               S D    ++VG L+  V +  +   F      ++ 
Sbjct: 58  LQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSG 117

Query: 65  HMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS 112
           H+  D  T + +GYGF+ F  ++DA  A+  M    L G+P+R+N A+
Sbjct: 118 HVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165

>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 = 68.3 bits (168), Expect = 3e-14
 Identities = 22/120 (18%), Positives = 44/120 (36%), Gaps = 40/120 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++GNLD  + E +L   F   G I                                ANI
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPI--------------------------------ANI 30

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                  +IM D     +  +AF+ Y     ++ ++  ++G+ + N  + +++AF+    
Sbjct: 31  -------KIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQS 82

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  219 bits (560), Expect = 1e-71
 Identities = 46/231 (19%), Positives = 88/231 (38%), Gaps = 49/231 (21%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
            +    + +YVG +  ++ E  + + F   GP+ ++ M  D VT  H+G+ F+E+   E 
Sbjct: 23  GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA 82

Query: 89  ADYAIKIMNMIKLYGKPIRVNKASSHQ----------KNLDVGANIFIGNLDPEVDEKLL 138
           A  A++ MN + L G+ I+V + S+            +       I++ ++  ++ +  +
Sbjct: 83  AQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 142

Query: 139 YDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT 198
              F AFG I                                           + RDP T
Sbjct: 143 KSVFEAFGKI---------------------------------------KSATLARDPTT 163

Query: 199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGS 249
           G  KG+ FI Y   ++S  ++ +M+   L  + + V  A           +
Sbjct: 164 GKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPAT 214

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 97.4 bits (243), Expect = 2e-24
 Identities = 28/151 (18%), Positives = 49/151 (32%), Gaps = 39/151 (25%)

Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
           G+ +    A+  Q  L + + +++G++  E+ E  +   F+ FG I              
Sbjct: 10  GQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIK------------- 56

Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
                                       ++  D  T   KGFAF+ Y   EA+  +++ M
Sbjct: 57  --------------------------SIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90

Query: 223 HGQYLCNRPISVSYAFKKDSKGDRHGSAAER 253
           +   L  R I V                AE 
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEE 121

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 92.0 bits (229), Expect = 2e-22
 Identities = 31/108 (28%), Positives = 53/108 (49%), Gaps = 2/108 (1%)

Query: 4   GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN 63
           GR I+ G  +   Q+  Q  ++   E       IYV  +   +S+  +  +F   G + +
Sbjct: 97  GRNIKVGRPSNIGQA--QPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKS 154

Query: 64  VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
             + +D  T  H+GYGFIE+   + +  A+  MN+  L G+ +RV KA
Sbjct: 155 ATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202

>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 =  215 bits (550), Expect = 8e-71
 Identities = 45/205 (21%), Positives = 85/205 (41%), Gaps = 42/205 (20%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
             + V  L   +++     LF   G + +  + +D++T    GYGF+ ++  +DA+ AI 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 95  IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI 154
            +N ++L  K I+V+ A     ++   AN+++  L   + +K L   FS +G I+ +   
Sbjct: 63  TLNGLRLQTKTIKVSYARPSSASIR-DANLYVSGLPKTMTQKELEQLFSQYGRIITS--- 118

Query: 155 MNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEA 214
                                                I+ D  TG S+G  FI +     
Sbjct: 119 ------------------------------------RILVDQVTGVSRGVGFIRFDKRIE 142

Query: 215 SDASIDAMHGQYL--CNRPISVSYA 237
           ++ +I  ++GQ       PI+V +A
Sbjct: 143 AEEAIKGLNGQKPSGATEPITVKFA 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 = 81.5 bits (202), Expect = 5e-19
 Identities = 22/124 (17%), Positives = 42/124 (33%), Gaps = 39/124 (31%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
            N+ +  L   + ++     F + G I                                 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESC------------------------------ 32

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                    +++RD  TG S G+ F+NY   + ++ +I+ ++G  L  + I VSYA    
Sbjct: 33  ---------KLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSS 83

Query: 242 SKGD 245
           +   
Sbjct: 84  ASIR 87

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 69.5 bits (171), Expect = 1e-14
 Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 2/85 (2%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
            +   DA +YV GL   +++  + +LF Q G ++   +  D+VT   +G GFI F    +
Sbjct: 83  SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIE 142

Query: 89  ADYAIKIMN--MIKLYGKPIRVNKA 111
           A+ AIK +N        +PI V  A
Sbjct: 143 AEEAIKGLNGQKPSGATEPITVKFA 167

>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 =  214 bits (547), Expect = 3e-70
 Identities = 46/207 (22%), Positives = 85/207 (41%), Gaps = 42/207 (20%)

Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
            +  + V  L   +++  ++ LF   GP+    + +D  T    GY F++F  E D+  A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 93  IKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
           IK++N I +  K ++V+ A    +++    N+++ NL   + +  L   F  +G I+Q  
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIK-DTNLYVTNLPRTITDDQLDTIFGKYGSIVQK- 119

Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
                                                  I+RD  TG  +G AF+ Y   
Sbjct: 120 --------------------------------------NILRDKLTGRPRGVAFVRYNKR 141

Query: 213 EASDASIDAMHGQYL--CNRPISVSYA 237
           E +  +I A++       ++P+SV  A
Sbjct: 142 EEAQEAISALNNVIPEGGSQPLSVRLA 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 = 85.7 bits (213), Expect = 1e-20
 Identities = 27/127 (21%), Positives = 43/127 (33%), Gaps = 39/127 (30%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
             N+ +  L  ++ ++ LY  F A G I                                
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTC----------------------------- 33

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                      IMRD  TG S G+AF+++ S   S  +I  ++G  + N+ + VSYA   
Sbjct: 34  ----------RIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG 83

Query: 241 DSKGDRH 247
                  
Sbjct: 84  GESIKDT 90

>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 =  210 bits (537), Expect = 1e-67
 Identities = 47/247 (19%), Positives = 83/247 (33%), Gaps = 55/247 (22%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           G ++      ++VG L   ++E     LF + G    V + +DR      G+GFI     
Sbjct: 15  GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESR 68

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFG 146
             A+ A   ++   L  +P+R+  A+        GA + + NL P V  +LL   FS FG
Sbjct: 69  TLAEIAKAELDGTILKSRPLRIRFATH-------GAALTVKNLSPVVSNELLEQAFSQFG 121

Query: 147 VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAF 206
            +                                           ++ D D G + G  F
Sbjct: 122 PV---------------------------------------EKAVVVVD-DRGRATGKGF 141

Query: 207 INYASFEASDASIDAMH-GQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQAD 265
           + +A+   +  +++    G +L             +   D  G   E+L+       +  
Sbjct: 142 VEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDG-LPEKLMQKTQQYHKER 200

Query: 266 RPHQLFA 272
                FA
Sbjct: 201 EQPPRFA 207

>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 = 74.7 bits (184), Expect = 9e-16
 Identities = 24/138 (17%), Positives = 43/138 (31%), Gaps = 46/138 (33%)

Query: 103 GKPIRVNKASSH-QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLY 161
           G  I +       +K       +F+GNL  ++ E+     F  +G               
Sbjct: 3   GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEP------------- 49

Query: 162 GKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
                              + +FI        RD      +GF FI   S   ++ +   
Sbjct: 50  -------------------SEVFI-------NRD------RGFGFIRLESRTLAEIAKAE 77

Query: 222 MHGQYLCNRPISVSYAFK 239
           + G  L +RP+ + +A  
Sbjct: 78  LDGTILKSRPLRIRFATH 95

>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 =  190 bits (486), Expect = 5e-61
 Identities = 35/211 (16%), Positives = 75/211 (35%), Gaps = 46/211 (21%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMP-----KDRVTQTHQGYGFIEFMGE 86
                +YVG +   ++E  M + F     +  +                + + F+EF   
Sbjct: 2   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFG 146
           ++   A+   + I   G+ +++ +   +Q  L     +FIG L   +++  + +  ++FG
Sbjct: 62  DETTQAMA-FDGIIFQGQSLKIRRPHDYQ-PLPGAHKLFIGGLPNYLNDDQVKELLTSFG 119

Query: 147 VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAF 206
            +                                           +++D  TG SKG+AF
Sbjct: 120 PL---------------------------------------KAFNLVKDSATGLSKGYAF 140

Query: 207 INYASFEASDASIDAMHGQYLCNRPISVSYA 237
             Y     +D +I  ++G  L ++ + V  A
Sbjct: 141 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 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 = 91.9 bits (229), Expect = 8e-23
 Identities = 24/81 (29%), Positives = 43/81 (53%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
            G   +++GGL + +++  + EL    GP+   ++ KD  T   +GY F E++     D 
Sbjct: 92  PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151

Query: 92  AIKIMNMIKLYGKPIRVNKAS 112
           AI  +N ++L  K + V +AS
Sbjct: 152 AIAGLNGMQLGDKKLLVQRAS 172

>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 = 63.8 bits (156), Expect = 2e-12
 Identities = 14/124 (11%), Positives = 34/124 (27%), Gaps = 35/124 (28%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++GN+   + E+ + D F+A   +                                   
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGG--------------------------------- 33

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
            +       +        K FAF+ + S + +  ++ A  G     + + +         
Sbjct: 34  -LTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPL 91

Query: 244 GDRH 247
              H
Sbjct: 92  PGAH 95

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  187 bits (477), Expect = 1e-59
 Identities = 49/213 (23%), Positives = 83/213 (38%), Gaps = 48/213 (22%)

Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQT--HQGYGFIEFMGEEDAD 90
               ++VG +    SE  + ELF Q G V  +++ +DR       +G  F+ F   + A 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 91  YAIKIMNMIKL---YGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGV 147
            A   ++ +K+      PI++  A S + N      +FIG +  +  E  +   FS+FG 
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 121

Query: 148 ILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFI 207
           I                                        +  I+R PD G S+G AF+
Sbjct: 122 I---------------------------------------EECRILRGPD-GLSRGCAFV 141

Query: 208 NYASFEASDASIDAMHGQYL---CNRPISVSYA 237
            + +   +  +I AMH       C+ P+ V +A
Sbjct: 142 TFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 75.3 bits (186), Expect = 1e-16
 Identities = 18/126 (14%), Positives = 38/126 (30%), Gaps = 41/126 (32%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            +F+G +     EK L + F  +G + +                                
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEI------------------------------- 33

Query: 183 IFIGNLDPEIMRDPDTGN--SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                    ++RD       SKG  F+ + + +A+  + +A+H   +             
Sbjct: 34  --------NVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPA 85

Query: 241 DSKGDR 246
           DS+ + 
Sbjct: 86  DSEKNN 91

>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 = 69.9 bits (172), Expect = 1e-14
 Identities = 20/111 (18%), Positives = 42/111 (37%), Gaps = 8/111 (7%)

Query: 4   GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN 63
             ++  G+  P     + ++     E    D  +++G +  K +E  +  +F   G +  
Sbjct: 69  NMKVLPGMHHPIQMKPADSEKNNAVE----DRKLFIGMISKKCTENDIRVMFSSFGQIEE 124

Query: 64  VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN---MIKLYGKPIRVNKA 111
             + +       +G  F+ F     A  AIK M+    ++    P+ V  A
Sbjct: 125 CRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>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 =  190 bits (486), Expect = 2e-59
 Identities = 43/215 (20%), Positives = 82/215 (38%), Gaps = 48/215 (22%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPV-VNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           + T+++       ++  + +L      V +++ +P  R   T + + +I+   +EDA Y 
Sbjct: 117 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYC 175

Query: 93  IKIMNMIKLYGKPIRVN--KASSHQKNLDV----GANIFIGNLDPEV-DEKLLYDTFSAF 145
           ++ +N +K+ G  +           K  D     G  I I NL  E+ DE LL ++F  F
Sbjct: 176 VEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGF 235

Query: 146 GVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFA 205
           G I +                                              +   +   A
Sbjct: 236 GSIEKINIPAGQ--------------------------------------KEHSFNNCCA 257

Query: 206 FINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
           F+ + + ++++ ++  M+   L NR ISVS A KK
Sbjct: 258 FMVFENKDSAERAL-QMNRSLLGNREISVSLADKK 291

>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 =  165 bits (421), Expect = 1e-49
 Identities = 30/240 (12%), Positives = 73/240 (30%), Gaps = 50/240 (20%)

Query: 13  TPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVT 72
           +P    L+  K            T+ V  L    ++  +++ F   GP+++V +      
Sbjct: 20  SPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--L 77

Query: 73  QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPE 132
           + +  +  IEF   + A  AI   + + +    I V+  +           +++ N  P 
Sbjct: 78  KKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSHLTE--------CTLWMTNFPPS 128

Query: 133 VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEI 192
             ++ + D      V+  +                                         
Sbjct: 129 YTQRNIRDLLQDINVVALS---------------------------------------IR 149

Query: 193 MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAE 252
           +       S+ FA+I+  S E +   ++ ++G  +    +    +   +       +  E
Sbjct: 150 LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLE 209

>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 = 73.5 bits (181), Expect = 3e-15
 Identities = 20/137 (14%), Positives = 34/137 (24%), Gaps = 46/137 (33%)

Query: 103 GKPIRVNKASSHQKNLDV----GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMI 158
           G P      S               + + NL    ++  +Y  F   G I+         
Sbjct: 19  GSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIH-------- 70

Query: 159 KLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDAS 218
                 + V                                 +  FA I +A ++ + A+
Sbjct: 71  ------VDVAD---------------------------SLKKNFRFARIEFARYDGALAA 97

Query: 219 IDAMHGQYLCNRPISVS 235
           I   H   +    I VS
Sbjct: 98  ITKTHK-VVGQNEIIVS 113

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 71.9 bits (177), Expect = 1e-14
 Identities = 22/110 (20%), Positives = 45/110 (40%), Gaps = 9/110 (8%)

Query: 4   GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVS-ETLMWELFVQSGPVV 62
           G  +   +S P  +     + +     G     I +  L  ++  E L+ E F   G + 
Sbjct: 186 GYTLVTKVSNPLEK---SKRTDSATLEG---REIMIRNLSTELLDENLLRESFEGFGSIE 239

Query: 63  NVHMPKDR-VTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
            +++P  +     +    F+ F  ++ A+ A++ MN   L  + I V+ A
Sbjct: 240 KINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA 288

>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 =  181 bits (461), Expect = 3e-57
 Identities = 35/210 (16%), Positives = 74/210 (35%), Gaps = 47/210 (22%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
                +++G L+   S   +     +     ++ +  D  T T++ +G+++F   ED + 
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEK 69

Query: 92  AIKIMNMIKLYGKPIRVNKASSH-QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQ 150
           A++ +  +K++G  I++ K      K +     +   NL   + E  L + F        
Sbjct: 70  ALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL---- 124

Query: 151 TPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYA 210
                                                   EI      G SKG A+I + 
Sbjct: 125 ----------------------------------------EIRLVSQDGKSKGIAYIEFK 144

Query: 211 SFEASDASIDAMHGQYLCNRPISVSYAFKK 240
           S   ++ +++   G  +  R +S+ Y  +K
Sbjct: 145 SEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>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 = 78.8 bits (195), Expect = 6e-18
 Identities = 21/127 (16%), Positives = 39/127 (30%), Gaps = 41/127 (32%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
            N+FIGNL+P      L    S          ++                          
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDL-AVV-------------------------- 46

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                        D  TG ++ F ++++ S E  + +++ + G  +    I +     +D
Sbjct: 47  -------------DVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRD 92

Query: 242 SKGDRHG 248
           SK  R  
Sbjct: 93  SKKVRAA 99

>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 = 71.1 bits (175), Expect = 4e-15
 Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 5/83 (6%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
           +      T+    L   ++E  + E+F  +  +              +G  +IEF  E D
Sbjct: 94  KKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEAD 148

Query: 89  ADYAIKIMNMIKLYGKPIRVNKA 111
           A+  ++     ++ G+ + +   
Sbjct: 149 AEKNLEEKQGAEIDGRSVSLYYT 171

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  159 bits (404), Expect = 1e-48
 Identities = 49/207 (23%), Positives = 82/207 (39%), Gaps = 43/207 (20%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
              +++GGL+   +E  + E F + G V ++ + KD  T   +G+GF+ F      D  +
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           K  +++   GK I   +A    +    G  IF+G + P+V  K   + FS +G I     
Sbjct: 63  KTQHILD--GKVIDPKRAIPRDEQDKTG-KIFVGGIGPDVRPKEFEEFFSQWGTI----- 114

Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
                                             +D ++M D DTG S+GF F+ Y S +
Sbjct: 115 ----------------------------------IDAQLMLDKDTGQSRGFGFVTYDSAD 140

Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKK 240
           A D            +R I +  A  +
Sbjct: 141 AVDRVC-QNKFIDFKDRKIEIKRAEPR 166

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 77.6 bits (192), Expect = 1e-17
 Identities = 18/79 (22%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VGG+   V      E F Q G +++  +  D+ T   +G+GF+ +   +  D   +  
Sbjct: 90  IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-N 148

Query: 97  NMIKLYGKPIRVNKASSHQ 115
             I    + I + +A    
Sbjct: 149 KFIDFKDRKIEIKRAEPRH 167

>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 = 67.6 bits (166), Expect = 5e-14
 Identities = 25/122 (20%), Positives = 42/122 (34%), Gaps = 41/122 (33%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
             +FIG L+ +  E  L + F  +G +                                 
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVT-------------------------------- 31

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                  D +IM+DP TG S+GF F+++    + D  +   H   L  + I    A  +D
Sbjct: 32  -------DLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH--ILDGKVIDPKRAIPRD 82

Query: 242 SK 243
            +
Sbjct: 83  EQ 84

>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 =  159 bits (404), Expect = 2e-48
 Identities = 38/242 (15%), Positives = 80/242 (33%), Gaps = 68/242 (28%)

Query: 31  GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMP-----KDRVTQTHQGYGFIEFMG 85
           G     +YVG +   ++E  M + F     +  +                + + F+EF  
Sbjct: 1   GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASSHQKNL-------------------DVGANIFI 126
            ++   A+   + I   G+ +++ +   +Q                      D    +FI
Sbjct: 61  VDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119

Query: 127 GNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIG 186
           G L   +++  + +  ++FG +                                      
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAF----------------------------------- 144

Query: 187 NLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDR 246
                +++D  TG SKG+AF  Y     +D +I  ++G  L ++ + V  A    S G +
Sbjct: 145 ----NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA----SVGAK 196

Query: 247 HG 248
           + 
Sbjct: 197 NA 198

>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 = 97.0 bits (242), Expect = 2e-24
 Identities = 26/92 (28%), Positives = 45/92 (48%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
                 D    +++GGL + +++  + EL    GP+   ++ KD  T   +GY F E++ 
Sbjct: 106 VSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 165

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
               D AI  +N ++L  K + V +AS   KN
Sbjct: 166 INVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 197

>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 = 65.1 bits (159), Expect = 7e-13
 Identities = 19/148 (12%), Positives = 46/148 (31%), Gaps = 36/148 (24%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++GN+   + E+ + D F+A        ++  + +  G P+                  
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQM------RLGGLTQAPGNPVL----------------- 43

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                             K FAF+ + S + +  ++ A  G     + + +         
Sbjct: 44  -----------AVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPL 91

Query: 244 GDRHGSAAERLLAAQNPLSQADRPHQLF 271
                + +  +    +     D  H+LF
Sbjct: 92  PGMSENPSVYVPGVVST-VVPDSAHKLF 118

>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 =  160 bits (408), Expect = 7e-48
 Identities = 41/229 (17%), Positives = 69/229 (30%), Gaps = 47/229 (20%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DA + V  L   +++    EL    G +    +     T   +GYGF E+M ++ A  A 
Sbjct: 95  DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNLDV--GANIFIGNLDPEV-DEKLLYDTFSAFGVILQ 150
             +    L  + + V+   + Q    +     + +  L P   D   L    SA      
Sbjct: 155 SDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTF 214

Query: 151 TPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYA 210
                          ++                               G  KGFA + Y 
Sbjct: 215 --------------CQL-------------------------ACGQ-DGQLKGFAVLEYE 234

Query: 211 SFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQN 259
           + E ++ +     G  L    + VS+            S    L+AAQ 
Sbjct: 235 TAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG----RSMLAALIAAQA 279

>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 =  150 bits (382), Expect = 4e-44
 Identities = 33/221 (14%), Positives = 68/221 (30%), Gaps = 53/221 (23%)

Query: 21  QTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGF 80
           + +LE           I + GL   V+   + +L      +    + K +      G  F
Sbjct: 9   RKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK------GTAF 61

Query: 81  IEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYD 140
           +  +  E A+ AI   +  +L  + + V    +        A + + NL P + ++   +
Sbjct: 62  VTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD-------ALLCVANLPPSLTQQQFEE 114

Query: 141 TFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN 200
               FG +                                           ++    TG 
Sbjct: 115 LVRPFGSLE---------------------------------------RCFLVYSERTGQ 135

Query: 201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
           SKG+ F  Y   +++  +   + G+ L  R + V +     
Sbjct: 136 SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ 176

>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 = 75.0 bits (185), Expect = 8e-16
 Identities = 12/109 (11%), Positives = 32/109 (29%), Gaps = 12/109 (11%)

Query: 4   GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSET-LMWELFVQSGPVV 62
            R +    +     + +                + V  L    ++   +           
Sbjct: 164 PRTLYVHWTDAGQLTPALLH----------SRCLCVDRLPPGFNDVDALCRALSAVHSPT 213

Query: 63  NVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
              +   +     +G+  +E+   E A+ A +  + + L G  +RV+  
Sbjct: 214 FCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261

>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 =  145 bits (368), Expect = 3e-44
 Identities = 70/85 (82%), Positives = 79/85 (92%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADYAI
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74

Query: 94  KIMNMIKLYGKPIRVNKASSHQKNL 118
           KIM+MIKLYGKPIRVNKAS+H KNL
Sbjct: 75  KIMDMIKLYGKPIRVNKASAHNKNL 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 = 81.5 bits (202), Expect = 9e-20
 Identities = 28/129 (21%), Positives = 48/129 (37%), Gaps = 41/129 (31%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
           A +++G LD +V E LL++ F   G +                +  +             
Sbjct: 16  ATVYVGGLDEKVSEPLLWELFLQAGPV----------------VNTH------------- 46

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF--K 239
                     + +D  TG  +G+ F+ + S E +D +I  M    L  +PI V+ A    
Sbjct: 47  ----------MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN 96

Query: 240 KDSKGDRHG 248
           K+  G   G
Sbjct: 97  KNLSGPSSG 105

>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 =  131 bits (332), Expect = 5e-39
 Identities = 76/129 (58%), Positives = 85/129 (65%), Gaps = 38/129 (29%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
           + IFIGNLDPE+DEKLLYDTFSAFGVILQTPKIM                          
Sbjct: 6   SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIM-------------------------- 39

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                       RDPDTGNSKG+AFIN+ASF+ASDA+I+AM+GQYLCNRPI+VSYAFKKD
Sbjct: 40  ------------RDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD 87

Query: 242 SKGDRHGSA 250
           SKG    S 
Sbjct: 88  SKGSGPSSG 96

>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 = 75.3 bits (186), Expect = 2e-17
 Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 1/87 (1%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNV-HMPKDRVTQTHQGYGFIEFMGEEDAD 90
            G + I++G LD ++ E L+++ F   G ++    + +D  T   +GY FI F   + +D
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62

Query: 91  YAIKIMNMIKLYGKPIRVNKASSHQKN 117
            AI+ MN   L  +PI V+ A      
Sbjct: 63  AAIEAMNGQYLCNRPITVSYAFKKDSK 89

>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 =  129 bits (326), Expect = 4e-38
 Identities = 34/82 (41%), Positives = 55/82 (67%), Gaps = 1/82 (1%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           + D T++VG L+ +V E +++ELF+Q+GP+  V + KDR  +  + +GF+ F   E   Y
Sbjct: 14  EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK-PKSFGFVCFKHPESVSY 72

Query: 92  AIKIMNMIKLYGKPIRVNKASS 113
           AI ++N I+LYG+PI V+  SS
Sbjct: 73  AIALLNGIRLYGRPINVSGPSS 94

>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 = 72.7 bits (179), Expect = 2e-16
 Identities = 26/127 (20%), Positives = 45/127 (35%), Gaps = 40/127 (31%)

Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
           +       +    +F+GNL+  V E++LY+ F   G +                 +V   
Sbjct: 6   SGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPL----------------TKVT-- 47

Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
                                I +D + G  K F F+ +   E+   +I  ++G  L  R
Sbjct: 48  ---------------------ICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGR 85

Query: 231 PISVSYA 237
           PI+VS  
Sbjct: 86  PINVSGP 92

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  128 bits (323), Expect = 4e-37
 Identities = 33/86 (38%), Positives = 51/86 (59%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G G S      +YVGGL ++V + ++   F+  G + ++ +P D  T+ H+G+ F+EF  
Sbjct: 55  GSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 114

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKA 111
            EDA  AI  MN  +L+G+ IRVN A
Sbjct: 115 AEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 82.9 bits (205), Expect = 7e-20
 Identities = 30/163 (18%), Positives = 52/163 (31%), Gaps = 46/163 (28%)

Query: 82  EFMGEEDADYAIKIMNMIKLYGKPIR-------VNKASSHQKNLDVGANIFIGNLDPEVD 134
           E + +E  +    +   +                  +     +      +++G L  EVD
Sbjct: 17  ENLSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVD 76

Query: 135 EKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR 194
           +K+L+  F  FG I                  +                        I  
Sbjct: 77  DKVLHAAFIPFGDI----------------TDIQ-----------------------IPL 97

Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           D +T   +GFAF+ +   E + A+ID M+   L  R I V+ A
Sbjct: 98  DYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 =  125 bits (317), Expect = 8e-37
 Identities = 31/84 (36%), Positives = 49/84 (58%)

Query: 28  GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           G        +YVGGL ++V + ++   F+  G + ++ +P D  T+ H+G+ F+EF   E
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60

Query: 88  DADYAIKIMNMIKLYGKPIRVNKA 111
           DA  AI  MN  +L+G+ IRVN A
Sbjct: 61  DAAAAIDNMNESELFGRTIRVNLA 84

>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 = 76.8 bits (190), Expect = 3e-18
 Identities = 29/116 (25%), Positives = 44/116 (37%), Gaps = 39/116 (33%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
             +++G L  EVD+K+L+  F  FG I                                 
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDIT-------------------------------- 35

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                  D +I  D +T   +GFAF+ +   E + A+ID M+   L  R I V+ A
Sbjct: 36  -------DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84

>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 =  125 bits (316), Expect = 2e-36
 Identities = 31/92 (33%), Positives = 46/92 (50%), Gaps = 2/92 (2%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G  E      T+YVG L   V+E L+ +LF Q GP  +  M  +  +  +  Y F+EF  
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYE 64

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
             DA  A+  MN  K+ GK ++VN A++    
Sbjct: 65  HRDAAAALAAMNGRKILGKEVKVNWATTPSSQ 96

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 67.3 bits (165), Expect = 2e-14
 Identities = 21/140 (15%), Positives = 47/140 (33%), Gaps = 43/140 (30%)

Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
           +S   ++      +++GNL  +V E L+   FS  G            K           
Sbjct: 5   SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKS-------CK----------- 46

Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
                                ++ +  +     + F+ +     + A++ AM+G+ +  +
Sbjct: 47  ---------------------MITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGK 83

Query: 231 PISVSYAFKKDSK--GDRHG 248
            + V++A    S+  G   G
Sbjct: 84  EVKVNWATTPSSQKSGPSSG 103

>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 =  117 bits (295), Expect = 2e-33
 Identities = 31/86 (36%), Positives = 49/86 (56%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G          +YVGGL ++V + ++   F+  G + ++ +P D  T+ H+G+ F+EF  
Sbjct: 4   GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKA 111
            EDA  AI  MN  +L+G+ IRVN A
Sbjct: 64  AEDAAAAIDNMNESELFGRTIRVNLA 89

>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 = 85.7 bits (213), Expect = 3e-21
 Identities = 31/128 (24%), Positives = 46/128 (35%), Gaps = 39/128 (30%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
             +++G L  EVD+K+L+  F  FG I                                 
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDIT-------------------------------- 40

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                  D +I  D +T   +GFAF+ +   E + A+ID M+   L  R I V+ A    
Sbjct: 41  -------DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR 93

Query: 242 SKGDRHGS 249
            K     S
Sbjct: 94  IKESGPSS 101

>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 =  112 bits (283), Expect = 2e-31
 Identities = 29/142 (20%), Positives = 56/142 (39%), Gaps = 43/142 (30%)

Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
           + +S  +       N+++ NLD  +D++ L   FS FG I                    
Sbjct: 3   SGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSA----------------- 45

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
                                 ++M +   G SKGF F+ ++S E +  ++  M+G+ + 
Sbjct: 46  ----------------------KVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVA 81

Query: 229 NRPISVSYAFKKDSK--GDRHG 248
            +P+ V+ A +K+ +  G   G
Sbjct: 82  TKPLYVALAQRKEERQSGPSSG 103

>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 = 68.0 bits (167), Expect = 1e-14
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
            +      +YV  LDD + +  + + F   G + +  +  +      +G+GF+ F   E+
Sbjct: 10  ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEE 67

Query: 89  ADYAIKIMNMIKLYGKPIRVNKA 111
           A  A+  MN   +  KP+ V  A
Sbjct: 68  ATKAVTEMNGRIVATKPLYVALA 90

>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 =  112 bits (282), Expect = 3e-31
 Identities = 36/132 (27%), Positives = 54/132 (40%), Gaps = 42/132 (31%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
            NIFI NLD  +D K LYDTFSAFG IL    +                           
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC-------------------------- 39

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA-FKK 240
                          D   SKG+ F+++ + EA++ +I+ M+G  L +R + V     +K
Sbjct: 40  ---------------DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 84

Query: 241 DSKGDRHGSAAE 252
           + + +    A E
Sbjct: 85  EREAELGARAKE 96

>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 = 24/110 (21%), Positives = 46/110 (41%), Gaps = 9/110 (8%)

Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           G   I++  LD  +    +++ F   G +++  +  D      +GYGF+ F  +E A+ A
Sbjct: 4   GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA 61

Query: 93  IKIMNMIKLYGKPIRVNKA-------SSHQKNLDVGANIFIGNLDPEVDE 135
           I+ MN + L  + + V +        +          N++I N  P    
Sbjct: 62  IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTR 111

>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 =  112 bits (283), Expect = 2e-30
 Identities = 44/230 (19%), Positives = 84/230 (36%), Gaps = 46/230 (20%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
           +  +    +++GGL  + ++  +   F Q G + +  + +D  T+  +G+GF+ +   E+
Sbjct: 8   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67

Query: 89  ADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFS 143
            D A+      K+ G+ +   +A S + +   GA+     IF+G +  + +E  L D F 
Sbjct: 68  VDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 126

Query: 144 AFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKG 203
            +G I                                          EIM D  +G  +G
Sbjct: 127 QYGKI---------------------------------------EVIEIMTDRGSGKKRG 147

Query: 204 FAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAER 253
           FAF+ +   ++ D  +       +      V  A  K        S   R
Sbjct: 148 FAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEMASASSSQRGR 196

>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 =  100 bits (250), Expect = 1e-26
 Identities = 28/141 (19%), Positives = 50/141 (35%), Gaps = 39/141 (27%)

Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
           G   +   A+  QK    GAN+FI +L  E  ++ L   F  FG ++             
Sbjct: 7   GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSA----------- 55

Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
                                       ++  D  T  SK F F++Y +  ++ A+I +M
Sbjct: 56  ----------------------------KVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 223 HGQYLCNRPISVSYAFKKDSK 243
           +G  +  + + V     K+  
Sbjct: 88  NGFQIGMKRLKVQLKRSKNDS 108

>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 = 74.3 bits (183), Expect = 6e-17
 Identities = 21/96 (21%), Positives = 45/96 (46%), Gaps = 2/96 (2%)

Query: 18  SLSQTKLEGGGESGDGD--ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTH 75
            L+Q  +   G   +G   A +++  L  +  +  + ++F+  G VV+  +  D+ T   
Sbjct: 7   GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 66

Query: 76  QGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
           + +GF+ +     A  AI+ MN  ++  K ++V   
Sbjct: 67  KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK 102

>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 = 96.8 bits (242), Expect = 9e-26
 Identities = 27/120 (22%), Positives = 51/120 (42%), Gaps = 39/120 (32%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
            N+F+G+L+  VD++ L + F  F   L                                
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYL-------------------------------- 29

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                     +M D  TG+S+G+ F+++ S + +  ++D+M GQ L  RP+ +++A K +
Sbjct: 30  -------SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE 82

>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 = 78.3 bits (194), Expect = 7e-19
 Identities = 23/78 (29%), Positives = 41/78 (52%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
             ++VG L+  V +  +   F      ++ H+  D  T + +GYGF+ F  ++DA  A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 95  IMNMIKLYGKPIRVNKAS 112
            M    L G+P+R+N A+
Sbjct: 62  SMQGQDLNGRPLRINWAA 79

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 95.0 bits (237), Expect = 7e-25
 Identities = 25/130 (19%), Positives = 46/130 (35%), Gaps = 40/130 (30%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
            ++F+G+L P+VD+ +LY+ F       +  K++                          
Sbjct: 10  YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVV-------------------------- 43

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY-LCNRPISVSYAFKK 240
                        D  TG SKG+ F+ +        ++    G   L ++P+ +S A  K
Sbjct: 44  ------------LDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPK 90

Query: 241 DSKGDRHGSA 250
            S+     S 
Sbjct: 91  ASRVKPVESG 100

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 68.1 bits (167), Expect = 9e-15
 Identities = 23/89 (25%), Positives = 44/89 (49%), Gaps = 3/89 (3%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVV-NVHMPKDRVTQTHQGYGFIEFM 84
           G   S   + +++VG L   V + +++E FV+  P      +  D+   + +GYGF++F 
Sbjct: 1   GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVS-KGYGFVKFT 59

Query: 85  GEEDADYAIKIMN-MIKLYGKPIRVNKAS 112
            E +   A+      + L  KP+R++ A 
Sbjct: 60  DELEQKRALTECQGAVGLGSKPVRLSVAI 88

>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 = 95.1 bits (237), Expect = 7e-25
 Identities = 22/131 (16%), Positives = 49/131 (37%), Gaps = 43/131 (32%)

Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
            + A++++G+L+P +DE  +   F+  G  + + KI+                       
Sbjct: 7   GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKII----------------------- 43

Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN----RPISV 234
                          R+  TG   G+ F+ +A    ++  +  ++G+ L      +   +
Sbjct: 44  ---------------RNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKL 88

Query: 235 SYA-FKKDSKG 244
           +YA +   S G
Sbjct: 89  NYATYSGPSSG 99

>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 = 83.1 bits (206), Expect = 2e-20
 Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 5/92 (5%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFM 84
           G   S    A++++G L+  + E  +   F   G  V++V + ++R+T    GY F+EF 
Sbjct: 1   GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60

Query: 85  GEEDADYAIKIMNMIKLYG----KPIRVNKAS 112
               A+  +  +N   L G    K  ++N A+
Sbjct: 61  DLATAEKCLHKINGKPLPGATPAKRFKLNYAT 92

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 94.0 bits (234), Expect = 3e-24
 Identities = 25/149 (16%), Positives = 52/149 (34%), Gaps = 41/149 (27%)

Query: 91  YAIKIMNMIKLYGKPIRVNKASSHQKNLD--VGANIFIGNLDPEVDEKLLYDTFSAFGVI 148
            +   ++   L    +    A++  K ++   G N+FI +L  E  +  L  TF  FG +
Sbjct: 8   GSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNV 67

Query: 149 LQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFIN 208
           +                                         ++  D  T  SK F F++
Sbjct: 68  ISA---------------------------------------KVFIDKQTSLSKCFGFVS 88

Query: 209 YASFEASDASIDAMHGQYLCNRPISVSYA 237
           + + +++  +I AM+G  +  + + V   
Sbjct: 89  FDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 70.9 bits (174), Expect = 1e-15
 Identities = 20/86 (23%), Positives = 40/86 (46%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G    G     +++  L  + ++T +   F+  G V++  +  D+ T   + +GF+ F  
Sbjct: 32  GKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDN 91

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKA 111
            + A  AIK MN  ++  K ++V   
Sbjct: 92  PDSAQVAIKAMNGFQVGTKRLKVQLK 117

>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 = 95.9 bits (238), Expect = 9e-24
 Identities = 29/205 (14%), Positives = 57/205 (27%), Gaps = 48/205 (23%)

Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
               +    +           ++IGNL     ++ L +   + GV               
Sbjct: 50  DDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVN-------------- 95

Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
                          D+        L+ +   +   G SKGFA +   S  +S   +D +
Sbjct: 96  ---------------DI--------LEIKFFENRANGQSKGFALVGVGSEASSKKLMDLL 132

Query: 223 HGQYLCNRPISVSYAFKKD-----------SKGDRHGSAAERLLAAQNPLSQADRPHQLF 271
             + L  +   V+   K+            ++  +     +      +  +   +  +  
Sbjct: 133 PKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGR 192

Query: 272 ADAPPPAPLPPPPPPINIMGLPPPP 296
              P   P     P     G PPPP
Sbjct: 193 GRFPGAVPGGDRFPGPAGPGGPPPP 217

>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 = 64.7 bits (157), Expect = 2e-12
 Identities = 11/85 (12%), Positives = 33/85 (38%), Gaps = 2/85 (2%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGP--VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
             +Y+G L    ++  + E     G   ++ +   ++R     +G+  +    E  +   
Sbjct: 69  IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 128

Query: 93  IKIMNMIKLYGKPIRVNKASSHQKN 117
           + ++   +L+G+   V   +    +
Sbjct: 129 MDLLPKRELHGQNPVVTPVNKQFLS 153

>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 = 91.9 bits (229), Expect = 1e-23
 Identities = 25/92 (27%), Positives = 46/92 (50%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
             G   DG  T+ V  L  + S   +  +F + G V +V++P++  T+  +G+ F+ F  
Sbjct: 5   SSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
             DA  A   M+  +L G+ +RV  A   +++
Sbjct: 65  RRDAQDAEAAMDGAELDGRELRVQVARYGRRD 96

>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 = 71.5 bits (176), Expect = 4e-16
 Identities = 23/133 (17%), Positives = 36/133 (27%), Gaps = 39/133 (29%)

Query: 117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKN 176
           ++D    + + NL        L   F  +G +                            
Sbjct: 9   DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVG--------------------------- 41

Query: 177 LDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
                       D  I R+P T   +GFAF+ +     +  +  AM G  L  R + V  
Sbjct: 42  ------------DVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV 89

Query: 237 AFKKDSKGDRHGS 249
           A           S
Sbjct: 90  ARYGRRDLSGPSS 102

>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 = 92.0 bits (229), Expect = 2e-23
 Identities = 29/145 (20%), Positives = 53/145 (36%), Gaps = 40/145 (27%)

Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
           + +S   +   +G+ +F+ NLD +V  K L + FS  GV+++                  
Sbjct: 3   SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRA----------------- 45

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
                                 +I+ D D G S+G   + +     +  +I   +GQ L 
Sbjct: 46  ----------------------DILEDKD-GKSRGIGTVTFEQSIEAVQAISMFNGQLLF 82

Query: 229 NRPISVSYAFKKDSKGDRHGSAAER 253
           +RP+ V    +   KGD       +
Sbjct: 83  DRPMHVKMDERALPKGDFFPPERPQ 107

>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 = 74.3 bits (183), Expect = 7e-17
 Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 1/87 (1%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
            G  ++G   +T++V  LD KV    + E+F  +G VV   + +D+  ++ +G G + F 
Sbjct: 6   SGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKS-RGIGTVTFE 64

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKA 111
              +A  AI + N   L+ +P+ V   
Sbjct: 65  QSIEAVQAISMFNGQLLFDRPMHVKMD 91

>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 = 92.9 bits (231), Expect = 2e-23
 Identities = 24/78 (30%), Positives = 45/78 (57%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
            T+YVG L    +E  ++ELF +SG +  + M  D++ +T  G+ F+E+    DA+ A++
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 95  IMNMIKLYGKPIRVNKAS 112
            +N  +L  + IR +  +
Sbjct: 100 YINGTRLDDRIIRTDWDA 117

>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 = 69.8 bits (171), Expect = 8e-15
 Identities = 23/126 (18%), Positives = 41/126 (32%), Gaps = 39/126 (30%)

Query: 112 SSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKAS 171
              +K L     +++GNL     E+ +Y+ FS  G I                       
Sbjct: 30  EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI----------------------- 66

Query: 172 SHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRP 231
                      I +G        D     + GF F+ Y S   ++ ++  ++G  L +R 
Sbjct: 67  ---------KKIIMG-------LDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI 110

Query: 232 ISVSYA 237
           I   + 
Sbjct: 111 IRTDWD 116

>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 = 90.7 bits (226), Expect = 2e-23
 Identities = 27/119 (22%), Positives = 48/119 (40%), Gaps = 39/119 (32%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
            ++F+G+L PE+    +   F+ FG I                 RV              
Sbjct: 7   FHVFVGDLSPEITTAAIAAAFAPFGRISD--------------ARV-------------- 38

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                      ++D  TG SKG+ F+++ +   ++ +I  M GQ+L  R I  ++A +K
Sbjct: 39  -----------VKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 78.4 bits (194), Expect = 8e-19
 Identities = 24/81 (29%), Positives = 40/81 (49%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
                ++VG L  +++   +   F   G + +  + KD  T   +GYGF+ F  + DA+ 
Sbjct: 4   GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63

Query: 92  AIKIMNMIKLYGKPIRVNKAS 112
           AI+ M    L G+ IR N A+
Sbjct: 64  AIQQMGGQWLGGRQIRTNWAT 84

>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 = 93.0 bits (231), Expect = 5e-23
 Identities = 39/241 (16%), Positives = 75/241 (31%), Gaps = 84/241 (34%)

Query: 33  GDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           G++ + V  L+ ++V+   ++ LF   G V  V     ++    +    ++      A  
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQL 56

Query: 92  AIKIMNMIKLYGKPIRVNKA------------------------SSHQKNLDVGAN---- 123
           A+  +N  KL+GKPIR+  +                          H+       N    
Sbjct: 57  AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI 116

Query: 124 ------IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNL 177
                 + + N+ P V E+ L   FS+ G +++  K                        
Sbjct: 117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ--------------------- 155

Query: 178 DVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL-CNRPISVSY 236
                                   +  A I   S E +  ++  +H   L  N  + VS+
Sbjct: 156 ----------------------KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF 193

Query: 237 A 237
           +
Sbjct: 194 S 194

>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 = 59.5 bits (144), Expect = 8e-11
 Identities = 20/174 (11%), Positives = 51/174 (29%), Gaps = 48/174 (27%)

Query: 122 ANIFIGNLDPE-VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           + + + NL+PE V  + L+  F  +G +                                
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQ------------------------------- 32

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                     +I+ +      K  A +  A    +  ++  ++G  L  +PI ++ +   
Sbjct: 33  --------RVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS--- 76

Query: 241 DSKGDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPP 294
             +  +     +           +         +     + PP   +++  +PP
Sbjct: 77  KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPP 130

>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 = 90.4 bits (225), Expect = 7e-23
 Identities = 25/134 (18%), Positives = 44/134 (32%), Gaps = 40/134 (29%)

Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
           +A   ++      N++I NL   +DE+ L +    FG ++ T                  
Sbjct: 14  QAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVIST------------------ 55

Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
                                 I+RD  +G S+G  F    S E  +A I   +G+++  
Sbjct: 56  ---------------------RILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKT 93

Query: 230 RPISVSYAFKKDSK 243
            P   +       K
Sbjct: 94  PPGVSAPTEPLLCK 107

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 64.2 bits (157), Expect = 3e-13
 Identities = 14/83 (16%), Positives = 28/83 (33%), Gaps = 1/83 (1%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
           +       +Y+  L   + E  +  +    G V++  + +D  + T +G GF      E 
Sbjct: 20  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEK 78

Query: 89  ADYAIKIMNMIKLYGKPIRVNKA 111
            +  I   N   +   P      
Sbjct: 79  CEAVIGHFNGKFIKTPPGVSAPT 101

>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 = 88.0 bits (219), Expect = 3e-22
 Identities = 27/86 (31%), Positives = 40/86 (46%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G     D +ATI V  L +   ET + ELF   G +  +++ KD+ T   +G+ FI F  
Sbjct: 7   GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 66

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKA 111
            EDA  AI  ++        + V  A
Sbjct: 67  REDAARAIAGVSGFGYDHLILNVEWA 92

>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 = 78.0 bits (193), Expect = 2e-18
 Identities = 28/138 (20%), Positives = 48/138 (34%), Gaps = 39/138 (28%)

Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
           +S   +  D  A I + NL  +  E  L + F  FG                    +++ 
Sbjct: 5   SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFG-------------------SISRI 45

Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
                                + +D  TG SKGFAFI++   E +  +I  + G    + 
Sbjct: 46  Y--------------------LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHL 85

Query: 231 PISVSYAFKKDSKGDRHG 248
            ++V +A    + G   G
Sbjct: 86  ILNVEWAKPSTNSGPSSG 103

>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 = 90.5 bits (224), Expect = 6e-22
 Identities = 30/246 (12%), Positives = 60/246 (24%), Gaps = 81/246 (32%)

Query: 31  GDGDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA 89
           G     + V GLD  K++   ++ +F   G V  V   K +      G   +E       
Sbjct: 1   GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAV 55

Query: 90  DYAIKIMNMIKLYGKPIRVNKA------------------------------------SS 113
           D AI  +N   ++G+ + V  +                                    ++
Sbjct: 56  DRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAA 115

Query: 114 HQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSH 173
             +       +   N   EV E+  ++     GV   T                      
Sbjct: 116 KNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPT---------------------- 153

Query: 174 QKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPIS 233
                             +              + + S   +  ++  ++   + N    
Sbjct: 154 -----------------SVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGP 196

Query: 234 VSYAFK 239
             Y  K
Sbjct: 197 YPYTLK 202

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 60.1 bits (145), Expect = 6e-11
 Identities = 12/106 (11%), Positives = 28/106 (26%)

Query: 4   GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN 63
           G       S       S  +             ++      +V+E   +E+  + G    
Sbjct: 93  GSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRP 152

Query: 64  VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN 109
             +            G +E+  + DA   +  +N  ++        
Sbjct: 153 TSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 198

>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 = 86.1 bits (214), Expect = 1e-21
 Identities = 26/88 (29%), Positives = 48/88 (54%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G   + D +  + V GL    +E  + E+F + GP+ +V +  D+ ++  +G+ F+ F  
Sbjct: 7   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASS 113
            +DA  A +  N ++L G+ IRV+  SS
Sbjct: 67  VDDAKEAKERANGMELDGRRIRVSGPSS 94

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 75.3 bits (186), Expect = 1e-17
 Identities = 24/129 (18%), Positives = 44/129 (34%), Gaps = 39/129 (30%)

Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
           + +S ++ N D    + +  L     E+ L + FS +G I                    
Sbjct: 3   SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIA------------------- 43

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
                               D  I+ D  +  S+GFAF+ + + + +  + +  +G  L 
Sbjct: 44  --------------------DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD 83

Query: 229 NRPISVSYA 237
            R I VS  
Sbjct: 84  GRRIRVSGP 92

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 86.7 bits (215), Expect = 2e-21
 Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 3/91 (3%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +    L+D V ET + ++  + G V  V +     T+ H G   + F     A   +K 
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 96  MNMIKLYGKPIRVN---KASSHQKNLDVGAN 123
           +++  + G  I      K     K  ++  N
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRMKYYELIVN 98

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 84.4 bits (209), Expect = 9e-21
 Identities = 19/138 (13%), Positives = 35/138 (25%), Gaps = 43/138 (31%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
              +    L+  V E  L D    +G + +                              
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEV----------------------------- 36

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                     EI+  P T    G A + + S   +  ++  +H   +    I        
Sbjct: 37  ----------EILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL---- 82

Query: 241 DSKGDRHGSAAERLLAAQ 258
           D KG +     E ++   
Sbjct: 83  DIKGQQRMKYYELIVNGS 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 = 89.3 bits (221), Expect = 3e-21
 Identities = 41/246 (16%), Positives = 77/246 (31%), Gaps = 84/246 (34%)

Query: 28  GESGDGDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           G +G G++ + V  L+ ++V+   ++ LF   G V  V     ++    +    ++    
Sbjct: 28  GLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADG 82

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKASSH-------------------------------- 114
             A  A+  +N  KL+GKPIR+  +                                   
Sbjct: 83  NQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSK 142

Query: 115 --QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASS 172
             Q      A + + N+ P V E+ L   FS+ G +++  K                   
Sbjct: 143 NFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---------------- 186

Query: 173 HQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL-CNRP 231
                                        +  A I   S E +  ++  +H   L  N  
Sbjct: 187 ---------------------------KDRKMALIQMGSVEEAVQALIDLHNHDLGENHH 219

Query: 232 ISVSYA 237
           + VS++
Sbjct: 220 LRVSFS 225

>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 = 53.8 bits (129), Expect = 8e-09
 Identities = 23/175 (13%), Positives = 56/175 (32%), Gaps = 48/175 (27%)

Query: 121 GANIFIGNLDPE-VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDV 179
            + + + NL+PE V  + L+  F  +G + +              +++            
Sbjct: 34  NSVLLVSNLNPERVTPQSLFILFGVYGDVQR--------------VKILF---------- 69

Query: 180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
                               N K  A +  A    +  ++  ++G  L  +PI ++ +  
Sbjct: 70  --------------------NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH 109

Query: 240 KDSKGDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPP 294
           ++ +  R G   + L         +         +     + PP   +++  +PP
Sbjct: 110 QNVQLPREGQEDQGL---TKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPP 161

>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 = 85.4 bits (212), Expect = 3e-21
 Identities = 24/94 (25%), Positives = 44/94 (46%), Gaps = 2/94 (2%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDR-VTQTHQGYGFIEFM 84
           G        + I V  +  + ++  + ELF   G +  V +PK    T  H+G+GF++F+
Sbjct: 7   GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66

Query: 85  GEEDADYAIKIM-NMIKLYGKPIRVNKASSHQKN 117
            ++DA  A   + +   LYG+ + +  A S    
Sbjct: 67  TKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTV 100

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 65.8 bits (161), Expect = 6e-14
 Identities = 18/144 (12%), Positives = 48/144 (33%), Gaps = 41/144 (28%)

Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
           + +S         + I + N+  + +++ + + FS FG +                    
Sbjct: 3   SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELK------------------- 43

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPD-TGNSKGFAFINYASFEASDASIDAM-HGQY 226
                                  + +    TG  +GF F+++ + + +  + +A+ H  +
Sbjct: 44  --------------------TVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTH 83

Query: 227 LCNRPISVSYAFKKDSKGDRHGSA 250
           L  R + + +A  + +      S 
Sbjct: 84  LYGRRLVLEWADSEVTVQSGPSSG 107

>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 = 85.5 bits (212), Expect = 4e-21
 Identities = 29/145 (20%), Positives = 57/145 (39%), Gaps = 39/145 (26%)

Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
           + +S  +K+     ++F+G+L PE+  + +   F+ FG I                 RV 
Sbjct: 3   SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISD--------------ARV- 47

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
                                   ++D  TG SKG+ F+++ +   ++ +I  M GQ+L 
Sbjct: 48  ------------------------VKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG 83

Query: 229 NRPISVSYAFKKDSKGDRHGSAAER 253
            R I  ++A +K         +  +
Sbjct: 84  GRQIRTNWATRKPPAPKSTYESNTK 108

>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 = 76.2 bits (188), Expect = 1e-17
 Identities = 24/84 (28%), Positives = 41/84 (48%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
           +       ++VG L  +++   +   F   G + +  + KD  T   +GYGF+ F  + D
Sbjct: 10  KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 69

Query: 89  ADYAIKIMNMIKLYGKPIRVNKAS 112
           A+ AI+ M    L G+ IR N A+
Sbjct: 70  AENAIQQMGGQWLGGRQIRTNWAT 93

>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 = 85.4 bits (212), Expect = 4e-21
 Identities = 22/96 (22%), Positives = 47/96 (48%)

Query: 16  LQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTH 75
           +++    +LE G +       ++V  + ++  E  + E F   G + N+H+  DR T   
Sbjct: 8   VRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS 67

Query: 76  QGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
           +GY  +E+   + A  A + +N  ++ G+ I+V+  
Sbjct: 68  KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC 103

>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 = 74.6 bits (184), Expect = 4e-17
 Identities = 24/120 (20%), Positives = 45/120 (37%), Gaps = 39/120 (32%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           G  +F+ ++  E  E  + + F  +G I                          KN+   
Sbjct: 26  GWILFVTSIHEEAQEDEIQEKFCDYGEI--------------------------KNIH-- 57

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                      +  D  TG SKG+A + Y + + + A+ +A++G  +  + I V + F K
Sbjct: 58  -----------LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 106

>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 = 84.6 bits (210), Expect = 5e-21
 Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 3/87 (3%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
            G         T++V GL +  +E  + E F      V   +  DR T + +G+GF++F 
Sbjct: 6   SGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFN 62

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKA 111
            EEDA  A + M   ++ G  + ++ A
Sbjct: 63  SEEDAKAAKEAMEDGEIDGNKVTLDWA 89

>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 = 70.0 bits (172), Expect = 2e-15
 Identities = 25/142 (17%), Positives = 48/142 (33%), Gaps = 42/142 (29%)

Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
           + +S           +F+  L  +  E+ L ++F                      +R  
Sbjct: 3   SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF-------------------DGSVRAR 43

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
                                  I+ D +TG+SKGF F+++ S E + A+ +AM    + 
Sbjct: 44  -----------------------IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEID 80

Query: 229 NRPISVSYAFKKDSKGDRHGSA 250
              +++ +A  K   G    S 
Sbjct: 81  GNKVTLDWAKPKGEGGSGPSSG 102

>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 = 85.5 bits (212), Expect = 6e-21
 Identities = 25/144 (17%), Positives = 55/144 (38%), Gaps = 40/144 (27%)

Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
                Q++++ G  +F+  +  E  E+ ++D F+ +G I                  ++ 
Sbjct: 12  DEPGPQRSVE-GWILFVTGVHEEATEEDIHDKFAEYGEI----------------KNIH- 53

Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
                                 +  D  TG  KG+  + Y +++ + A+++ ++GQ L  
Sbjct: 54  ----------------------LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG 91

Query: 230 RPISVSYAFKKDSKGDRHGSAAER 253
           +PISV + F +     +      R
Sbjct: 92  QPISVDWCFVRGPPKGKRRGGRRR 115

>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 = 84.3 bits (209), Expect = 2e-20
 Identities = 25/95 (26%), Positives = 49/95 (51%)

Query: 17  QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
            S+ Q   E G +       ++V G+ ++ +E  + + F + G + N+H+  DR T   +
Sbjct: 5   DSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64

Query: 77  GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
           GY  +E+   ++A  A++ +N   L G+PI V+  
Sbjct: 65  GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 99

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 84.2 bits (209), Expect = 7e-21
 Identities = 22/78 (28%), Positives = 40/78 (51%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
             +Y+G +    +E  + +L    GPV+N+ M  D  T   +GY FIEF   E +  A++
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 95  IMNMIKLYGKPIRVNKAS 112
            +N  +L  + ++   +S
Sbjct: 63  NLNGYQLGSRFLKCGYSS 80

>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 = 77.7 bits (192), Expect = 2e-18
 Identities = 24/125 (19%), Positives = 48/125 (38%), Gaps = 39/125 (31%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
             +++G++  +  E+ + D  S  G ++                                
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVI-------------------------------- 30

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                  + ++M DP TG SKG+AFI +   E+S +++  ++G  L +R +   Y+   D
Sbjct: 31  -------NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD 83

Query: 242 SKGDR 246
             G  
Sbjct: 84  ISGVS 88

>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 = 84.2 bits (209), Expect = 9e-21
 Identities = 28/87 (32%), Positives = 47/87 (54%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
            G       +  ++VGGL    +E  + ++F + G +  V + KDR TQ  +G+GF+ F 
Sbjct: 3   SGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFE 62

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKA 111
             +DA  A+  MN   + G+ IRV++A
Sbjct: 63  NIDDAKDAMMAMNGKSVDGRQIRVDQA 89

>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 = 76.5 bits (189), Expect = 7e-18
 Identities = 26/140 (18%), Positives = 48/140 (34%), Gaps = 40/140 (28%)

Query: 111 ASSHQK-NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
            SS           +F+G L  + +E+ L   FS +G I +                   
Sbjct: 1   GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEV------------------ 42

Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
                                 +++D +T  S+GF F+ + + + +  ++ AM+G+ +  
Sbjct: 43  ---------------------VVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG 81

Query: 230 RPISVSYAFKKDSKGDRHGS 249
           R I V  A K         S
Sbjct: 82  RQIRVDQAGKSSDNRSGPSS 101

>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 = 85.3 bits (211), Expect = 2e-20
 Identities = 22/95 (23%), Positives = 46/95 (48%)

Query: 17  QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
           ++    +LE G +       ++V  + ++  E  + E F   G + N+H+  DR T   +
Sbjct: 55  RNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114

Query: 77  GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
           GY  +E+   + A  A + +N  ++ G+ I+V+  
Sbjct: 115 GYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC 149

>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 = 83.0 bits (205), Expect = 1e-19
 Identities = 24/133 (18%), Positives = 47/133 (35%), Gaps = 39/133 (29%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           G  +F+ ++  E  E  + + F  +G I                  ++            
Sbjct: 72  GWILFVTSIHEEAQEDEIQEKFCDYGEI----------------KNIH------------ 103

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                      +  D  TG SKG+A + Y + + + A+ +A++G  +  + I V + F K
Sbjct: 104 -----------LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 152

Query: 241 DSKGDRHGSAAER 253
             K  +      R
Sbjct: 153 GPKRVKKSEKRRR 165

>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 = 82.3 bits (204), Expect = 3e-20
 Identities = 25/92 (27%), Positives = 49/92 (53%), Gaps = 1/92 (1%)

Query: 20  SQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYG 79
           S +    GG +    +T+YV  L   ++   ++ +F + G VV V + KD+ T+  +G  
Sbjct: 3   SGSSGMSGGLAPSK-STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVA 61

Query: 80  FIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
           FI F+ ++ A    + +N  +L+G+ I+ + A
Sbjct: 62  FILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 70.7 bits (174), Expect = 8e-16
 Identities = 26/117 (22%), Positives = 42/117 (35%), Gaps = 39/117 (33%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
            + +++ NL   +    LY  FS +G                   +V K +         
Sbjct: 16  KSTVYVSNLPFSLTNNDLYRIFSKYG-------------------KVVKVT--------- 47

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                      IM+D DT  SKG AFI +   +++     A++ + L  R I  S A
Sbjct: 48  -----------IMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 82.7 bits (205), Expect = 4e-20
 Identities = 25/95 (26%), Positives = 49/95 (51%)

Query: 17  QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
            S+ Q   E G +       ++V G+ ++ +E  + + F + G + N+H+  DR T   +
Sbjct: 6   DSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65

Query: 77  GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
           GY  +E+   ++A  A++ +N   L G+PI V+  
Sbjct: 66  GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 100

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 78.5 bits (194), Expect = 2e-18
 Identities = 24/132 (18%), Positives = 53/132 (40%), Gaps = 40/132 (30%)

Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
                 Q++++ G  +F+  +  E  E+ ++D F+ +G I                  ++
Sbjct: 12  GDEPGPQRSVE-GWILFVTGVHEEATEEDIHDKFAEYGEI----------------KNIH 54

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
                                  +  D  TG  KG+  + Y +++ + A+++ ++GQ L 
Sbjct: 55  -----------------------LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM 91

Query: 229 NRPISVSYAFKK 240
            +PISV + F +
Sbjct: 92  GQPISVDWCFVR 103

>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 = 82.3 bits (204), Expect = 5e-20
 Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 2/86 (2%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G  ES      ++V  +  +  +  + ++F Q G +++V +  +   +  +G+GF+ F  
Sbjct: 7   GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFEN 64

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKA 111
             DAD A + ++   + G+ I VN A
Sbjct: 65  SADADRAREKLHGTVVEGRKIEVNNA 90

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 66.5 bits (163), Expect = 3e-14
 Identities = 24/139 (17%), Positives = 44/139 (31%), Gaps = 41/139 (29%)

Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
           +S + ++      + + N+     +  L   F  FG IL                     
Sbjct: 5   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKIL--------------------- 43

Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
                             D EI+ +     SKGF F+ + +   +D + + +HG  +  R
Sbjct: 44  ------------------DVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGR 83

Query: 231 PISVSYAFKKDSKGDRHGS 249
            I V+ A  +        S
Sbjct: 84  KIEVNNATARVMTNSGPSS 102

>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 = 82.0 bits (203), Expect = 8e-20
 Identities = 29/82 (35%), Positives = 46/82 (56%), Gaps = 1/82 (1%)

Query: 30  SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA 89
             D    +++GGL+ + +E ++  +F + GP+  V + KDR T   +G+ FI F    DA
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61

Query: 90  DYAIKIMNMIKLYGKPIRVNKA 111
             A K MN   L+GK I+V +A
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQA 83

>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 = 73.5 bits (181), Expect = 1e-16
 Identities = 27/128 (21%), Positives = 44/128 (34%), Gaps = 40/128 (31%)

Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
           D    +FIG L+ E +EK+L   F   G I                              
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPIS----------------------------- 35

Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
                     +  +++D  T  S+GFAFI + +   +  +   M+G+ L  + I V  A 
Sbjct: 36  ----------EVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK 84

Query: 239 KKDSKGDR 246
           K   +   
Sbjct: 85  KPSFQSGG 92

>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 = 81.0 bits (201), Expect = 1e-19
 Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRV-TQTHQGYGFIEFMGEEDADYAI 93
             +++G L   V++  + E+F   G +  + MP +R+     +GY ++EF   ++A+ A+
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 94  KIMNMIKLYGKPIRVNKA 111
           K M+  ++ G+ I     
Sbjct: 65  KHMDGGQIDGQEITATAV 82

>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 = 64.5 bits (158), Expect = 1e-13
 Identities = 17/116 (14%), Positives = 39/116 (33%), Gaps = 38/116 (32%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
             + IG L   V +  + + FS +G I                          K +D+  
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKI--------------------------KMIDM-- 36

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                      +       SKG+A++ + + + ++ ++  M G  +  + I+ +  
Sbjct: 37  ----------PVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV 82

>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 = 85.7 bits (211), Expect = 1e-19
 Identities = 29/188 (15%), Positives = 53/188 (28%), Gaps = 47/188 (25%)

Query: 122 ANIFIGNLDPEVDE----KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNL 177
             I+I NL+ ++ +    K LY  FS FG IL                            
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILD--------------------------- 42

Query: 178 DVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                          +    +   +G AF+ +    ++  ++ +M G    ++P+ + YA
Sbjct: 43  ---------------ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87

Query: 238 -FKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPP 296
               D      G+  ER    +    ++                P        +   PP 
Sbjct: 88  KTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPM 147

Query: 297 PSGLRASA 304
               R   
Sbjct: 148 TQAPRIMH 155

>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 = 68.4 bits (166), Expect = 2e-13
 Identities = 19/83 (22%), Positives = 41/83 (49%), Gaps = 7/83 (8%)

Query: 35  ATIYVGGLDDKVSE----TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
            TIY+  L++K+ +      ++ +F Q G ++++ + +   +   +G  F+ F     A 
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66

Query: 91  YAIKIMNMIKLYGKPIRVNKASS 113
            A++ M     Y KP+R+  A +
Sbjct: 67  NALRSMQGFPFYDKPMRIQYAKT 89

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 46.0 bits (108), Expect = 5e-06
 Identities = 17/103 (16%), Positives = 34/103 (33%), Gaps = 6/103 (5%)

Query: 8   QAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMP 67
             G   P      Q            +  +++  L ++ +E ++  LF Q      V + 
Sbjct: 181 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 240

Query: 68  KDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY-GKPIRVN 109
             R         F+EF  E  A  A   +   K+     ++++
Sbjct: 241 PGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS 278

>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 = 46.0 bits (108), Expect = 5e-06
 Identities = 24/184 (13%), Positives = 49/184 (26%), Gaps = 50/184 (27%)

Query: 57  QSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQK 116
              P +  HMP         G      +              +     P     + +   
Sbjct: 148 TQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPN 207

Query: 117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKN 176
           +      +F+ NL  E +E +L   F+ F    +  +++                     
Sbjct: 208 H-----ILFLTNLPEETNELMLSMLFNQFPGF-KEVRLVP-------------------- 241

Query: 177 LDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC-NRPISVS 235
                                       AF+ + +   + A+ DA+ G  +  N  + +S
Sbjct: 242 -----------------------GRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS 278

Query: 236 YAFK 239
           +A K
Sbjct: 279 FAKK 282

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 83.0 bits (205), Expect = 1e-19
 Identities = 26/110 (23%), Positives = 50/110 (45%)

Query: 2   SLGREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPV 61
            +  E     +T        +         +G  ++ V  L  + S   +  +F + G V
Sbjct: 38  GVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRV 97

Query: 62  VNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
            +V++P+DR T+  +G+ F+ F  + DA+ A+  M+   L G+ +RV  A
Sbjct: 98  GDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147

>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 = 77.2 bits (190), Expect = 2e-17
 Identities = 31/188 (16%), Positives = 53/188 (28%), Gaps = 51/188 (27%)

Query: 72  TQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS------------HQKNLD 119
            +T +G    E +    A+   K              + A+             H  +++
Sbjct: 9   GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVE 68

Query: 120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDV 179
              ++ + NL        L   F  +G +                               
Sbjct: 69  GMTSLKVDNLTYRTSPDTLRRVFEKYGRVG------------------------------ 98

Query: 180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
                    D  I RD  T  S+GFAF+ +     ++ ++DAM G  L  R + V  A  
Sbjct: 99  ---------DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARY 149

Query: 240 KDSKGDRH 247
                  H
Sbjct: 150 GRPPDSHH 157

>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 = 80.7 bits (200), Expect = 1e-19
 Identities = 23/85 (27%), Positives = 39/85 (45%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           G     G   ++V  L    SE  + +LF   GP+  +H P D +T+  +G+ F+ FM  
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKA 111
           E A  A   ++     G+ + V  +
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPS 85

>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 = 67.2 bits (165), Expect = 2e-14
 Identities = 24/127 (18%), Positives = 38/127 (29%), Gaps = 39/127 (30%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+ NL     E+ L   FSA+G +                     +  H          
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPL---------------------SELH---------- 39

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                      D  T   KGFAF+ +   E +  +   + GQ    R + V  +  K   
Sbjct: 40  --------YPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA 91

Query: 244 GDRHGSA 250
                S+
Sbjct: 92  SQSGPSS 98

>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 = 80.8 bits (200), Expect = 2e-19
 Identities = 24/95 (25%), Positives = 45/95 (47%)

Query: 17  QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
             ++        +   G   +YVG L   ++E ++  +F   G + ++ +  D  T   +
Sbjct: 9   SHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68

Query: 77  GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
           GYGFI F   E A  A++ +N  +L G+P++V   
Sbjct: 69  GYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV 103

>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 = 69.3 bits (170), Expect = 4e-15
 Identities = 26/132 (19%), Positives = 50/132 (37%), Gaps = 39/132 (29%)

Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
            A++ QK       +++G+L   + E +L   F  FG                   R+  
Sbjct: 15  MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFG-------------------RIES 55

Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
                                 +M D +TG SKG+ FI ++  E +  +++ ++G  L  
Sbjct: 56  IQ--------------------LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG 95

Query: 230 RPISVSYAFKKD 241
           RP+ V +  ++ 
Sbjct: 96  RPMKVGHVTERT 107

>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 = 80.4 bits (199), Expect = 2e-19
 Identities = 29/141 (20%), Positives = 50/141 (35%), Gaps = 43/141 (30%)

Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
           +S  +        +F+G L+ +  E+ +   F  FGVI +                    
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDEC------------------- 45

Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL--- 227
                                ++R PD G+SKG AF+ ++S   + A+I A+HG      
Sbjct: 46  --------------------TVLRGPD-GSSKGCAFVKFSSHTEAQAAIHALHGSQTMPG 84

Query: 228 CNRPISVSYAFKKDSKGDRHG 248
            +  + V +A      G   G
Sbjct: 85  ASSSLVVKFADTDKESGPSSG 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 = 64.2 bits (157), Expect = 2e-13
 Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 4/95 (4%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G    G  D  ++VG L+ + SE  +  LF   G +    + +     + +G  F++F  
Sbjct: 7   GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSS 65

Query: 86  EEDADYAIKIMN---MIKLYGKPIRVNKASSHQKN 117
             +A  AI  ++    +      + V  A + +++
Sbjct: 66  HTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES 100

>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 = 80.0 bits (198), Expect = 3e-19
 Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 6/88 (6%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           GG ++    + ++VG L   ++E  M +LF + G    V + KD+      G+GFI    
Sbjct: 7   GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLET 60

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASS 113
              A+ A   ++ + L GK +RV  A  
Sbjct: 61  RTLAEIAKVELDNMPLRGKQLRVRFACH 88

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 62.7 bits (153), Expect = 8e-13
 Identities = 20/135 (14%), Positives = 43/135 (31%), Gaps = 45/135 (33%)

Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
           + +S  +K     + +F+GNL P++ E+ +   F  +G   +              + ++
Sbjct: 3   SGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGE--------------VFIH 48

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
           K                                KGF FI   +   ++ +   +    L 
Sbjct: 49  K-------------------------------DKGFGFIRLETRTLAEIAKVELDNMPLR 77

Query: 229 NRPISVSYAFKKDSK 243
            + + V +A    S 
Sbjct: 78  GKQLRVRFACHSASL 92

>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 = 80.9 bits (200), Expect = 3e-19
 Identities = 24/87 (27%), Positives = 47/87 (54%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
            G   + D +  + V GL    +E  + E+F + GP+ +V +  D+ ++  +G+ F+ F 
Sbjct: 37  VGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 96

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKA 111
             +DA  A +  N ++L G+ IRV+ +
Sbjct: 97  NVDDAKEAKERANGMELDGRRIRVDFS 123

>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 = 22/122 (18%), Positives = 40/122 (32%), Gaps = 39/122 (31%)

Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
           D    + +  L     E+ L + FS +G I                              
Sbjct: 44  DPNCCLGVFGLSLYTTERDLREVFSKYGPIA----------------------------- 74

Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
                     D  I+ D  +  S+GFAF+ + + + +  + +  +G  L  R I V ++ 
Sbjct: 75  ----------DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI 124

Query: 239 KK 240
            K
Sbjct: 125 TK 126

>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 = 79.5 bits (197), Expect = 4e-19
 Identities = 27/80 (33%), Positives = 44/80 (55%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
            G + +YVG L   ++E ++  +F   G + N+ + KD  T   +GYGFI F   E A  
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 92  AIKIMNMIKLYGKPIRVNKA 111
           A++ +N  +L G+P+RV   
Sbjct: 63  ALEQLNGFELAGRPMRVGHV 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 = 74.9 bits (185), Expect = 2e-17
 Identities = 26/128 (20%), Positives = 49/128 (38%), Gaps = 39/128 (30%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
           + +++G+L   + E +L   F  FG I                                 
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKID-------------------------------- 33

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                  +  +M+D DTG SKG+ FI ++  E +  +++ ++G  L  RP+ V +  ++ 
Sbjct: 34  -------NIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERL 86

Query: 242 SKGDRHGS 249
             G    S
Sbjct: 87  DGGSGPSS 94

>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 = 78.8 bits (195), Expect = 8e-19
 Identities = 24/77 (31%), Positives = 46/77 (59%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
            +++VG +  + +E  + ++F + GPVV+  +  DR T   +GYGF E+  +E A  A++
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 95  IMNMIKLYGKPIRVNKA 111
            +N  +  G+ +RV+ A
Sbjct: 69  NLNGREFSGRALRVDNA 85

>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 = 66.1 bits (162), Expect = 4e-14
 Identities = 23/125 (18%), Positives = 44/125 (35%), Gaps = 39/125 (31%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
            ++F+GN+  E  E+ L D FS                  G  +                
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSE----------------VGPVVSFR------------- 39

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                     ++ D +TG  KG+ F  Y   E + +++  ++G+    R + V  A  + 
Sbjct: 40  ----------LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK 89

Query: 242 SKGDR 246
           +K + 
Sbjct: 90  NKEEL 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 = 78.5 bits (194), Expect = 1e-18
 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 6/74 (8%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T Y+G +    +E  +  LF   G +++     ++      G  FI++   E A   I  
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQAAVCIVA 82

Query: 96  MNMIKLYGKPIRVN 109
           +      G+ +R  
Sbjct: 83  LANFPFQGRNLRTG 96

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 60.0 bits (146), Expect = 6e-12
 Identities = 23/141 (16%), Positives = 34/141 (24%), Gaps = 48/141 (34%)

Query: 100 KLYGKPIRVNKASSHQKNLDVGAN---IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN 156
           +  G P +VN  +               +IGN+     E  L   F  FG IL       
Sbjct: 3   QTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILD------ 56

Query: 157 MIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASD 216
                    +                                   KG  FI Y + E + 
Sbjct: 57  --------FKHYP-------------------------------EKGCCFIKYDTHEQAA 77

Query: 217 ASIDAMHGQYLCNRPISVSYA 237
             I A+       R +   + 
Sbjct: 78  VCIVALANFPFQGRNLRTGWG 98

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 78.1 bits (193), Expect = 1e-18
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ---GYGFIEFMGEEDA 89
           G + +++  L+   +E  +  +F + G + +  + K +         G+GF+E+   E A
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 90  DYAIKIMNMIKLYGKPIRVNKA 111
             A+K +    + G  + V  +
Sbjct: 64  QKALKQLQGHTVDGHKLEVRIS 85

>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 = 71.1 bits (175), Expect = 5e-16
 Identities = 20/133 (15%), Positives = 35/133 (26%), Gaps = 42/133 (31%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
            + +FI NL+    E+ L   FS  G I                                
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIK------------------------------- 33

Query: 181 ANIFIGNLDPEIMRDPDTGN---SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                      I +  +      S GF F+ Y   E +  ++  + G  +    + V  +
Sbjct: 34  --------SCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS 85

Query: 238 FKKDSKGDRHGSA 250
            +         S 
Sbjct: 86  ERATKPASGPSSG 98

>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 = 78.5 bits (194), Expect = 2e-18
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+++  L     E  + E+  Q G +  V +     T+  +G  F +FM +E A   +  
Sbjct: 17  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76

Query: 96  MNM------IKLYGKPIRVNKASS 113
            ++      +KL G+ ++V+ A +
Sbjct: 77  ASLEAEGGGLKLDGRQLKVDLAVT 100

>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 = 70.5 bits (173), Expect = 1e-15
 Identities = 27/143 (18%), Positives = 45/143 (31%), Gaps = 45/143 (31%)

Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
            +S    ++  G  +FI NL  + +E+ L +    FG +                     
Sbjct: 4   GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLK-------------------- 43

Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMH------ 223
                                 ++  PDT +SKG AF  + + EA+   + A        
Sbjct: 44  -------------------YVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGG 84

Query: 224 GQYLCNRPISVSYAFKKDSKGDR 246
           G  L  R + V  A  +D     
Sbjct: 85  GLKLDGRQLKVDLAVTRDEAASG 107

>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 = 78.1 bits (193), Expect = 2e-18
 Identities = 29/89 (32%), Positives = 37/89 (41%), Gaps = 11/89 (12%)

Query: 28  GESGDGDA-----TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIE 82
           G SGD D       +YV  L    SE ++ + F    P     + K R       Y F+ 
Sbjct: 4   GSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR------DYAFVH 57

Query: 83  FMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
           F   EDA  A+K +N   L G PI V  A
Sbjct: 58  FSNREDAVEAMKALNGKVLDGSPIEVTLA 86

>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 = 62.3 bits (152), Expect = 1e-12
 Identities = 23/142 (16%), Positives = 48/142 (33%), Gaps = 47/142 (33%)

Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
           + +S  +  +     +++ NL     E+++   F+                      RV 
Sbjct: 3   SGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPG--------------AVERVK 48

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
           K                                + +AF+++++ E +  ++ A++G+ L 
Sbjct: 49  K-------------------------------IRDYAFVHFSNREDAVEAMKALNGKVLD 77

Query: 229 NRPISVSYA--FKKDSKGDRHG 248
             PI V+ A    KDS G   G
Sbjct: 78  GSPIEVTLAKPVDKDSSGPSSG 99

>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 = 78.1 bits (193), Expect = 2e-18
 Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++   L  ++    + + F   G V +V +  DR ++  +G  ++EF   +    AI  
Sbjct: 27  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG- 85

Query: 96  MNMIKLYGKPIRVNKA 111
           +   +L G PI V  +
Sbjct: 86  LTGQRLLGVPIIVQAS 101

>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 = 64.3 bits (157), Expect = 3e-13
 Identities = 23/127 (18%), Positives = 41/127 (32%), Gaps = 40/127 (31%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F   L   +  + L D FSA G +                  V                
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKV----------------RDVR--------------- 56

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                   I+ D ++  SKG A++ +   ++   +I  + GQ L   PI V  +  + ++
Sbjct: 57  --------IISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNR 107

Query: 244 GDRHGSA 250
                S 
Sbjct: 108 LSGPSSG 114

>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 = 78.1 bits (193), Expect = 2e-18
 Identities = 21/85 (24%), Positives = 39/85 (45%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
             G+ +  +Y+  L  +V+E  +  LF +        +    +T   +G  FI F  +E 
Sbjct: 20  NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 79

Query: 89  ADYAIKIMNMIKLYGKPIRVNKASS 113
           A  A+ ++N  KLYGK + +    +
Sbjct: 80  AWQALHLVNGYKLYGKILVIEFGKN 104

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 75.0 bits (185), Expect = 3e-17
 Identities = 27/148 (18%), Positives = 46/148 (31%), Gaps = 41/148 (27%)

Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
           G+ IR     S     +    +++ NL P V E+ L   F+ F                 
Sbjct: 7   GEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKK------------- 53

Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
                                      P I     TG  +G AFI + + E +  ++  +
Sbjct: 54  --------------------------GPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87

Query: 223 HGQYLCNRPISVSYAFKKD--SKGDRHG 248
           +G  L  + + + +   K   S G   G
Sbjct: 88  NGYKLYGKILVIEFGKNKKQRSSGPSSG 115

>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 = 77.3 bits (191), Expect = 3e-18
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
            T+YV G D  ++ TL+   F   G ++++ M   R         F+ +   E AD A+ 
Sbjct: 16  NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVA 67

Query: 95  IMNMIKLYGKPIRVNKA 111
            +N  ++    ++VN A
Sbjct: 68  ELNGTQVESVQLKVNIA 84

>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 = 66.2 bits (162), Expect = 4e-14
 Identities = 20/141 (14%), Positives = 45/141 (31%), Gaps = 47/141 (33%)

Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
           + +S  ++    G  +++   D  +   LL   FS FG I+               + ++
Sbjct: 3   SGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIID--------------LSMD 46

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
                                            +  AF+ Y   E++D ++  ++G  + 
Sbjct: 47  P-------------------------------PRNCAFVTYEKMESADQAVAELNGTQVE 75

Query: 229 NRPISVSYAFKKDSKGDRHGS 249
           +  + V+ A K+        S
Sbjct: 76  SVQLKVNIARKQPMLDSGPSS 96

>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 = 76.9 bits (190), Expect = 3e-18
 Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 7/86 (8%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           G     G   +Y+G L   V+   + +LF          +P         GY F+++  +
Sbjct: 1   GSSGSSGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQ 54

Query: 87  EDADYAIKIMN-MIKLYGKPIRVNKA 111
             A  AI+ ++  ++L+GK + V+ +
Sbjct: 55  NWAIRAIETLSGKVELHGKIMEVDYS 80

>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 = 66.1 bits (162), Expect = 3e-14
 Identities = 19/123 (15%), Positives = 34/123 (27%), Gaps = 46/123 (37%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           ++IGNL P V    L   F    + L                                  
Sbjct: 11  LYIGNLSPAVTADDLRQLFGDRKLPL---------------------------------- 36

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY-LCNRPISVSYAFKKDS 242
                              G+AF++Y     +  +I+ + G+  L  + + V Y+  K  
Sbjct: 37  -----------AGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL 85

Query: 243 KGD 245
           +  
Sbjct: 86  RSS 88

>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 = 77.4 bits (191), Expect = 3e-18
 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
            T+Y GG+   +++ LM + F   G ++ + +  ++      GY F+ F   E A +AI 
Sbjct: 26  CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIV 79

Query: 95  IMNMIKLYGKPIRVN 109
            +N   + G  ++  
Sbjct: 80  SVNGTTIEGHVVKCY 94

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 61.2 bits (149), Expect = 4e-12
 Identities = 19/130 (14%), Positives = 48/130 (36%), Gaps = 47/130 (36%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
             ++ G +   + ++L+  TFS FG I++              IR               
Sbjct: 26  CTVYCGGIASGLTDQLMRQTFSPFGQIME--------------IR--------------- 56

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                     +  +      KG++F+ +++ E++  +I +++G  +    +   +   K+
Sbjct: 57  ----------VFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG--KE 98

Query: 242 SKGDRHGSAA 251
           S     G ++
Sbjct: 99  SPDMTSGPSS 108

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 76.6 bits (189), Expect = 4e-18
 Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 6/93 (6%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSG--PVVNVHMPKDRVTQTHQGYGFIEFM 84
           G        TI +  +        +           V N+ + KD+ TQ ++G+ F++  
Sbjct: 2   GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61

Query: 85  GEEDADYAIKIMN----MIKLYGKPIRVNKASS 113
              DA   ++I+      +K+ GK I V+ A S
Sbjct: 62  SAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 69.7 bits (171), Expect = 2e-15
 Identities = 14/123 (11%), Positives = 34/123 (27%), Gaps = 41/123 (33%)

Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
                I + N+ P      +    S +  +                +             
Sbjct: 7   HHMDTIILRNIAPHTVVDSIMTALSPYASL---------------AVN------------ 39

Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQ----YLCNRPISV 234
                     +  +++D  T  ++GFAF+  +S   +   +  +        +  + I V
Sbjct: 40  ----------NIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV 89

Query: 235 SYA 237
            +A
Sbjct: 90  DFA 92

>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 = 76.4 bits (189), Expect = 5e-18
 Identities = 30/76 (39%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            IYVG L    +   + ELF Q G V NV +  DR T+  +G+GF+E M EE    AI  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAK 61

Query: 96  MNMIKLYGKPIRVNKA 111
           ++     G+ IRV +A
Sbjct: 62  LDNTDFMGRTIRVTEA 77

>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 = 63.0 bits (154), Expect = 4e-13
 Identities = 26/125 (20%), Positives = 39/125 (31%), Gaps = 40/125 (32%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           NI++GNL      + + + FS FG                   +V               
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFG-------------------KVFNVK----------- 32

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
                    ++ D +T   KGF F+       S+A I  +       R I V+ A  K S
Sbjct: 33  ---------LIYDRETKKPKGFGFVEMQEESVSEA-IAKLDNTDFMGRTIRVTEANPKKS 82

Query: 243 KGDRH 247
               H
Sbjct: 83  LEHHH 87

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 77.9 bits (192), Expect = 5e-18
 Identities = 24/87 (27%), Positives = 45/87 (51%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
                  +G  ++ V  L  + S   +  +F + G V +V++P+DR T+  +G+ F+ F 
Sbjct: 38  GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFH 97

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKA 111
            + DA+ A+  M+   L G+ +RV  A
Sbjct: 98  DKRDAEDAMDAMDGAVLDGRELRVQMA 124

>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 = 2e-15
 Identities = 27/140 (19%), Positives = 43/140 (30%), Gaps = 40/140 (28%)

Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
                  +++   ++ + NL        L   F  +G                   RV  
Sbjct: 36  SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYG-------------------RVGD 76

Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
                                 I RD  T  S+GFAF+ +     ++ ++DAM G  L  
Sbjct: 77  VY--------------------IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 116

Query: 230 RPISVSYAFKKDSKGDRHGS 249
           R + V  A +     D H S
Sbjct: 117 RELRVQMA-RYGRPPDSHHS 135

>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 = 6e-18
 Identities = 34/139 (24%), Positives = 48/139 (34%), Gaps = 43/139 (30%)

Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
            SS  K+ D    +FIG +   +DEK L   F  FG I                      
Sbjct: 4   GSSGMKDHD-AIKLFIGQIPRNLDEKDLKPLFEEFGKIY--------------------- 41

Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL--- 227
                             +  +++D  TG  KG AF+ Y   E++  +  A+H Q     
Sbjct: 42  ------------------ELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPG 83

Query: 228 CNRPISVSYAFKKDSKGDR 246
            NRPI V  A  +   G  
Sbjct: 84  MNRPIQVKPADSESRGGSG 102

>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 = 75.8 bits (187), Expect = 1e-17
 Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 3/95 (3%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
             G        +++G +   + E  +  LF + G +  + + KDR T  H+G  F+ +  
Sbjct: 5   SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64

Query: 86  EEDADYAIKIMN---MIKLYGKPIRVNKASSHQKN 117
            E A  A   ++    +    +PI+V  A S  + 
Sbjct: 65  RESALKAQSALHEQKTLPGMNRPIQVKPADSESRG 99

>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 = 77.5 bits (191), Expect = 7e-18
 Identities = 28/113 (24%), Positives = 48/113 (42%)

Query: 17  QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
           Q              D    + V  +   V E  + +LF + GP+ +V +  DR T+  +
Sbjct: 25  QQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSR 84

Query: 77  GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNL 129
           GYGF++F     A  AI  +N   +  K ++V  A+S  +   +   +  GN 
Sbjct: 85  GYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNG 137

>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 = 77.1 bits (190), Expect = 1e-17
 Identities = 25/173 (14%), Positives = 55/173 (31%), Gaps = 41/173 (23%)

Query: 81  IEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYD 140
           I  + + D       +   +L  +  +    +      DV  N+ +  +   VDE  L  
Sbjct: 4   IPLVSQYDPYGQTAQLQ--QLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQ 61

Query: 141 TFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN 200
            F  +G                    +                        I+ D +T  
Sbjct: 62  LFERYG-------------------PIESVK--------------------IVCDRETRQ 82

Query: 201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAER 253
           S+G+ F+ + S  ++  +I  ++G  + N+ + V+ A     +    G+  + 
Sbjct: 83  SRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDG 135

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 75.4 bits (186), Expect = 1e-17
 Identities = 15/83 (18%), Positives = 38/83 (45%), Gaps = 1/83 (1%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
             +++ GL    ++  + E+    G V ++ +  +R     +G  ++E+  E  A  A+ 
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVM 76

Query: 95  IMNMIKLYGKPIRVNKASSHQKN 117
            M+ + +    I+V  ++S   +
Sbjct: 77  KMDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 18/124 (14%), Positives = 35/124 (28%), Gaps = 40/124 (32%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
              +FI  L     ++ L +   A G +                                
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVK------------------------------- 45

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                   D  ++ +   G  KG A++ Y +   +  ++  M G  +    I V+ +   
Sbjct: 46  --------DLRLVTN-RAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSG 96

Query: 241 DSKG 244
            S G
Sbjct: 97  PSSG 100

>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 = 75.9 bits (187), Expect = 2e-17
 Identities = 26/89 (29%), Positives = 41/89 (46%), Gaps = 1/89 (1%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
            GGGE  +  A + V  LD  VS+  + ELF + G +    +  DR +    G   + F 
Sbjct: 26  CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFE 84

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKASS 113
              DA  A+K    + L G+P+ +   +S
Sbjct: 85  RRADALKAMKQYKGVPLDGRPMDIQLVAS 113

>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 = 67.0 bits (164), Expect = 3e-14
 Identities = 18/134 (13%), Positives = 41/134 (30%), Gaps = 40/134 (29%)

Query: 107 RVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIR 166
             +      + ++ GA + + NLD  V +  + + F+ FG + +                
Sbjct: 21  LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA--------------- 65

Query: 167 VNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY 226
                                    +  D  +G S G A +++     +  ++    G  
Sbjct: 66  ------------------------AVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVP 100

Query: 227 LCNRPISVSYAFKK 240
           L  RP+ +     +
Sbjct: 101 LDGRPMDIQLVASQ 114

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 74.5 bits (184), Expect = 2e-17
 Identities = 18/81 (22%), Positives = 37/81 (45%)

Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           G + +Y+ GL    ++  + +L    G +V+     D+ T   +GYGF++F     A  A
Sbjct: 4   GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 93  IKIMNMIKLYGKPIRVNKASS 113
           +  +    +  +  + +  SS
Sbjct: 64  VTALKASGVQAQMAKQSGPSS 84

>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 = 72.6 bits (179), Expect = 1e-16
 Identities = 16/115 (13%), Positives = 35/115 (30%), Gaps = 39/115 (33%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
            + ++I  L P   ++ L      +G I+                     S+        
Sbjct: 5   SSGLYIRGLQPGTTDQDLVKLCQPYGKIV---------------------STK------- 36

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS 235
                       + D  T   KG+ F+++ S  A+  ++ A+    +  +    S
Sbjct: 37  -----------AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQS 80

>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 = 74.2 bits (183), Expect = 3e-17
 Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 8/87 (9%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
            G SG     ++VG +    +   +   F + GPV+   + K         Y F+     
Sbjct: 3   SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERA 54

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKASS 113
           EDA  AI+ ++  +  GK + V  ++S
Sbjct: 55  EDAVEAIRGLDNTEFQGKRMHVQLSTS 81

>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 = 47.2 bits (113), Expect = 2e-07
 Identities = 13/129 (10%), Positives = 34/129 (26%), Gaps = 47/129 (36%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
              + +GN+ P    + L   F  +G ++                               
Sbjct: 10  STKLHVGNISPTCTNQELRAKFEEYGPVI------------------------------- 38

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                   + +I++         +AF++    E +  +I  +       + + V  +  +
Sbjct: 39  --------ECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSR 82

Query: 241 DSKGDRHGS 249
                   S
Sbjct: 83  LRTASGPSS 91

>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 = 74.6 bits (184), Expect = 3e-17
 Identities = 28/117 (23%), Positives = 41/117 (35%), Gaps = 33/117 (28%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN-MIKLYGKPIRVNKASSHQKNLDVG 180
             IF+  L   V  + + D F   G+I    K    MI LY                   
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLY------------------- 54

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                         D +TG  KG A +++    ++ A+ID   G+     PI VS+A
Sbjct: 55  -------------TDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 72.0 bits (177), Expect = 3e-16
 Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 8/86 (9%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPV--------VNVHMPKDRVTQTHQGYGFIEFMGE 86
            TI+V GL + V+   + + F Q G +          +++  DR T   +G   + F   
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKAS 112
             A  AI   +  +  G PI+V+ A+
Sbjct: 74  PSAKAAIDWFDGKEFSGNPIKVSFAT 99

>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 = 74.6 bits (184), Expect = 4e-17
 Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 1/88 (1%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           GGG   +    + V  LD  VS+  + ELF + G +    +  DR +    G   + F  
Sbjct: 21  GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFER 79

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASS 113
           + DA  A+K  N + L G+P+ +   +S
Sbjct: 80  KADALKAMKQYNGVPLDGRPMNIQLVTS 107

>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 = 66.9 bits (164), Expect = 2e-14
 Identities = 17/131 (12%), Positives = 40/131 (30%), Gaps = 40/131 (30%)

Query: 107 RVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIR 166
             +        ++ G  + + NLD  V +  + + F+ FG + +                
Sbjct: 15  LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKA--------------- 59

Query: 167 VNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY 226
                                    +  D  +G S G A +++     +  ++   +G  
Sbjct: 60  ------------------------AVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVP 94

Query: 227 LCNRPISVSYA 237
           L  RP+++   
Sbjct: 95  LDGRPMNIQLV 105

>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 = 74.1 bits (183), Expect = 4e-17
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 32  DGDA-TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
           + DA +IYVG +D   +   +   F   G V  V +  D+ +   +G+ +IEF  +E   
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 91  YAIKIMNMIKLYGKPIRVNKA 111
            ++  ++     G+ I+V   
Sbjct: 63  TSLA-LDESLFRGRQIKVIPK 82

>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 = 61.4 bits (150), Expect = 1e-12
 Identities = 23/115 (20%), Positives = 38/115 (33%), Gaps = 40/115 (34%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           +I++GN+D     + L   F   G +                 RV               
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVN----------------RVT-------------- 37

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                    I+ D  +G+ KGFA+I ++  E+   S+ A+       R I V   
Sbjct: 38  ---------ILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPK 82

>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 = 75.7 bits (186), Expect = 4e-17
 Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
           +S   D  +YVG L +  ++T +   F   GP+ +V + ++       G+ F+EF    D
Sbjct: 68  DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRD 122

Query: 89  ADYAIKIMNMIKLYGKPIRVNKA 111
           A  A++ ++   L G  +RV  +
Sbjct: 123 AADAVRELDGRTLCGCRVRVELS 145

>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 = 59.9 bits (145), Expect = 3e-11
 Identities = 17/135 (12%), Positives = 40/135 (29%), Gaps = 44/135 (32%)

Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
            +    +    H+ +  +   +++GNL    ++  L   F  +G +              
Sbjct: 55  TEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLR------------- 101

Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
                                        + R+P      GFAF+ +     +  ++  +
Sbjct: 102 --------------------------SVWVARNP-----PGFAFVEFEDPRDAADAVREL 130

Query: 223 HGQYLCNRPISVSYA 237
            G+ LC   + V  +
Sbjct: 131 DGRTLCGCRVRVELS 145

>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 = 74.3 bits (183), Expect = 5e-17
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 3/84 (3%)

Query: 28  GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           G +G+ D  IYVG L   +    + ++F + G + ++ +   R       + F+EF    
Sbjct: 16  GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPR 72

Query: 88  DADYAIKIMNMIKLYGKPIRVNKA 111
           DA+ A+   +     G  +RV   
Sbjct: 73  DAEDAVYGRDGYDYDGYRLRVEFP 96

>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 = 49.6 bits (119), Expect = 4e-08
 Identities = 18/127 (14%), Positives = 35/127 (27%), Gaps = 44/127 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           I++GNL P++  K + D F  +G I                                   
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIR---------------------------------- 50

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA--FKKD 241
                D ++           FAF+ +     ++ ++    G       + V +    +  
Sbjct: 51  -----DIDLKNRR---GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 102

Query: 242 SKGDRHG 248
             G   G
Sbjct: 103 GSGPSSG 109

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 74.7 bits (184), Expect = 5e-17
 Identities = 29/131 (22%), Positives = 45/131 (34%), Gaps = 33/131 (25%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN-MIKLYGKPIRVNKASSHQKNLDVGA 181
            IF+  L   V  + + D F   G+I    K    MI LY                    
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLY-------------------- 48

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                        D +TG  KG A +++    ++ A+ID   G+     PI VS+A ++ 
Sbjct: 49  ------------TDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA 96

Query: 242 SKGDRHGSAAE 252
                 G+   
Sbjct: 97  DFNRGGGNGRG 107

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 72.0 bits (177), Expect = 4e-16
 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 8/84 (9%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPV--------VNVHMPKDRVTQTHQGYGFIEFMGEE 87
           TI+V GL + V+   + + F Q G +          +++  DR T   +G   + F    
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 88  DADYAIKIMNMIKLYGKPIRVNKA 111
            A  AI   +  +  G PI+V+ A
Sbjct: 69  SAKAAIDWFDGKEFSGNPIKVSFA 92

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 74.3 bits (183), Expect = 5e-17
 Identities = 19/85 (22%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
             E+      ++V  +  +  +  + ++F Q G +++V +  +   +  +G+GF+ F   
Sbjct: 22  NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENS 79

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKA 111
            DAD A + ++   + G+ I VN A
Sbjct: 80  ADADRAREKLHGTVVEGRKIEVNNA 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 = 67.0 bits (164), Expect = 2e-14
 Identities = 23/136 (16%), Positives = 43/136 (31%), Gaps = 41/136 (30%)

Query: 105 PIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKP 164
            +    +  + +N      + + N+     +  L   F  FG IL               
Sbjct: 13  GLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKIL--------------- 57

Query: 165 IRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHG 224
                                   D EI+ +     SKGF F+ + +   +D + + +HG
Sbjct: 58  ------------------------DVEIIFNERG--SKGFGFVTFENSADADRAREKLHG 91

Query: 225 QYLCNRPISVSYAFKK 240
             +  R I V+ A  +
Sbjct: 92  TVVEGRKIEVNNATAR 107

>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 = 73.9 bits (182), Expect = 7e-17
 Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 8/76 (10%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            ++V  L + V+E ++ + F Q G +  V   KD        Y FI F   + A  A++ 
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEE 64

Query: 96  MNMIKLYGKPIRVNKA 111
           MN   L G+ I +  A
Sbjct: 65  MNGKDLEGENIEIVFA 80

>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 = 63.1 bits (154), Expect = 6e-13
 Identities = 24/139 (17%), Positives = 45/139 (32%), Gaps = 47/139 (33%)

Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
            SS    +     +F+ NL   V E++L   FS FG + +  K +               
Sbjct: 1   GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERV-KKL--------------- 44

Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
                                          K +AFI++   + +  +++ M+G+ L   
Sbjct: 45  -------------------------------KDYAFIHFDERDGAVKAMEEMNGKDLEGE 73

Query: 231 PISVSYAFKKDSKGDRHGS 249
            I + +A   D K     +
Sbjct: 74  NIEIVFAKPPDQKRKERKA 92

>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 = 73.9 bits (182), Expect = 9e-17
 Identities = 13/76 (17%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +Y+  L  K++   M+++F + GP+  + +     T+   G  ++ +    DA  A+  
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAVDH 66

Query: 96  MNMIKLYGKPIRVNKA 111
           ++   +  + + V   
Sbjct: 67  LSGFNVSNRYLVVLYY 82

>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 = 67.0 bits (164), Expect = 3e-14
 Identities = 25/141 (17%), Positives = 45/141 (31%), Gaps = 42/141 (29%)

Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
           +V   ++I NL  ++  + +YD F  +G I Q              IRV           
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ--------------IRV----------- 40

Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
                             +T  ++G A++ Y     +  ++D + G  + NR + V Y  
Sbjct: 41  -----------------GNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN 83

Query: 239 KKDSKGDRHGSAAERLLAAQN 259
              +         E  L    
Sbjct: 84  ANRAFQKMDTKKKEEQLKLLK 104

>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 = 73.1 bits (180), Expect = 1e-16
 Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 4/87 (4%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
            G         T+ +  L    +E  + E+F ++  +              +GY FIEF 
Sbjct: 6   SGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYAFIEFA 61

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKA 111
             EDA  A+   N  ++ G+ IR+   
Sbjct: 62  SFEDAKEALNSCNKREIEGRAIRLELQ 88

>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 = 63.5 bits (155), Expect = 4e-13
 Identities = 20/123 (16%), Positives = 37/123 (30%), Gaps = 43/123 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           + + NL     E+ L + F     I                                   
Sbjct: 18  LVLSNLSYSATEETLQEVFEKATFIK---------------------------------- 43

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                    +     G SKG+AFI +ASFE +  ++++ + + +  R I +     + S 
Sbjct: 44  ---------VPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP 94

Query: 244 GDR 246
              
Sbjct: 95  NSG 97

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 72.8 bits (179), Expect = 1e-16
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 38  YVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN 97
            +      V +  +  LF ++G VVN+  P D  T   +G+ F+E     DA   IK  +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 98  MIKLYGKP-IRVNKASSHQK 116
             +L  K  + +      ++
Sbjct: 76  GKRLDLKHRLFLYTMKDVER 95

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 20/103 (19%), Positives = 30/103 (29%), Gaps = 39/103 (37%)

Query: 125 FIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIF 184
            I +    V +K L   FS  G ++                                   
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVV----------------------------------- 40

Query: 185 IGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
               + E   D  TG +KGF F+   S   +   I + HG+ L
Sbjct: 41  ----NMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 72.6 bits (179), Expect = 1e-16
 Identities = 23/121 (19%), Positives = 36/121 (29%), Gaps = 41/121 (33%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
              IF+ NL  +   K+L D F+  G +L                               
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNECGHVLYA----------------------------- 38

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                     +I  +   G SKG   + + S E ++ +   M+G  L  R I V      
Sbjct: 39  ----------DIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNA 86

Query: 241 D 241
            
Sbjct: 87  S 87

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 66.4 bits (163), Expect = 2e-14
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 2/85 (2%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           G     G   I+V  L    +  ++ + F + G V+   +  +      +G G ++F   
Sbjct: 1   GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKA 111
           E A+ A ++MN +KL G+ I V   
Sbjct: 59  EVAERACRMMNGMKLSGREIDVRID 83

>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 = 72.7 bits (179), Expect = 2e-16
 Identities = 16/90 (17%), Positives = 40/90 (44%), Gaps = 2/90 (2%)

Query: 28  GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           G        +++G L+   S   +     +     ++ +  D  T T++ +G+++F   E
Sbjct: 11  GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAE 69

Query: 88  DADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
           D + A++ +  +K++G  I++ K       
Sbjct: 70  DLEKALE-LTGLKVFGNEIKLEKPKGRDGT 98

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 68.8 bits (169), Expect = 5e-15
 Identities = 19/121 (15%), Positives = 36/121 (29%), Gaps = 41/121 (33%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           N+FIGNL+P      L    S                        N              
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFA-------------------KNDL------------ 47

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
                     + D  TG ++ F ++++ S E  + +++ + G  +    I +     +D 
Sbjct: 48  ---------AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDG 97

Query: 243 K 243
            
Sbjct: 98  T 98

>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 = 72.8 bits (179), Expect = 2e-16
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 29  ESGDGDA-TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           E  + D  ++YVG +D   +   +   F   G +  + +  D+ +   +GY +IEF    
Sbjct: 30  EKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERN 89

Query: 88  DADYAIKIMNMIKLYGKPIRVNKA 111
             D A+  M+     G+ I+V   
Sbjct: 90  SVDAAVA-MDETVFRGRTIKVLPK 112

>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 = 59.3 bits (144), Expect = 2e-11
 Identities = 24/115 (20%), Positives = 41/115 (35%), Gaps = 40/115 (34%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           ++++GN+D     + L   FS+ G I                 R+               
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSI----------------NRIT-------------- 67

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                    I+ D  +G+ KG+A+I +A   + DA++ AM       R I V   
Sbjct: 68  ---------ILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK 112

>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 = 72.4 bits (178), Expect = 2e-16
 Identities = 26/131 (19%), Positives = 42/131 (32%), Gaps = 33/131 (25%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN-MIKLYGKPIRVNKASSHQKNLDV 179
            + I++  L+  V    L D F   GV+    +    MI +Y                  
Sbjct: 15  NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIY------------------ 56

Query: 180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
                          D +TG  KG A ++Y     + A+++   G+      + VS A K
Sbjct: 57  --------------LDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 102

Query: 240 KDSKGDRHGSA 250
           K        S 
Sbjct: 103 KPPMNSGPSSG 113

>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 = 69.7 bits (171), Expect = 3e-15
 Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 8/95 (8%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPV--------VNVHMPKDRVTQTHQ 76
            G  +    ++ IYV GL+D V+   + + F Q G V          +H+  D+ T   +
Sbjct: 6   SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65

Query: 77  GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
           G   + +     A  A++  +     G  ++V+ A
Sbjct: 66  GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 100

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 71.9 bits (177), Expect = 4e-16
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            ++V      V E+ + E+F   GP+  V +          G+ F+EF   E A  AI+ 
Sbjct: 33  RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEE 84

Query: 96  MNMIKLYGKPIRVNKA 111
           ++      +P+ V  +
Sbjct: 85  VHGKSFANQPLEVVYS 100

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 24/135 (17%), Positives = 44/135 (32%), Gaps = 51/135 (37%)

Query: 113 SHQKNLDVGA----NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
           SH  +   G      +F+     +V E  L + F  FG + +  KI+             
Sbjct: 19  SHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEV-KIL------------- 64

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
                                             GFAF+ +   E++  +I+ +HG+   
Sbjct: 65  ---------------------------------NGFAFVEFEEAESAAKAIEEVHGKSFA 91

Query: 229 NRPISVSYAFKKDSK 243
           N+P+ V Y+     +
Sbjct: 92  NQPLEVVYSKLPAKR 106

>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 = 71.1 bits (175), Expect = 5e-16
 Identities = 22/125 (17%), Positives = 41/125 (32%), Gaps = 37/125 (29%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            ++IGNL     ++ L +   + GV                              D+   
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVN-----------------------------DI--- 30

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
                L+ +   +   G SKGFA +   S  +S   +D +  + L  +   V+ + K + 
Sbjct: 31  -----LEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEH 85

Query: 243 KGDRH 247
               H
Sbjct: 86  HHHHH 90

>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 = 69.5 bits (171), Expect = 2e-15
 Identities = 11/83 (13%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGP--VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           +Y+G L    ++  + E     G   ++ +   ++R     +G+  +    E  +   + 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 95  IMNMIKLYGKPIRVNKASSHQKN 117
           ++   +L+G+   V  ++  + +
Sbjct: 64  LLPKRELHGQNPVVTPSNKLEHH 86

>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 = 71.4 bits (175), Expect = 6e-16
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 7/86 (8%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           GG  S   +  + V GL    S   + +   ++G V    + +D       G G +EF+ 
Sbjct: 7   GGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVR 59

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKA 111
           +ED  YA++ ++  K           
Sbjct: 60  KEDMTYAVRKLDNTKFRSHEGETAYI 85

>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 = 39.8 bits (93), Expect = 1e-04
 Identities = 12/130 (9%), Positives = 25/130 (19%), Gaps = 46/130 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           + +  L P    + L D     G +                                   
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYA-------------------------------- 45

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                  ++ RD       G   + +   E    ++  +      +     +Y   K   
Sbjct: 46  -------DVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG 91

Query: 244 GDRHGSAAER 253
                    R
Sbjct: 92  PRSPSYGRSR 101

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 70.4 bits (173), Expect = 7e-16
 Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 10/88 (11%)

Query: 26  GGGESGDGDA---TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIE 82
           G   S   D    T+YVGGL D ++ET +   F Q G +  + + + +         FI+
Sbjct: 1   GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQ 54

Query: 83  FMGEEDADYAI-KIMNMIKLYGKPIRVN 109
           F   + A+ A  K  N + + G+ + V 
Sbjct: 55  FATRQAAEVAAEKSFNKLIVNGRRLNVK 82

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 48.4 bits (116), Expect = 5e-08
 Identities = 18/116 (15%), Positives = 35/116 (30%), Gaps = 46/116 (39%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            +++G L   + E  L + F  FG I                I V +             
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRT--------------ITVVQ------------- 46

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFE-ASDASIDAMHGQYLCNRPISVSYA 237
                              +  AFI +A+ + A  A+  + +   +  R ++V + 
Sbjct: 47  ------------------RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG 84

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 70.8 bits (174), Expect = 8e-16
 Identities = 16/89 (17%), Positives = 40/89 (44%), Gaps = 9/89 (10%)

Query: 29  ESGDGDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
                 + +++G L    VS+  ++ +F   G ++ +++           +GFI+F   +
Sbjct: 17  RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQ 68

Query: 88  DADYAIKIMNMIKLYGKPIRVNKASSHQK 116
               AI+  +    +GK + +  +SS+ +
Sbjct: 69  SVRDAIEXESQEMNFGKKLILEVSSSNAR 97

>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 = 43.5 bits (103), Expect = 5e-06
 Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 13/72 (18%)

Query: 179 VGANIFIGNLDPEIMRDPDT-------GN------SKGFAFINYASFEASDASIDAMHGQ 225
           + + +FIGNL  + +   D        G+         F FI + + ++   +I+    +
Sbjct: 21  MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQE 80

Query: 226 YLCNRPISVSYA 237
               + + +  +
Sbjct: 81  MNFGKKLILEVS 92

>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 = 70.3 bits (173), Expect = 8e-16
 Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 8/91 (8%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G   S      I+VG +    +   +  LF + G V+   + K         Y F+    
Sbjct: 1   GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEK 52

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASSHQK 116
           E DA  AI  +N  ++ GK I V  ++  QK
Sbjct: 53  EADAKAAIAQLNGKEVKGKRINVELSTKGQK 83

>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 = 48.7 bits (117), Expect = 6e-08
 Identities = 19/129 (14%), Positives = 40/129 (31%), Gaps = 48/129 (37%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
              IF+GN+      + L   F   G ++                               
Sbjct: 9   TWKIFVGNVSAACTSQELRSLFERRGRVI------------------------------- 37

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                   + +++        K +AF++      + A+I  ++G+ +  + I+V  + K 
Sbjct: 38  --------ECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG 81

Query: 241 DSK-GDRHG 248
             K G   G
Sbjct: 82  QKKSGPSSG 90

>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 = 69.9 bits (172), Expect = 1e-15
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 8/85 (9%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           G     G   +++G L  + +E  +  LF Q G V+   + K         YGF+    +
Sbjct: 1   GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDK 52

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKA 111
             A+ AI+ ++  KL+G  I V  +
Sbjct: 53  TAAEDAIRNLHHYKLHGVNINVEAS 77

>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 = 48.3 bits (116), Expect = 6e-08
 Identities = 21/127 (16%), Positives = 37/127 (29%), Gaps = 47/127 (37%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            +FIGNL  E  E+ +   F  +G +L+   I+                           
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLEC-DII--------------------------- 41

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
                              K + F++     A++ +I  +H   L    I+V  +  K  
Sbjct: 42  -------------------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK 82

Query: 243 KGDRHGS 249
                 S
Sbjct: 83  ASSGPSS 89

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 72.6 bits (178), Expect = 1e-15
 Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 1/88 (1%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           GGGE  +  A + V  LD  VS+  + ELF + G +    +  DR +    G   + F  
Sbjct: 80  GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFER 138

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASS 113
             DA  A+K    + L G+P+ +   +S
Sbjct: 139 RADALKAMKQYKGVPLDGRPMDIQLVAS 166

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 61.8 bits (150), Expect = 7e-12
 Identities = 21/141 (14%), Positives = 43/141 (30%), Gaps = 40/141 (28%)

Query: 107 RVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIR 166
             +      + ++ GA + + NLD  V +  + + F+ FG                    
Sbjct: 74  LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG-------------------T 114

Query: 167 VNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY 226
           + KA                     +  D  +G S G A +++     +  ++    G  
Sbjct: 115 LKKA--------------------AVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVP 153

Query: 227 LCNRPISVSYAFKKDSKGDRH 247
           L  RP+ +     +      H
Sbjct: 154 LDGRPMDIQLVASQIDLEHHH 174

>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 = 70.3 bits (173), Expect = 1e-15
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VGG+D ++ ET +   F + G V  V +  DR T   +GYGF+ F  + D      + 
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKI--VE 68

Query: 97  NMIKLYGKPIRVNKA 111
           + I  +GK +++  A
Sbjct: 69  SQINFHGKKLKLGPA 83

>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 = 68.4 bits (168), Expect = 7e-15
 Identities = 18/131 (13%), Positives = 42/131 (32%), Gaps = 42/131 (32%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            +F+G +D  +DE  +   F+ +G +                                  
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVK--------------------------------- 37

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
                 + +I+ D  TG SKG+ F+++ +       +++        + + +  A +K +
Sbjct: 38  ------EVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQI--NFHGKKLKLGPAIRKQN 88

Query: 243 KGDRHGSAAER 253
               H      
Sbjct: 89  LSTYHVQPRPL 99

>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 = 69.2 bits (170), Expect = 3e-15
 Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 36  TIYVGGLDDKVSE----TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           TIY+  L++K+ +      +  +F + G ++++ + +   +   +G  F+ F     A  
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66

Query: 92  AIKIMNMIKLYGKPIRVNKASS 113
           A++ M     Y KP+R+  A +
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKT 88

>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 = 62.2 bits (152), Expect = 8e-13
 Identities = 25/125 (20%), Positives = 46/125 (36%), Gaps = 47/125 (37%)

Query: 123 NIFIGNLDPEVDE----KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
            I+I NL+ ++ +    K L+  FS FG IL               I V++         
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILD--------------ILVSR--------- 46

Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
                              +   +G AF+ +    ++  ++ +M G    ++P+ + YA 
Sbjct: 47  -------------------SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA- 86

Query: 239 KKDSK 243
           K DS 
Sbjct: 87  KTDSD 91

>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 = 69.3 bits (170), Expect = 4e-15
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 9/83 (10%)

Query: 36  TIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
            +++G L+   V ++ +  +F + G V    + K        GY F+++  E  A  A+ 
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAVL 80

Query: 95  IMNMIKLYGKPIRVNKASSHQKN 117
             N   L G+ + +N A   + +
Sbjct: 81  GENGRVLAGQTLDINMAGEPKPD 103

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 53.2 bits (128), Expect = 3e-09
 Identities = 20/97 (20%), Positives = 46/97 (47%), Gaps = 15/97 (15%)

Query: 165 IRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT-------GN------SKGFAFINYAS 211
           ++ +  ++      + + +FIGNL+  +++  D        G        KG+AF+ Y++
Sbjct: 12  LQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSN 71

Query: 212 FEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHG 248
              + A++   +G+ L  + + ++ A   + K DR G
Sbjct: 72  ERHARAAVLGENGRVLAGQTLDINMA--GEPKPDRSG 106

>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 = 68.8 bits (169), Expect = 4e-15
 Identities = 30/87 (34%), Positives = 42/87 (48%), Gaps = 1/87 (1%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
            G SG     I+VGG+     ET + E F + G V  V M  D   Q  +G+GFI F  E
Sbjct: 3   SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKASS 113
           +  D A+  M+   + GK + V +A  
Sbjct: 63  QSVDQAVN-MHFHDIMGKKVEVKRAEP 88

>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 = 66.1 bits (162), Expect = 4e-14
 Identities = 23/126 (18%), Positives = 41/126 (32%), Gaps = 40/126 (31%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+G +     E  L + F  FGV+                                   
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVT---------------------------------- 38

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                +  ++ D +    +GF FI +   ++ D ++  MH   +  + + V  A  +DSK
Sbjct: 39  -----EVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NMHFHDIMGKKVEVKRAEPRDSK 92

Query: 244 GDRHGS 249
                S
Sbjct: 93  SSGPSS 98

>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 = 69.1 bits (169), Expect = 4e-15
 Identities = 15/80 (18%), Positives = 37/80 (46%), Gaps = 6/80 (7%)

Query: 36  TIYVGGLDDKVSETLMW---ELFVQSGPVVNVHMPKDRVT---QTHQGYGFIEFMGEEDA 89
            ++V GL  ++++  +    E F + G +  V +         Q      ++ ++  EDA
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 90  DYAIKIMNMIKLYGKPIRVN 109
             AI+ +N + + G+ ++ +
Sbjct: 77  LRAIQCVNNVVVDGRTLKAS 96

>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 = 53.7 bits (129), Expect = 1e-09
 Identities = 18/126 (14%), Positives = 34/126 (26%), Gaps = 44/126 (34%)

Query: 115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQ 174
           QKNL     +F+  L   + +  +      F               +GK  +V       
Sbjct: 14  QKNL-----VFVVGLSQRLADPEVLKRPEYF-------------GKFGKIHKV------- 48

Query: 175 KNLDVGANIFIGNLDPEIMRDPDTGNSK---GFAFINYASFEASDASIDAMHGQYLCNRP 231
                            I        S+     A++ Y   E +  +I  ++   +  R 
Sbjct: 49  ----------------VINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT 92

Query: 232 ISVSYA 237
           +  S  
Sbjct: 93  LKASLG 98

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 68.0 bits (167), Expect = 7e-15
 Identities = 16/83 (19%), Positives = 40/83 (48%), Gaps = 9/83 (10%)

Query: 35  ATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           + +++G L    VS+  ++ +F   G ++ +++           +GFI+F   +    AI
Sbjct: 11  SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 62

Query: 94  KIMNMIKLYGKPIRVNKASSHQK 116
           +  +    +GK + +  +SS+ +
Sbjct: 63  ECESQEMNFGKKLILEVSSSNAR 85

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 14/87 (16%), Positives = 31/87 (35%), Gaps = 13/87 (14%)

Query: 176 NLDVGANIFIGNLDPEIMRDPDT-------GN------SKGFAFINYASFEASDASIDAM 222
           N+   + +FIGNL  + +   D        G+         F FI + + ++   +I+  
Sbjct: 6   NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECE 65

Query: 223 HGQYLCNRPISVSYAFKKDSKGDRHGS 249
             +    + + +  +         HG 
Sbjct: 66  SQEMNFGKKLILEVSSSNARPQFDHGD 92

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 21/80 (26%)

Query: 117 NLDVGANIFIGNLDPE-VDEKLLYDTFSAFGVILQ-------------TP-------KIM 155
           N+   + +FIGNL  + V ++ L+  FS +G I+Q              P       +  
Sbjct: 6   NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECE 65

Query: 156 NMIKLYGKPIRVNKASSHQK 175
           +    +GK + +  +SS+ +
Sbjct: 66  SQEMNFGKKLILEVSSSNAR 85

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 68.8 bits (168), Expect = 8e-15
 Identities = 14/104 (13%), Positives = 39/104 (37%), Gaps = 7/104 (6%)

Query: 17  QSLSQTKLEGGGESGDGDATIYVGGLDDKVSE----TLMWELFVQSGPVVNVHMPKDRVT 72
           Q +    L       +    + +  ++ +V +     L++ L    G ++++ +     +
Sbjct: 12  QHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---S 68

Query: 73  QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQK 116
             + G  +I F  +E A   ++        G P+ +  + + Q 
Sbjct: 69  DDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 62.2 bits (151), Expect = 2e-12
 Identities = 27/154 (17%), Positives = 53/154 (34%), Gaps = 46/154 (29%)

Query: 104 KPIRVNKASSHQKNLDVGANIFIGNLDPEVDE----KLLYDTFSAFGVILQTPKIMNMIK 159
           + +      S   + +    + I N++PEV +     LLY   S+ G IL          
Sbjct: 12  QHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD--------- 62

Query: 160 LYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASI 219
                I V+                             + ++ G A+I +A+ E++ A +
Sbjct: 63  -----IVVDL----------------------------SDDNSGKAYIVFATQESAQAFV 89

Query: 220 DAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAER 253
           +A  G      P+ ++++    S+    GS    
Sbjct: 90  EAFQGYPFQGNPLVITFSETPQSQVAEDGSLEHH 123

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 67.7 bits (166), Expect = 1e-14
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +YVG L     +  +   F   GP+  V + ++       G+ F+EF    DA+ A++ +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 57

Query: 97  NMIKLYGKPIRVNKA 111
           +   + G  +RV  +
Sbjct: 58  DGKVICGSRVRVELS 72

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 19/131 (14%), Positives = 38/131 (29%), Gaps = 45/131 (34%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            +++GNL     +  L   FS +G +                                  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLR--------------------------------- 28

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
                    I R+P      GFAF+ +     ++ ++  + G+ +C   + V  +     
Sbjct: 29  ------TVWIARNP-----PGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS-TGMP 76

Query: 243 KGDRHGSAAER 253
           +  R      R
Sbjct: 77  RRSRFDRPPAR 87

>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 = 67.5 bits (165), Expect = 2e-14
 Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVV-NVHMPKD-RVTQTHQGYGFIEFMGEEDADYAI 93
            +++GG+        + E   +    V +V +         ++G+ F+E+     A  A 
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 94  KIMNM--IKLYGKPIRVNKA 111
           + +    I+L+G  I V+ A
Sbjct: 70  RKLMPGRIQLWGHQIAVDWA 89

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 54.8 bits (132), Expect = 7e-10
 Identities = 15/125 (12%), Positives = 33/125 (26%), Gaps = 39/125 (31%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FIG +      + + +  +     +    +                             
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAA------------------------ 46

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQ--YLCNRPISVSYAFKKD 241
                        D   ++GFAF+ Y S  A+  +   +      L    I+V +A  + 
Sbjct: 47  -------------DKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEI 93

Query: 242 SKGDR 246
              + 
Sbjct: 94  DVDED 98

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 66.9 bits (164), Expect = 2e-14
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 2/82 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T YVG L     +  +  +F     + +V + +D+ T   +G+ ++EF   +    A+  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74

Query: 96  MNMIKLYGKPIRVNKASSHQKN 117
            +   L  + +RV+ A   +++
Sbjct: 75  YDGALLGDRSLRVDIAEGRKQD 96

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 57.3 bits (139), Expect = 7e-11
 Identities = 18/126 (14%), Positives = 37/126 (29%), Gaps = 41/126 (32%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
            ++GNL     +  +   F    +               + +R                 
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLSI---------------RSVR----------------- 45

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                   ++RD DT   KGF ++ +   ++   ++    G  L +R + V  A  +   
Sbjct: 46  --------LVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQD 96

Query: 244 GDRHGS 249
                S
Sbjct: 97  KSGPSS 102

>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 = 66.1 bits (162), Expect = 4e-14
 Identities = 13/96 (13%), Positives = 32/96 (33%), Gaps = 5/96 (5%)

Query: 22  TKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFI 81
            +     +      T+    L   ++E  + E+F  +  +              +G  +I
Sbjct: 4   LEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYI 58

Query: 82  EFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
           EF  E DA+  ++     ++ G+ + +         
Sbjct: 59  EFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 62.7 bits (153), Expect = 6e-13
 Identities = 20/134 (14%), Positives = 36/134 (26%), Gaps = 44/134 (32%)

Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
           +     K +     +   NL   + E  L + F                           
Sbjct: 5   EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDAL----------------------- 41

Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
                                EI      G SKG A+I + S   ++ +++   G  +  
Sbjct: 42  ---------------------EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG 80

Query: 230 RPISVSYAFKKDSK 243
           R +S+ Y  +K   
Sbjct: 81  RSVSLYYTGEKGGT 94

>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 = 66.2 bits (162), Expect = 5e-14
 Identities = 28/111 (25%), Positives = 43/111 (38%), Gaps = 6/111 (5%)

Query: 26  GGGESGDGDAT---IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIE 82
            G      D T   I+VGGL    ++  + + F   G +    +  DR T   +GYGF+ 
Sbjct: 6   SGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 65

Query: 83  FMGEEDADYAIKIMNMIKLYGKPIRVNKASS--HQKNLDVGANIFIGNLDP 131
                 A+ A K  N   + G+   VN A      ++L  G  I +     
Sbjct: 66  MADRAAAERACKDPN-PIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSS 115

>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 = 58.8 bits (143), Expect = 3e-11
 Identities = 20/118 (16%), Positives = 36/118 (30%), Gaps = 40/118 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+G L     +  L   F  FG I                                   
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIE---------------------------------- 45

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                +  ++ D  TG S+G+ F+  A   A++ +    +   +  R  +V+ A+   
Sbjct: 46  -----EAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PIIDGRKANVNLAYLGA 97

>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 = 64.8 bits (159), Expect = 6e-14
 Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VGGL     E  + E F   G V ++ +P D  T   +G+ FI F  EE     ++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 97  NMIKLYGKPIRVNKA 111
               +      +  A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 57.5 bits (140), Expect = 3e-11
 Identities = 18/114 (15%), Positives = 30/114 (26%), Gaps = 40/114 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+G L P+  E+ + + F  FG +                                   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVE---------------------------------- 27

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                  E+  D  T   +GF FI +   E     +       +      +  A
Sbjct: 28  -----SIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EKKYHNVGLSKCEIKVA 75

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 67.3 bits (164), Expect = 7e-14
 Identities = 15/95 (15%), Positives = 35/95 (36%), Gaps = 2/95 (2%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGP--VVNVHMPKDRVTQTHQGYGFIE 82
                  +  A +YVG      ++  + ++    G   VV +   ++R     +GY  + 
Sbjct: 46  YTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVV 105

Query: 83  FMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
              E      ++++    L G+ + V  A+    +
Sbjct: 106 VASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 66.9 bits (163), Expect = 8e-14
 Identities = 18/145 (12%), Positives = 44/145 (30%), Gaps = 37/145 (25%)

Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
               ++    +  A +++G+      ++ L     + GV                     
Sbjct: 43  AILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVY-------------------- 82

Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
                    DV        ++ +   +   G SKG+A +  AS  +    ++ + G+ L 
Sbjct: 83  ---------DV--------VELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLN 125

Query: 229 NRPISVSYAFKKDSKGDRHGSAAER 253
              + V  A +++       +    
Sbjct: 126 GEKVDVRPATRQNLSQFEAQARKRE 150

>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 = 65.0 bits (159), Expect = 1e-13
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTH-QGYGFIEFMGEEDADYAIK 94
           T ++G L   V+E  + E F     +  V +P++       +G+G+ EF   +    A+ 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 95  IMNMIKLYGKPIRVNKA 111
            +N   L  + IRV+ A
Sbjct: 80  -LNEESLGNRRIRVDVA 95

>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 = 49.5 bits (119), Expect = 4e-08
 Identities = 19/115 (16%), Positives = 40/115 (34%), Gaps = 42/115 (36%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
            F+GNL  +V E+ + + F    +                 +R                 
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLNI---------------SAVR----------------- 49

Query: 184 FIGNLDPEIMRDP-DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                   + R+P +    KGF +  +   ++  +++ +++ + L NR I V  A
Sbjct: 50  --------LPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVA 95

>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 = 65.6 bits (160), Expect = 2e-13
 Identities = 23/100 (23%), Positives = 38/100 (38%), Gaps = 5/100 (5%)

Query: 17  QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
           + +    +    E G+ +  IYV  L   V E  +  +F +     +         +  +
Sbjct: 28  EEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK 87

Query: 77  -----GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
                G  FI    E+ A  A+K  N   L+GKP+ V  A
Sbjct: 88  EGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFA 127

>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 = 64.8 bits (158), Expect = 3e-13
 Identities = 27/168 (16%), Positives = 50/168 (29%), Gaps = 44/168 (26%)

Query: 89  ADYAIKIMNMIKLYGKPIRVNKASSHQ-------KNLDVGA---NIFIGNLDPEVDEKLL 138
                  M    +  + +   + S  +       ++ + G     I++ NL   V EK L
Sbjct: 3   LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDL 62

Query: 139 YDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT 198
              F  +                          + +   D+              R    
Sbjct: 63  KYIFGRYVDFSS--------------------ETQRIMFDI--------------RLMKE 88

Query: 199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDR 246
           G  KG AFI   + +A+  ++   +G  L  +P+ V +A     K D 
Sbjct: 89  GRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQDP 136

>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 = 64.4 bits (157), Expect = 2e-13
 Identities = 14/79 (17%), Positives = 27/79 (34%), Gaps = 6/79 (7%)

Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
               I    L        + E F + G +  V +P+            +EF+   +A  A
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEFLEPLEARKA 62

Query: 93  IKIMNMIKLYGKPIRVNKA 111
            + +   K +  P+ +  A
Sbjct: 63  FRHLAYSKFHHVPLYLEWA 81

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 63.8 bits (156), Expect = 2e-13
 Identities = 19/89 (21%), Positives = 34/89 (38%), Gaps = 12/89 (13%)

Query: 31  GDGDA----TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           G G A     ++VGGL    S   +   F + G +  +   K         + +I++   
Sbjct: 10  GYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESL 63

Query: 87  EDADYAIKIMN--MIKLYGKPIRVNKASS 113
           + A  A   M    +    + +RV+ A S
Sbjct: 64  DAAQAACAKMRGFPLGGPDRRLRVDFAKS 92

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 21/117 (17%), Positives = 33/117 (28%), Gaps = 47/117 (40%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            +++G L P      L   F  FG I                                  
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTI------------------------------- 47

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN--RPISVSYA 237
                   + ++         FA+I Y S +A+ A+   M G  L    R + V +A
Sbjct: 48  --------DHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA 90

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 64.0 bits (156), Expect = 3e-13
 Identities = 21/90 (23%), Positives = 41/90 (45%), Gaps = 9/90 (10%)

Query: 34  DATIYVGGL----DDKVS--ETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           D+ I V  +     D++   + ++ ++F + G + N   P++      +GY F+E+    
Sbjct: 15  DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 72

Query: 88  DADYAIKIMNMIKLYGK-PIRVNKASSHQK 116
            A  A+K  +  KL  +   RVN  +   K
Sbjct: 73  HAVDAVKNADGYKLDKQHTFRVNLFTDFDK 102

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 43.2 bits (102), Expect = 7e-06
 Identities = 18/115 (15%), Positives = 33/115 (28%), Gaps = 49/115 (42%)

Query: 120 VGANIFIGNLDPEVDE-------KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASS 172
           + + I + N+ P+V          +++  FS FG I                        
Sbjct: 14  IDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKIT----------------------- 49

Query: 173 HQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
                                   + G +KG+ F+ YAS   +  ++    G  L
Sbjct: 50  ------------------NDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL 86

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 64.0 bits (156), Expect = 3e-13
 Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           ++Y+ G     +   + E     G V+N+ M +    +  +G  F+ F   E A   ++ 
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE- 70

Query: 96  MNMIKLYGKPIRV 108
               K     + +
Sbjct: 71  TPGQKYKETDLLI 83

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 12/104 (11%), Positives = 27/104 (25%), Gaps = 40/104 (38%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           +++I     +     + +     G +L               I+                
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLN--------------IQ---------------- 42

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY 226
                     MR       KG  F+ + S E++   ++    +Y
Sbjct: 43  ----------MRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKY 76

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 62.5 bits (153), Expect = 4e-13
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VGGL    +   +   F Q G V +  +  D+ T  H+G+GF+ F  E+  +   + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 97  NMIKLYGKPIRVNKA 111
           +  ++  K +   KA
Sbjct: 61  HFHEINNKMVECKKA 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 60.9 bits (149), Expect = 1e-12
 Identities = 18/114 (15%), Positives = 32/114 (28%), Gaps = 40/114 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+G L      + +   F  FG +                                   
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVD---------------------------------- 27

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                D  +M D  T   +GF F+ + S +  +     +H   + N+ +    A
Sbjct: 28  -----DAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHFHEINNKMVECKKA 75

>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 = 63.4 bits (155), Expect = 4e-13
 Identities = 21/120 (17%), Positives = 37/120 (30%), Gaps = 41/120 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           + +  L  +  E+ L + FS FG +L                                  
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVL---------------------------------- 43

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                  ++ +D  TG+SKGF F+ +  +E     +   H   +  R         K S+
Sbjct: 44  -----MVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQ 96

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 2/89 (2%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
            G   +    + + V GL  K +E  + E F   G V+ V + KD  T   +G+GF+ F 
Sbjct: 6   SGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 65

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKASS 113
             E     +   +MI   G+       +S
Sbjct: 66  EYETQVKVMSQRHMID--GRWCDCKLPNS 92

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 63.1 bits (154), Expect = 4e-13
 Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 7/87 (8%)

Query: 28  GESGDGDA-TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           G SG     +++V G    V    + E F+  GPV +V M KD+       +  +E    
Sbjct: 1   GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDV 55

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKASS 113
              +  +   +   L G  +RV     
Sbjct: 56  GAREAVLS-QSQHSLGGHRLRVRPREQ 81

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 19/128 (14%), Positives = 34/128 (26%), Gaps = 45/128 (35%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           ++F+      VD   L + F AFG +                                  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVA--------------------------------- 36

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
                    ++ D D G    FA +      A +A + +     L    + V    +K+ 
Sbjct: 37  --------SVVMDKDKG---VFAIVEMGDVGAREAVL-SQSQHSLGGHRLRVRPREQKEF 84

Query: 243 KGDRHGSA 250
           +     S 
Sbjct: 85  QSPASKSP 92

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 62.9 bits (153), Expect = 6e-13
 Identities = 18/86 (20%), Positives = 30/86 (34%), Gaps = 5/86 (5%)

Query: 28  GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           GE     A +YVG L      + +     + G V     P     Q  +   F+ +    
Sbjct: 13  GEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSA 67

Query: 88  DADYAIKIMNMIKLYGKPIRVNKASS 113
            A  A+  +  ++L    +RV  A  
Sbjct: 68  AAQQAVSCLQGLRLGTDTLRVALARQ 93

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 19/141 (13%), Positives = 40/141 (28%), Gaps = 44/141 (31%)

Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
           G        S   +   + A++++GNL  +     L       G +              
Sbjct: 1   GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-------------- 46

Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
            P+R+                                  +  AF++Y    A+  ++  +
Sbjct: 47  -PLRLT-----------------------------WQGPRRRAFLHYPDSAAAQQAVSCL 76

Query: 223 HGQYLCNRPISVSYAFKKDSK 243
            G  L    + V+ A ++  K
Sbjct: 77  QGLRLGTDTLRVALARQQRDK 97

>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 = 61.7 bits (150), Expect = 1e-12
 Identities = 14/79 (17%), Positives = 34/79 (43%), Gaps = 6/79 (7%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNV-HMPKDRV----TQTHQGYGFIEFMGEEDADY 91
           +YVG +   ++E  M + F     +  +   P + V        + + F+EF   ++   
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 92  AIKIMNMIKLYGKPIRVNK 110
           A+   + I   G+ +++ +
Sbjct: 69  AMA-FDGIIFQGQSLKIRR 86

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 15/111 (13%), Positives = 37/111 (33%), Gaps = 35/111 (31%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++GN+   + E+ + D F+A        ++  + +  G P+                  
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQM------RLGGLTQAPGNPVL----------------- 45

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
                             K FAF+ + S + +  ++ A  G     + + +
Sbjct: 46  -----------AVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKI 84

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 61.6 bits (150), Expect = 2e-12
 Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 2/90 (2%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEF 83
            G      G   I V  +   VS   + + F     +   V +  +       G   + F
Sbjct: 6   SGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMVAF 64

Query: 84  MGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
              ++A  A+  +N   +  + ++++  SS
Sbjct: 65  ESRDEATAAVIDLNDRPIGSRKVKLSGPSS 94

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 50.4 bits (121), Expect = 1e-08
 Identities = 17/134 (12%), Positives = 38/134 (28%), Gaps = 43/134 (32%)

Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
           +S           I + N+   V    + D F  + VI                      
Sbjct: 5   SSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIP--------------------- 43

Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
                                 ++  + G   G A + + S + + A++  ++ + + +R
Sbjct: 44  ------------------GSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSR 85

Query: 231 PISVSYAFKKDSKG 244
            + +S      S G
Sbjct: 86  KVKLSGP----SSG 95

>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 = 60.7 bits (148), Expect = 2e-12
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 7/81 (8%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VG     ++E  + E F Q G V++V +PK       + + F+ F  ++ A       
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGED 62

Query: 97  NMIKLYGKPIRVNKASSHQKN 117
            +IK  G  + ++ A     +
Sbjct: 63  LIIK--GISVHISNAEPKHNS 81

>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 = 46.1 bits (110), Expect = 4e-07
 Identities = 17/126 (13%), Positives = 36/126 (28%), Gaps = 46/126 (36%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+G    ++ E  L + FS +G ++                                  
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVM---------------------------------- 33

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                D  I +       + FAF+ +A  + + +         +    + +S A  K + 
Sbjct: 34  -----DVFIPKP-----FRAFAFVTFADDQIAQSLCGEDL--IIKGISVHISNAEPKHNS 81

Query: 244 GDRHGS 249
                S
Sbjct: 82  NSGPSS 87

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 61.1 bits (149), Expect = 3e-12
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 3/83 (3%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKD-RVTQTHQGYGFIEFMGEEDADYAIK 94
           T ++G L   V+E  + E F     +  V +P++    +  +G+G+ EF   +    A+ 
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 95  IMNMIKLYGKPIRVNKASSHQKN 117
            +N   L  K IRV+ A   Q  
Sbjct: 76  -LNEESLGNKRIRVDVADQAQDK 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 = 51.1 bits (123), Expect = 1e-08
 Identities = 20/128 (15%), Positives = 43/128 (33%), Gaps = 44/128 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
            F+GNL  +V E+ + + F    +                 +R                 
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNI---------------SAVR----------------- 45

Query: 184 FIGNLDPEIMRDP-DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF--KK 240
                   + R+P +    KGF +  +   ++  +++ +++ + L N+ I V  A   + 
Sbjct: 46  --------LPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD 96

Query: 241 DSKGDRHG 248
              G   G
Sbjct: 97  KDSGPSSG 104

>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 = 65.3 bits (158), Expect = 4e-12
 Identities = 22/87 (25%), Positives = 40/87 (45%)

Query: 30  SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA 89
            GD   T++V  ++   +E+ +   F   GP+  +HM   + +   +GY FIE+  E D 
Sbjct: 98  QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDM 157

Query: 90  DYAIKIMNMIKLYGKPIRVNKASSHQK 116
             A K  +  K+ G+ + V+       
Sbjct: 158 HSAYKHADGKKIDGRRVLVDVERGRTV 184

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 52.5 bits (125), Expect = 7e-08
 Identities = 24/178 (13%), Positives = 46/178 (25%), Gaps = 39/178 (21%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+  ++ +  E  L   F  +G I +                                 
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRI-------------------------------- 132

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                   ++    +G  +G+AFI Y       ++     G+ +  R + V     +  K
Sbjct: 133 -------HMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVK 185

Query: 244 GDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLR 301
           G R       L   +   +  +  H    D       P P P  +             
Sbjct: 186 GWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRE 243

>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 = 60.3 bits (147), Expect = 4e-12
 Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 7/88 (7%)

Query: 24  LEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEF 83
           + G        + ++VG   + ++   + + F Q G VV+V +PK       + + F+ F
Sbjct: 1   MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTF 55

Query: 84  MGEEDADYAIKIMNMIKLYGKPIRVNKA 111
             ++ A        +IK  G  + ++ A
Sbjct: 56  ADDKVAQSLCGEDLIIK--GISVHISNA 81

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 15/120 (12%), Positives = 34/120 (28%), Gaps = 46/120 (38%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+G    ++  + L   F  +G ++                                  
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVV---------------------------------- 39

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                D  I +       + FAF+ +A  + + +         +    + +S A  K +K
Sbjct: 40  -----DVFIPKP-----FRAFAFVTFADDKVAQSLCGEDL--IIKGISVHISNAEPKHNK 87

>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 = 60.4 bits (147), Expect = 5e-12
 Identities = 14/90 (15%), Positives = 30/90 (33%), Gaps = 2/90 (2%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEF 83
            G      G   I V  +   VS   + + F     +   V +  +       G   + F
Sbjct: 6   SGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMVAF 64

Query: 84  MGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
              ++A  A+  +N   +  + +++   S 
Sbjct: 65  ESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>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 = 49.2 bits (118), Expect = 4e-08
 Identities = 15/121 (12%), Positives = 35/121 (28%), Gaps = 40/121 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           I + N+   V    + D F  + VI                                   
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGYQVIP---------------------------------- 43

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                    ++  + G   G A + + S + + A++  ++ + + +R + +       S 
Sbjct: 44  -----GSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG-SGPSS 97

Query: 244 G 244
           G
Sbjct: 98  G 98

>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 = 60.6 bits (147), Expect = 5e-12
 Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 7/85 (8%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           G  S   +  + V GL    S   + +   ++G V    + +D       G G +EF+ +
Sbjct: 9   GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRK 61

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKA 111
           ED  YA++ ++  K           
Sbjct: 62  EDMTYAVRKLDNTKFRSHEGETAYI 86

>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 = 39.4 bits (92), Expect = 2e-04
 Identities = 9/85 (10%), Positives = 18/85 (21%), Gaps = 15/85 (17%)

Query: 183 IFIGNLDPEIMRDPD-------TG-------NSKGFAFINYASFEASDASIDAMHGQYLC 228
           + +  L P      D        G          G   + +   E    ++  +      
Sbjct: 19  VVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFR 77

Query: 229 NRPISVSYAFKKDSKGDRHGSAAER 253
           +     +Y   K            R
Sbjct: 78  SHEGETAYIRVKVDGPRSPSYGRSR 102

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 59.7 bits (145), Expect = 5e-12
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 11/84 (13%)

Query: 34  DATIYVGGL-------DDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           D+ I V  +        +K+   +  ++F + G + N   P++      +GY F+E+   
Sbjct: 1   DSVIVVDNVPQVGPDRLEKLKNVIH-KIFSKFGKITNDFYPEE--DGKTKGYIFLEYASP 57

Query: 87  EDADYAIKIMNMIKLYGK-PIRVN 109
             A  A+K  +  KL  +   RVN
Sbjct: 58  AHAVDAVKNADGYKLDKQHTFRVN 81

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 18/111 (16%), Positives = 31/111 (27%), Gaps = 49/111 (44%)

Query: 124 IFIGNLDPEVDE-------KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKN 176
           I + N+ P+V          +++  FS FG I                            
Sbjct: 4   IVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKIT--------------------------- 35

Query: 177 LDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
                               + G +KG+ F+ YAS   +  ++    G  L
Sbjct: 36  --------------NDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL 72

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 59.4 bits (145), Expect = 7e-12
 Identities = 23/115 (20%), Positives = 37/115 (32%), Gaps = 40/115 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FIG L  +  ++ L + F  FG +                                   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVK---------------------------------- 28

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
                +  +MRDP T  S+GF F+ +      D  + A     L ++ I    AF
Sbjct: 29  -----ECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKVAF 77

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 57.1 bits (139), Expect = 5e-11
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL  + ++  + E F Q G V    + +D +T+  +G+GF+ FM +   D  +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 97  NMIKLYGKPIRVNKA 111
           +  +L  K I    A
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 59.1 bits (144), Expect = 9e-12
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           ++VGGL    S+  + + F + G VV+  +  D  T   +G+GFI F      +  +   
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 97  NMIKLYGKPIRVNKA 111
              +L G+ I   KA
Sbjct: 74  E-HRLDGRVIDPKKA 87

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 55.7 bits (135), Expect = 2e-10
 Identities = 25/114 (21%), Positives = 38/114 (33%), Gaps = 40/114 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+G L  +  +K L D F+ FG ++                                  
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVV---------------------------------- 39

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                D  I  DP+TG S+GF FI +    + +  +D      L  R I    A
Sbjct: 40  -----DCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKE-HRLDGRVIDPKKA 87

>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 = 60.0 bits (146), Expect = 9e-12
 Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 2/98 (2%)

Query: 17  QSLSQTKLEGGGESGDGDAT-IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTH 75
                + L   G         +++GGL  + ++  + E F Q G V    + +D +T+  
Sbjct: 7   HHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRS 66

Query: 76  QGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
           +G+GF+ FM +   D  +   +  +L  K I    A  
Sbjct: 67  RGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVAFP 103

>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 = 58.4 bits (142), Expect = 3e-11
 Identities = 23/120 (19%), Positives = 40/120 (33%), Gaps = 40/120 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FIG L  +  ++ L + F  FG +                                   
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVK---------------------------------- 53

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                +  +MRDP T  S+GF F+ +      D  + A     L ++ I    AF + ++
Sbjct: 54  -----ECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKVAFPRRAQ 107

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 58.6 bits (142), Expect = 2e-11
 Identities = 11/84 (13%), Positives = 27/84 (32%), Gaps = 3/84 (3%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G          + +  +   +   ++  L VQ G V +                 + +  
Sbjct: 7   GSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSS 63

Query: 86  EEDADYAIKIMNMIKLYGKPIRVN 109
           ++ A  A+  +N  +L    ++V 
Sbjct: 64  KDQARQALDKLNGFQLENFTLKVA 87

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 53.6 bits (129), Expect = 1e-09
 Identities = 15/122 (12%), Positives = 37/122 (30%), Gaps = 42/122 (34%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
              + I N+ P +  ++L      +GV+    ++                          
Sbjct: 15  IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVN------------------------- 49

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                            T +      + Y+S + +  ++D ++G  L N  + V+Y   +
Sbjct: 50  -----------------TDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE 92

Query: 241 DS 242
            +
Sbjct: 93  MA 94

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 58.3 bits (141), Expect = 3e-11
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 9/83 (10%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            ++V GL + V E  + E   + G +  V M   +          +EF   + A   +  
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFENIDSAKECVTF 70

Query: 96  MNMIKLY--GKPIRVNKASSHQK 116
              + +Y  G+    N  S+ ++
Sbjct: 71  AADVPVYIAGQQAFFNY-STSKR 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 = 38.2 bits (89), Expect = 4e-04
 Identities = 14/137 (10%), Positives = 32/137 (23%), Gaps = 47/137 (34%)

Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
           +S     + V   + +  L   V E  L +    FG I                + +   
Sbjct: 5   SSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTI--------------CYVMMMP- 49

Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM--HGQYLC 228
                                          K  A + + + +++   +        Y+ 
Sbjct: 50  ------------------------------FKRQALVEFENIDSAKECVTFAADVPVYIA 79

Query: 229 NRPISVSYAFKKDSKGD 245
            +    +Y+  K     
Sbjct: 80  GQQAFFNYSTSKRITRP 96

>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 = 58.1 bits (141), Expect = 4e-11
 Identities = 25/126 (19%), Positives = 43/126 (34%), Gaps = 40/126 (31%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FIG L  E  E+ L + +  +G +                                   
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLT---------------------------------- 55

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                D  +MRDP +  S+GF F+ ++S    DA++ A     +  R +    A  ++  
Sbjct: 56  -----DCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAREES 109

Query: 244 GDRHGS 249
           G    S
Sbjct: 110 GSGPSS 115

>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 = 56.9 bits (138), Expect = 1e-10
 Identities = 15/77 (19%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL  + +E  +   + Q G + +  + +D  ++  +G+GF+ F    + D A+   
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-A 88

Query: 97  NMIKLYGKPIRVNKASS 113
               + G+ +   +A +
Sbjct: 89  RPHSIDGRVVEPKRAVA 105

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 57.8 bits (140), Expect = 5e-11
 Identities = 21/83 (25%), Positives = 33/83 (39%), Gaps = 9/83 (10%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +++ GL D V E  + E   + GP+  V +   +          +EF     A  A+  
Sbjct: 23  VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK------RQALVEFEDVLGACNAVNY 76

Query: 96  MNM--IKLYGKPIRVNKASSHQK 116
                I + G P  VN  S+ QK
Sbjct: 77  AADNQIYIAGHPAFVNY-STSQK 98

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 14/119 (11%), Positives = 29/119 (24%), Gaps = 47/119 (39%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           + I  L   V E  L +    FG I      + ++                         
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISY----VVVMP------------------------ 55

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQ--YLCNRPISVSYAFKK 240
                             K  A + +     +  +++       Y+   P  V+Y+  +
Sbjct: 56  -----------------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ 97

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 57.9 bits (140), Expect = 6e-11
 Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 3/88 (3%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
              +       I +  L +  S   + +L  ++             T+   G G +EF  
Sbjct: 20  HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTF---SSVNTRDFDGTGALEFPS 76

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASS 113
           EE    A++ +N I+  G  I V +  +
Sbjct: 77  EEILVEALERLNNIEFRGSVITVERDDN 104

>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 = 57.4 bits (139), Expect = 6e-11
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 3/88 (3%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEFM 84
           G       D  + + GL    S+  + + F     V N + +P D   +   G  F++F 
Sbjct: 7   GNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR-STGEAFVQFA 65

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKAS 112
            +E A+ A+K  +  ++  + I + K+S
Sbjct: 66  SQEIAEKALK-KHKERIGHRYIEIFKSS 92

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 56.9 bits (138), Expect = 6e-11
 Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 3/88 (3%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
             G SG    T+ + G    V+E  + E      PV  + + ++       GY F++F  
Sbjct: 2   SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGNKT-GYIFVDFSN 59

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASS 113
           EE+   A+K  N   + G+ I V +  S
Sbjct: 60  EEEVKQALK-CNREYMGGRYIEVFREKS 86

>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 = 41.5 bits (98), Expect = 2e-05
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 5/64 (7%)

Query: 184 FIGNLDPE---IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
           F+  L P    I+R+   GN  G+ F+++++ E    ++   + +Y+  R I V      
Sbjct: 30  FLAPLKPVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSG 87

Query: 241 DSKG 244
            S G
Sbjct: 88  PSSG 91

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 57.6 bits (139), Expect = 7e-11
 Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 8/90 (8%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK- 94
            I++  L   V+E  +  L +  G V N+ M K +         FIE   EE A+  +  
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANTMVNY 71

Query: 95  -IMNMIKLYGKPIRVNKASSHQKNLDVGAN 123
                  L G+PI +  ++  +   D   N
Sbjct: 72  YTSVTPVLRGQPIYIQFSNHKELKTDSSPN 101

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 22/143 (15%), Positives = 40/143 (27%), Gaps = 47/143 (32%)

Query: 106 IRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPI 165
           +R +    H  +      I I  L  +V E  +      FG +                +
Sbjct: 1   MRGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN--------------L 46

Query: 166 RVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDA--MH 223
            + K                                K  AFI   + EA++  ++     
Sbjct: 47  LMLK-------------------------------GKNQAFIEMNTEEAANTMVNYYTSV 75

Query: 224 GQYLCNRPISVSYAFKKDSKGDR 246
              L  +PI + ++  K+ K D 
Sbjct: 76  TPVLRGQPIYIQFSNHKELKTDS 98

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 57.2 bits (139), Expect = 7e-11
 Identities = 21/120 (17%), Positives = 35/120 (29%), Gaps = 40/120 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +F+G LD    ++ L   FS +G ++                                  
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVV---------------------------------- 44

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                D  IM+D  T  S+GF F+ +         + A     L  R I       +  +
Sbjct: 45  -----DCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-ASRPHTLDGRNIDPKPCTPRGMQ 98

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 2/90 (2%)

Query: 25  EGGGESGDGDAT-IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEF 83
            G   SG  +   ++VGGLD   ++  +   F Q G VV+  + KD+ T   +G+GF++F
Sbjct: 6   SGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65

Query: 84  MGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
                    +       L G+ I     + 
Sbjct: 66  KDPNCVGTVLA-SRPHTLDGRNIDPKPCTP 94

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 57.1 bits (138), Expect = 1e-10
 Identities = 15/92 (16%), Positives = 35/92 (38%), Gaps = 3/92 (3%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEFM 84
           G G+        ++  +   +++  + +         N VH+  D       G   ++F 
Sbjct: 7   GEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFK 65

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKASSHQK 116
            E+DA  + + ++  KL G+   V+  +    
Sbjct: 66  NEDDARKSER-LHRKKLNGREAFVHVVTLEDM 96

>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 = 39.7 bits (93), Expect = 1e-04
 Identities = 14/134 (10%), Positives = 32/134 (23%), Gaps = 40/134 (29%)

Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
            +S             I N+   + +  +        V                 +    
Sbjct: 4   GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENA-------------VH--- 47

Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
                                 ++ D + G   G A + + + + +  S   +H + L  
Sbjct: 48  ----------------------VLVDNN-GQGLGQALVQFKNEDDARKSE-RLHRKKLNG 83

Query: 230 RPISVSYAFKKDSK 243
           R   V     +D +
Sbjct: 84  REAFVHVVTLEDMR 97

>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 = 56.3 bits (136), Expect = 2e-10
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
                D  + V G+     E  + + F     V  VH+ KD V + + G G ++F+  +D
Sbjct: 11  PINPDDLYVSVHGMPFSAMENDVRDFF-HGLRVDAVHLLKDHVGR-NNGNGLVKFLSPQD 68

Query: 89  ADYAIKIMNMIKLYGKPIRVNKASSHQ 115
              A+K  N + +  + + V+ A+  Q
Sbjct: 69  TFEALK-RNRMLMIQRYVEVSPATERQ 94

>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 = 40.5 bits (95), Expect = 7e-05
 Identities = 8/50 (16%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
           +++D   G + G   + + S + +  ++   +   +  R + VS A ++ 
Sbjct: 47  LLKDHV-GRNNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPATERQ 94

>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 = 54.5 bits (131), Expect = 8e-10
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 9/75 (12%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +  GGL + VS   +  +  + G V  + MP ++       Y F  +   E++  A   +
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTL 83

Query: 97  N---MIKLYGKPIRV 108
           N   ++   G+ I +
Sbjct: 84  NGKEVVDDLGQKITL 98

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 54.8 bits (132), Expect = 8e-10
 Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 3/91 (3%)

Query: 23  KLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFI 81
           K        +    +Y+ GL  +     + + F +   V + +++      +   G GF+
Sbjct: 14  KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT-GEGFV 72

Query: 82  EFMGEEDADYAIKIMNMIKLYGKPIRVNKAS 112
           EF  E D   A+   +   +  + I+V+  +
Sbjct: 73  EFRNEADYKAALC-RHKQYMGNRFIQVHPIT 102

>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 = 41.0 bits (96), Expect = 7e-05
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
           I   P+ G + G  F+ + +     A++   H QY+ NR I V    KK 
Sbjct: 58  IAYGPN-GKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKG 105

>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 = 54.1 bits (130), Expect = 9e-10
 Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 9/83 (10%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK- 94
            +++  L  +V+ET +  L +  G V N+ M K +         F+E   EE A   +  
Sbjct: 17  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAITMVNY 70

Query: 95  -IMNMIKLYGKPIRVNKASSHQK 116
                  L  +PI +   S+H++
Sbjct: 71  YSAVTPHLRNQPIYIQY-SNHKE 92

>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 = 53.6 bits (129), Expect = 1e-09
 Identities = 13/81 (16%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           G + I V  L    +   + +L          ++ +++         F+  +  E A  A
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYDLKY-CYVDRNK------RTAFVTLLNGEQAQNA 56

Query: 93  IKIMNMIKLYGKPIRVNKASS 113
           I++ +     GK + V    +
Sbjct: 57  IQMFHQYSFRGKDLIVQLQPT 77

>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 = 48.6 bits (116), Expect = 7e-08
 Identities = 10/71 (14%), Positives = 21/71 (29%), Gaps = 13/71 (18%)

Query: 183 IFIGNLDPEI-------------MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
           I + NL  +              ++      +K  AF+   + E +  +I   H      
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRG 67

Query: 230 RPISVSYAFKK 240
           + + V      
Sbjct: 68  KDLIVQLQPTD 78

>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 = 54.2 bits (130), Expect = 1e-09
 Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 8/90 (8%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK- 94
            I++  L   V+E  +  L +  G V N+ M K +         FIE   EE A+  +  
Sbjct: 33  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANTMVNY 86

Query: 95  -IMNMIKLYGKPIRVNKASSHQKNLDVGAN 123
                  L G+PI +  ++  +   D   N
Sbjct: 87  YTSVTPVLRGQPIYIQFSNHKELKTDSSPN 116

>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 = 39.1 bits (91), Expect = 2e-04
 Identities = 22/146 (15%), Positives = 39/146 (26%), Gaps = 47/146 (32%)

Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
           G   R +     +        I I  L  +V E  +      FG +              
Sbjct: 13  GLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN------------ 60

Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASID-- 220
             + + K                                K  AFI   + EA++  ++  
Sbjct: 61  --LLMLK-------------------------------GKNQAFIEMNTEEAANTMVNYY 87

Query: 221 AMHGQYLCNRPISVSYAFKKDSKGDR 246
                 L  +PI + ++  K+ K D 
Sbjct: 88  TSVTPVLRGQPIYIQFSNHKELKTDS 113

>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 = 53.3 bits (128), Expect = 3e-09
 Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 3/85 (3%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEFMGEE 87
                D  + + GL    ++  + + F     V N + +P D   +   G  F++F  +E
Sbjct: 37  ADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK-ITGEAFVQFASQE 95

Query: 88  DADYAIKIMNMIKLYGKPIRVNKAS 112
            A+ A+   +  ++  + I V K+S
Sbjct: 96  LAEKALG-KHKERIGHRYIEVFKSS 119

>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 = 51.8 bits (124), Expect = 9e-09
 Identities = 20/96 (20%), Positives = 32/96 (33%), Gaps = 5/96 (5%)

Query: 20  SQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQ---SGPVVNVHMPKDRVTQTHQ 76
           S +     G  G     + + GL    S   +            V  VH    R  +   
Sbjct: 3   SGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR-QS 61

Query: 77  GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS 112
           G  F+E   E+D   A+K  +   +  + I V K+ 
Sbjct: 62  GEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSH 96

>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 = 51.4 bits (123), Expect = 1e-08
 Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 5/87 (5%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQ---SGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           E  D    I   GL    +   +   F           +H   +R     +G   IE   
Sbjct: 6   EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR-DGKRRGDALIEMES 64

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKAS 112
           E+D   A++  + + +  + + V + +
Sbjct: 65  EQDVQKALE-KHRMYMGQRYVEVYEIN 90

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 53.6 bits (128), Expect = 1e-08
 Identities = 20/104 (19%), Positives = 42/104 (40%), Gaps = 15/104 (14%)

Query: 26  GGGESGDGDATIYVGGLDDKVS---------ETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
           G G     + T+YVGG+D  ++         E+ +  +F + G +  +   + +      
Sbjct: 126 GIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------ 179

Query: 77  GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDV 120
             GF++F  + +A++A + M+   L     +          L V
Sbjct: 180 NCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLV 223

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 50.6 bits (121), Expect = 4e-08
 Identities = 17/89 (19%), Positives = 32/89 (35%), Gaps = 3/89 (3%)

Query: 25  EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
                       +++ GL  K +E  ++  F    PV  VH+          G   +EF 
Sbjct: 37  SEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGP-DGRVTGEADVEFA 94

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKASS 113
             E+A  A+   +   +  + I +   S+
Sbjct: 95  THEEAVAAMS-KDRANMQHRYIELFLNST 122

>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 = 39.8 bits (93), Expect = 2e-04
 Identities = 20/126 (15%), Positives = 38/126 (30%), Gaps = 42/126 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           + +  L  +  E  +Y+ FS                    P+RV                
Sbjct: 49  VHMRGLPYKATENDIYNFFSPLN-----------------PVRV---------------- 75

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                   I   PD G   G A + +A+ E + A++ +     + +R I +       + 
Sbjct: 76  -------HIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGAS 126

Query: 244 GDRHGS 249
              + S
Sbjct: 127 NGAYSS 132

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 49.3 bits (118), Expect = 5e-08
 Identities = 17/94 (18%), Positives = 35/94 (37%), Gaps = 10/94 (10%)

Query: 27  GGESGDGDA-------TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYG 79
           G     G +        +++ GL  + +E  ++  F    P+  VH+          G  
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEA 58

Query: 80  FIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
            +EF   EDA  A+   +   +  + + +   S+
Sbjct: 59  DVEFATHEDAVAAMA-KDKANMQHRYVELFLNST 91

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 40.1 bits (94), Expect = 8e-05
 Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 5/69 (7%)

Query: 184 FIGNLDPE---IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
           F   L+P    I   PD G   G A + +A+ E + A++ A     + +R + +      
Sbjct: 35  FFSPLNPMRVHIEIGPD-GRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLNSTA 92

Query: 241 DSKGDRHGS 249
            + G    S
Sbjct: 93  GTSGSGPSS 101

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 49.1 bits (117), Expect = 9e-08
 Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 6/88 (6%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN----VHMPKDRVTQTHQGYGFIEFM 84
            S +    + + GL    +   +   F Q  P+      +        +   G  F+ F 
Sbjct: 18  LSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR-PTGDAFVLFA 76

Query: 85  GEEDADYAIKIMNMIKLYGKPIRVNKAS 112
            EE A  A++  +   L  + I + +++
Sbjct: 77  CEEYAQNALR-KHKDLLGKRYIELFRST 103

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 47.9 bits (114), Expect = 1e-07
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 9/83 (10%)

Query: 36  TIYVGGL-DDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
            +++      K     + +L    G + N  +             FIE    EDA  A+ 
Sbjct: 17  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVD 70

Query: 95  --IMNMIKLYGKPIRVNKASSHQ 115
                   ++GKP+RV+ +  ++
Sbjct: 71  YYTTTPALVFGKPVRVHLSQKYK 93

>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 = 49.8 bits (118), Expect = 2e-07
 Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           ++Y+ G     +   + E     G V+N+ M +    +  +G  F+ F   E A   ++ 
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVET 169

Query: 96  MNMIKLYGKPIRV 108
               K     + +
Sbjct: 170 PGQ-KYKETDLLI 181

>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 = 46.9 bits (111), Expect = 4e-07
 Identities = 15/84 (17%), Positives = 35/84 (41%), Gaps = 9/84 (10%)

Query: 36  TIYVGGL-DDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
            I++  L     S++ + +L    G + N  + + +         FIE    EDA   + 
Sbjct: 27  VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK------SQAFIEMETREDAMAMVD 80

Query: 95  --IMNMIKLYGKPIRVNKASSHQK 116
             +   +   G+ ++V+ +  ++K
Sbjct: 81  HCLKKALWFQGRCVKVDLSEKYKK 104

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 46.1 bits (109), Expect = 5e-07
 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 12/92 (13%)

Query: 28  GESGDGDATIYVGGLDDKVSETLM----WELFVQSGPVVNV--HMPKDRVTQTHQGYGFI 81
           G SG+G A + V  +D ++S   +     E F + G V +V      D     +Q    +
Sbjct: 4   GSSGNG-ADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD-----YQLKAVV 57

Query: 82  EFMGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
           +    +DA  A+  ++  K+  K I V+ A+ 
Sbjct: 58  QMENLQDAIGAVNSLHRYKIGSKKILVSLATG 89

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 20/93 (21%), Positives = 31/93 (33%), Gaps = 9/93 (9%)

Query: 28  GESGDGDAT-IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ--GYGFIEFM 84
           G SG   +  ++VGGL   + E  +   F + GP+V     K          GY F+ F 
Sbjct: 1   GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 85  GEEDADYAIKIMNM------IKLYGKPIRVNKA 111
            E      I           + +    I+    
Sbjct: 61  EESSVQALIDACLEEDGKLYLCVSSPTIKDKPV 93

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 37.3 bits (86), Expect = 9e-04
 Identities = 12/41 (29%), Positives = 20/41 (48%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKP 164
           +F+G L P++DE  +  +F  FG ++         K Y  P
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPP 51

>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 = 45.0 bits (106), Expect = 3e-06
 Identities = 16/80 (20%), Positives = 27/80 (33%), Gaps = 5/80 (6%)

Query: 36  TIYVGGLDDKVSETLMWELFVQ---SGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
            + + GL    S   +               VH    R  +   G  F+E   E+D   A
Sbjct: 46  VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR-QSGEAFVELGSEDDVKMA 104

Query: 93  IKIMNMIKLYGKPIRVNKAS 112
           +K  +   +  + I V K+ 
Sbjct: 105 LK-KDRESMGHRYIEVFKSH 123

>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 = 44.3 bits (104), Expect = 7e-06
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 4/87 (4%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I V  L   V+  ++ ++F + G V+ +          +Q    +++     A +A   +
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 104

Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGAN 123
           +   +Y     +    S   +L+V  N
Sbjct: 105 DGQNIYNACCTLRIDFSKLTSLNVKYN 131

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 13/87 (14%), Positives = 29/87 (33%), Gaps = 5/87 (5%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           + +      ++  +++ +    G V  + + K    Q       +EF     A  A   +
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQ-----AMVEFESVLCAQKAKAAL 82

Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGAN 123
           N   +Y     +    +    L+V  N
Sbjct: 83  NGADIYAGCCTLKIEYARPTRLNVIRN 109

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 4/87 (4%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I V  L   V+  ++ ++F + G V+ +          +Q    +++     A +A   +
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 86

Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGAN 123
           +   +Y     +    S   +L+V  N
Sbjct: 87  DGQNIYNACCTLRIDFSKLTSLNVKYN 113

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 39.3 bits (91), Expect = 1e-04
 Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 6/88 (6%)

Query: 28  GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           G    G + + +  L  ++    +  L +Q GP+V+ H         +QG    ++   E
Sbjct: 1   GAMAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPY------LNQGIALCKYTTRE 54

Query: 88  DADYAIKIMNMIKLYGKPIRVNKASSHQ 115
           +A+ A   +N   L    I     S ++
Sbjct: 55  EANKAQMALNNCVLANTTIFAESPSENE 82

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 37.5 bits (87), Expect = 7e-04
 Identities = 5/42 (11%), Positives = 18/42 (42%)

Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
           D    +  G  ++ +   E ++ ++  ++ ++   +PI    
Sbjct: 61  DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

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
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	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
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.98
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.98
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.98
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.89
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.89
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.86
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.84
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.83
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.82
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.81
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.81
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.81
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.81
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.81
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.81
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.81
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.81
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.8
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.8
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.8
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.8
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.8
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.8
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.8
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.8
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.8
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.8
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.8
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.79
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.79
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.79
2div_A	99	TRNA selenocysteine associated protein; structural	99.79
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.79
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.79
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.79
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.79
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.79
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.79
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.79
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.79
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.79
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.79
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.78
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.78
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.78
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.78
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.78
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.78
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.78
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.78
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.78
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.78
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.78
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.78
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.78
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.77
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.77
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.77
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.77
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.77
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.77
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.77
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.77
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.77
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.77
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.77
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.77
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.77
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.77
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.77
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.76
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.76
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.76
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.76
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.76
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.76
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.76
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.76
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.75
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.75
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.75
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.75
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.75
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.75
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.75
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.75
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.75
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.74
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.74
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.74
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.74
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.74
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.74
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.74
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.74
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.74
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.73
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.73
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.73
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.73
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.73
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.73
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.73
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.73
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.73
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.73
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.73
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.73
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.73
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.72
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.72
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.72
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.72
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.72
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.72
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.72
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.72
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.72
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.72
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.72
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.71
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.71
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.71
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.71
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.71
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.71
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.71
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.71
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.71
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.71
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.71
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.71
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.7
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.7
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.7
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.7
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.7
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.7
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.7
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.7
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.7
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.7
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.7
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.7
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.7
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.7
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.7
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.7
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.7
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.7
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.7
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.69
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.69
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.69
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.69
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.69
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.69
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.69
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.69
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.69
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.69
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.69
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.52
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.69
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.69
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.68
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.68
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.68
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.68
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.68
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.68
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.68
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.68
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.68
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.68
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.67
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.67
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.67
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.67
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.67
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.67
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.67
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.66
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.66
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.66
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.66
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.66
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.66
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.66
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.66
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.66
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.66
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.66
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.66
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.66
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.66
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.66
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.66
2div_A	99	TRNA selenocysteine associated protein; structural	99.66
1x5p_A	97	Negative elongation factor E; structure genomics,	99.66
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.65
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.65
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.65
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.65
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.65
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.65
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.65
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.65
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.65
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.65
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.65
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.65
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.65
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.65
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.65
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.64
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.64
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.64
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.64
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.64
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.64
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.64
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.64
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.64
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.64
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.64
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.63
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.63
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.63
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.63
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.63
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.63
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.63
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.63
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.63
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.63
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.63
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.63
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.63
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.62
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.62
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.62
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.62
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.62
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.62
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.62
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.62
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.62
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.62
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.62
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.61
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.61
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.61
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.61
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.61
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.61
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.6
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.6
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.6
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.6
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.6
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.6
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.6
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.59
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.59
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.59
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.37
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.59
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.58
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.58
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.58
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.58
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.58
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.58
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.58
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.58
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.58
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.58
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.58
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.57
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.57
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.57
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.57
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.57
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.57
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.57
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.56
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.56
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.56
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.56
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.56
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.56
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.56
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.56
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.55
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.55
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.55
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.55
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.55
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.54
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.54
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.53
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.53
1x5p_A	97	Negative elongation factor E; structure genomics,	99.53
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.53
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.53
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.52
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.52
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.52
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.52
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.51
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.51
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.51
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.5
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.5
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.5
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.5
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.5
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.49
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.49
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.48
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.48
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.47
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.47
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.45
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.45
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.44
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.44
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.44
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.43
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.4
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.4
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.36
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.36
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.36
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.35
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.35
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.33
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.31
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.29
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.13
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.13
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.11
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.07
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.02
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.89
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.83
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.76
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.75
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.69
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.58
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.52
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.24
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.13
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.71
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.5
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.45
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.14
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.95
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.66
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.61
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.25
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.91
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.52
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.3
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	95.27
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.96
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	94.44
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.21
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	93.11
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	92.26
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	89.5
2v8f_C	26	MDIA1, profilin IIA; alternative splicing, protein	86.69

>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=3.5e-37  Score=265.44  Aligned_cols=171  Identities=34%  Similarity=0.605  Sum_probs=153.2

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||||||.++|+++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|.+|++.+++..+.|+.|++.
T Consensus        11 p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~   90 (213)
T 4f02_A           11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM   90 (213)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccc
Confidence            34456899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCcccc-ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccC
Q psy3016         110 KASSHQKN-LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNL  188 (305)
Q Consensus       110 ~~~~~~~~-~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  188 (305)
                      ++...... .....+|||+||+..+|+++|+++|+.||.|..+                                     
T Consensus        91 ~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~-------------------------------------  133 (213)
T 4f02_A           91 WSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSC-------------------------------------  133 (213)
T ss_dssp             ECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEE-------------------------------------
T ss_pred             cccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEE-------------------------------------
Confidence            98765432 2345789999999999999999999999999887                                     


Q ss_pred             CCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       189 ~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                        .++.|.  +.++|||||+|.+.++|.+|++.|||..|+|+.|+|.|+..+.
T Consensus       134 --~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          134 --KVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             --EEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             --EeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence              566663  4579999999999999999999999999999999999997654

>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=6.5e-35  Score=239.85  Aligned_cols=164  Identities=29%  Similarity=0.596  Sum_probs=152.2

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (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            689999999999999999999999999999999987 5779999999999999999999999999999999999998765


Q ss_pred             cc-cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcc
Q psy3016         115 QK-NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIM  193 (305)
Q Consensus       115 ~~-~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~  193 (305)
                      .. ......+|||+|||..+|+++|+++|+.||.|..+                                       .++
T Consensus        80 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~---------------------------------------~i~  120 (166)
T 3md3_A           80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSG---------------------------------------HVM  120 (166)
T ss_dssp             CCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEE---------------------------------------EEE
T ss_pred             CCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEE---------------------------------------EEE
Confidence            43 33456899999999999999999999999999877                                       678


Q ss_pred             cCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         194 RDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       194 ~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      .|..++.++|||||+|.+.++|.+|+..|||..++|+.|+|+|++
T Consensus       121 ~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          121 WDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             ECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             ecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            888889999999999999999999999999999999999999985

>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=7e-35  Score=240.50  Aligned_cols=165  Identities=28%  Similarity=0.495  Sum_probs=154.0

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (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            46899999999999999999999999999999999998889999999999999999999999999999999999999988


Q ss_pred             CccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCc
Q psy3016         113 SHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEI  192 (305)
Q Consensus       113 ~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i  192 (305)
                      +.... ...++|||+|||..+++++|+++|+.||.|..+                                       .+
T Consensus        82 ~~~~~-~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~---------------------------------------~i  121 (168)
T 1b7f_A           82 PGGES-IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQK---------------------------------------NI  121 (168)
T ss_dssp             CCSST-TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEE---------------------------------------EE
T ss_pred             CCccc-CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEE---------------------------------------EE
Confidence            76543 346789999999999999999999999999876                                       67


Q ss_pred             ccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecC--eeeEEEEe
Q psy3016         193 MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN--RPISVSYA  237 (305)
Q Consensus       193 ~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g--~~l~v~~a  237 (305)
                      +.+..++.++|||||+|.+.++|.+|+..|||..+.|  ++|+|+||
T Consensus       122 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            7887789999999999999999999999999999977  99999986

>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=1.3e-34  Score=238.26  Aligned_cols=165  Identities=27%  Similarity=0.481  Sum_probs=152.7

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      +.++|||+|||.++|+++|+++|+.||.|.+++++.+..+|.++|||||+|.+.++|.+|++.|++..+.|+.|.|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            36899999999999999999999999999999999998889999999999999999999999999999999999999988


Q ss_pred             CccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCc
Q psy3016         113 SHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEI  192 (305)
Q Consensus       113 ~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i  192 (305)
                      +.... ....+|||+|||..+++++|+++|+.||.|..+                                       .+
T Consensus        81 ~~~~~-~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~---------------------------------------~i  120 (167)
T 1fxl_A           81 PSSAS-IRDANLYVSGLPKTMTQKELEQLFSQYGRIITS---------------------------------------RI  120 (167)
T ss_dssp             CCCGG-GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EE
T ss_pred             CCccc-CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEE---------------------------------------EE
Confidence            66533 346789999999999999999999999999876                                       67


Q ss_pred             ccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCee--eEEEEe
Q psy3016         193 MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRP--ISVSYA  237 (305)
Q Consensus       193 ~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~--l~v~~a  237 (305)
                      +.+..+|.++|||||+|.+.++|.+|++.|||..+.|+.  |+|+||
T Consensus       121 ~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            778778999999999999999999999999999999975  888885

>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=9.2e-35  Score=245.87  Aligned_cols=173  Identities=23%  Similarity=0.420  Sum_probs=152.1

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+++.+..++.++|||||+|.+.++|.+|++. ++..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            445678999999999999999999999999999999999988899999999999999999999985 9999999999999


Q ss_pred             eCCCccccc-----cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeE
Q psy3016         110 KASSHQKNL-----DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIF  184 (305)
Q Consensus       110 ~~~~~~~~~-----~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  184 (305)
                      ++.......     ...++|||+|||.++|+++|+++|+.||.|..+                                 
T Consensus        88 ~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v---------------------------------  134 (196)
T 1l3k_A           88 RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI---------------------------------  134 (196)
T ss_dssp             ECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEE---------------------------------
T ss_pred             cccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEE---------------------------------
Confidence            987654322     235789999999999999999999999999887                                 


Q ss_pred             eccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         185 IGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       185 ~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                            .++.|..++.++|||||+|.+.++|.+|+.. ++..++|+.|.|.|+.++...
T Consensus       135 ------~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          135 ------EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             ------EEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             ------EEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence                  6788888899999999999999999999986 899999999999999887654

>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=2.4e-34  Score=246.96  Aligned_cols=170  Identities=27%  Similarity=0.478  Sum_probs=154.0

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+++.+..++.++|||||+|.+.++|.+|++.|++..+.|+.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            34679999999999999999999999999999999999888999999999999999999999999999999999999988


Q ss_pred             CCcccc----------ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcc
Q psy3016         112 SSHQKN----------LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA  181 (305)
Q Consensus       112 ~~~~~~----------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (305)
                      ......          ....++|||+||+..+|+++|+++|+.||.|..+                              
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v------------------------------  155 (216)
T 2qfj_A          106 SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSA------------------------------  155 (216)
T ss_dssp             SCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEE------------------------------
T ss_pred             CCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEE------------------------------
Confidence            765422          2345799999999999999999999999999887                              


Q ss_pred             eeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       182 ~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                               .++.+..++.++|||||+|.+.++|.+|+..|||..|+|+.|+|.|+..+
T Consensus       156 ---------~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~  205 (216)
T 2qfj_A          156 ---------TLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP  205 (216)
T ss_dssp             ---------EEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSC
T ss_pred             ---------EEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCC
Confidence                     67888888999999999999999999999999999999999999998654

>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=1.6e-34  Score=238.22  Aligned_cols=165  Identities=30%  Similarity=0.511  Sum_probs=151.9

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      .+++|||+|||.++|+++|+++|+.||.|.+|+++.+..+|.++|||||+|.+.++|.+|++  ++..+.|+.|.+.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            46899999999999999999999999999999999998889999999999999999999999  4689999999999987


Q ss_pred             CccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCc
Q psy3016         113 SHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEI  192 (305)
Q Consensus       113 ~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i  192 (305)
                      ..... ....+|||+|||..+|+++|+++|+.||.|..+                                       .+
T Consensus        80 ~~~~~-~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~---------------------------------------~i  119 (167)
T 2cjk_A           80 PRDEQ-DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDA---------------------------------------QL  119 (167)
T ss_dssp             CHHHH-HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEE---------------------------------------EC
T ss_pred             chhhc-cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEE---------------------------------------EE
Confidence            65432 346789999999999999999999999999877                                       67


Q ss_pred             ccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         193 MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       193 ~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +.|..+|.++|||||+|.+.++|.+|++ +|+..++|+.|+|.|+.++
T Consensus       120 ~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          120 MLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             CCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             EEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            8887889999999999999999999998 8999999999999999765

>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=7.1e-34  Score=235.80  Aligned_cols=165  Identities=28%  Similarity=0.477  Sum_probs=151.2

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCC--CcceEEEEEEcCHHHHHHHHHHhcCceeC---CeeeE
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQ--THQGYGFIEFMGEEDADYAIKIMNMIKLY---GKPIR  107 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~--~~~g~afV~f~~~e~A~~Ai~~l~g~~~~---g~~l~  107 (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            57899999999999999999999999999999999998776  89999999999999999999999998776   68899


Q ss_pred             EeeCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEecc
Q psy3016         108 VNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGN  187 (305)
Q Consensus       108 v~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  187 (305)
                      +.++..........++|||+|||..+|+++|+++|+.||.|..+                                    
T Consensus        82 ~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v------------------------------------  125 (175)
T 3nmr_A           82 MKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC------------------------------------  125 (175)
T ss_dssp             EEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEE------------------------------------
T ss_pred             EccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEE------------------------------------
Confidence            98888777666678899999999999999999999999999877                                    


Q ss_pred             CCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeec---CeeeEEEEe
Q psy3016         188 LDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC---NRPISVSYA  237 (305)
Q Consensus       188 l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~---g~~l~v~~a  237 (305)
                         .++.+. +|.++|||||+|.+.++|.+|+..|||..+.   +++|+|.||
T Consensus       126 ---~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          126 ---RILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             ---EEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             ---EEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence               567774 4899999999999999999999999998775   499999997

>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=3.8e-32  Score=225.06  Aligned_cols=159  Identities=24%  Similarity=0.501  Sum_probs=144.7

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccC----C-------CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQS----G-------PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL  101 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~  101 (305)
                      ..++|||+|||.++|+++|+++|+.|    |       .|.++++..      ++|||||+|.+.++|.+|+ .+++..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46899999999999999999999999    7       788888744      4699999999999999999 7999999


Q ss_pred             CCeeeEEeeCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcc
Q psy3016         102 YGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA  181 (305)
Q Consensus       102 ~g~~l~v~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (305)
                      .|+.|.|.++...... ....+|||+|||..+|+++|+++|+.||.|..+                              
T Consensus        76 ~g~~i~v~~~~~~~~~-~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v------------------------------  124 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQPL-PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF------------------------------  124 (172)
T ss_dssp             TTEECEEECCSSCCCC-TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEE------------------------------
T ss_pred             cCceeeecCCcccCCC-CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEE------------------------------
Confidence            9999999998765432 336889999999999999999999999999877                              


Q ss_pred             eeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       182 ~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                               .++.+..+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.||.
T Consensus       125 ---------~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          125 ---------NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             ---------EEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ---------EEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence                     678887789999999999999999999999999999999999999973

>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=5e-32  Score=242.60  Aligned_cols=170  Identities=21%  Similarity=0.256  Sum_probs=156.3

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||+|||..+|+++|+++|+.||.|..++++.+..+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            35799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             Cccccc--cccccccccCCCchh-cHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCC
Q psy3016         113 SHQKNL--DVGANIFIGNLDPEV-DEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLD  189 (305)
Q Consensus       113 ~~~~~~--~~~~~l~v~nl~~~~-t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  189 (305)
                      ......  ...++|||+|||..+ |+++|+++|+.||.|..+                                      
T Consensus       174 ~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v--------------------------------------  215 (284)
T 3smz_A          174 AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFC--------------------------------------  215 (284)
T ss_dssp             GGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEE--------------------------------------
T ss_pred             CCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEE--------------------------------------
Confidence            765432  356889999999995 999999999999999877                                      


Q ss_pred             CCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         190 PEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       190 ~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                       .++.+. +|.++|||||+|.+.++|.+|+..|||..++|+.|+|.|+.++..
T Consensus       216 -~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          216 -QLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             -EEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             -EEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence             567775 689999999999999999999999999999999999999977654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.98  E-value=4.2e-32  Score=229.83  Aligned_cols=164  Identities=24%  Similarity=0.483  Sum_probs=145.7

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccC----C-------CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQS----G-------PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL  101 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~  101 (305)
                      ..++|||+|||.++|+++|+++|+.|    |       .|.++++      +.++|||||+|.+.++|.+|+ .||+..+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            47899999999999999999999999    5       6777776      345799999999999999999 7999999


Q ss_pred             CCeeeEEeeCCCcccc-------------------ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcC
Q psy3016         102 YGKPIRVNKASSHQKN-------------------LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG  162 (305)
Q Consensus       102 ~g~~l~v~~~~~~~~~-------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~  162 (305)
                      .|+.|.|.++......                   ....++|||+||+..+++++|+++|+.||.|..+           
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~-----------  144 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF-----------  144 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEE-----------
T ss_pred             cCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEE-----------
Confidence            9999999998754211                   1345899999999999999999999999999876           


Q ss_pred             cceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                                                  .++.+..++.++|||||+|.+.++|.+|+..|||..++|+.|+|.|+.++..
T Consensus       145 ----------------------------~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          145 ----------------------------NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             ----------------------------EEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             ----------------------------EEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence                                        6788877899999999999999999999999999999999999999977643

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.98  E-value=7.7e-33  Score=230.20  Aligned_cols=166  Identities=20%  Similarity=0.347  Sum_probs=146.3

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||.++|+++|+++|+.||.+.. .++.+..++.++|||||+|.+.++|.+|++ |++..+.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v   85 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL   85 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEE
Confidence            35567899999999999999999999999998766 334444567899999999999999999995 9999999999999


Q ss_pred             eeCCCcccc-ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEecc
Q psy3016         109 NKASSHQKN-LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGN  187 (305)
Q Consensus       109 ~~~~~~~~~-~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  187 (305)
                      .++...... ....++|||+|||..+|+++|+++|+.||.|..                                     
T Consensus        86 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~-------------------------------------  128 (175)
T 1fje_B           86 EKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-------------------------------------  128 (175)
T ss_dssp             ECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEE-------------------------------------
T ss_pred             ecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEE-------------------------------------
Confidence            998865433 335689999999999999999999999998863                                     


Q ss_pred             CCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         188 LDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       188 l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                           +  ..++.++|||||+|.+.++|.+|+..|||..++|+.|+|+|+.++
T Consensus       129 -----~--~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          129 -----V--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             -----E--CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             -----e--cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence                 2  356889999999999999999999999999999999999999765

>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=99.98  E-value=8.1e-32  Score=230.64  Aligned_cols=159  Identities=17%  Similarity=0.254  Sum_probs=137.3

Q ss_pred             CCceEEEcCCC-ccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          33 GDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        33 ~~~~l~V~nLp-~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (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            46899999999 89999999999999999999999875     3699999999999999999999999999999999988


Q ss_pred             CCcccc------------------------------------ccccccccccCCCchhcHHHHHHHHhhcCcc--cchhh
Q psy3016         112 SSHQKN------------------------------------LDVGANIFIGNLDPEVDEKLLYDTFSAFGVI--LQTPK  153 (305)
Q Consensus       112 ~~~~~~------------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v--~~~~~  153 (305)
                      ......                                    ....++|||+|||.++|+++|+++|+.||.|  ..+  
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v--  155 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV--  155 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEE--
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEE--
Confidence            632100                                    0123579999999999999999999999998  544  


Q ss_pred             hhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCe---
Q psy3016         154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR---  230 (305)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~---  230 (305)
                                                           +++.+.  +..+|+|||+|++.++|.+|+..|||..+.|+   
T Consensus       156 -------------------------------------~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~  196 (205)
T 3tyt_A          156 -------------------------------------KVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGP  196 (205)
T ss_dssp             -------------------------------------EECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSS
T ss_pred             -------------------------------------EEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCC
Confidence                                                 344443  56679999999999999999999999999776   


Q ss_pred             -eeEEEEe
Q psy3016         231 -PISVSYA  237 (305)
Q Consensus       231 -~l~v~~a  237 (305)
                       ++.|.||
T Consensus       197 ~p~~vk~~  204 (205)
T 3tyt_A          197 YPYTLKLC  204 (205)
T ss_dssp             SCEECEEE
T ss_pred             cceEEEec
Confidence             6777776

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.97  E-value=4.9e-31  Score=235.90  Aligned_cols=162  Identities=22%  Similarity=0.410  Sum_probs=142.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHH----HHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMW----ELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      .....++|||+|||.++|+++|+    ++|+.||.|.+|++++   +++++|||||+|.+.++|.+|++.|||..+.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            44568899999999999999966    8999999999999986   5678999999999999999999999999999999


Q ss_pred             eEEeeCCCccc---------------------------------------------------------------------
Q psy3016         106 IRVNKASSHQK---------------------------------------------------------------------  116 (305)
Q Consensus       106 l~v~~~~~~~~---------------------------------------------------------------------  116 (305)
                      |+|.++.....                                                                     
T Consensus        82 l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  161 (282)
T 3pgw_A           82 MRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQP  161 (282)
T ss_pred             EEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCC
Confidence            99998865331                                                                     


Q ss_pred             -----------------------------------------cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhh
Q psy3016         117 -----------------------------------------NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIM  155 (305)
Q Consensus       117 -----------------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~  155 (305)
                                                               .....++|||+||+..+|+++|+++|+.||.|..+    
T Consensus       162 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v----  237 (282)
T 3pgw_A          162 PYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEV----  237 (282)
T ss_pred             CCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEE----
Confidence                                                     01134679999999999999999999999999876    


Q ss_pred             hhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeec-CeeeEE
Q psy3016         156 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC-NRPISV  234 (305)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~-g~~l~v  234 (305)
                                                         .++.+.     +|||||+|.+.++|.+|+..|||..+. |+.|+|
T Consensus       238 -----------------------------------~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  277 (282)
T 3pgw_A          238 -----------------------------------RLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKI  277 (282)
T ss_pred             -----------------------------------EEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEE
Confidence                                               344331     589999999999999999999999999 999999


Q ss_pred             EEee
Q psy3016         235 SYAF  238 (305)
Q Consensus       235 ~~a~  238 (305)
                      +|++
T Consensus       278 ~~ak  281 (282)
T 3pgw_A          278 SFAK  281 (282)
T ss_pred             EEec
Confidence            9985

>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=3.2e-31  Score=238.29  Aligned_cols=167  Identities=25%  Similarity=0.429  Sum_probs=145.0

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCC-CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (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            478999999999999999999999999 999999999874 788999999999999999999999999999999999998


Q ss_pred             CCcccc------ccccccccccCCCch-hcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeE
Q psy3016         112 SSHQKN------LDVGANIFIGNLDPE-VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIF  184 (305)
Q Consensus       112 ~~~~~~------~~~~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  184 (305)
                      .+....      .....+|||+|||.. +|+++|+++|+.||.|..+                                 
T Consensus       195 ~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v---------------------------------  241 (292)
T 2ghp_A          195 NPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKI---------------------------------  241 (292)
T ss_dssp             CCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEE---------------------------------
T ss_pred             CCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEE---------------------------------
Confidence            865432      234688999999999 9999999999999999877                                 


Q ss_pred             eccCCCCcccCCC-CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         185 IGNLDPEIMRDPD-TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       185 ~~~l~~~i~~d~~-~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                            .++.+.. +|.++|||||+|.+.++|.+|+ .|||..|+|+.|+|.|+.++
T Consensus       242 ------~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          242 ------NIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             ------ECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             ------EEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence                  5677765 5899999999999999999999 99999999999999999765

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.97  E-value=7.4e-31  Score=228.29  Aligned_cols=166  Identities=24%  Similarity=0.385  Sum_probs=144.8

Q ss_pred             CCCCcCCCCceEEEcCCCc-cccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe
Q psy3016          26 GGGESGDGDATIYVGGLDD-KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK  104 (305)
Q Consensus        26 ~~~~~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~  104 (305)
                      .+.......++|||+|||. .+|+++|+++|+.||.|.+|+++.++     +|||||+|.+.++|++|++.|++..+.|+
T Consensus        26 ~p~~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~  100 (229)
T 2adc_A           26 IPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGK  100 (229)
T ss_dssp             CGGGGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSS
T ss_pred             CCCCCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            3445566789999999999 99999999999999999999998874     68999999999999999999999999999


Q ss_pred             eeEEeeCCCcccc----------------------------------ccccccccccCCCchhcHHHHHHHHhhcC-ccc
Q psy3016         105 PIRVNKASSHQKN----------------------------------LDVGANIFIGNLDPEVDEKLLYDTFSAFG-VIL  149 (305)
Q Consensus       105 ~l~v~~~~~~~~~----------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g-~v~  149 (305)
                      .|.|.++......                                  ....++|||+||+..+++++|+++|+.|| .|.
T Consensus       101 ~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~  180 (229)
T 2adc_A          101 PIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK  180 (229)
T ss_dssp             BCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEE
T ss_pred             EEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCee
Confidence            9999988743100                                  11257899999999999999999999999 888


Q ss_pred             chhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeec-
Q psy3016         150 QTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC-  228 (305)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~-  228 (305)
                      .+                                       .++.+     .+|||||+|.+.++|.+|+..|||..+. 
T Consensus       181 ~v---------------------------------------~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~  216 (229)
T 2adc_A          181 GF---------------------------------------KFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGE  216 (229)
T ss_dssp             EE---------------------------------------EECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             EE---------------------------------------EEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCC
Confidence            76                                       33322     3789999999999999999999999999 


Q ss_pred             CeeeEEEEeeec
Q psy3016         229 NRPISVSYAFKK  240 (305)
Q Consensus       229 g~~l~v~~a~~~  240 (305)
                      |+.|+|+|++++
T Consensus       217 g~~l~v~~a~~~  228 (229)
T 2adc_A          217 NHHLRVSFSKST  228 (229)
T ss_dssp             SCBCEEEECSSC
T ss_pred             CCeEEEEEecCC
Confidence            999999998653

>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=8.1e-31  Score=222.49  Aligned_cols=159  Identities=24%  Similarity=0.391  Sum_probs=140.6

Q ss_pred             CCceEEEcCCCc-cccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          33 GDATIYVGGLDD-KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        33 ~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (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            368999999999 99999999999999999999998874     689999999999999999999999999999999988


Q ss_pred             CCcccc----------------------------------ccccccccccCCCchhcHHHHHHHHhhcC-cccchhhhhh
Q psy3016         112 SSHQKN----------------------------------LDVGANIFIGNLDPEVDEKLLYDTFSAFG-VILQTPKIMN  156 (305)
Q Consensus       112 ~~~~~~----------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~g-~v~~~~~~~~  156 (305)
                      ......                                  ....++|||+||+..+++++|+++|+.|| .|..+     
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v-----  151 (198)
T 1qm9_A           77 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF-----  151 (198)
T ss_dssp             CCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEE-----
T ss_pred             cCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEE-----
Confidence            643110                                  11267899999999999999999999999 88876     


Q ss_pred             hhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeec-CeeeEEE
Q psy3016         157 MIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC-NRPISVS  235 (305)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~-g~~l~v~  235 (305)
                                                        .++.+     .+|+|||+|.+.++|.+|+..|||..++ |+.|+|.
T Consensus       152 ----------------------------------~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          152 ----------------------------------KFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             ----------------------------------EESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             ----------------------------------EEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence                                              33332     3789999999999999999999999999 9999999


Q ss_pred             Eeeec
Q psy3016         236 YAFKK  240 (305)
Q Consensus       236 ~a~~~  240 (305)
                      |++++
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            98653

>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=9e-30  Score=227.94  Aligned_cols=158  Identities=19%  Similarity=0.336  Sum_probs=145.9

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ....++|||+|||.++|+++|+++|+.|| |.+|++      +.++|||||+|.+.++|.+|++.|++..+.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   91 (284)
T 3smz_A           19 FRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL   91 (284)
T ss_dssp             HHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEe
Confidence            34578999999999999999999999999 999998      34679999999999999999999999999999999998


Q ss_pred             CCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCC
Q psy3016         111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDP  190 (305)
Q Consensus       111 ~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  190 (305)
                      +.       ...+|||+|||..+|+++|+++|+.||.|..+                                       
T Consensus        92 ~~-------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~---------------------------------------  125 (284)
T 3smz_A           92 QP-------TDALLCVANLPPSLTQQQFEELVRPFGSLERC---------------------------------------  125 (284)
T ss_dssp             CC-------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------
T ss_pred             cC-------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEE---------------------------------------
Confidence            54       24689999999999999999999999999876                                       


Q ss_pred             CcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         191 EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       191 ~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .++.|..+|.++|||||+|.+.++|.+|+..|||..+.|+.|.|.|+..+.
T Consensus       126 ~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          126 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             EEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGG
T ss_pred             EEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            678888889999999999999999999999999999999999999997654

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.97  E-value=6.1e-30  Score=226.84  Aligned_cols=159  Identities=26%  Similarity=0.462  Sum_probs=143.6

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (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 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            355679999999999999999999999999999999653      59999999999999999999999999999999999


Q ss_pred             CCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCC
Q psy3016         111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDP  190 (305)
Q Consensus       111 ~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  190 (305)
                      +..       ..+|||+||+..+|+++|+++|+.||.|..+                                       
T Consensus        93 a~~-------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v---------------------------------------  126 (261)
T 3sde_A           93 ATH-------GAALTVKNLSPVVSNELLEQAFSQFGPVEKA---------------------------------------  126 (261)
T ss_dssp             CCC-------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------
T ss_pred             ccc-------CCcccccCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------
Confidence            874       4689999999999999999999999999887                                       


Q ss_pred             CcccCCCCCCccceEEEEeCChHHHHHHHHHhcC-eeec---CeeeEEEEeeecCC
Q psy3016         191 EIMRDPDTGNSKGFAFINYASFEASDASIDAMHG-QYLC---NRPISVSYAFKKDS  242 (305)
Q Consensus       191 ~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~-~~~~---g~~l~v~~a~~~~~  242 (305)
                      .++.| .+|.++|||||+|.+.++|.+|+..||+ ..+.   +++|.|.++.....
T Consensus       127 ~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~~  181 (261)
T 3sde_A          127 VVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDD  181 (261)
T ss_dssp             EEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEES
T ss_pred             EeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccCc
Confidence            66777 5799999999999999999999999955 4444   99999999976543

>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=99.96  E-value=2e-29  Score=226.58  Aligned_cols=163  Identities=17%  Similarity=0.240  Sum_probs=138.8

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||..+|+++|+++|+.||.|.+|+++.+..+  ++|||||+|.+.++|.+|++ +++..+.|+.|.
T Consensus        35 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~  111 (292)
T 2ghp_A           35 LTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEII  111 (292)
T ss_dssp             -------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEE
Confidence            335567889999999999999999999999999999999998633  57999999999999999996 999999999999


Q ss_pred             EeeCCCccccccccccccccCCCchhcHHHHHHHHhhcC-cccchhhhhhhhhhcCcceeeecCccccccCCCcceeEec
Q psy3016         108 VNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFG-VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIG  186 (305)
Q Consensus       108 v~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  186 (305)
                      |.++.        .++|||+|||..+++++|+++|+.|| .|..+                                   
T Consensus       112 v~~~~--------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v-----------------------------------  148 (292)
T 2ghp_A          112 VSHLT--------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSI-----------------------------------  148 (292)
T ss_dssp             EEECC--------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEE-----------------------------------
T ss_pred             EEECC--------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEE-----------------------------------
Confidence            99863        57899999999999999999999999 99876                                   


Q ss_pred             cCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         187 NLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       187 ~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                          .++.+.. +.++|||||+|.+.++|.+|+..|||..+.|+.|.|.|+.+..
T Consensus       149 ----~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  198 (292)
T 2ghp_A          149 ----RLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLE  198 (292)
T ss_dssp             ----ECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-
T ss_pred             ----EEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCc
Confidence                5666654 7889999999999999999999999999999999999987654

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.89  E-value=2.9e-23  Score=161.19  Aligned_cols=103  Identities=24%  Similarity=0.468  Sum_probs=75.5

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      +..+|||+|||.++|+++|+++|+.||.|.+|+|+.+.  +.++|||||+|.+.++|++|++.|++..+.|+.|.|.++.
T Consensus         4 ~~~~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            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            46789999999999999999999999999999999986  4589999999999999999999999999999999999987


Q ss_pred             Cccccc-------cccccccccCCCchhcHHH
Q psy3016         113 SHQKNL-------DVGANIFIGNLDPEVDEKL  137 (305)
Q Consensus       113 ~~~~~~-------~~~~~l~v~nl~~~~t~~~  137 (305)
                      .+....       ....+|||+||++++|++-
T Consensus        82 ~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           82 SRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCCC----------------------------
T ss_pred             CccccccccccccCCCCceEeCCCCCCccccc
Confidence            654322       2346799999999999863

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.89  E-value=9.5e-23  Score=166.84  Aligned_cols=139  Identities=20%  Similarity=0.244  Sum_probs=111.8

Q ss_pred             EEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe-------eCCC-----ccccccccccccccCCC
Q psy3016          63 NVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN-------KASS-----HQKNLDVGANIFIGNLD  130 (305)
Q Consensus        63 ~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~-------~~~~-----~~~~~~~~~~l~v~nl~  130 (305)
                      .++|+.+.  ..++|||||+|.+.++|++|++.+++....+..+.+.       ....     .........+|||+||+
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~   79 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT   79 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCC
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCC
Confidence            45666665  3689999999999999999999887533222222222       1111     11122346899999999


Q ss_pred             chhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeC
Q psy3016         131 PEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYA  210 (305)
Q Consensus       131 ~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~  210 (305)
                      .++|+++|+++|+.||.|..+                                       .++.|..+|.++|||||+|.
T Consensus        80 ~~~~~~~l~~~F~~~G~v~~~---------------------------------------~i~~~~~~g~~~g~afV~f~  120 (158)
T 2kn4_A           80 YRTSPDTLRRVFEKYGRVGDV---------------------------------------YIPRDRYTKESRGFAFVRFH  120 (158)
T ss_dssp             TTCCHHHHHHHHHHHSCEEEE---------------------------------------ECCCCSSCTTSCCEEEEEES
T ss_pred             CCCCHHHHHHHHHhcCCeEEE---------------------------------------EEeecCCCCccceEEEEEEC
Confidence            999999999999999999877                                       67888888999999999999


Q ss_pred             ChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         211 SFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       211 ~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +.++|.+|+..|||..+.|+.|+|.|+..+..
T Consensus       121 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A          121 DKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             BHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             CHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            99999999999999999999999999977643

>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=2.4e-21  Score=146.37  Aligned_cols=81  Identities=27%  Similarity=0.490  Sum_probs=77.8

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (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~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            45789999999999999999999999999999999999899999999999999999999999999999999999999986


Q ss_pred             C
Q psy3016         113 S  113 (305)
Q Consensus       113 ~  113 (305)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            4

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.84  E-value=4.9e-21  Score=155.45  Aligned_cols=123  Identities=19%  Similarity=0.333  Sum_probs=108.5

Q ss_pred             CCcceEEEEEEcCHHHHHHHHHHh-cCceeCCeeeEEeeCCCcc---------------ccccccccccccCCCchhcHH
Q psy3016          73 QTHQGYGFIEFMGEEDADYAIKIM-NMIKLYGKPIRVNKASSHQ---------------KNLDVGANIFIGNLDPEVDEK  136 (305)
Q Consensus        73 ~~~~g~afV~f~~~e~A~~Ai~~l-~g~~~~g~~l~v~~~~~~~---------------~~~~~~~~l~v~nl~~~~t~~  136 (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 9999999 99999876521               122346899999999999999


Q ss_pred             HHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHH
Q psy3016         137 LLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASD  216 (305)
Q Consensus       137 ~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~  216 (305)
                      +|+++|+.||.|..+                                       .++.|     ++|||||+|.+.++|.
T Consensus        89 ~l~~~F~~~G~i~~v---------------------------------------~i~~~-----~~g~afV~f~~~~~a~  124 (150)
T 2i2y_A           89 ELERAFGYYGPLRSV---------------------------------------WVARN-----PPGFAFVEFEDPRDAA  124 (150)
T ss_dssp             HHHHHHHHHSCEEEE---------------------------------------EECSS-----SCSEEEEEESSHHHHH
T ss_pred             HHHHHHHhhCCEEEE---------------------------------------EEeeC-----CCcEEEEEECCHHHHH
Confidence            999999999999876                                       44544     5899999999999999


Q ss_pred             HHHHHhcCeeecCeeeEEEEeeec
Q psy3016         217 ASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       217 ~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +|+..|||..+.|+.|+|.|+.++
T Consensus       125 ~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A          125 DAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHcCCCEECCeEEEEEEcCCC
Confidence            999999999999999999998765

>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=3e-20  Score=142.97  Aligned_cols=84  Identities=20%  Similarity=0.251  Sum_probs=79.6

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+||+..+|+++|+++|++||.|.+|+|+.+..+++++|||||+|.+.++|++|++.|||..+.|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34689999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             CCcc
Q psy3016         112 SSHQ  115 (305)
Q Consensus       112 ~~~~  115 (305)
                      ....
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            7544

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.82  E-value=1.1e-20  Score=140.45  Aligned_cols=84  Identities=14%  Similarity=0.291  Sum_probs=77.5

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCC-CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc-CceeCCeeeEEeeC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN-MIKLYGKPIRVNKA  111 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~-g~~~~g~~l~v~~~  111 (305)
                      +.+|||+|||.++|+++|+++|+.|| .|.+|+|++++.++.++|||||+|.+.++|.+|++.++ +..+.|+.|+|+++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 89999999999999999999999999999999999774 67899999999999


Q ss_pred             CCcccc
Q psy3016         112 SSHQKN  117 (305)
Q Consensus       112 ~~~~~~  117 (305)
                      .++.+.
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.4e-19  Score=137.21  Aligned_cols=92  Identities=29%  Similarity=0.385  Sum_probs=84.6

Q ss_pred             CCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        26 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      .+.......++|||+|||..+|+++|+++|+.||.|..|.++.++.++.++|||||+|.+.++|.+|++.||+..+.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   86 (103)
T 2cq0_A            7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI   86 (103)
T ss_dssp             CSCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcE
Confidence            34445667899999999999999999999999999999999999888999999999999999999999999999999999


Q ss_pred             eEEeeCCCcccc
Q psy3016         106 IRVNKASSHQKN  117 (305)
Q Consensus       106 l~v~~~~~~~~~  117 (305)
                      |+|.++..+...
T Consensus        87 l~v~~a~~~~~~   98 (103)
T 2cq0_A           87 LNVEWAKPSTNS   98 (103)
T ss_dssp             CEEEESSCCCCS
T ss_pred             EEEEECCCCCCC
Confidence            999999876543

>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=99.81  E-value=2.2e-19  Score=130.61  Aligned_cols=82  Identities=28%  Similarity=0.493  Sum_probs=78.0

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (305)
                      .++|||+|||..+|+++|+++|+.||.|.++.++.+..++.++|||||+|.+.++|++|++.|||..+.|+.|+|.++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999999988899999999999999999999999999999999999999886


Q ss_pred             cc
Q psy3016         114 HQ  115 (305)
Q Consensus       114 ~~  115 (305)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.81  E-value=1.5e-19  Score=132.14  Aligned_cols=83  Identities=36%  Similarity=0.661  Sum_probs=78.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||.++++++|+++|+.||.|.+|.++.+..++.++|||||+|.+.++|.+|++.|||..+.|+.|+|+
T Consensus         3 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eCC
Q psy3016         110 KAS  112 (305)
Q Consensus       110 ~~~  112 (305)
                      ++.
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            874

>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=99.81  E-value=1.5e-19  Score=132.70  Aligned_cols=83  Identities=29%  Similarity=0.470  Sum_probs=76.9

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||..+|+++|+++|+.||.|.+|+++.+..++.++|||||+|.+.++|++|++.||+..+.|+.|+|+++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            45789999999999999999999999999999999999888999999999999999999999999999999999999998


Q ss_pred             CCc
Q psy3016         112 SSH  114 (305)
Q Consensus       112 ~~~  114 (305)
                      ..+
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            754

>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=99.81  E-value=1.3e-19  Score=140.31  Aligned_cols=106  Identities=15%  Similarity=0.284  Sum_probs=95.5

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ....++|||+|||..+|+++|+++|+.||.|.+|.++.+   +.++|||||+|.+.++|.+|++.|||..+.|+.|.|.+
T Consensus         5 ~~~~~~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            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            345789999999999999999999999999999999876   35689999999999999999999999999999999999


Q ss_pred             CCCccccccccccccccCCCchhcHHHHHHHHhhcCcc
Q psy3016         111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVI  148 (305)
Q Consensus       111 ~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v  148 (305)
                      +.+....         .+++...+++++.++|+.||.-
T Consensus        82 a~~~~~~---------~~~~~~~~~~~l~~~~~~~g~~  110 (115)
T 3lqv_A           82 YNANRAF---------QKMDTKKKEEQLKLLKEKYGIN  110 (115)
T ss_dssp             CCHHHHT---------TTSCHHHHHHHHHHHHHHHCCC
T ss_pred             ecCChhh---------hhhhHhHhHHHHHHHHHHhCCC
Confidence            9865533         5778899999999999999864

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.81  E-value=5.3e-19  Score=136.81  Aligned_cols=91  Identities=26%  Similarity=0.404  Sum_probs=83.7

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||..+|+++|+++|+.||.|..|+|+.++.++.++|||||+|.+.++|++|++.|++..+.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   88 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            33556788999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EeeCCCccccc
Q psy3016         108 VNKASSHQKNL  118 (305)
Q Consensus       108 v~~~~~~~~~~  118 (305)
                      |.++..+....
T Consensus        89 V~~a~~~~~~~   99 (115)
T 2dgo_A           89 TNWATRKPPAP   99 (115)
T ss_dssp             EEESSCCCCCS
T ss_pred             EEEccCCCCCC
Confidence            99998765443

>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=99.81  E-value=2.4e-19  Score=136.37  Aligned_cols=91  Identities=76%  Similarity=1.231  Sum_probs=84.2

Q ss_pred             CCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        27 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      +.......++|||+|||..+|+++|+++|+.||.|..|+++.+..++.++|||||+|.+.++|.+|++.|++..+.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (105)
T 1x5u_A            8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   87 (105)
T ss_dssp             CCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            34455678899999999999999999999999999999999998889999999999999999999999999999999999


Q ss_pred             EEeeCCCcccc
Q psy3016         107 RVNKASSHQKN  117 (305)
Q Consensus       107 ~v~~~~~~~~~  117 (305)
                      +|.++......
T Consensus        88 ~v~~a~~~~~~   98 (105)
T 1x5u_A           88 RVNKASAHNKN   98 (105)
T ss_dssp             EEEETTTTSCC
T ss_pred             EEEECCCCCcC
Confidence            99999876544

>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=99.81  E-value=2.6e-19  Score=134.72  Aligned_cols=88  Identities=25%  Similarity=0.410  Sum_probs=82.2

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|+++.+..++.++|||||+|.+.++|.+|++.||+..+.|+.|.|.
T Consensus         4 ~~~~~~~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            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eCCCcccc
Q psy3016         110 KASSHQKN  117 (305)
Q Consensus       110 ~~~~~~~~  117 (305)
                      ++..+...
T Consensus        84 ~a~~~~~~   91 (99)
T 1whw_A           84 PSTIKKEA   91 (99)
T ss_dssp             ECCCCSTT
T ss_pred             EcCCCccc
Confidence            99876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.80  E-value=8.7e-20  Score=136.58  Aligned_cols=84  Identities=24%  Similarity=0.352  Sum_probs=77.1

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCC--eEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCc----eeCC
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGP--VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMI----KLYG  103 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~--i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~----~~~g  103 (305)
                      ....-.||||+|||+.+|+++|+++|++||.  |.+|++++|+.+|.++|||||+|.+.++|.+|++.||+.    .+.|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            3455679999999999999999999999995  679999999999999999999999999999999999986    5899


Q ss_pred             eeeEEeeCCC
Q psy3016         104 KPIRVNKASS  113 (305)
Q Consensus       104 ~~l~v~~~~~  113 (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            9999999874

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.9e-19  Score=133.31  Aligned_cols=86  Identities=29%  Similarity=0.421  Sum_probs=80.5

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||..+|+++|+++|+.||.|..|+++.+..++.++|||||+|.+.++|.+|++.||+..+.|+.|+
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34556678999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EeeCCC
Q psy3016         108 VNKASS  113 (305)
Q Consensus       108 v~~~~~  113 (305)
                      |+++..
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999864

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=3.8e-19  Score=132.49  Aligned_cols=84  Identities=26%  Similarity=0.478  Sum_probs=79.1

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||..+++++|+++|+.||.|.+|+++.++.++.++|||||+|.+.++|.+|++.||+..+.|+.|+|
T Consensus        11 ~~~~~~~~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           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             eeCC
Q psy3016         109 NKAS  112 (305)
Q Consensus       109 ~~~~  112 (305)
                      ++++
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=5.1e-19  Score=133.44  Aligned_cols=85  Identities=18%  Similarity=0.319  Sum_probs=79.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (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~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      ++.++.
T Consensus        92 ~a~~~~   97 (100)
T 2do4_A           92 ISNSGP   97 (100)
T ss_dssp             ECCCCS
T ss_pred             ECCCCC
Confidence            998754

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=3.8e-19  Score=133.91  Aligned_cols=88  Identities=33%  Similarity=0.561  Sum_probs=81.7

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||..+|+++|+++|+.||.|.+|+++.++.++.++|||||+|.+.++|.+|++ |++..+.|+.|+|
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V   83 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEV   83 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEE
Confidence            345567899999999999999999999999999999999998889999999999999999999999 9999999999999


Q ss_pred             eeCCCcccc
Q psy3016         109 NKASSHQKN  117 (305)
Q Consensus       109 ~~~~~~~~~  117 (305)
                      .++..+...
T Consensus        84 ~~a~~~~~~   92 (99)
T 2dgs_A           84 KRAEPRDSK   92 (99)
T ss_dssp             EECCCCCCC
T ss_pred             EECCCCccc
Confidence            999876543

>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=99.80  E-value=3.4e-19  Score=133.46  Aligned_cols=83  Identities=27%  Similarity=0.436  Sum_probs=79.3

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (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~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            57999999999999999999999999999999999988899999999999999999999999999999999999999987


Q ss_pred             ccc
Q psy3016         114 HQK  116 (305)
Q Consensus       114 ~~~  116 (305)
                      ...
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            653

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.3e-19  Score=135.78  Aligned_cols=88  Identities=34%  Similarity=0.621  Sum_probs=82.3

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|+++.+..++.++|||||+|.+.++|++|++.||+..+.|+.|+|.
T Consensus         8 ~~~~~~~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            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eCCCcccc
Q psy3016         110 KASSHQKN  117 (305)
Q Consensus       110 ~~~~~~~~  117 (305)
                      ++......
T Consensus        88 ~a~~~~~~   95 (102)
T 2cqb_A           88 LAKPMRIK   95 (102)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            99876544

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=2.2e-19  Score=136.23  Aligned_cols=90  Identities=28%  Similarity=0.438  Sum_probs=83.3

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||..+|+++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|++|++.||+..+.|+.|.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            34556788999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EeeCCCcccc
Q psy3016         108 VNKASSHQKN  117 (305)
Q Consensus       108 v~~~~~~~~~  117 (305)
                      |.++......
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dnm_A           87 VQVARYGRRD   96 (103)
T ss_dssp             EEECSSCCSC
T ss_pred             EEECCcCCCC
Confidence            9999876543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=3.6e-19  Score=132.91  Aligned_cols=85  Identities=32%  Similarity=0.567  Sum_probs=80.6

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||..+|+++|+++|+.||.|.+|+++.+..++.++|||||+|.+.++|.+|++.||+..+.|+.|+|+++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            45789999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             CCccc
Q psy3016         112 SSHQK  116 (305)
Q Consensus       112 ~~~~~  116 (305)
                      ..+..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87654

>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=99.80  E-value=3.7e-19  Score=137.74  Aligned_cols=88  Identities=22%  Similarity=0.357  Sum_probs=82.0

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|+.+..++.++|||||+|.+.++|++|++.||+..+.|+.|+|.
T Consensus        21 ~~~~~~~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           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44466899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eCCCcccc
Q psy3016         110 KASSHQKN  117 (305)
Q Consensus       110 ~~~~~~~~  117 (305)
                      ++..+...
T Consensus       101 ~a~~~~~~  108 (115)
T 2cpz_A          101 LKRSKNDS  108 (115)
T ss_dssp             CCCCSCCC
T ss_pred             EcCCCCcC
Confidence            99876543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.80  E-value=3.9e-19  Score=138.21  Aligned_cols=84  Identities=23%  Similarity=0.362  Sum_probs=78.4

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||.++|+++|+++|+.||.|.+|+++.++.++.++|||||+|.+.++|++|++.|||..+.|+.|+|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             eeCC
Q psy3016         109 NKAS  112 (305)
Q Consensus       109 ~~~~  112 (305)
                      ++++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9863

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.80  E-value=4.2e-19  Score=136.11  Aligned_cols=88  Identities=27%  Similarity=0.529  Sum_probs=82.0

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||..+|+++|+++|+.||.|..|+++.++.++.++|||||+|.+.++|.+|++.|+|..+.|+.|+
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~   99 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK   99 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34556778999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EeeCCCcc
Q psy3016         108 VNKASSHQ  115 (305)
Q Consensus       108 v~~~~~~~  115 (305)
                      |+++..+.
T Consensus       100 V~~a~~k~  107 (108)
T 2jrs_A          100 VGHVTERT  107 (108)
T ss_dssp             EECSCSSC
T ss_pred             EEEcccCC
Confidence            99987653

>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=2.4e-19  Score=141.86  Aligned_cols=90  Identities=27%  Similarity=0.418  Sum_probs=83.5

Q ss_pred             CCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        26 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      .+.......++|||+|||..+|+++|+++|+.||.|..|+++.++.++.++|||||+|.+.++|++|++.|++..+.|+.
T Consensus        38 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~  117 (129)
T 2kxn_B           38 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR  117 (129)
T ss_dssp             CCSSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            34456677889999999999999999999999999999999999888999999999999999999999999999999999


Q ss_pred             eEEeeCCCcc
Q psy3016         106 IRVNKASSHQ  115 (305)
Q Consensus       106 l~v~~~~~~~  115 (305)
                      |+|.++..+.
T Consensus       118 l~V~~a~~~~  127 (129)
T 2kxn_B          118 IRVDFSITKR  127 (129)
T ss_dssp             CEESCCSSSS
T ss_pred             EEEEEecCCC
Confidence            9999988654

>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=99.79  E-value=7.9e-19  Score=133.53  Aligned_cols=87  Identities=21%  Similarity=0.349  Sum_probs=80.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC---eee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG---KPI  106 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g---~~l  106 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|++|++.||+..+.|   +.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34567899999999999999999999999999999999997 78999999999999999999999999999998   999


Q ss_pred             EEeeCCCcccc
Q psy3016         107 RVNKASSHQKN  117 (305)
Q Consensus       107 ~v~~~~~~~~~  117 (305)
                      .|.++......
T Consensus        90 ~V~~a~~~~~~  100 (105)
T 2dnh_A           90 VVKFADTDKES  100 (105)
T ss_dssp             EEEESCSSCCC
T ss_pred             EEEECccCccc
Confidence            99999876544

>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=99.79  E-value=4.8e-19  Score=135.95  Aligned_cols=86  Identities=22%  Similarity=0.350  Sum_probs=80.7

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..|+++.+..++.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      ++..+.
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            987654

>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=3.1e-19  Score=134.34  Aligned_cols=86  Identities=26%  Similarity=0.425  Sum_probs=80.7

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeE-EEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee---
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVV-NVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP---  105 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~-~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~---  105 (305)
                      .....++|||+|||..+|+++|+++|+.||.|. +|+++.++.++.++|||||+|.+.++|++|++.||+..+.|+.   
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   84 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK   84 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCE
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcce
Confidence            455678999999999999999999999999999 9999999889999999999999999999999999999999999   


Q ss_pred             -eEEeeCCCcc
Q psy3016         106 -IRVNKASSHQ  115 (305)
Q Consensus       106 -l~v~~~~~~~  115 (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             9999987653

>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=99.79  E-value=7.3e-20  Score=135.55  Aligned_cols=82  Identities=13%  Similarity=0.275  Sum_probs=72.8

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCC--CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSG--PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G--~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (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~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999899999999999999999999999999999999999999988


Q ss_pred             Cccc
Q psy3016         113 SHQK  116 (305)
Q Consensus       113 ~~~~  116 (305)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=7.1e-19  Score=133.35  Aligned_cols=88  Identities=23%  Similarity=0.353  Sum_probs=81.2

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||..+|+++|+++|+.||.|..|+++.+  ++.++|||||+|.+.++|.+|++.||+..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            44557889999999999999999999999999999999998  7889999999999999999999999999999999999


Q ss_pred             eeCCCccccc
Q psy3016         109 NKASSHQKNL  118 (305)
Q Consensus       109 ~~~~~~~~~~  118 (305)
                      .++..+....
T Consensus        88 ~~a~~~~~~~   97 (103)
T 2d9p_A           88 ALAQRKEERQ   97 (103)
T ss_dssp             EECSSCCCCC
T ss_pred             EEecccccCC
Confidence            9998765443

>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=99.79  E-value=8.1e-19  Score=134.75  Aligned_cols=88  Identities=22%  Similarity=0.321  Sum_probs=82.2

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc------CceeCC
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN------MIKLYG  103 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~------g~~~~g  103 (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            45567899999999999999999999999999999999998889999999999999999999999999      999999


Q ss_pred             eeeEEeeCCCcccc
Q psy3016         104 KPIRVNKASSHQKN  117 (305)
Q Consensus       104 ~~l~v~~~~~~~~~  117 (305)
                      +.|+|.++..+...
T Consensus        91 ~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           91 RQLKVDLAVTRDEA  104 (111)
T ss_dssp             CEEEEECCCCCCCC
T ss_pred             EEEEEEECCCCccC
Confidence            99999999876543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=7.4e-19  Score=134.10  Aligned_cols=89  Identities=26%  Similarity=0.464  Sum_probs=82.1

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEccc-CCCCCcceEEEEEEcCHHHHHHHHHHh-cCceeCCeee
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKD-RVTQTHQGYGFIEFMGEEDADYAIKIM-NMIKLYGKPI  106 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~-~~~~~~~g~afV~f~~~e~A~~Ai~~l-~g~~~~g~~l  106 (305)
                      ......++|||+|||..+|+++|+++|+.||.|..|+++.+ ..++.++|||||+|.+.++|.+|++.| |+..+.|+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            34556789999999999999999999999999999999998 778999999999999999999999999 9999999999


Q ss_pred             EEeeCCCcccc
Q psy3016         107 RVNKASSHQKN  117 (305)
Q Consensus       107 ~v~~~~~~~~~  117 (305)
                      .|.++..+...
T Consensus        90 ~v~~a~~~~~~  100 (107)
T 2cph_A           90 VLEWADSEVTV  100 (107)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999876543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.7e-19  Score=135.42  Aligned_cols=89  Identities=31%  Similarity=0.524  Sum_probs=82.4

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||.++|+++|+++|+.||.|..|+++.+..++.++|||||+|.+.++|.+|++.||+..+.|+.|+|
T Consensus         7 ~~~~~~~~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            7 GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   86 (102)
T ss_dssp             CCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             eeCCCcccc
Q psy3016         109 NKASSHQKN  117 (305)
Q Consensus       109 ~~~~~~~~~  117 (305)
                      .++......
T Consensus        87 ~~a~~~~~~   95 (102)
T 1x5s_A           87 DQAGKSSDN   95 (102)
T ss_dssp             EEEECCCCC
T ss_pred             EECCCCCCC
Confidence            998876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.3e-19  Score=133.33  Aligned_cols=86  Identities=30%  Similarity=0.551  Sum_probs=80.8

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEE-EEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNV-HMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i-~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ...++|||+|||..+|+++|+++|+.||.|..| +++.++.++.++|||||+|.+.++|++|++.||+..+.|+.|+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            457899999999999999999999999999999 9999988899999999999999999999999999999999999999


Q ss_pred             CCCcccc
Q psy3016         111 ASSHQKN  117 (305)
Q Consensus       111 ~~~~~~~  117 (305)
                      +..+...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9876543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=4.6e-19  Score=135.08  Aligned_cols=86  Identities=24%  Similarity=0.403  Sum_probs=80.3

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|.++.+..++.++|||||+|.+.++|++|++.|||..+.|+.|.|.
T Consensus        19 ~~~~~~~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           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34456899999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      ++..+.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            987653

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.79  E-value=1.1e-19  Score=137.40  Aligned_cols=83  Identities=27%  Similarity=0.324  Sum_probs=78.5

Q ss_pred             CCceEEEcCCCc------cccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC-ee
Q psy3016          33 GDATIYVGGLDD------KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG-KP  105 (305)
Q Consensus        33 ~~~~l~V~nLp~------~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g-~~  105 (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            357999999999      99999999999999999999999999889999999999999999999999999999999 99


Q ss_pred             eEEeeCCCcc
Q psy3016         106 IRVNKASSHQ  115 (305)
Q Consensus       106 l~v~~~~~~~  115 (305)
                      |+|.++.+..
T Consensus        85 l~V~~a~~~~   94 (100)
T 3ns6_A           85 LFLYTMKDVE   94 (100)
T ss_dssp             CEEEESHHHH
T ss_pred             EEEEECchhh
Confidence            9999987543

>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=99.79  E-value=8.9e-19  Score=128.60  Aligned_cols=83  Identities=25%  Similarity=0.433  Sum_probs=76.2

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||.++|+++|+++|+.||.|.+|+++.++.++.++|||||+|.+.++|.+|++ +++..+.|+.|.
T Consensus         5 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~   83 (87)
T 3s7r_A            5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVID   83 (87)
T ss_dssp             --CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEE
Confidence            3455678899999999999999999999999999999999998889999999999999999999997 588899999999


Q ss_pred             EeeC
Q psy3016         108 VNKA  111 (305)
Q Consensus       108 v~~~  111 (305)
                      |+++
T Consensus        84 v~~A   87 (87)
T 3s7r_A           84 PKKA   87 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9875

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.79  E-value=7.4e-19  Score=132.34  Aligned_cols=84  Identities=27%  Similarity=0.392  Sum_probs=78.9

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEE--------EEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCce
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN--------VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIK  100 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~--------i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~  100 (305)
                      ......++|||+|||.++|+++|+++|+.||.|..        |+++.++.+|.++|||||+|.+.++|.+|++.|||..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34556789999999999999999999999999999        9999998899999999999999999999999999999


Q ss_pred             eCCeeeEEeeCC
Q psy3016         101 LYGKPIRVNKAS  112 (305)
Q Consensus       101 ~~g~~l~v~~~~  112 (305)
                      +.|+.|+|+++.
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999874

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=6.8e-19  Score=132.20  Aligned_cols=86  Identities=20%  Similarity=0.386  Sum_probs=79.3

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCC---CCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRV---TQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~---~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ...++|||+|||.++|+++|+++|+.||.|..|.++.+..   ++.++|||||+|.+.++|++|++.||+..+.|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4578999999999999999999999999999999998875   5589999999999999999999999999999999999


Q ss_pred             eeCCCcccc
Q psy3016         109 NKASSHQKN  117 (305)
Q Consensus       109 ~~~~~~~~~  117 (305)
                      .++......
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>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=99.78  E-value=5.5e-19  Score=134.66  Aligned_cols=90  Identities=24%  Similarity=0.423  Sum_probs=82.5

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee---CCe
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL---YGK  104 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~---~g~  104 (305)
                      .......++|||+|||..+|+++|+++|+.||.|.+|+++.++.++.++|||||+|.+.++|.+|++.||+..+   .|+
T Consensus         7 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~   86 (106)
T 2dgp_A            7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNR   86 (106)
T ss_dssp             SCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCc
Confidence            34556678999999999999999999999999999999999988899999999999999999999999999887   899


Q ss_pred             eeEEeeCCCcccc
Q psy3016         105 PIRVNKASSHQKN  117 (305)
Q Consensus       105 ~l~v~~~~~~~~~  117 (305)
                      .|.|.++......
T Consensus        87 ~l~v~~a~~~~~~   99 (106)
T 2dgp_A           87 PIQVKPADSESRG   99 (106)
T ss_dssp             CCEEEECCCCSCC
T ss_pred             eEEEEECCccccc
Confidence            9999999876543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.78  E-value=3e-19  Score=134.95  Aligned_cols=91  Identities=23%  Similarity=0.441  Sum_probs=81.6

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (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            58999999999999999999999999999999887     6799999999999999999999999999999999999875


Q ss_pred             cccc---------cccccccccCCC
Q psy3016         115 QKNL---------DVGANIFIGNLD  130 (305)
Q Consensus       115 ~~~~---------~~~~~l~v~nl~  130 (305)
                      ....         ....+|||+||+
T Consensus        76 ~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           76 PRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CCcccCCCCCccccCCCceecCCCC
Confidence            4321         125789999997

>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=99.78  E-value=3.5e-19  Score=134.36  Aligned_cols=80  Identities=29%  Similarity=0.564  Sum_probs=75.9

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||.++|+++|+++|+.||.|..+                                       .+++|..+|.
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v---------------------------------------~i~~d~~tg~   59 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESA---------------------------------------KLIRDKVAGH   59 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------EEEECSSSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEe---------------------------------------EeeecCCCCc
Confidence            5689999999999999999999999999887                                       7788988999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      ++|||||+|.+.++|.+|++.|||..+.|+.|+|+||++
T Consensus        60 ~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           60 SLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             EEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             ccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            999999999999999999999999999999999999965

>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=99.78  E-value=2.8e-18  Score=130.07  Aligned_cols=89  Identities=22%  Similarity=0.359  Sum_probs=80.5

Q ss_pred             CCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        27 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      ..+.....++|||+|||..+|+++|+++|+.||.|.+|+|+.+..  .++|||||+|.+.++|++|++.|++..+.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   85 (103)
T 2cq3_A            8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKI   85 (103)
T ss_dssp             CSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            345566789999999999999999999999999999999998863  388999999999999999999999999999999


Q ss_pred             EEeeCCCcccc
Q psy3016         107 RVNKASSHQKN  117 (305)
Q Consensus       107 ~v~~~~~~~~~  117 (305)
                      +|.++..+...
T Consensus        86 ~v~~a~~~~~~   96 (103)
T 2cq3_A           86 EVNNATARVMT   96 (103)
T ss_dssp             EEEECCSSCCC
T ss_pred             EEEEcccCCCC
Confidence            99999876543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.8e-18  Score=134.06  Aligned_cols=88  Identities=26%  Similarity=0.353  Sum_probs=81.0

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||..+|+++|+++|+.||.|..|+|+.++.++.++|||||+|.+.++|++|++.+++ .+.|+.|+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            34556678999999999999999999999999999999999988899999999999999999999999998 89999999


Q ss_pred             EeeCCCccc
Q psy3016         108 VNKASSHQK  116 (305)
Q Consensus       108 v~~~~~~~~  116 (305)
                      |+++.....
T Consensus        90 V~~a~~~~~   98 (116)
T 2cqd_A           90 VNLAYLGAK   98 (116)
T ss_dssp             EEESTTTCC
T ss_pred             EEEcccCCC
Confidence            999976543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.78  E-value=1.1e-18  Score=139.47  Aligned_cols=90  Identities=28%  Similarity=0.426  Sum_probs=83.4

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||.++|+++|+++|+.||.|.+|+++.++.++.++|||||+|.+.++|.+|++.||+..+.|+.|+
T Consensus        36 ~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  115 (139)
T 1u6f_A           36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             SCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            34556678999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EeeCCCcccc
Q psy3016         108 VNKASSHQKN  117 (305)
Q Consensus       108 v~~~~~~~~~  117 (305)
                      |.++......
T Consensus       116 v~~a~~~~~~  125 (139)
T 1u6f_A          116 VALAASGHQR  125 (139)
T ss_dssp             EEESSCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999876544

>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=99.78  E-value=2.3e-18  Score=130.58  Aligned_cols=88  Identities=34%  Similarity=0.538  Sum_probs=79.6

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||..+|+++|+++|+.||.|.+|+++.+..+  ++|||||+|.+.++|.+|++.|++..+.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cqi_A            9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVK   86 (103)
T ss_dssp             CCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEE
Confidence            345567899999999999999999999999999999999998633  689999999999999999999999999999999


Q ss_pred             EeeCCCcccc
Q psy3016         108 VNKASSHQKN  117 (305)
Q Consensus       108 v~~~~~~~~~  117 (305)
                      |.++......
T Consensus        87 V~~a~~~~~~   96 (103)
T 2cqi_A           87 VNWATTPSSQ   96 (103)
T ss_dssp             EEECCCTTCC
T ss_pred             EEECCCCccc
Confidence            9999876543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.3e-18  Score=134.15  Aligned_cols=88  Identities=23%  Similarity=0.345  Sum_probs=81.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeE--------EEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVV--------NVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL  101 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~--------~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~  101 (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            455678999999999999999999999999999        699999988899999999999999999999999999999


Q ss_pred             CCeeeEEeeCCCcccc
Q psy3016         102 YGKPIRVNKASSHQKN  117 (305)
Q Consensus       102 ~g~~l~v~~~~~~~~~  117 (305)
                      .|+.|+|.++..+...
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999876543

>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=99.78  E-value=4.6e-19  Score=136.96  Aligned_cols=85  Identities=21%  Similarity=0.365  Sum_probs=79.1

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..|+|+.++.++.++|||||+|.+.++|++|+ .||+..+.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   99 (114)
T 2cq4_A           21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQ   99 (114)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEE
Confidence            3445689999999999999999999999999999999999988999999999999999999999 899999999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      ++..+.
T Consensus       100 ~a~~~~  105 (114)
T 2cq4_A          100 ASQAEK  105 (114)
T ss_dssp             EHHHHH
T ss_pred             ecCCCc
Confidence            987643

>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=1.1e-18  Score=130.26  Aligned_cols=83  Identities=41%  Similarity=0.795  Sum_probs=77.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+++++|+++|+.||.|.+|+++.+.. +.++|||||+|.+.++|.+|++.||+..+.|+.|+|+
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            445678999999999999999999999999999999999975 8899999999999999999999999999999999999


Q ss_pred             eCCC
Q psy3016         110 KASS  113 (305)
Q Consensus       110 ~~~~  113 (305)
                      ++..
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            8763

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.78  E-value=9.7e-19  Score=134.26  Aligned_cols=91  Identities=24%  Similarity=0.412  Sum_probs=76.6

Q ss_pred             CCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe
Q psy3016          25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK  104 (305)
Q Consensus        25 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~  104 (305)
                      ....+.....++|||+|||..+|+++|+++|+.||.|.+|+++.+..+|.++|||||+|.+.++|.+|++.+ +..+.|+
T Consensus        16 ~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~   94 (109)
T 2rs2_A           16 PRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSK   94 (109)
T ss_dssp             ----------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTE
T ss_pred             ccccccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCE
Confidence            344456677899999999999999999999999999999999999888999999999999999999999975 5999999


Q ss_pred             eeEEeeCCCccc
Q psy3016         105 PIRVNKASSHQK  116 (305)
Q Consensus       105 ~l~v~~~~~~~~  116 (305)
                      .|.|.++..+..
T Consensus        95 ~l~V~~a~~~~~  106 (109)
T 2rs2_A           95 TIDPKVAFPRRA  106 (109)
T ss_dssp             EEEEEECCCCCC
T ss_pred             EEEEEEccCCCC
Confidence            999999987653

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=1.9e-18  Score=130.99  Aligned_cols=86  Identities=20%  Similarity=0.320  Sum_probs=79.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.|| |.+|+++.+..++.++|||||+|.+.++|++|+ .||+..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            445678999999999999999999999997 999999999988999999999999999999999 799999999999999


Q ss_pred             eCCCcccc
Q psy3016         110 KASSHQKN  117 (305)
Q Consensus       110 ~~~~~~~~  117 (305)
                      ++......
T Consensus        89 ~a~~~~~~   96 (103)
T 2dng_A           89 IAEGRKQD   96 (103)
T ss_dssp             ECCCCCCC
T ss_pred             EecCCCCC
Confidence            99876543

>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=99.78  E-value=8.8e-19  Score=128.72  Aligned_cols=83  Identities=23%  Similarity=0.446  Sum_probs=77.0

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCC-cceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQT-HQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~-~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ..++|||+|||.++|+++|+++|+.||.|.+|.++.+..++. ++|||||+|.+.++|.+|++.|||..+.|+.|+|+++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            467999999999999999999999999999999999876655 8999999999999999999999999999999999998


Q ss_pred             CCcc
Q psy3016         112 SSHQ  115 (305)
Q Consensus       112 ~~~~  115 (305)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=2.9e-18  Score=132.34  Aligned_cols=88  Identities=26%  Similarity=0.383  Sum_probs=80.7

Q ss_pred             CCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        27 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      +.......++|||+|||..+|+++|+++|+.||.|.+|+|+.++ ++.++|||||+|.+.++|++|++.||+..+.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   86 (114)
T 2do0_A            8 ALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPM   86 (114)
T ss_dssp             CCCCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEE
Confidence            33455668899999999999999999999999999999999997 58999999999999999999999999999999999


Q ss_pred             EEeeCCCcc
Q psy3016         107 RVNKASSHQ  115 (305)
Q Consensus       107 ~v~~~~~~~  115 (305)
                      .|.++....
T Consensus        87 ~v~~a~~~~   95 (114)
T 2do0_A           87 HVKMDERAL   95 (114)
T ss_dssp             EEEECSCCC
T ss_pred             EEEEcccCC
Confidence            999987543

>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=99.78  E-value=2.1e-18  Score=131.06  Aligned_cols=86  Identities=26%  Similarity=0.381  Sum_probs=79.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCC-CCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVT-QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~-~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      .....++|||+|||..+|+++|+++|+.|| |.+|.|+.+..+ +.++|||||+|.+.++|++|+ .|++..+.|+.|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            345568999999999999999999999999 999999999877 899999999999999999999 89999999999999


Q ss_pred             eeCCCcccc
Q psy3016         109 NKASSHQKN  117 (305)
Q Consensus       109 ~~~~~~~~~  117 (305)
                      .++..+...
T Consensus        89 ~~a~~~~~~   97 (104)
T 1wi8_A           89 DVADQAQDK   97 (104)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCCCCC
Confidence            999876544

>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=99.77  E-value=1.9e-18  Score=129.40  Aligned_cols=84  Identities=23%  Similarity=0.236  Sum_probs=76.7

Q ss_pred             cCCCCceEEEcCCCccccHHHHH----HHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMW----ELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      .....++|||+|||..+++++|+    ++|+.||.|.+|+++.++.+   +|||||+|.+.++|.+|++.|||..+.|+.
T Consensus         5 ~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~   81 (96)
T 2dgx_A            5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKK   81 (96)
T ss_dssp             CCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            34456899999999999999999    99999999999999998754   799999999999999999999999999999


Q ss_pred             eEEeeCCCccc
Q psy3016         106 IRVNKASSHQK  116 (305)
Q Consensus       106 l~v~~~~~~~~  116 (305)
                      |+|+++.+...
T Consensus        82 l~V~~a~~~~~   92 (96)
T 2dgx_A           82 ILVSLATGASG   92 (96)
T ss_dssp             EEEEECCCSSC
T ss_pred             EEEEEcCCCCC
Confidence            99999976543

>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=1.7e-18  Score=132.16  Aligned_cols=84  Identities=26%  Similarity=0.362  Sum_probs=78.7

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||..+|+++|+++|+.||.|.+|+++.+. ++.++|||||+|.+.++|++|++.|++..+.|+.|+
T Consensus        23 ~~~~~~~~~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           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN  101 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            3455678899999999999999999999999999999999998 899999999999999999999999999999999999


Q ss_pred             EeeCC
Q psy3016         108 VNKAS  112 (305)
Q Consensus       108 v~~~~  112 (305)
                      |+++.
T Consensus       102 V~~a~  106 (107)
T 3ulh_A          102 IQLVT  106 (107)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99875

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.77  E-value=3.2e-19  Score=142.28  Aligned_cols=126  Identities=20%  Similarity=0.237  Sum_probs=82.0

Q ss_pred             eEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhh
Q psy3016          77 GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN  156 (305)
Q Consensus        77 g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~  156 (305)
                      -++|++|.+...+..|++.++|....|+. .+.+..+ .......++|||+|||.++|+++|+++|+.||.|..+     
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~~-~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v-----   77 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGRP-PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV-----   77 (135)
T ss_dssp             -------------------------------CCSCCS-CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEE-----
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCC-CCCcCCC-CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE-----
Confidence            46899999999999999999876655543 2223332 2233456889999999999999999999999999877     


Q ss_pred             hhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEE
Q psy3016         157 MIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY  236 (305)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~  236 (305)
                                                        .++.+..++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|
T Consensus        78 ----------------------------------~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           78 ----------------------------------YIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             ----------------------------------ECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             ----------------------------------EEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence                                              6788888899999999999999999999999999999999999999


Q ss_pred             eeecCCc
Q psy3016         237 AFKKDSK  243 (305)
Q Consensus       237 a~~~~~~  243 (305)
                      ++.+...
T Consensus       124 a~~~~~~  130 (135)
T 2lea_A          124 ARYGRPP  130 (135)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9776543

>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=99.77  E-value=8.1e-19  Score=131.76  Aligned_cols=85  Identities=15%  Similarity=0.130  Sum_probs=79.2

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|++|++.||+..+.|+.|+|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            44567899999999999999999999999999998888888889999999999999999999999999999999999999


Q ss_pred             eCCCc
Q psy3016         110 KASSH  114 (305)
Q Consensus       110 ~~~~~  114 (305)
                      ++...
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98754

>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=99.77  E-value=1.2e-18  Score=135.23  Aligned_cols=84  Identities=35%  Similarity=0.588  Sum_probs=79.5

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (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~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             CCCcc
Q psy3016         111 ASSHQ  115 (305)
Q Consensus       111 ~~~~~  115 (305)
                      +....
T Consensus        83 a~~~~   87 (116)
T 2fy1_A           83 AKKPS   87 (116)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            98654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=3.1e-19  Score=130.50  Aligned_cols=81  Identities=21%  Similarity=0.399  Sum_probs=76.8

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||..+|+++|+++|+.||.|.+|+++.++.++.++|||||+|.+.++|.+|++.|||..+.|+.+++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            46789999999999999999999999999999999999888999999999999999999999999999999999988775


Q ss_pred             C
Q psy3016         112 S  112 (305)
Q Consensus       112 ~  112 (305)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.77  E-value=3.5e-18  Score=134.04  Aligned_cols=88  Identities=28%  Similarity=0.381  Sum_probs=81.7

Q ss_pred             CCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        27 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      .+......++|||+|||..+++++|+++|+.||.|.+|+++.+. ++.++|||||+|.+.++|.+|++.||+..+.|+.|
T Consensus        28 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  106 (124)
T 2kt5_A           28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM  106 (124)
T ss_dssp             CCCCCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            34456677899999999999999999999999999999999998 89999999999999999999999999999999999


Q ss_pred             EEeeCCCcc
Q psy3016         107 RVNKASSHQ  115 (305)
Q Consensus       107 ~v~~~~~~~  115 (305)
                      +|+++....
T Consensus       107 ~V~~a~~~~  115 (124)
T 2kt5_A          107 DIQLVASQI  115 (124)
T ss_dssp             EEEEECCTT
T ss_pred             EEEEeCCCC
Confidence            999988654

>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=1.4e-18  Score=141.88  Aligned_cols=83  Identities=18%  Similarity=0.349  Sum_probs=77.5

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCC--CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSG--PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G--~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ...++|||+|||.++|+++|+++|+.||  .|.+|+|+.|+.+|.++|||||+|.+.++|++||+.|||..+.|+.|.|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            3568999999999999999999999999  99999999999999999999999999999999999999999999999999


Q ss_pred             eCCCc
Q psy3016         110 KASSH  114 (305)
Q Consensus       110 ~~~~~  114 (305)
                      ++...
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            98754

>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=1.7e-18  Score=127.58  Aligned_cols=80  Identities=23%  Similarity=0.401  Sum_probs=76.5

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (305)
                      .++|||+|||.++|+++|+++|+.||.|.+++++.+..++.++|||||+|.+.++|++|+ .||+..+.|+.|+|.++..
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            579999999999999999999999999999999999888999999999999999999999 8999999999999999876


Q ss_pred             c
Q psy3016         114 H  114 (305)
Q Consensus       114 ~  114 (305)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=1.4e-18  Score=132.13  Aligned_cols=88  Identities=24%  Similarity=0.412  Sum_probs=81.7

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||..+|+++|+++|+.||.|..|+++.++.++.++|||||+|.+.++|.+|++. ++..+.|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            3456778999999999999999999999999999999999988899999999999999999999998 999999999999


Q ss_pred             eeCCCcccc
Q psy3016         109 NKASSHQKN  117 (305)
Q Consensus       109 ~~~~~~~~~  117 (305)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (105)
T 2dh8_A           90 KPCTPRGMQ   98 (105)
T ss_dssp             CCSCCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.3e-18  Score=133.54  Aligned_cols=92  Identities=21%  Similarity=0.335  Sum_probs=80.2

Q ss_pred             ccccCCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCce
Q psy3016          21 QTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIK  100 (305)
Q Consensus        21 ~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~  100 (305)
                      ....+.+.+.....++|||+|||..+|+++|+++|+.||.|.+|+++.+.  +.++|||||+|.+.++|++|++.|+|..
T Consensus        16 ~~~~S~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~   93 (109)
T 2err_A           16 PRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTV   93 (109)
T ss_dssp             ------CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCE
T ss_pred             CCCCCCCccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCE
Confidence            33445666777888999999999999999999999999999999999885  3488999999999999999999999999


Q ss_pred             eCCeeeEEeeCCCc
Q psy3016         101 LYGKPIRVNKASSH  114 (305)
Q Consensus       101 ~~g~~l~v~~~~~~  114 (305)
                      +.|+.|+|+++..+
T Consensus        94 ~~g~~l~V~~a~~~  107 (109)
T 2err_A           94 VEGRKIEVNNATAR  107 (109)
T ss_dssp             ETTEECEEEECCCS
T ss_pred             ECCEEEEEEECCCC
Confidence            99999999998764

>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=1e-18  Score=135.42  Aligned_cols=88  Identities=17%  Similarity=0.394  Sum_probs=80.9

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||..+|+++|+++|+.||.|..|+|+.+..++.++|||||+|.+.++|++|++. ++..+.|+.|+|
T Consensus        22 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V  100 (116)
T 1x4b_A           22 REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEP  100 (116)
T ss_dssp             CHHHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEE
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEE
Confidence            3444568999999999999999999999999999999999988899999999999999999999997 999999999999


Q ss_pred             eeCCCcccc
Q psy3016         109 NKASSHQKN  117 (305)
Q Consensus       109 ~~~~~~~~~  117 (305)
                      .++..+...
T Consensus       101 ~~a~~~~~~  109 (116)
T 1x4b_A          101 KRAVAREES  109 (116)
T ss_dssp             ECCSSCCCC
T ss_pred             EECCCCccC
Confidence            999876543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.77  E-value=2.6e-18  Score=127.42  Aligned_cols=85  Identities=24%  Similarity=0.384  Sum_probs=78.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..|+++.+  ++.++|||||+|.+.++|++|++.|++..+.|+.|+|+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   81 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVR   81 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456789999999999999999999999999999999885  68899999999999999999999999999999999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      ++.....
T Consensus        82 ~a~~~~~   88 (92)
T 2dgv_A           82 IDRNASG   88 (92)
T ss_dssp             ECSCCSS
T ss_pred             EcCCCCC
Confidence            9887653

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.77  E-value=6.8e-19  Score=131.37  Aligned_cols=84  Identities=17%  Similarity=0.161  Sum_probs=75.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|++|++.||+..+.|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~   90 (95)
T 2ek1_A           11 GKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLS   90 (95)
T ss_dssp             ----CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEE
Confidence            34456899999999999999999999999999999999988889999999999999999999999999999999999999


Q ss_pred             eCCC
Q psy3016         110 KASS  113 (305)
Q Consensus       110 ~~~~  113 (305)
                      ++..
T Consensus        91 ~a~s   94 (95)
T 2ek1_A           91 GPSS   94 (95)
T ss_dssp             CCC-
T ss_pred             eccC
Confidence            8753

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.5e-18  Score=131.67  Aligned_cols=87  Identities=25%  Similarity=0.445  Sum_probs=80.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhcc-CCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCce-eCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQ-SGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIK-LYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~-~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~-~~g~~l~  107 (305)
                      .....++|||+|||..+|+++|+++|+. ||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.|++.. +.|+.|.
T Consensus         5 ~~~~~~~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            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3456789999999999999999999999 9999999999998 89999999999999999999999999999 9999999


Q ss_pred             EeeCCCcccc
Q psy3016         108 VNKASSHQKN  117 (305)
Q Consensus       108 v~~~~~~~~~  117 (305)
                      |.++..+...
T Consensus        84 v~~a~~~~~~   93 (104)
T 2dhg_A           84 LSVAIPKASR   93 (104)
T ss_dssp             CCBCCCCCSC
T ss_pred             EEEccCCCcC
Confidence            9999765543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.8e-18  Score=131.17  Aligned_cols=83  Identities=27%  Similarity=0.286  Sum_probs=74.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc--CceeCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN--MIKLYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~--g~~~~g~~l~  107 (305)
                      +....++|||+|||.++|+++|+++|++||.|.+|+|+++      +|||||+|.+.++|++|++.|+  +..+.|+.|+
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4556889999999999999999999999999999999875      5999999999999999999886  4789999999


Q ss_pred             EeeCCCccccc
Q psy3016         108 VNKASSHQKNL  118 (305)
Q Consensus       108 v~~~~~~~~~~  118 (305)
                      |.++..+....
T Consensus        86 V~~A~~~~~~~   96 (105)
T 1sjq_A           86 IQFSNHKELKT   96 (105)
T ss_dssp             BCCCSSSSCCC
T ss_pred             EEEcCCCCCCc
Confidence            99998765443

>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=8.3e-18  Score=127.44  Aligned_cols=88  Identities=24%  Similarity=0.277  Sum_probs=80.3

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||..+|+++|+++|+.||.|..|+++.++.++.++|||||+|.+.++|.+|++  ++..+.|+.|.
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~   86 (103)
T 2cqg_A            9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCD   86 (103)
T ss_dssp             SCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEE
T ss_pred             CCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEE
Confidence            3455667899999999999999999999999999999999998889999999999999999999999  57899999999


Q ss_pred             EeeCCCcccc
Q psy3016         108 VNKASSHQKN  117 (305)
Q Consensus       108 v~~~~~~~~~  117 (305)
                      |.++..+...
T Consensus        87 v~~a~~~~~~   96 (103)
T 2cqg_A           87 CKLPNSKQSQ   96 (103)
T ss_dssp             EECCCTTCCC
T ss_pred             EEecCCCCcC
Confidence            9999876543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.76  E-value=5e-18  Score=135.59  Aligned_cols=85  Identities=38%  Similarity=0.683  Sum_probs=78.9

Q ss_pred             CCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        27 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      ........++|||+|||..+|+++|+++|+.||.|..++++.++.++.++|||||+|.+.++|++|++.||+..+.|+.|
T Consensus        56 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  135 (140)
T 2ku7_A           56 SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI  135 (140)
T ss_dssp             SCSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEE
T ss_pred             CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34455678899999999999999999999999999999999998889999999999999999999999999999999999


Q ss_pred             EEeeC
Q psy3016         107 RVNKA  111 (305)
Q Consensus       107 ~v~~~  111 (305)
                      +|+++
T Consensus       136 ~v~~A  140 (140)
T 2ku7_A          136 RVNLA  140 (140)
T ss_dssp             EEEC-
T ss_pred             EEEeC
Confidence            99875

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.76  E-value=3e-18  Score=124.72  Aligned_cols=75  Identities=23%  Similarity=0.309  Sum_probs=70.4

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      -++..|||+||+..+|+++|+++|.+||+|.+++++.      ++|||||+|.+.++|.+|++.||+..+.|+.|+|+.+
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            3577999999999999999999999999999999965      5799999999999999999999999999999999987


Q ss_pred             C
Q psy3016         112 S  112 (305)
Q Consensus       112 ~  112 (305)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.76  E-value=9.4e-19  Score=132.16  Aligned_cols=86  Identities=24%  Similarity=0.353  Sum_probs=75.2

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccC-CCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDR-VTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~-~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      .......++|||+|||.++|+++|+++|+.|| |.+|+++.+. .+|+++|||||+|.+.++|.+|+ .|+|..+.|+.|
T Consensus        13 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l   90 (100)
T 2j76_E           13 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRI   90 (100)
T ss_dssp             -------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCC
T ss_pred             cCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEE
Confidence            34556789999999999999999999999999 9999999998 58999999999999999999999 899999999999


Q ss_pred             EEeeCCCcc
Q psy3016         107 RVNKASSHQ  115 (305)
Q Consensus       107 ~v~~~~~~~  115 (305)
                      +|+++..+.
T Consensus        91 ~V~~a~~~~   99 (100)
T 2j76_E           91 RVDVADQAQ   99 (100)
T ss_dssp             CCEECCCSC
T ss_pred             EEEeccCCC
Confidence            999987653

>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=1.2e-18  Score=132.31  Aligned_cols=80  Identities=16%  Similarity=0.215  Sum_probs=75.5

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||.++|+++|+++|+.||.|.+|.|+.+.. +.++|||||+|.+.++|.+|++ +++..+.|+.|.|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3468999999999999999999999999999999999986 9999999999999999999999 8999999999999987


Q ss_pred             CC
Q psy3016         112 SS  113 (305)
Q Consensus       112 ~~  113 (305)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            65

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.4e-18  Score=131.90  Aligned_cols=84  Identities=30%  Similarity=0.547  Sum_probs=79.5

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||+|||..+++++|+++|+.||.|..|+++.+..+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            45799999999999999999999999999999999998889999999999999999999999999999999999999998


Q ss_pred             Cccc
Q psy3016         113 SHQK  116 (305)
Q Consensus       113 ~~~~  116 (305)
                      ....
T Consensus        87 ~~~~   90 (104)
T 1p1t_A           87 SEKN   90 (104)
T ss_dssp             CTTH
T ss_pred             Cccc
Confidence            7653

>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=99.76  E-value=5.4e-18  Score=138.30  Aligned_cols=88  Identities=27%  Similarity=0.475  Sum_probs=82.1

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||..+|+++|+++|+.||.|..|+|+.+..++.++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        34 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           34 KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34456789999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             eeCCCccc
Q psy3016         109 NKASSHQK  116 (305)
Q Consensus       109 ~~~~~~~~  116 (305)
                      .++.....
T Consensus       114 ~~a~~~~~  121 (156)
T 1h2v_Z          114 DWDAGFKE  121 (156)
T ss_dssp             EEESCCCT
T ss_pred             EECCCCCC
Confidence            99987543

>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=8.9e-19  Score=124.93  Aligned_cols=75  Identities=27%  Similarity=0.461  Sum_probs=72.2

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (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-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            59999999999999999999999999999999998889999999999999999999998 9999999999999875

>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=99.75  E-value=3.3e-18  Score=134.49  Aligned_cols=87  Identities=24%  Similarity=0.396  Sum_probs=80.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|.|+.+..++.++|||||+|.+.++|++|++.||+..+.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            33456799999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      ++.....
T Consensus        98 ~a~~~~~  104 (126)
T 3ex7_B           98 WCFVRGP  104 (126)
T ss_dssp             ESEESSS
T ss_pred             EecCCCC
Confidence            9976543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.75  E-value=3e-18  Score=130.56  Aligned_cols=87  Identities=23%  Similarity=0.309  Sum_probs=77.7

Q ss_pred             CCCcCCCCceEEEcCCCccc------cHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCce
Q psy3016          27 GGESGDGDATIYVGGLDDKV------SETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIK  100 (305)
Q Consensus        27 ~~~~~~~~~~l~V~nLp~~~------te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~  100 (305)
                      +.......++|||+|||..+      |+++|+++|+.||.|.+|.++.  .+|.++|||||+|.+.++|.+|++.|||..
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~   85 (105)
T 2nlw_A            8 PQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYK   85 (105)
T ss_dssp             CCSCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSSEE
T ss_pred             CCCCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCCcc
Confidence            33445557899999999999      7899999999999999999983  578999999999999999999999999999


Q ss_pred             eCCe-eeEEeeCCCcc
Q psy3016         101 LYGK-PIRVNKASSHQ  115 (305)
Q Consensus       101 ~~g~-~l~v~~~~~~~  115 (305)
                      +.|+ .|+|.++....
T Consensus        86 ~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           86 LDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             CSTTCEEEEECSCCCC
T ss_pred             cCCCceEEEEEcchHh
Confidence            9998 99999987543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.75  E-value=7.7e-19  Score=139.26  Aligned_cols=86  Identities=22%  Similarity=0.366  Sum_probs=80.1

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEE--EEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCc----eeCC
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN--VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMI----KLYG  103 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~--i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~----~~~g  103 (305)
                      .....++|||+|||.++|+++|+++|+.||.|..  |+|+.++.+|.++|||||+|.+. +|.+|++.||+.    .+.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            4466789999999999999999999999999977  99999998999999999999999 999999999999    9999


Q ss_pred             eeeEEeeCCCccc
Q psy3016         104 KPIRVNKASSHQK  116 (305)
Q Consensus       104 ~~l~v~~~~~~~~  116 (305)
                      +.|.|.++.+...
T Consensus        98 r~l~V~~a~~~~~  110 (131)
T 2m2b_A           98 KTINVEFAKGSKR  110 (131)
T ss_dssp             CCCCCEECCCSCC
T ss_pred             EEEEEEECCCCCC
Confidence            9999999987643

>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=99.75  E-value=1.4e-17  Score=127.58  Aligned_cols=84  Identities=23%  Similarity=0.394  Sum_probs=76.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..|++..+   +.++|||||+|.+.++|++|++.||+..+.|+.|+|+
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            4456789999999999999999999999999999999665   4578999999999999999999999999999999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      ++.....
T Consensus        95 ~a~~~~~  101 (109)
T 1x4a_A           95 FPRSGRG  101 (109)
T ss_dssp             CCCCCCC
T ss_pred             EcccCCC
Confidence            9987654

>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=1.1e-17  Score=129.03  Aligned_cols=85  Identities=16%  Similarity=0.288  Sum_probs=77.8

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee-------
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL-------  101 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~-------  101 (305)
                      ......++|||+|||..+|+++|+++|+.||.|.+|+++.+. ++.++|||||+|.+.++|++|++.|||..+       
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~   98 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   98 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcccc
Confidence            344567899999999999999999999999999999999998 899999999999999999999999999999       


Q ss_pred             -CCeeeEEeeCCCc
Q psy3016         102 -YGKPIRVNKASSH  114 (305)
Q Consensus       102 -~g~~l~v~~~~~~  114 (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             5778999888753

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.75  E-value=2.2e-18  Score=127.90  Aligned_cols=83  Identities=19%  Similarity=0.399  Sum_probs=75.1

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcC-cccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFG-VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      +++|||+|||.++|+++|+++|+.|| .|..+                                       .+++|..++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v---------------------------------------~i~~d~~t~   41 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREV---------------------------------------RLMRNKSSG   41 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBC---------------------------------------CSSSCSSSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEE---------------------------------------EEEecCCCC
Confidence            36899999999999999999999999 78766                                       789999999


Q ss_pred             CccceEEEEeCChHHHHHHHHHh-cCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAM-HGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l-~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++|||||+|.+.++|.+|++.+ |+..++|++|+|.|+.++..
T Consensus        42 ~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~   85 (91)
T 2lxi_A           42 QSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPK   85 (91)
T ss_dssp             CCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCCC
T ss_pred             CcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCCC
Confidence            99999999999999999999987 45679999999999977643

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=8e-18  Score=124.59  Aligned_cols=83  Identities=25%  Similarity=0.346  Sum_probs=77.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.| .|.+|+++.+ .+|.++|||||+|.+.++|.+|++ ||+..+.|+.|.|.
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEE
Confidence            44567899999999999999999999999 9999999999 689999999999999999999999 99999999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      ++..+.
T Consensus        83 ~a~~~~   88 (91)
T 2dgw_A           83 REKSGP   88 (91)
T ss_dssp             EESSCC
T ss_pred             ECCcCC
Confidence            987653

>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=99.75  E-value=5.2e-18  Score=130.54  Aligned_cols=86  Identities=16%  Similarity=0.299  Sum_probs=78.1

Q ss_pred             cCCCCceEEEcCCCccccHHHHH---HHhccCCCeEEEEEcccCCCC---CcceEEEEEEcCHHHHHHHHHHhcCceeCC
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMW---ELFVQSGPVVNVHMPKDRVTQ---THQGYGFIEFMGEEDADYAIKIMNMIKLYG  103 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~---~~F~~~G~i~~i~~~~~~~~~---~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g  103 (305)
                      .....++|||+|||..+++++|+   ++|++||.|.+|.++.+..++   .++|||||+|.+.++|++|++.||+..+.|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            44457799999999999999999   999999999999999887643   556999999999999999999999999999


Q ss_pred             eeeEEeeCCCcc
Q psy3016         104 KPIRVNKASSHQ  115 (305)
Q Consensus       104 ~~l~v~~~~~~~  115 (305)
                      +.|+|.++..+.
T Consensus        91 r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 RTLKASLGTTKY  102 (111)
T ss_dssp             EEEEEESCCCCS
T ss_pred             EEEEEEeccccc
Confidence            999999988764

>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=99.75  E-value=6.5e-18  Score=137.93  Aligned_cols=87  Identities=28%  Similarity=0.462  Sum_probs=81.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|+++.+..+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus        66 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  145 (158)
T 2kn4_A           66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  145 (158)
T ss_dssp             CCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            44557899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      ++.....
T Consensus       146 ~a~~~~~  152 (158)
T 2kn4_A          146 MARYGRP  152 (158)
T ss_dssp             EECCSSC
T ss_pred             ECCCCCC
Confidence            9987643

>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=99.74  E-value=2.8e-18  Score=141.41  Aligned_cols=125  Identities=24%  Similarity=0.382  Sum_probs=78.5

Q ss_pred             EEEcCHHHHHHHHHHhcCceeC--CeeeEEeeCCC-------------------ccccccccccccccCCCchhcHHHHH
Q psy3016          81 IEFMGEEDADYAIKIMNMIKLY--GKPIRVNKASS-------------------HQKNLDVGANIFIGNLDPEVDEKLLY  139 (305)
Q Consensus        81 V~f~~~e~A~~Ai~~l~g~~~~--g~~l~v~~~~~-------------------~~~~~~~~~~l~v~nl~~~~t~~~l~  139 (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            7889999999999988876554  55555544211                   01112235689999999999999999


Q ss_pred             HHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHH
Q psy3016         140 DTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASI  219 (305)
Q Consensus       140 ~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al  219 (305)
                      ++|..||.|..+                                       .++.+..+|.++|||||+|.+.++|.+|+
T Consensus        91 ~~F~~~G~i~~v---------------------------------------~i~~~~~~g~~~g~afV~f~~~~~A~~Ai  131 (165)
T 1rk8_A           91 EKFCDYGEIKNI---------------------------------------HLNLDRRTGFSKGYALVEYETHKQALAAK  131 (165)
T ss_dssp             HHHGGGSCEEEE---------------------------------------EEEECTTTSSEEEEEEEEESSHHHHHHHH
T ss_pred             HHhhcCCCEEEE---------------------------------------EEEecCCCCcEeeEEEEEECCHHHHHHHH
Confidence            999999999887                                       67888888999999999999999999999


Q ss_pred             HHhcCeeecCeeeEEEEeeecCCcC
Q psy3016         220 DAMHGQYLCNRPISVSYAFKKDSKG  244 (305)
Q Consensus       220 ~~l~~~~~~g~~l~v~~a~~~~~~~  244 (305)
                      ..|||..|.|+.|.|.|+..+..+.
T Consensus       132 ~~l~g~~~~g~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A          132 EALNGAEIMGQTIQVDWCFVKGPKR  156 (165)
T ss_dssp             HHHTTCEETTEECEEEESEECC---
T ss_pred             HHhCCCEECCEEEEEEEecCCCCCC
Confidence            9999999999999999998876543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=1e-18  Score=125.16  Aligned_cols=76  Identities=26%  Similarity=0.452  Sum_probs=73.2

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (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-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            589999999999999999999999999999999998889999999999999999999999988 9999999999986

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.3e-17  Score=125.90  Aligned_cols=85  Identities=24%  Similarity=0.386  Sum_probs=76.2

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .+.....++|||+|||..+|+++|+++|+.||.|   +++.+ .++.++|||||+|.+.++|++|++.||+..+.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   84 (101)
T 2fc9_A            9 STWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIR   84 (101)
T ss_dssp             CCCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            3455678999999999999999999999999987   56666 5788999999999999999999999999999999999


Q ss_pred             EeeCCCccc
Q psy3016         108 VNKASSHQK  116 (305)
Q Consensus       108 v~~~~~~~~  116 (305)
                      |.++..+..
T Consensus        85 v~~a~~~~~   93 (101)
T 2fc9_A           85 LELQGPRGS   93 (101)
T ss_dssp             EEECSSCCC
T ss_pred             EEEcCCCCC
Confidence            999987654

>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=99.74  E-value=4.7e-18  Score=130.06  Aligned_cols=85  Identities=20%  Similarity=0.386  Sum_probs=78.4

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCC-eEEEEEc-ccCCCCCcceEEEEEEcCHHHHHHHHHHhc--CceeCCeeeE
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGP-VVNVHMP-KDRVTQTHQGYGFIEFMGEEDADYAIKIMN--MIKLYGKPIR  107 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~-i~~i~~~-~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~--g~~~~g~~l~  107 (305)
                      ...++|||+|||..+|+++|+++|+.||. |.+|.++ .+..++.++|||||+|.+.++|.+|++.|+  +..+.|+.|+
T Consensus         6 ~~~~~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            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            35689999999999999999999999998 9999998 788788999999999999999999999996  5899999999


Q ss_pred             EeeCCCccc
Q psy3016         108 VNKASSHQK  116 (305)
Q Consensus       108 v~~~~~~~~  116 (305)
                      |.++.++..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987654

>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=99.74  E-value=6.4e-18  Score=127.85  Aligned_cols=80  Identities=20%  Similarity=0.270  Sum_probs=72.1

Q ss_pred             cCCCCceEEEcCCCc-cccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcC--ceeCCeee
Q psy3016          30 SGDGDATIYVGGLDD-KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM--IKLYGKPI  106 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g--~~~~g~~l  106 (305)
                      ..+..++|||+|||. .+|+++|+++|++||.|.+|.|++++      |||||+|.+.++|.+|++.|++  ..+.|+.|
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k------g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC------CEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            344678999999999 99999999999999999999998753      8999999999999999999885  46999999


Q ss_pred             EEeeCCCcc
Q psy3016         107 RVNKASSHQ  115 (305)
Q Consensus       107 ~v~~~~~~~  115 (305)
                      .|.++....
T Consensus        85 ~V~~a~~~~   93 (102)
T 1x4d_A           85 RVHLSQKYK   93 (102)
T ss_dssp             EEEEECCCT
T ss_pred             EEEECCCCC
Confidence            999998654

>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=4.3e-18  Score=131.66  Aligned_cols=85  Identities=14%  Similarity=0.190  Sum_probs=78.7

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCe-EEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPV-VNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i-~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      ......++|||+|||.++|+++|+++|+.||.| ..|+|+.+. +++++|||||+|.+.++|++|++. |+..+.|+.|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~   87 (114)
T 2cpy_A           10 DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAF   87 (114)
T ss_dssp             SCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEE
T ss_pred             CCCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEE
Confidence            345667899999999999999999999999999 899999998 899999999999999999999996 99999999999


Q ss_pred             EeeCCCcc
Q psy3016         108 VNKASSHQ  115 (305)
Q Consensus       108 v~~~~~~~  115 (305)
                      |.++..+.
T Consensus        88 v~~a~~~~   95 (114)
T 2cpy_A           88 VHVVTLED   95 (114)
T ss_dssp             EEEECHHH
T ss_pred             EEECCHHH
Confidence            99987643

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.74  E-value=8.1e-18  Score=131.84  Aligned_cols=83  Identities=22%  Similarity=0.412  Sum_probs=78.0

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+++.++.++.++|||||+|.+.++|.+|+ .|||..+.|+.|+|.++.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4579999999999999999999999999999999999888999999999999999999999 799999999999999988


Q ss_pred             Cccc
Q psy3016         113 SHQK  116 (305)
Q Consensus       113 ~~~~  116 (305)
                      ....
T Consensus       114 ~~~~  117 (124)
T 2jwn_A          114 TNMP  117 (124)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.74  E-value=2.5e-18  Score=137.09  Aligned_cols=91  Identities=26%  Similarity=0.425  Sum_probs=83.7

Q ss_pred             CCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        26 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      .+.......++|||+|||..+|+++|+++|+.||.|..|+++.++.++.++|||||+|.+.++|++|++.||+..+.|+.
T Consensus        39 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~  118 (135)
T 2lea_A           39 RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRE  118 (135)
T ss_dssp             CSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSC
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            44455667789999999999999999999999999999999999888999999999999999999999999999999999


Q ss_pred             eEEeeCCCccc
Q psy3016         106 IRVNKASSHQK  116 (305)
Q Consensus       106 l~v~~~~~~~~  116 (305)
                      |+|.++.....
T Consensus       119 l~V~~a~~~~~  129 (135)
T 2lea_A          119 LRVQMARYGRP  129 (135)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999987543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.74  E-value=4.1e-18  Score=127.46  Aligned_cols=82  Identities=17%  Similarity=0.355  Sum_probs=72.9

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      =.+|||+||+..+|+++|+++|++||.+...                                     ++.+++|..+|.
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~-------------------------------------~v~i~~d~~tg~   51 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVN-------------------------------------NIRLIKDKQTQQ   51 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGG-------------------------------------GEECCCCSSSSS
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEE-------------------------------------EEEEEecCCCCC
Confidence            3689999999999999999999999975422                                     126789999999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCe----eecCeeeEEEEeee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQ----YLCNRPISVSYAFK  239 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~----~~~g~~l~v~~a~~  239 (305)
                      ++|||||+|.+.++|.+|++.|||.    .++||+|.|+||+.
T Consensus        52 srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           52 NRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             CSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             CceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            9999999999999999999999997    58999999999864

>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=99.74  E-value=7.6e-19  Score=129.82  Aligned_cols=81  Identities=35%  Similarity=0.538  Sum_probs=74.1

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (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~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            68999999999999999999999999999999999888999999999999999 99999999999999999999998865


Q ss_pred             cc
Q psy3016         115 QK  116 (305)
Q Consensus       115 ~~  116 (305)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.73  E-value=1.1e-17  Score=128.23  Aligned_cols=85  Identities=24%  Similarity=0.353  Sum_probs=72.9

Q ss_pred             cCCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC
Q psy3016          24 LEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG  103 (305)
Q Consensus        24 ~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g  103 (305)
                      ...........++|||+|||..+|+++|+++|+.||.|..|+++        +|||||+|.+.++|++|++.|||..+.|
T Consensus        21 ~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (108)
T 2jvo_A           21 MHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFAN   92 (108)
T ss_dssp             -------CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             cccccCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            33444566778999999999999999999999999999999996        5999999999999999999999999999


Q ss_pred             eeeEEeeCCCccc
Q psy3016         104 KPIRVNKASSHQK  116 (305)
Q Consensus       104 ~~l~v~~~~~~~~  116 (305)
                      +.|.|.++.....
T Consensus        93 ~~l~V~~a~~~~~  105 (108)
T 2jvo_A           93 QPLEVVYSKLPAK  105 (108)
T ss_dssp             EECEEESCSCCC-
T ss_pred             eEEEEEEecCCCC
Confidence            9999999887543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=125.16  Aligned_cols=79  Identities=23%  Similarity=0.264  Sum_probs=71.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCce--eCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIK--LYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~--~~g~~l~  107 (305)
                      ....+++|||+|||..+|+++|+++|++||.|.+++++++      ||||||+|.+.++|.+|++.|++..  +.|+.|.
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~   90 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAF   90 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEE
Confidence            3446789999999999999999999999999999999753      5999999999999999999999764  7899999


Q ss_pred             EeeCCCc
Q psy3016         108 VNKASSH  114 (305)
Q Consensus       108 v~~~~~~  114 (305)
                      |+++..+
T Consensus        91 V~~S~~k   97 (100)
T 3r27_A           91 VNYSTSQ   97 (100)
T ss_dssp             EEECSCS
T ss_pred             EEecccc
Confidence            9998765

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2e-17  Score=124.96  Aligned_cols=88  Identities=27%  Similarity=0.435  Sum_probs=78.7

Q ss_pred             CCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        26 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      .+.......++|||+|||..+|+++|+++|+.|+   .|.++.+..++.++|||||+|.+.++|++|++.||+..+.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 2fc8_A            7 GPNARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNK   83 (102)
T ss_dssp             TTSSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            3445566789999999999999999999999874   6778888778999999999999999999999999999999999


Q ss_pred             eEEeeCCCccc
Q psy3016         106 IRVNKASSHQK  116 (305)
Q Consensus       106 l~v~~~~~~~~  116 (305)
                      |+|.++.++..
T Consensus        84 l~V~~a~~~~~   94 (102)
T 2fc8_A           84 VTLDWAKPKGE   94 (102)
T ss_dssp             CEEEECCCCCS
T ss_pred             EEEEEecCCCC
Confidence            99999987654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=9.2e-18  Score=125.88  Aligned_cols=84  Identities=19%  Similarity=0.283  Sum_probs=74.8

Q ss_pred             CCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        27 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      ........++|||+|||..+|+++|+++|+.||.|. +.++.+    .++|||||+|.+.++|++|++.|||..+.|+.|
T Consensus        12 ~~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   86 (97)
T 2e5j_A           12 PGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTL   86 (97)
T ss_dssp             CCSSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            344556688999999999999999999999999997 666654    478999999999999999999999999999999


Q ss_pred             EEeeCCCcc
Q psy3016         107 RVNKASSHQ  115 (305)
Q Consensus       107 ~v~~~~~~~  115 (305)
                      +|.++..+.
T Consensus        87 ~V~~a~~~~   95 (97)
T 2e5j_A           87 RVALARQQR   95 (97)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEcCCCC
Confidence            999988754

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.8e-17  Score=122.51  Aligned_cols=80  Identities=26%  Similarity=0.473  Sum_probs=73.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+++        +|||||+|.+.++|++|++.||+..+.|+.|+|+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   75 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVE   75 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEE
Confidence            44567899999999999999999999999999999996        5899999999999999999999999999999999


Q ss_pred             eCCCcccc
Q psy3016         110 KASSHQKN  117 (305)
Q Consensus       110 ~~~~~~~~  117 (305)
                      ++..+...
T Consensus        76 ~a~~~~~~   83 (90)
T 2dnq_A           76 ASKNKSKA   83 (90)
T ss_dssp             CSSCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=3.1e-18  Score=134.43  Aligned_cols=84  Identities=18%  Similarity=0.217  Sum_probs=76.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||+ ||+..+.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            44567899999999999999999999999999986666666789999999999999999999999 99999999999999


Q ss_pred             eCCCc
Q psy3016         110 KASSH  114 (305)
Q Consensus       110 ~~~~~  114 (305)
                      ++..+
T Consensus       100 ~a~~~  104 (124)
T 1wel_A          100 PITKK  104 (124)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            98754

>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=9.3e-18  Score=130.61  Aligned_cols=83  Identities=22%  Similarity=0.241  Sum_probs=76.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCC---eEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGP---VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      .....++|||+|||.++|+++|+++|+.||.   |..|+|+.+.. |+++|||||+|.+.++|++|++ +|+..+.|+.|
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   90 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYI   90 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEE
Confidence            4556789999999999999999999999999   89999999975 8999999999999999999999 99999999999


Q ss_pred             EEeeCCCc
Q psy3016         107 RVNKASSH  114 (305)
Q Consensus       107 ~v~~~~~~  114 (305)
                      .|.++...
T Consensus        91 ~V~~a~~~   98 (118)
T 2db1_A           91 EVFKSHRT   98 (118)
T ss_dssp             EEEEECHH
T ss_pred             EEEECCHH
Confidence            99987643

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.73  E-value=6.6e-18  Score=129.83  Aligned_cols=81  Identities=20%  Similarity=0.310  Sum_probs=76.5

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+.++++++|+++|++||.|..+                                       .+++|..++
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v---------------------------------------~i~~d~~tg   45 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEV---------------------------------------EILLHPRTR   45 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEE---------------------------------------EEEECTTTC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEE---------------------------------------EEEECCCCC
Confidence            45789999999999999999999999999987                                       788999999


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      +++|||||+|++.++|.+|+..|||..+.|+.|+|.++..
T Consensus        46 ~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~   85 (110)
T 3s8s_A           46 KHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIK   85 (110)
T ss_dssp             CEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECST
T ss_pred             ceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            9999999999999999999999999999999999999853

>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=1.1e-17  Score=127.24  Aligned_cols=85  Identities=22%  Similarity=0.287  Sum_probs=77.4

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEE-EEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~-i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      ......++|||+|||..+|+++|+++|+.||.|.. |.|+.+ .+++++|||||+|.+.++|++|++. ++..+.|+.|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~   87 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIE   87 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEE
Confidence            34456789999999999999999999999999998 889888 6899999999999999999999997 99999999999


Q ss_pred             EeeCCCcc
Q psy3016         108 VNKASSHQ  115 (305)
Q Consensus       108 v~~~~~~~  115 (305)
                      |.++....
T Consensus        88 v~~~~~~~   95 (104)
T 1wg5_A           88 IFKSSRAE   95 (104)
T ss_dssp             EEEECTTT
T ss_pred             EEECCHHH
Confidence            99877543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.73  E-value=3.3e-18  Score=123.99  Aligned_cols=73  Identities=25%  Similarity=0.367  Sum_probs=67.9

Q ss_pred             CceEEEcCCCccc------cHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe-ee
Q psy3016          34 DATIYVGGLDDKV------SETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK-PI  106 (305)
Q Consensus        34 ~~~l~V~nLp~~~------te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~-~l  106 (305)
                      +++|||+|||..+      |+++|+++|++||.|.+|.+..  .+|.++|||||+|.+.++|.+|++.|||..+.|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            4799999999999      7899999999999999999883  4788999999999999999999999999999999 88


Q ss_pred             EE
Q psy3016         107 RV  108 (305)
Q Consensus       107 ~v  108 (305)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=4.8e-17  Score=122.94  Aligned_cols=82  Identities=23%  Similarity=0.300  Sum_probs=73.1

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc--CceeCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN--MIKLYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~--g~~~~g~~l~  107 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|.++.+      +|||||+|.+.++|.+|++.|+  +..+.|+.|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3445789999999999999999999999999999999765      5999999999999999999774  6789999999


Q ss_pred             EeeCCCcccc
Q psy3016         108 VNKASSHQKN  117 (305)
Q Consensus       108 v~~~~~~~~~  117 (305)
                      |.++..+...
T Consensus        85 V~~a~~~~~~   94 (101)
T 2cq1_A           85 IQYSNHKELK   94 (101)
T ss_dssp             EEECSCSSCC
T ss_pred             EEEcCcccCc
Confidence            9999876543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.73  E-value=1.3e-17  Score=131.40  Aligned_cols=82  Identities=13%  Similarity=0.310  Sum_probs=74.1

Q ss_pred             CCCCceEEEcCCCccccHHHHH----HHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMW----ELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      ....++|||+|||..+++++|+    ++|++||.|.+|.+..   ++.++|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            4457899999999999999876    7999999999998854   46789999999999999999999999999999999


Q ss_pred             EEeeCCCcc
Q psy3016         107 RVNKASSHQ  115 (305)
Q Consensus       107 ~v~~~~~~~  115 (305)
                      +|.++..+.
T Consensus       103 ~V~~a~~~~  111 (127)
T 2a3j_A          103 VITFSETPQ  111 (127)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            999998754

>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=99.73  E-value=4.1e-17  Score=124.80  Aligned_cols=80  Identities=25%  Similarity=0.371  Sum_probs=74.2

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC-----e
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG-----K  104 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g-----~  104 (305)
                      .....++|||+|||.++|+++|+++|+.||.|..|+|+.+       |||||+|.+.++|++||+.||+..+.|     +
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~   83 (108)
T 1x4c_A           11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   83 (108)
T ss_dssp             CCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcce
Confidence            3456789999999999999999999999999999999876       899999999999999999999999999     9


Q ss_pred             eeEEeeCCCccc
Q psy3016         105 PIRVNKASSHQK  116 (305)
Q Consensus       105 ~l~v~~~~~~~~  116 (305)
                      .|+|.++.++..
T Consensus        84 ~i~V~~a~~~~~   95 (108)
T 1x4c_A           84 YIRVKVDGPRSP   95 (108)
T ss_dssp             EEEEEESSCCSC
T ss_pred             EEEEEeCCCCCC
Confidence            999999987654

>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=99.72  E-value=2e-17  Score=128.44  Aligned_cols=83  Identities=25%  Similarity=0.281  Sum_probs=74.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc--CceeCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN--MIKLYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~--g~~~~g~~l~  107 (305)
                      .....++|||+|||.++|+++|+++|++||.|.+|+|+.+      +|||||+|.+.++|.+|++.|+  +..+.|+.|+
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            4456789999999999999999999999999999999875      5999999999999999999887  4689999999


Q ss_pred             EeeCCCccccc
Q psy3016         108 VNKASSHQKNL  118 (305)
Q Consensus       108 v~~~~~~~~~~  118 (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            99998765443

>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=99.72  E-value=2.4e-17  Score=135.74  Aligned_cols=87  Identities=22%  Similarity=0.344  Sum_probs=79.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..|.|+.+..+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34456789999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      ++.....
T Consensus       148 ~a~~~~~  154 (165)
T 1rk8_A          148 WCFVKGP  154 (165)
T ss_dssp             ESEECC-
T ss_pred             EecCCCC
Confidence            9876543

>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=1e-17  Score=127.05  Aligned_cols=84  Identities=18%  Similarity=0.234  Sum_probs=76.0

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||.++|+++|+++|+.||.+ +|+|+.++ +++++|||||+|.+.++|++|++ +|+..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (102)
T 1wez_A           10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVEL   86 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEE
Confidence            345567899999999999999999999999954 99999997 89999999999999999999996 7999999999999


Q ss_pred             eeCCCcc
Q psy3016         109 NKASSHQ  115 (305)
Q Consensus       109 ~~~~~~~  115 (305)
                      .++....
T Consensus        87 ~~~~~~~   93 (102)
T 1wez_A           87 FLNSTAG   93 (102)
T ss_dssp             EEECCCC
T ss_pred             EECCCCC
Confidence            9877554

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.7e-17  Score=124.25  Aligned_cols=87  Identities=33%  Similarity=0.490  Sum_probs=79.9

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+|||..+++++|+++|+.||.|..+                                       .++.|..
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v---------------------------------------~i~~~~~   49 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI---------------------------------------QIPLDYE   49 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCE---------------------------------------ECCCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEE---------------------------------------EEEecCC
Confidence            3456899999999999999999999999999876                                       6788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ++.++|||||+|.+.++|.+|+..||+..|.|+.|+|.|+..+..+
T Consensus        50 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2cqb_A           50 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK   95 (102)
T ss_dssp             SCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCCC
Confidence            8999999999999999999999999999999999999999877554

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.72  E-value=1.5e-17  Score=127.91  Aligned_cols=81  Identities=20%  Similarity=0.174  Sum_probs=72.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCC-CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      .....++|||+|||.++|+++|+++|+.|| .|..+++..+    .++|||||+|.+.++|++|++.|||..+.|+.|+|
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V   99 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            445678999999999999999999999999 9999998643    47899999999999999999999999999999999


Q ss_pred             eeCCCc
Q psy3016         109 NKASSH  114 (305)
Q Consensus       109 ~~~~~~  114 (305)
                      +++...
T Consensus       100 ~~a~~~  105 (111)
T 2jvr_A          100 ERDDNP  105 (111)
T ss_dssp             EESCC-
T ss_pred             EECCCC
Confidence            998754

>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=2.8e-17  Score=119.92  Aligned_cols=77  Identities=27%  Similarity=0.434  Sum_probs=71.1

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHh-cCceeCCeeeEE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM-NMIKLYGKPIRV  108 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l-~g~~~~g~~l~v  108 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|+++.+      +|||||+|.+.++|.+|++.| ++..+.|+.|+|
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v   81 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV   81 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEE
Confidence            3456789999999999999999999999999999999864      599999999999999999998 999999999999


Q ss_pred             eeCC
Q psy3016         109 NKAS  112 (305)
Q Consensus       109 ~~~~  112 (305)
                      +++.
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=4.6e-17  Score=120.25  Aligned_cols=81  Identities=28%  Similarity=0.425  Sum_probs=73.8

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||..+|+++|+++|+.||.|.+|++++        +||||+|.+.++|++|++.||+..+.|+.|+|
T Consensus         4 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   75 (90)
T 2dnp_A            4 GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINV   75 (90)
T ss_dssp             CSSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            3456788999999999999999999999999999999963        59999999999999999999999999999999


Q ss_pred             eeCCCcccc
Q psy3016         109 NKASSHQKN  117 (305)
Q Consensus       109 ~~~~~~~~~  117 (305)
                      .++......
T Consensus        76 ~~a~~~~~~   84 (90)
T 2dnp_A           76 ELSTKGQKK   84 (90)
T ss_dssp             EESCCCCCC
T ss_pred             EECCCCCCC
Confidence            999876543

>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=99.72  E-value=4.7e-17  Score=121.93  Aligned_cols=80  Identities=21%  Similarity=0.322  Sum_probs=73.2

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC--CeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY--GKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~--g~~l~  107 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|.+..+      +|||||+|.+.++|++|++.||+..+.  |+.|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            3445689999999999999999999999999999999754      589999999999999999999999999  99999


Q ss_pred             EeeCCCcc
Q psy3016         108 VNKASSHQ  115 (305)
Q Consensus       108 v~~~~~~~  115 (305)
                      |.++.++.
T Consensus        87 V~~a~~~~   94 (97)
T 1why_A           87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998754

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.72  E-value=1.6e-17  Score=125.40  Aligned_cols=77  Identities=19%  Similarity=0.305  Sum_probs=71.4

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ....++|||+|||.++|+++|+++|+.||.|.+|++..      ++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   97 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW   97 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCB
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEe
Confidence            34568999999999999999999999999999999973      569999999999999999999999999999999999


Q ss_pred             CCC
Q psy3016         111 ASS  113 (305)
Q Consensus       111 ~~~  113 (305)
                      +.+
T Consensus        98 a~~  100 (101)
T 2la4_A           98 GKE  100 (101)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            865

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=3.6e-17  Score=124.36  Aligned_cols=82  Identities=18%  Similarity=0.193  Sum_probs=72.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcC--ceeCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM--IKLYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g--~~~~g~~l~  107 (305)
                      .....++|||+|||..+|+++|+++|++||.|.+|.++.+      +|||||+|.+.++|.+|++.|++  ..+.|+.|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            3345789999999999999999999999999999999764      59999999999999999998875  458999999


Q ss_pred             EeeCCCcccc
Q psy3016         108 VNKASSHQKN  117 (305)
Q Consensus       108 v~~~~~~~~~  117 (305)
                      |.++..+...
T Consensus        85 V~~a~~~~~~   94 (104)
T 1wex_A           85 FNYSTSKRIT   94 (104)
T ss_dssp             EEECSSSSCC
T ss_pred             EEEccCcccc
Confidence            9999876543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=5.7e-17  Score=120.23  Aligned_cols=81  Identities=25%  Similarity=0.439  Sum_probs=73.8

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||..+|+++|+++|+.||.|.+|++++        +||||+|.+.++|.+|++.||+..+.|+.|+|
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   76 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHV   76 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Confidence            3456678999999999999999999999999999999953        59999999999999999999999999999999


Q ss_pred             eeCCCcccc
Q psy3016         109 NKASSHQKN  117 (305)
Q Consensus       109 ~~~~~~~~~  117 (305)
                      +++..+...
T Consensus        77 ~~a~~~~~~   85 (92)
T 2dgt_A           77 QLSTSRLRT   85 (92)
T ss_dssp             EESSCCCSC
T ss_pred             EEccCCCCC
Confidence            999876543

>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=99.72  E-value=1e-17  Score=133.51  Aligned_cols=84  Identities=20%  Similarity=0.219  Sum_probs=77.6

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCC---eEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGP---VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      ......++|||+|||.++|+++|+++|+.||.   |.+|+|+.++. |+++|||||+|.+.++|++|++ +|+..+.||.
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~  116 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRY  116 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEE
Confidence            34556789999999999999999999999999   89999999986 9999999999999999999999 9999999999


Q ss_pred             eEEeeCCCc
Q psy3016         106 IRVNKASSH  114 (305)
Q Consensus       106 l~v~~~~~~  114 (305)
                      |.|.++...
T Consensus       117 i~V~~a~~~  125 (136)
T 2hgl_A          117 IEVFKSHRT  125 (136)
T ss_dssp             EEEEECCHH
T ss_pred             EEEEECChH
Confidence            999988644

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.72  E-value=2.2e-18  Score=130.20  Aligned_cols=85  Identities=18%  Similarity=0.325  Sum_probs=76.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||.++|+++|+++|+.||.|.. .++.+..++.++|||||+|.+.++|.+|++ ||+..+.|+.|+|.
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~   90 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   90 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEE
Confidence            3456789999999999999999999999999888 667776678899999999999999999999 99999999999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      ++..+..
T Consensus        91 ~a~~~~~   97 (101)
T 1fj7_A           91 KPKGRDG   97 (101)
T ss_dssp             CCSCCCC
T ss_pred             EcCCCCC
Confidence            9987543

>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=99.71  E-value=3.8e-17  Score=125.14  Aligned_cols=81  Identities=23%  Similarity=0.458  Sum_probs=74.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|+++.+      +|||||+|.+.++|.+|++.|++..+.|+.|+|.
T Consensus        21 ~~~~~~~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           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            4456789999999999999999999999999999999876      5999999999999999999999999999999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      ++.....
T Consensus        95 ~a~~~~~  101 (109)
T 1x4g_A           95 WGKESPD  101 (109)
T ss_dssp             CCCCCCS
T ss_pred             ecCCCCC
Confidence            9987654

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.71  E-value=5.5e-17  Score=121.75  Aligned_cols=78  Identities=21%  Similarity=0.430  Sum_probs=71.2

Q ss_pred             CcCCCCceEEEcCCCc-cccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          29 ESGDGDATIYVGGLDD-KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      ......++|||+|||. .+++++|+++|+.||.|.+|++        ++|||||+|.+.++|.+|++.|||..+.|+.|+
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   88 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI   88 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE--------CSSEEEEEESSHHHHHHHHHHHTTSEETTEECE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3455688999999998 9999999999999999999999        369999999999999999999999999999999


Q ss_pred             EeeCCCc
Q psy3016         108 VNKASSH  114 (305)
Q Consensus       108 v~~~~~~  114 (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

>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=99.71  E-value=3.2e-17  Score=123.30  Aligned_cols=80  Identities=29%  Similarity=0.436  Sum_probs=73.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..|++.++      +|||||+|.+.++|.+|++.|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            4456789999999999999999999999999999999764      5999999999999999999999999999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      ++....
T Consensus        85 ~a~~~~   90 (99)
T 2cpj_A           85 FACHSA   90 (99)
T ss_dssp             ESSCCS
T ss_pred             EcCCCC
Confidence            998754

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.9e-17  Score=124.13  Aligned_cols=87  Identities=26%  Similarity=0.502  Sum_probs=79.8

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+|||.++++++|+++|+.||.|..+                                       .++.+..
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v---------------------------------------~i~~~~~   49 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEV---------------------------------------VVVKDRE   49 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEE---------------------------------------EECCCSS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEeCCC
Confidence            3456899999999999999999999999999877                                       6788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ++.++|||||+|.+.++|.+|++.||+..|.|+.|+|.|+..+...
T Consensus        50 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   95 (102)
T 1x5s_A           50 TQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN   95 (102)
T ss_dssp             SCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCC
T ss_pred             CCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            8999999999999999999999999999999999999999877654

>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=99.71  E-value=1.9e-17  Score=123.95  Aligned_cols=83  Identities=22%  Similarity=0.470  Sum_probs=75.5

Q ss_pred             CCCCceEEEcCCCccccHHHHH----HHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMW----ELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      ....++|||+|||..+|+++|+    ++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            4567899999999999999999    9999999999999974   46688999999999999999999999999999999


Q ss_pred             EEeeCCCccc
Q psy3016         107 RVNKASSHQK  116 (305)
Q Consensus       107 ~v~~~~~~~~  116 (305)
                      +|.++.....
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999987643

>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=99.71  E-value=4.1e-18  Score=121.41  Aligned_cols=75  Identities=27%  Similarity=0.418  Sum_probs=71.5

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            69999999999999999999999999999999998889999999999999999999999 4899999999999875

>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=99.71  E-value=3.9e-17  Score=122.73  Aligned_cols=85  Identities=26%  Similarity=0.310  Sum_probs=78.7

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||..+|+++|+++|+.||.|..+                                       .++.|..++
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~~   47 (99)
T 1whw_A            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSEL---------------------------------------HYPIDSLTK   47 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCCCTTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEE---------------------------------------EEEecCCCC
Confidence            46789999999999999999999999999877                                       678888789


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|+|.++..+...
T Consensus        48 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   91 (99)
T 1whw_A           48 KPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             CCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             CcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCccc
Confidence            99999999999999999999999999999999999999877543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.8e-17  Score=125.56  Aligned_cols=88  Identities=30%  Similarity=0.409  Sum_probs=80.6

Q ss_pred             cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      .....++|||+|||..+++++|+++|+.||.|..+                                       .++.+.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v---------------------------------------~i~~~~   51 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRI---------------------------------------YLAKDK   51 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEE---------------------------------------EEEECS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEE---------------------------------------EEeecC
Confidence            34457899999999999999999999999999877                                       678888


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .++.++|||||+|.+.++|.+|+..|||..|.|+.|+|.|+..+...
T Consensus        52 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (103)
T 2cq0_A           52 TTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS   98 (103)
T ss_dssp             SSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCS
T ss_pred             CCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCCCC
Confidence            88999999999999999999999999999999999999999877554

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.71  E-value=5.8e-17  Score=122.83  Aligned_cols=80  Identities=25%  Similarity=0.325  Sum_probs=73.0

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..|+++        ++||||+|.+.++|++|++.||+..+.|+.|.|.
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   78 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIV   78 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEE
Confidence            34567899999999999999999999999999999985        4699999999999999999999999999999999


Q ss_pred             eCCCcccc
Q psy3016         110 KASSHQKN  117 (305)
Q Consensus       110 ~~~~~~~~  117 (305)
                      ++......
T Consensus        79 ~a~~~~~~   86 (103)
T 2dgu_A           79 FAKPPDQK   86 (103)
T ss_dssp             ECCCCCCC
T ss_pred             EcCCCccc
Confidence            99876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.71  E-value=1e-16  Score=130.74  Aligned_cols=83  Identities=30%  Similarity=0.517  Sum_probs=78.7

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.++.++.+..++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            44567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eCC
Q psy3016         110 KAS  112 (305)
Q Consensus       110 ~~~  112 (305)
                      ++.
T Consensus       163 ~a~  165 (166)
T 3md3_A          163 WAA  165 (166)
T ss_dssp             ESC
T ss_pred             ecC
Confidence            985

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.8e-17  Score=126.01  Aligned_cols=81  Identities=23%  Similarity=0.331  Sum_probs=74.0

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ....++|||+|||.++|+++|+++|+.| .|.+|.|+.++. |+++|||||+|.+.++|++|+ .+|+..+.||.|.|..
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   89 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSP   89 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEE
Confidence            3445799999999999999999999999 899999999974 899999999999999999999 5999999999999988


Q ss_pred             CCCc
Q psy3016         111 ASSH  114 (305)
Q Consensus       111 ~~~~  114 (305)
                      +...
T Consensus        90 a~~~   93 (109)
T 2dnn_A           90 ATER   93 (109)
T ss_dssp             CCHH
T ss_pred             CCcc
Confidence            7643

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=2.9e-17  Score=122.45  Aligned_cols=85  Identities=28%  Similarity=0.566  Sum_probs=78.7

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+..+++++|+++|+.||.|..+                                       .++.|..++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v---------------------------------------~i~~~~~~~   44 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNI---------------------------------------VLMKDSDTG   44 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEE---------------------------------------EEECCSSSC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEE---------------------------------------EEeecCCCC
Confidence            45789999999999999999999999999877                                       678888889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      +++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+...
T Consensus        45 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   88 (95)
T 2dnz_A           45 RSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDG   88 (95)
T ss_dssp             CCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCCC
T ss_pred             ceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccCC
Confidence            99999999999999999999999999999999999999777554

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.71  E-value=3.6e-17  Score=126.47  Aligned_cols=86  Identities=28%  Similarity=0.460  Sum_probs=79.2

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+.++++++|+++|+.||.|..+                                       .++.|..+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~   63 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSA---------------------------------------KVFIDKQT   63 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEE---------------------------------------EEEECSSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEECCCC
Confidence            346899999999999999999999999999877                                       67888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      +.++|||||+|.+.++|.+|+..||+..|.|+.|+|.|++.+...
T Consensus        64 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~  108 (115)
T 2cpz_A           64 NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS  108 (115)
T ss_dssp             CSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCC
T ss_pred             CCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCcC
Confidence            999999999999999999999999999999999999999876543

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.71  E-value=2.3e-17  Score=119.72  Aligned_cols=80  Identities=34%  Similarity=0.679  Sum_probs=75.5

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      .+|||+|||.++++++|+++|+.||.|..+                                       .++.+..++.+
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~---------------------------------------~i~~~~~~~~~   42 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSG---------------------------------------HVMWDMQTGSS   42 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEE---------------------------------------EEEECTTTCCE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEE---------------------------------------EEEEcCCCCCc
Confidence            579999999999999999999999999877                                       67888888999


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +|||||+|.+.++|.+|+..|||..+.|+.|+|.|+.++
T Consensus        43 ~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A           43 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             cceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            999999999999999999999999999999999999765

>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=99.70  E-value=1.5e-17  Score=144.19  Aligned_cols=82  Identities=13%  Similarity=0.268  Sum_probs=77.1

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCC--CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSG--PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G--~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ..++|||+||+.++|+++|+++|+.||  .|.+|+|+.++.+++++|||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  999999999998999999999999999999999999999999999999999


Q ss_pred             CCCc
Q psy3016         111 ASSH  114 (305)
Q Consensus       111 ~~~~  114 (305)
                      +...
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8743

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=3.2e-17  Score=124.19  Aligned_cols=87  Identities=24%  Similarity=0.336  Sum_probs=79.5

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+++++|+++|+.||.|..+                                       .++.|..
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v---------------------------------------~i~~~~~   50 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDV---------------------------------------YIPREPH   50 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEE---------------------------------------ECCBCSS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEeCCC
Confidence            3456899999999999999999999999999877                                       6788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+......
T Consensus        51 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dnm_A           51 TKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRD   96 (103)
T ss_dssp             SCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCCSC
T ss_pred             CCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCCCC
Confidence            8999999999999999999999999999999999999999766543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.4e-16  Score=119.79  Aligned_cols=79  Identities=32%  Similarity=0.373  Sum_probs=72.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccC--CCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQS--GPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~--G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .....++|||+|||..+|+++|+++|+.|  |.|..|++.        +|||||+|.+.++|.+|++.||+..+.|+.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIE   82 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            44567899999999999999999999999  999999873        58999999999999999999999999999999


Q ss_pred             EeeCCCccc
Q psy3016         108 VNKASSHQK  116 (305)
Q Consensus       108 v~~~~~~~~  116 (305)
                      |.++.....
T Consensus        83 v~~a~~~~~   91 (99)
T 2cpd_A           83 VTLAKPVDK   91 (99)
T ss_dssp             EECCCCCCC
T ss_pred             EEECCCCCC
Confidence            999987654

>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=99.70  E-value=2.5e-17  Score=120.64  Aligned_cols=82  Identities=30%  Similarity=0.616  Sum_probs=75.0

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+.++++++|+++|+.||.|..+                                       .++.+..++
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~~   45 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDA---------------------------------------RVVKDMATG   45 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECTTTC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEE---------------------------------------EEEecCCCC
Confidence            35789999999999999999999999999877                                       678888889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+
T Consensus        46 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           46 KSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             CEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             ccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            99999999999999999999999999999999999999754

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.70  E-value=5.1e-17  Score=131.57  Aligned_cols=83  Identities=27%  Similarity=0.443  Sum_probs=76.0

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .......++|||+|||..+|+++|+++|+.||.|.+|+++.+     ++|||||+|.+.++|.+|++.|||..+.|+.|+
T Consensus        67 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  141 (150)
T 2i2y_A           67 RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVR  141 (150)
T ss_dssp             SSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            345566789999999999999999999999999999999876     579999999999999999999999999999999


Q ss_pred             EeeCCCcc
Q psy3016         108 VNKASSHQ  115 (305)
Q Consensus       108 v~~~~~~~  115 (305)
                      |.++.++.
T Consensus       142 v~~a~~~~  149 (150)
T 2i2y_A          142 VELSNGEK  149 (150)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99987653

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.2e-17  Score=121.27  Aligned_cols=90  Identities=82%  Similarity=1.311  Sum_probs=79.9

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||..+++++|+++|+.||.|..+.                                      .++.|..++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~--------------------------------------~i~~~~~~g   45 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTP--------------------------------------KIMRDPDTG   45 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCC--------------------------------------EECCCTTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE--------------------------------------EEEEcCCCC
Confidence            467899999999999999999999999997541                                      357777889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcCCCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRH  247 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~~~~  247 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..+..++
T Consensus        46 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~   93 (96)
T 1x5t_A           46 NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGSGP   93 (96)
T ss_dssp             SCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCCCCCC
T ss_pred             CcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCCCCCCC
Confidence            999999999999999999999999999999999999998877655444

>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=9.4e-18  Score=128.23  Aligned_cols=84  Identities=18%  Similarity=0.194  Sum_probs=77.6

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCC---eEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGP---VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      ......++|||+|||.++|+++|+++|+.||.   |..|.|+.+.. |+++|||||+|.+.++|++|++ +++..+.|+.
T Consensus         6 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~   83 (107)
T 2lmi_A            6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRY   83 (107)
T ss_dssp             CCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSC
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeE
Confidence            34567889999999999999999999999998   89999999986 9999999999999999999999 9999999999


Q ss_pred             eEEeeCCCc
Q psy3016         106 IRVNKASSH  114 (305)
Q Consensus       106 l~v~~~~~~  114 (305)
                      |.|.++...
T Consensus        84 i~V~~a~~~   92 (107)
T 2lmi_A           84 VEVYEINNE   92 (107)
T ss_dssp             CCCEECCHH
T ss_pred             EEEEECCHH
Confidence            999988754

>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=99.70  E-value=3.7e-17  Score=122.25  Aligned_cols=83  Identities=28%  Similarity=0.556  Sum_probs=77.4

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+||+..+++++|+++|+.||.|..+                                       .++.+..+|.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~g~   42 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINL---------------------------------------KMMFDPQTGR   42 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCBCTTTCC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEeCCCCCc
Confidence            4789999999999999999999999999877                                       6788888899


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      ++|||||+|.+.++|.+|+..|||..++|+.|+|.|+..+..
T Consensus        43 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           43 SKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             BCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSSG
T ss_pred             cceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCCC
Confidence            999999999999999999999999999999999999977643

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=4.5e-17  Score=123.74  Aligned_cols=88  Identities=30%  Similarity=0.525  Sum_probs=80.2

Q ss_pred             cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      .....++|||+||+..+++++|+++|+.||.|..+                                       .++.+.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~   51 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNT---------------------------------------HMPKDR   51 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCBCS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEecC
Confidence            34457899999999999999999999999999877                                       678888


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .++.++|||||+|.+.++|.+|+..||+..+.|+.|+|.|+..+...
T Consensus        52 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (105)
T 1x5u_A           52 VTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKN   98 (105)
T ss_dssp             SSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSCC
T ss_pred             CCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCcC
Confidence            88999999999999999999999999999999999999999776543

>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=99.70  E-value=1.1e-16  Score=122.77  Aligned_cols=77  Identities=23%  Similarity=0.425  Sum_probs=71.3

Q ss_pred             CCCCceEEEcCCCcc-ccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          31 GDGDATIYVGGLDDK-VSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ....++|||+|||.. +|+++|+++|+.||.|.+|.+        ++|||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   95 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            344689999999999 999999999999999999999        56999999999999999999999999999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      ++....
T Consensus        96 ~a~~~~  101 (110)
T 1wf1_A           96 MAGEPK  101 (110)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            997544

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.70  E-value=1.1e-17  Score=126.45  Aligned_cols=82  Identities=30%  Similarity=0.558  Sum_probs=76.4

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ....++|||+|||..+|+++|+++|+.||.|.+|+++.+. ++.++|||||+|.+.++|++|++  ++..++|+.|.|.+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEE
Confidence            3456899999999999999999999999999999999998 89999999999999999999999  99999999999998


Q ss_pred             CCCcc
Q psy3016         111 ASSHQ  115 (305)
Q Consensus       111 ~~~~~  115 (305)
                      +..+.
T Consensus        83 a~~~~   87 (102)
T 2xs2_A           83 AIRKQ   87 (102)
T ss_dssp             EEECC
T ss_pred             CCcCc
Confidence            87544

>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=99.70  E-value=1.1e-17  Score=123.76  Aligned_cols=81  Identities=25%  Similarity=0.351  Sum_probs=70.9

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcC--cccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFG--VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      .+|||+||+.++|+++|+++|+.||  .|..+                                       .++.|..+|
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v---------------------------------------~i~~~~~~g   42 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEI---------------------------------------KFFENRANG   42 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCE---------------------------------------EEEECTTTC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEE---------------------------------------EEEecCCCC
Confidence            4799999999999999999999999  88766                                       778898899


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.+..
T Consensus        43 ~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~   84 (90)
T 3p5t_L           43 QSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLE   84 (90)
T ss_dssp             CEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC----
T ss_pred             ccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCCc
Confidence            999999999999999999999999999999999999986653

>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=99.70  E-value=3.7e-17  Score=125.56  Aligned_cols=81  Identities=19%  Similarity=0.222  Sum_probs=71.9

Q ss_pred             cCCCCceEEEcCCCcc-ccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc--CceeCCeee
Q psy3016          30 SGDGDATIYVGGLDDK-VSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN--MIKLYGKPI  106 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~--g~~~~g~~l  106 (305)
                      .....++|||+|||.+ +|+++|+++|+.||.|.+|.|++      ++|||||+|.+.++|.+|++.|+  +..+.|+.|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3556889999999998 99999999999999999999964      46999999999999999999886  456999999


Q ss_pred             EEeeCCCccc
Q psy3016         107 RVNKASSHQK  116 (305)
Q Consensus       107 ~v~~~~~~~~  116 (305)
                      +|.++..+..
T Consensus        95 ~V~~a~~~~~  104 (112)
T 1x4f_A           95 KVDLSEKYKK  104 (112)
T ss_dssp             EEEEECSCSS
T ss_pred             EEEECccccc
Confidence            9999876543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.70  E-value=8.5e-17  Score=134.05  Aligned_cols=86  Identities=27%  Similarity=0.339  Sum_probs=80.3

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      ......++|||+|||..+++++|+++|+.||.|.+|.|+.+. ++.++|||||+|.+.++|.+|++.||+..+.|+.|.|
T Consensus        83 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V  161 (177)
T 2f3j_A           83 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI  161 (177)
T ss_dssp             SSCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345667899999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             eeCCCcc
Q psy3016         109 NKASSHQ  115 (305)
Q Consensus       109 ~~~~~~~  115 (305)
                      .++....
T Consensus       162 ~~a~~~~  168 (177)
T 2f3j_A          162 QLVASQI  168 (177)
T ss_dssp             EEESSGG
T ss_pred             EEecCCC
Confidence            9987654

>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=99.70  E-value=9.3e-18  Score=129.69  Aligned_cols=84  Identities=26%  Similarity=0.414  Sum_probs=74.6

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCe----EEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPV----VNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i----~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      .....++|||+|||..+|+++|+++|+.||.|    ..+++.    ++.++|||||+|.+.++|.+|++.|++..+.|+.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~----~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   96 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKI   96 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE----CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC----CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            34467899999999999999999999999998    455554    6788999999999999999999999999999999


Q ss_pred             eEEeeCCCcccc
Q psy3016         106 IRVNKASSHQKN  117 (305)
Q Consensus       106 l~v~~~~~~~~~  117 (305)
                      |+|.++......
T Consensus        97 l~v~~a~~~~~~  108 (115)
T 2cpx_A           97 LVIEFGKNKKQR  108 (115)
T ss_dssp             CEEEECCCCSCC
T ss_pred             EEEEEccCCCCC
Confidence            999999876543

>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=99.70  E-value=3.4e-17  Score=119.38  Aligned_cols=80  Identities=35%  Similarity=0.542  Sum_probs=75.1

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||.++++++|+++|+.||.|..+                                       .++.|..++
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v---------------------------------------~i~~~~~~~   46 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI---------------------------------------QIPLDYETE   46 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------ECCEETTTT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEE---------------------------------------EEEECCCCC
Confidence            46789999999999999999999999999877                                       678888889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|+|+|++
T Consensus        47 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A           47 KHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             EECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            999999999999999999999999999999999999974

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=7.9e-17  Score=122.72  Aligned_cols=87  Identities=18%  Similarity=0.432  Sum_probs=79.2

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC-C
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD-P  196 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d-~  196 (305)
                      ....++|||+|||..+++++|+++|+.||.|..+                                       .++.+ .
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~   52 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTV---------------------------------------RLPKKMT   52 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCCCCS
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEE---------------------------------------EEecCCC
Confidence            3457899999999999999999999999999877                                       67777 6


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHh-cCeeecCeeeEEEEeeecCCc
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAM-HGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l-~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .++.++|||||+|.+.++|.+|+..| |+..|.|+.|+|.|+..+...
T Consensus        53 ~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~~  100 (107)
T 2cph_A           53 GTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTV  100 (107)
T ss_dssp             SSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCCC
T ss_pred             CCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCCC
Confidence            78999999999999999999999999 999999999999999877554

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=4.4e-17  Score=121.36  Aligned_cols=84  Identities=26%  Similarity=0.362  Sum_probs=77.4

Q ss_pred             cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      .....++|||+|||..+++++|+++|+.||.|..+                                       .++.+.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v---------------------------------------~i~~~~   51 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADV---------------------------------------SIVYDQ   51 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEE---------------------------------------EEEECS
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEE---------------------------------------EEEEcC
Confidence            34457899999999999999999999999999877                                       678888


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      .++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|++.
T Consensus        52 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           52 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             SSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             CCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            8899999999999999999999999999999999999999853

>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=99.70  E-value=8.2e-17  Score=123.47  Aligned_cols=87  Identities=30%  Similarity=0.483  Sum_probs=80.1

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+|+++|+++|..||.|..+                                       .++.|..
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~   52 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYV---------------------------------------RVVLHPD   52 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCBCSS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEecCC
Confidence            3456899999999999999999999999999877                                       7788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhc------CeeecCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMH------GQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~------~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ++.++|||||+|.+.++|.+|+..||      +..+.|+.|+|.|+..+...
T Consensus        53 ~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           53 TEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCCC
T ss_pred             CCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCccC
Confidence            89999999999999999999999999      99999999999999877554

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=6.2e-17  Score=121.66  Aligned_cols=85  Identities=26%  Similarity=0.507  Sum_probs=78.3

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+++++|+++|+.||.|..+                                       .++.|..+
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~   48 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEV---------------------------------------VMIYDAEK   48 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEE---------------------------------------EECCCTTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEeCCCC
Confidence            346889999999999999999999999999877                                       67888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      +.++|||||+|.+.++|.+|+. ||+..+.|+.|+|.++..+...
T Consensus        49 ~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~~   92 (99)
T 2dgs_A           49 QRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDSK   92 (99)
T ss_dssp             CSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCCCC
T ss_pred             CCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCccc
Confidence            9999999999999999999999 9999999999999999877554

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.69  E-value=7.4e-17  Score=124.62  Aligned_cols=87  Identities=29%  Similarity=0.576  Sum_probs=79.5

Q ss_pred             cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      .....++|||+||+..+++++|+++|+.||.|..+                                       .++.+.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~   51 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDA---------------------------------------RVVKDM   51 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEEcC
Confidence            34457899999999999999999999999999877                                       678888


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++.++|||||+|.+.++|.+|+..|||..|.|+.|+|.|+..+..
T Consensus        52 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   97 (115)
T 2dgo_A           52 ATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPP   97 (115)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCC
Confidence            8899999999999999999999999999999999999999976643

>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=99.69  E-value=1.2e-16  Score=131.47  Aligned_cols=81  Identities=30%  Similarity=0.496  Sum_probs=77.4

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||..+|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|||..+.|+.|.|+++
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            44789999999999999999999999999999999999888999999999999999999999999999999999999987


Q ss_pred             C
Q psy3016         112 S  112 (305)
Q Consensus       112 ~  112 (305)
                      .
T Consensus       172 s  172 (172)
T 2g4b_A          172 S  172 (172)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.69  E-value=7.1e-17  Score=122.82  Aligned_cols=87  Identities=33%  Similarity=0.462  Sum_probs=79.3

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+++++|+++|+.||.|..+                                       .++.|..
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~   50 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYEL---------------------------------------TVLKDRF   50 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEE---------------------------------------ECCCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEE---------------------------------------EEEecCC
Confidence            3456889999999999999999999999999877                                       7788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeee---cCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYL---CNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~---~g~~l~v~~a~~~~~~  243 (305)
                      ++.++|||||+|.+.++|.+|+..||+..+   .|+.|+|.|+..+..+
T Consensus        51 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~~   99 (106)
T 2dgp_A           51 TGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRG   99 (106)
T ss_dssp             SCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSCC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCccccc
Confidence            899999999999999999999999999987   8999999999776543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.69  E-value=2.2e-16  Score=132.80  Aligned_cols=86  Identities=29%  Similarity=0.461  Sum_probs=81.0

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ....++|||+|||..+|+++|+++|+.||.|.+|.+..+..++.++|||||+|.+.++|.+|++.|||..+.|+.|.|.+
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            46778999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             CCCccc
Q psy3016         111 ASSHQK  116 (305)
Q Consensus       111 ~~~~~~  116 (305)
                      +.+...
T Consensus       191 a~~~~~  196 (198)
T 2yh0_A          191 ASVGAK  196 (198)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            987643

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=8.9e-17  Score=123.77  Aligned_cols=95  Identities=25%  Similarity=0.319  Sum_probs=79.1

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+|+++|+++|+.||.|..+..                               ...-...++.|..
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~-------------------------------~~~~~v~i~~~~~   60 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKR-------------------------------TGQPMIHIYLDKE   60 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSS-------------------------------SCCBSEECCBCTT
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccc-------------------------------cCccCEEEEEeCC
Confidence            345689999999999999999999999999973100                               0000116788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ++.++|||||+|.+.++|.+|+..||+..|.|+.|+|.++..+...
T Consensus        61 ~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCCS
T ss_pred             CCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCCC
Confidence            8999999999999999999999999999999999999999776543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.69  E-value=3.8e-17  Score=122.05  Aligned_cols=82  Identities=17%  Similarity=0.239  Sum_probs=73.3

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|++.|++..+.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34467899999999999999999999999988766     2367899999999999999999999999999999999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      ++..+..
T Consensus        87 ~a~~~~~   93 (96)
T 1fjc_A           87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EcCCCCC
Confidence            9876543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.69  E-value=1.9e-17  Score=125.02  Aligned_cols=81  Identities=25%  Similarity=0.322  Sum_probs=76.6

Q ss_pred             cccccccCCCc------hhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc
Q psy3016         121 GANIFIGNLDP------EVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR  194 (305)
Q Consensus       121 ~~~l~v~nl~~------~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  194 (305)
                      .++|||+|||.      ++++++|+++|+.||.|..+                                       .++.
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v---------------------------------------~i~~   46 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNM---------------------------------------EFPI   46 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEE---------------------------------------ECCE
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEE---------------------------------------EEEE
Confidence            57899999999      99999999999999999887                                       7889


Q ss_pred             CCCCCCccceEEEEeCChHHHHHHHHHhcCeeecC-eeeEEEEeeec
Q psy3016         195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN-RPISVSYAFKK  240 (305)
Q Consensus       195 d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g-~~l~v~~a~~~  240 (305)
                      |..+|+++|||||+|.+.++|.+|+..|||..+.| +.|+|.++.++
T Consensus        47 d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~~   93 (100)
T 3ns6_A           47 DEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDV   93 (100)
T ss_dssp             ETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHHH
T ss_pred             cCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECchh
Confidence            98899999999999999999999999999999999 99999999764

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.69  E-value=8.5e-17  Score=123.27  Aligned_cols=85  Identities=26%  Similarity=0.472  Sum_probs=78.8

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+|+++|+++|+.||.|..+                                       .++.+..+
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~   64 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNI---------------------------------------HLNLDRRT   64 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------ECCBCTTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEecCCC
Confidence            346889999999999999999999999999877                                       67888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..
T Consensus        65 ~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  108 (110)
T 1oo0_B           65 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  108 (110)
T ss_dssp             SSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESSC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCCC
Confidence            99999999999999999999999999999999999999987654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=6.5e-17  Score=123.03  Aligned_cols=84  Identities=27%  Similarity=0.561  Sum_probs=78.2

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+++++|+++|+.||.|..+                                       .++.|..+
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v---------------------------------------~i~~~~~~   61 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNI---------------------------------------HLNLDRRT   61 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECTTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEE---------------------------------------EEEecCCC
Confidence            346789999999999999999999999999877                                       67888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+.
T Consensus        62 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  104 (106)
T 1p27_B           62 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG  104 (106)
T ss_dssp             SSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             CceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCCC
Confidence            9999999999999999999999999999999999999997764

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.69  E-value=7.2e-17  Score=122.57  Aligned_cols=86  Identities=30%  Similarity=0.569  Sum_probs=78.0

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+++++|+++|+.||.|..+                                       .++.+. +
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~-~   52 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDEC---------------------------------------TVLRGP-D   52 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEE---------------------------------------EEEECS-S
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEECC-C
Confidence            357899999999999999999999999999877                                       667776 6


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecC---eeeEEEEeeecCCcC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCN---RPISVSYAFKKDSKG  244 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g---~~l~v~~a~~~~~~~  244 (305)
                      +.++|||||+|.+.++|.+|+..|||..+.|   +.|+|.|+..+..+.
T Consensus        53 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~~~  101 (105)
T 2dnh_A           53 GSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESG  101 (105)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCCCS
T ss_pred             CCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCcccC
Confidence            8999999999999999999999999999988   999999998776543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.69  E-value=4.1e-17  Score=122.12  Aligned_cols=79  Identities=20%  Similarity=0.419  Sum_probs=70.9

Q ss_pred             cCCCCceEEEcCCCc-cccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          30 SGDGDATIYVGGLDD-KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      .....++|||+|||. .+|+++|+++|+.||.|.+|.+        ++|||||+|.+.++|.+|++.|++..+.|+.|+|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE--------ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            445688999999998 9999999999999999999999        3699999999999999999999999999999999


Q ss_pred             eeCCCccc
Q psy3016         109 NKASSHQK  116 (305)
Q Consensus       109 ~~~~~~~~  116 (305)
                      +++.....
T Consensus        78 ~~a~~~~~   85 (96)
T 2kvi_A           78 EVSSSNAR   85 (96)
T ss_dssp             EEEECCCC
T ss_pred             EEcCcCCC
Confidence            99876543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.52  E-value=1.9e-18  Score=133.96  Aligned_cols=87  Identities=25%  Similarity=0.366  Sum_probs=80.7

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEE--------EEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVN--------VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY  102 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~--------i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~  102 (305)
                      ....++|||+|||..+|+++|+++|+.||.|..        |+++.++.++.++|||||+|.+.++|.+|++.||+..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            346789999999999999999999999999999        999999888999999999999999999999999999999


Q ss_pred             CeeeEEeeCCCcccc
Q psy3016         103 GKPIRVNKASSHQKN  117 (305)
Q Consensus       103 g~~l~v~~~~~~~~~  117 (305)
                      |+.|+|.++..+...
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999998876543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=8.3e-17  Score=121.20  Aligned_cols=84  Identities=19%  Similarity=0.307  Sum_probs=77.0

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||..+|+++|+++|+.||.|..+                                       .++.+. +
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~-~   54 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDL---------------------------------------RLVTNR-A   54 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEE---------------------------------------EEEECT-T
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEE---------------------------------------EEEECC-C
Confidence            346889999999999999999999999999877                                       677776 7


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+.++..
T Consensus        55 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   98 (100)
T 2do4_A           55 GKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPS   98 (100)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCSC
T ss_pred             CCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            99999999999999999999999999999999999999977654

>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=99.69  E-value=8.7e-18  Score=158.84  Aligned_cols=154  Identities=16%  Similarity=0.264  Sum_probs=107.9

Q ss_pred             HHHHHhccCCCeEEEEEcc----cC-CCCCcceEE--EEEEcCHHHHHHHHHHhcCceeCC---------------eeeE
Q psy3016          50 LMWELFVQSGPVVNVHMPK----DR-VTQTHQGYG--FIEFMGEEDADYAIKIMNMIKLYG---------------KPIR  107 (305)
Q Consensus        50 ~L~~~F~~~G~i~~i~~~~----~~-~~~~~~g~a--fV~f~~~e~A~~Ai~~l~g~~~~g---------------~~l~  107 (305)
                      .|..+|..+|+|..|..+.    +. .+....|++  |+.|.....+..++..++.....+               ..+.
T Consensus         8 ~L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~   87 (437)
T 3pgw_S            8 NLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELK   87 (437)
T ss_pred             cHHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            3788999999998873332    21 111122333  778877655443332221111110               0111


Q ss_pred             Ee-eCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEec
Q psy3016         108 VN-KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIG  186 (305)
Q Consensus       108 v~-~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  186 (305)
                      +. ............++|||+||+..+|+++|.++|+.||.|..|                                   
T Consensus        88 ~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v-----------------------------------  132 (437)
T 3pgw_S           88 MWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRI-----------------------------------  132 (437)
T ss_pred             hcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEE-----------------------------------
Confidence            11 111111222345799999999999999999999999999877                                   


Q ss_pred             cCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         187 NLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       187 ~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                          .|+.|..++.++|||||+|.+.++|.+||..|||.+|.|+.|.|.|+.....
T Consensus       133 ----~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~~  184 (437)
T 3pgw_S          133 ----HMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV  184 (437)
T ss_pred             ----EeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence                6788888899999999999999999999999999999999999999987654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=8.5e-17  Score=119.61  Aligned_cols=81  Identities=30%  Similarity=0.502  Sum_probs=75.7

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||..+++++|+++|+.||.|..+                                       .++.+..+
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v---------------------------------------~i~~~~~~   54 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKV---------------------------------------TIMKDKDT   54 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEE---------------------------------------EECCCSSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEeCCCC
Confidence            356899999999999999999999999999877                                       67888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      +.++|||||+|.+.++|.+|++.||+..+.|+.|+|.|++
T Consensus        55 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           55 RKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             CCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            9999999999999999999999999999999999999974

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=5.9e-17  Score=120.35  Aligned_cols=80  Identities=23%  Similarity=0.383  Sum_probs=71.2

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCC-eEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcC-ceeCCeeeEE
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGP-VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM-IKLYGKPIRV  108 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~-i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g-~~~~g~~l~v  108 (305)
                      ....++|||+|||..+|+++|+++|+.||. |..+.+.       ++|||||+|.+.++|++|++.||+ ..+.|+.|+|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            456789999999999999999999999999 6666662       469999999999999999999999 9999999999


Q ss_pred             eeCCCcccc
Q psy3016         109 NKASSHQKN  117 (305)
Q Consensus       109 ~~~~~~~~~  117 (305)
                      +++..+...
T Consensus        78 ~~a~~~~~~   86 (93)
T 2cqh_A           78 DYSVSKKLR   86 (93)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCcccc
Confidence            999876543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=7.4e-17  Score=122.13  Aligned_cols=86  Identities=30%  Similarity=0.591  Sum_probs=77.6

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+|+++|+++|+.||.|..+                                       .++.+  
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~--   50 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSA---------------------------------------KVMME--   50 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEE---------------------------------------EEEEC--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEcC--
Confidence            3457899999999999999999999999999877                                       56666  


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKG  244 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~  244 (305)
                      ++.++|||||+|.+.++|.+|+..||+..+.|+.|+|.|+..+..+.
T Consensus        51 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   97 (103)
T 2d9p_A           51 GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQ   97 (103)
T ss_dssp             SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCCCC
T ss_pred             CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccccCC
Confidence            68999999999999999999999999999999999999998776543

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.68  E-value=4e-17  Score=126.35  Aligned_cols=81  Identities=41%  Similarity=0.696  Sum_probs=73.3

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ..+|||+|||.++|+++|+++|+.||.|..+                                       +++.|.  +.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v---------------------------------------~i~~d~--~~   43 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSC---------------------------------------KVVCDE--NG   43 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEEET--TE
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEE---------------------------------------EEeecC--CC
Confidence            4679999999999999999999999999877                                       567764  45


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      ++|||||+|.+.++|.+|+..|||..+.|+.|+|.++..+..
T Consensus        44 ~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~   85 (115)
T 4f25_A           44 SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE   85 (115)
T ss_dssp             EEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC
T ss_pred             CCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCccc
Confidence            799999999999999999999999999999999999876554

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1e-16  Score=119.66  Aligned_cols=82  Identities=15%  Similarity=0.169  Sum_probs=73.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEE-EEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNV-HMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i-~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+| .++.+..+    +.|||+|.+.++|.+|++.|||..+.|+.|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V   86 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKV   86 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEE
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            34557899999999999999999999999999999 58877643    44999999999999999999999999999999


Q ss_pred             eeCCCcc
Q psy3016         109 NKASSHQ  115 (305)
Q Consensus       109 ~~~~~~~  115 (305)
                      .++.++.
T Consensus        87 ~~a~~~~   93 (96)
T 2e44_A           87 AYIPDEM   93 (96)
T ss_dssp             EECCCCC
T ss_pred             EEcCccc
Confidence            9998763

>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=99.68  E-value=4.7e-17  Score=125.23  Aligned_cols=76  Identities=18%  Similarity=0.216  Sum_probs=70.6

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||..+|+++|+++|+.||.|..|.++.      ++|||||+|.+.++|++|++.|||..+.|+.|.|.|+
T Consensus         8 ~~~~~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            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3467999999999999999999999999999999864      4589999999999999999999999999999999998


Q ss_pred             CC
Q psy3016         112 SS  113 (305)
Q Consensus       112 ~~  113 (305)
                      ..
T Consensus        82 ~~   83 (111)
T 1whx_A           82 PI   83 (111)
T ss_dssp             ET
T ss_pred             CC
Confidence            64

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.68  E-value=1.2e-16  Score=123.95  Aligned_cols=83  Identities=31%  Similarity=0.515  Sum_probs=76.5

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+.++|+++|+++|+.||.|..+                                       .++.+. ++
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~-~g   45 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEV---------------------------------------LLIKDR-TS   45 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEE---------------------------------------EEECST-TT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEECC-CC
Confidence            45789999999999999999999999999876                                       677776 79


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..
T Consensus        46 ~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   88 (116)
T 2fy1_A           46 KSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF   88 (116)
T ss_dssp             TCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSSC
T ss_pred             CcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            9999999999999999999999999999999999999976643

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=2.3e-16  Score=117.43  Aligned_cols=80  Identities=20%  Similarity=0.340  Sum_probs=70.2

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ....++|||+|||.++|+++|+++|+.||.|.+|  +.+..++.   ||||+|.+.++|.+|++ |++..+.|+.|.|++
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEE
Confidence            3456799999999999999999999999999998  44444444   99999999999999999 999999999999998


Q ss_pred             CCCccc
Q psy3016         111 ASSHQK  116 (305)
Q Consensus       111 ~~~~~~  116 (305)
                      +..+..
T Consensus        79 a~~~~~   84 (94)
T 2e5g_A           79 REQKEF   84 (94)
T ss_dssp             SCCSCC
T ss_pred             CCcCCC
Confidence            876543

>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=99.68  E-value=1.2e-16  Score=125.43  Aligned_cols=88  Identities=26%  Similarity=0.523  Sum_probs=80.5

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+|+++|+++|+.||.|..+                                       .++.|..
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~   59 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNI---------------------------------------HLNLDRR   59 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCBCTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEecCC
Confidence            3346799999999999999999999999999877                                       6788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKG  244 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~  244 (305)
                      ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+..+....
T Consensus        60 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  106 (126)
T 3ex7_B           60 TGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPK  106 (126)
T ss_dssp             TSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSSCC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCCC
Confidence            89999999999999999999999999999999999999998876543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.68  E-value=1.1e-16  Score=120.35  Aligned_cols=89  Identities=28%  Similarity=0.423  Sum_probs=75.3

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+.++++++|+++|+.||.|......                               ..-...++.|..+
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~-------------------------------~~~~v~i~~~~~~   59 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKT-------------------------------GQPMINLYTDRET   59 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTT-------------------------------TEESEEEEECTTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeecccc-------------------------------ccccEEEEecCCC
Confidence            356899999999999999999999999999861000                               0000167888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      |.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+|+
T Consensus        60 g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           60 GKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             CSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             CCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEecC
Confidence            9999999999999999999999999999999999999974

>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=99.67  E-value=1.5e-17  Score=144.20  Aligned_cols=83  Identities=24%  Similarity=0.314  Sum_probs=76.1

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcC--cccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFG--VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ..++|||+||+.++|+++|+++|+.||  .|..+                                       .|+.|..
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v---------------------------------------~i~~d~~  107 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEI---------------------------------------KFFENRA  107 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEE---------------------------------------EEEECTT
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEE---------------------------------------EEEecCC
Confidence            356899999999999999999999999  88876                                       7889988


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +++++|||||+|.+.++|.+||..||+..|.|+.|+|.++....
T Consensus       108 tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~~~  151 (229)
T 3q2s_C          108 NGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQF  151 (229)
T ss_dssp             TCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCHHH
T ss_pred             CCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCCCc
Confidence            99999999999999999999999999999999999999987543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=6.4e-17  Score=121.31  Aligned_cols=84  Identities=23%  Similarity=0.371  Sum_probs=75.6

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC--
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD--  197 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~--  197 (305)
                      ..++|||+||+.++++++|+++|+.||.|..+                                       .++.+..  
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~~   44 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSC---------------------------------------TISKKKNKA   44 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------EEEEEECTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEecCCCC
Confidence            35789999999999999999999999999876                                       5666655  


Q ss_pred             -CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         198 -TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       198 -~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                       ++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..
T Consensus        45 gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   90 (98)
T 2cpf_A           45 GVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK   90 (98)
T ss_dssp             CCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSSC
T ss_pred             CCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCCC
Confidence             568999999999999999999999999999999999999977654

>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=1.8e-16  Score=116.61  Aligned_cols=76  Identities=17%  Similarity=0.277  Sum_probs=70.4

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||..+|+++|+++|++| .|.++++.      +++|||||+|.+.++|++|++.|||..+.|+.|+|+++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   75 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEc
Confidence            356899999999999999999999999 99999984      47899999999999999999999999999999999998


Q ss_pred             CCc
Q psy3016         112 SSH  114 (305)
Q Consensus       112 ~~~  114 (305)
                      ...
T Consensus        76 ~~~   78 (88)
T 1wg1_A           76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.67  E-value=9.8e-17  Score=126.79  Aligned_cols=86  Identities=26%  Similarity=0.411  Sum_probs=79.0

Q ss_pred             cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      .....++|||+||+.++++++|+++|+.||.|..+                                       .++.|.
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v---------------------------------------~i~~d~   82 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADV---------------------------------------SIVYDQ   82 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEE---------------------------------------EEECCS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEecC
Confidence            34457899999999999999999999999999877                                       678888


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .++.++|||||+|.+.++|.+|+..|||..|.|+.|+|.|+..+.
T Consensus        83 ~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~  127 (129)
T 2kxn_B           83 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR  127 (129)
T ss_dssp             SSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSS
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            889999999999999999999999999999999999999997654

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.7e-16  Score=120.35  Aligned_cols=84  Identities=23%  Similarity=0.419  Sum_probs=76.8

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+++++|+++|+.|| |..+                                       .++.+..+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v---------------------------------------~i~~~~~~   52 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAV---------------------------------------RLPREPSN   52 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEE---------------------------------------ECCBCSSC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEE---------------------------------------EEecCCCC
Confidence            3568999999999999999999999999 8776                                       67888877


Q ss_pred             -CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         199 -GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 -~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                       +.++|||||+|.+.++|.+|+ .||+..+.|+.|+|.++..+..+
T Consensus        53 ~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   97 (104)
T 1wi8_A           53 PERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             TTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCCC
T ss_pred             CCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCCCC
Confidence             899999999999999999999 89999999999999999877554

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.67  E-value=1.4e-16  Score=127.27  Aligned_cols=86  Identities=26%  Similarity=0.460  Sum_probs=79.3

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+.++++++|+++|+.||.|..+                                       .++.|..+
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~   80 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESV---------------------------------------KIVCDRET   80 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEE---------------------------------------EEEEETTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEEcCCC
Confidence            346899999999999999999999999999877                                       67888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ++++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..+
T Consensus        81 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  125 (139)
T 1u6f_A           81 RQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR  125 (139)
T ss_dssp             TEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            999999999999999999999999999999999999999877554

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.67  E-value=7.7e-17  Score=123.39  Aligned_cols=85  Identities=27%  Similarity=0.555  Sum_probs=78.2

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+++++|+++|+.||.|..+                                       .++.+..
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~   63 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESI---------------------------------------QLMMDSE   63 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEE---------------------------------------EEEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEEcCC
Confidence            3456899999999999999999999999999877                                       6788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      ++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.++.
T Consensus        64 ~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k~  107 (108)
T 2jrs_A           64 TGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT  107 (108)
T ss_dssp             TTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSSC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccCC
Confidence            89999999999999999999999999999999999999997653

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.66  E-value=9.7e-17  Score=127.06  Aligned_cols=86  Identities=17%  Similarity=0.412  Sum_probs=77.1

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+.++|+++|+++|+.||.|...                                     ++.+++|..+
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~-------------------------------------~v~i~~d~~t   63 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSS-------------------------------------NVRVIKDKQT   63 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTT-------------------------------------TEECCBCSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccee-------------------------------------eEEEEEcCCC
Confidence            346789999999999999999999999999761                                     1167999889


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCe----eecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQ----YLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~----~~~g~~l~v~~a~~~~~  242 (305)
                      |+++|||||+|.+. +|.+|+..|||.    .++|+.|+|.|+..+..
T Consensus        64 g~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           64 QLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSKR  110 (131)
T ss_dssp             SSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSCC
T ss_pred             CCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCCC
Confidence            99999999999999 999999999999    99999999999976543

>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=99.66  E-value=1.1e-16  Score=117.49  Aligned_cols=82  Identities=18%  Similarity=0.389  Sum_probs=74.3

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+||+.++|+++|+++|+.||.|..+                                       .++.+..++.
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~---------------------------------------~i~~~~~~~~   44 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMI---------------------------------------DMPVERMHPH   44 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCEETTEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEE---------------------------------------EEEeCCCCCC
Confidence            4689999999999999999999999999876                                       6677766555


Q ss_pred             -ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         201 -SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       201 -~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                       ++|||||+|.+.++|.+|+..|||..++|+.|+|+++....
T Consensus        45 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (88)
T 4a8x_A           45 LSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPW   86 (88)
T ss_dssp             EECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECCCC
T ss_pred             CCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCCCC
Confidence             89999999999999999999999999999999999996553

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.66  E-value=9.4e-17  Score=124.60  Aligned_cols=81  Identities=27%  Similarity=0.461  Sum_probs=75.2

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+.++++++|+++|+.||.|..+                                       .++.|..+
T Consensus        38 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~---------------------------------------~i~~~~~~   78 (118)
T 2khc_A           38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISA---------------------------------------KVFIDKQT   78 (118)
T ss_dssp             CCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEE---------------------------------------EECCCSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEeCCCC
Confidence            346899999999999999999999999999877                                       67888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      ++++|||||+|.+.++|.+|++.|||..++|+.|+|.|++
T Consensus        79 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~ak  118 (118)
T 2khc_A           79 SLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK  118 (118)
T ss_dssp             SCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC-
T ss_pred             CCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            9999999999999999999999999999999999999974

>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=99.66  E-value=2.1e-16  Score=118.45  Aligned_cols=83  Identities=16%  Similarity=0.207  Sum_probs=76.1

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||..+++++|+++|..||.|..+                                       .++.+..+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~---------------------------------------~~~~~~~~   53 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGS---------------------------------------VCLKYNEK   53 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTT---------------------------------------CEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccce---------------------------------------EEEEECCC
Confidence            346789999999999999999999999999865                                       66778788


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +.++|||||+|.+.++|.+|++.|||..|.|+.|+|.++..+
T Consensus        54 g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (98)
T 2cqp_A           54 GMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP   95 (98)
T ss_dssp             SCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSCS
T ss_pred             CCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCCC
Confidence            999999999999999999999999999999999999998654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=1.7e-16  Score=120.62  Aligned_cols=86  Identities=23%  Similarity=0.405  Sum_probs=78.8

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+++++|+++|+.||.|..+                                       .++.+..
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v---------------------------------------~i~~~~~   53 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDC---------------------------------------VIMKDKT   53 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------EEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEeeCCC
Confidence            3456899999999999999999999999999887                                       6788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ++.++|||||+|.+.++|.+|+.. |+..|.|+.|+|.++..+...
T Consensus        54 ~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~~~   98 (105)
T 2dh8_A           54 TNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQ   98 (105)
T ss_dssp             SCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSCCSSCC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEccCCCCC
Confidence            899999999999999999999998 999999999999999877554

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.66  E-value=1.9e-16  Score=119.87  Aligned_cols=84  Identities=20%  Similarity=0.398  Sum_probs=76.5

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+++++|+++|+.|| |..+                                       .++.|..+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v---------------------------------------~i~~~~~~   52 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSV---------------------------------------RLVRDKDT   52 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEE---------------------------------------EEEECSSS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEE---------------------------------------EEeecCCC
Confidence            4568999999999999999999999997 7766                                       67888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ++++|||||+|.+.++|.+|+ .||+..+.|+.|+|.|+..+...
T Consensus        53 g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dng_A           53 DKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQD   96 (103)
T ss_dssp             CSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCCCC
T ss_pred             CccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCCCC
Confidence            999999999999999999999 89999999999999999776543

>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=5e-17  Score=130.59  Aligned_cols=87  Identities=28%  Similarity=0.316  Sum_probs=74.3

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEE--Eccc---CCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVH--MPKD---RVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK  104 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~--~~~~---~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~  104 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..+.  ++.+   ..++.++|||||+|.+.++|.+|++.|||..+.|+
T Consensus        41 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            456678999999999999999999999999987741  1111   13578999999999999999999999999999999


Q ss_pred             eeEEeeCCCccc
Q psy3016         105 PIRVNKASSHQK  116 (305)
Q Consensus       105 ~l~v~~~~~~~~  116 (305)
                      .|.|.++.....
T Consensus       121 ~l~V~~a~~~~~  132 (143)
T 3egn_A          121 PMVVQFARSARP  132 (143)
T ss_dssp             ECEEEECCCSCC
T ss_pred             EEEEEECCCCCC
Confidence            999999976543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.66  E-value=7.2e-16  Score=120.57  Aligned_cols=75  Identities=15%  Similarity=0.209  Sum_probs=67.3

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceE-EEEEEcCHHHHHHHHHHhcCceeCC--eeeEEeeC
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGY-GFIEFMGEEDADYAIKIMNMIKLYG--KPIRVNKA  111 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~-afV~f~~~e~A~~Ai~~l~g~~~~g--~~l~v~~~  111 (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            45789999999999999999999999999999652      286 9999999999999999999999988  68999998


Q ss_pred             CCcc
Q psy3016         112 SSHQ  115 (305)
Q Consensus       112 ~~~~  115 (305)
                      ....
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            8654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.66  E-value=1.2e-16  Score=123.94  Aligned_cols=80  Identities=14%  Similarity=0.088  Sum_probs=71.9

Q ss_pred             CceEEEcCC----CccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcC----HHH----HHHHHH--HhcCc
Q psy3016          34 DATIYVGGL----DDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG----EED----ADYAIK--IMNMI   99 (305)
Q Consensus        34 ~~~l~V~nL----p~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~----~e~----A~~Ai~--~l~g~   99 (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    9999999999999999999999999999999999999999996    333    788888  78999


Q ss_pred             eeCCeeeEEeeCCC
Q psy3016         100 KLYGKPIRVNKASS  113 (305)
Q Consensus       100 ~~~g~~l~v~~~~~  113 (305)
                      .+.|+.|+|..-..
T Consensus        82 ~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           82 FIMGFKFEVILNKH   95 (136)
T ss_dssp             EETTEEEEEEECCT
T ss_pred             eecCcEEEEEECcc
Confidence            99999999997543

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4.1e-16  Score=118.03  Aligned_cols=86  Identities=24%  Similarity=0.410  Sum_probs=76.0

Q ss_pred             cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..+                                       .++.+.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v---------------------------------------~i~~~~   51 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV---------------------------------------EIIFNE   51 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEE---------------------------------------EEECCT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEecC
Confidence            33456899999999999999999999999999876                                       566664


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .  .++|||||+|.+.++|.+|+..||+..|.|+.|+|.|+..+...
T Consensus        52 ~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cq3_A           52 R--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMT   96 (103)
T ss_dssp             T--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCCC
T ss_pred             C--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCCC
Confidence            3  38999999999999999999999999999999999999877554

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.66  E-value=5.1e-16  Score=130.39  Aligned_cols=86  Identities=23%  Similarity=0.383  Sum_probs=75.9

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ....++|||+|||..+|+++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|.+|++. ++..+.|+.|.|.+
T Consensus       101 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~  179 (196)
T 1l3k_A          101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRK  179 (196)
T ss_dssp             --CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEE
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEe
Confidence            34568999999999999999999999999999999999988899999999999999999999985 89999999999999


Q ss_pred             CCCcccc
Q psy3016         111 ASSHQKN  117 (305)
Q Consensus       111 ~~~~~~~  117 (305)
                      +.++...
T Consensus       180 a~~k~~~  186 (196)
T 1l3k_A          180 ALSKQEM  186 (196)
T ss_dssp             CC-----
T ss_pred             cCChhHh
Confidence            9876543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=1.2e-16  Score=121.17  Aligned_cols=86  Identities=27%  Similarity=0.543  Sum_probs=78.2

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhh-cCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSA-FGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~-~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      ....++|||+||+.++|+++|+++|+. ||.|..+                                       .++.|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v---------------------------------------~i~~~~   46 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGG---------------------------------------KVVLDQ   46 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEE---------------------------------------EEEECT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEE---------------------------------------EEEECC
Confidence            345689999999999999999999999 9999877                                       678887


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCee-ecCeeeEEEEeeecCCc
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQY-LCNRPISVSYAFKKDSK  243 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~-~~g~~l~v~~a~~~~~~  243 (305)
                       ++.++|||||+|.+.++|.+|+..||+.. +.|+.|+|.++..+...
T Consensus        47 -~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~~~   93 (104)
T 2dhg_A           47 -TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASR   93 (104)
T ss_dssp             -TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCCSC
T ss_pred             -CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCCcC
Confidence             89999999999999999999999999999 99999999999766543

>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=99.66  E-value=4.4e-16  Score=117.86  Aligned_cols=85  Identities=20%  Similarity=0.439  Sum_probs=75.3

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+++++|+++|+.||.|..+                                       .++.|..
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~   52 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSC---------------------------------------KMITEHT   52 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEE---------------------------------------EEECCCC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEE---------------------------------------EEEecCC
Confidence            3456899999999999999999999999999877                                       5666643


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                        .++|||||+|.+.++|.+|+..||+..+.|+.|+|.|+..+..+
T Consensus        53 --~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2cqi_A           53 --SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ   96 (103)
T ss_dssp             --SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTCC
T ss_pred             --CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCccc
Confidence              36899999999999999999999999999999999999876544

>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=99.66  E-value=6.4e-16  Score=126.49  Aligned_cols=81  Identities=25%  Similarity=0.448  Sum_probs=76.3

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC--eeeEE
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG--KPIRV  108 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g--~~l~v  108 (305)
                      ....++|||+|||..+|+++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|.+|++.|||..+.|  +.|+|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            3456899999999999999999999999999999999998889999999999999999999999999999988  99999


Q ss_pred             eeC
Q psy3016         109 NKA  111 (305)
Q Consensus       109 ~~~  111 (305)
                      .+|
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            875

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.66  E-value=2.5e-16  Score=134.86  Aligned_cols=81  Identities=26%  Similarity=0.506  Sum_probs=75.5

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||+|||..+|+++|+++|+.||.|.+|+|+.+.  +.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999999985  4478999999999999999999999999999999999998


Q ss_pred             Ccc
Q psy3016         113 SHQ  115 (305)
Q Consensus       113 ~~~  115 (305)
                      ++.
T Consensus       180 ~~~  182 (213)
T 4f02_A          180 SRK  182 (213)
T ss_dssp             CHH
T ss_pred             CCc
Confidence            754

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.66  E-value=1.6e-16  Score=118.38  Aligned_cols=80  Identities=18%  Similarity=0.223  Sum_probs=74.1

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||..+++++|+++|+.||.|..+                                       .++.+..++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~---------------------------------------~~~~~~~~g   54 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGS---------------------------------------VCLKYNEKG   54 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTC---------------------------------------CEEEECTTS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccce---------------------------------------EEEEeCCCC
Confidence            45789999999999999999999999999865                                       667787889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      .++|||||+|.+.++|.+|++.||+..+.|+.|+|.++.
T Consensus        55 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           55 MPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             CEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            999999999999999999999999999999999999875

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=1.3e-16  Score=119.75  Aligned_cols=83  Identities=23%  Similarity=0.565  Sum_probs=76.8

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCccc-chhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVIL-QTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ...++|||+|||.++++++|+++|+.||.|. .+                                       .++.|..
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v---------------------------------------~i~~~~~   47 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSV---------------------------------------KIIRNRL   47 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEE---------------------------------------EEEECSS
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEE---------------------------------------EEeecCC
Confidence            3468899999999999999999999999998 76                                       6788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCee----eEEEEeeec
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRP----ISVSYAFKK  240 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~----l~v~~a~~~  240 (305)
                      ++.++|||||+|.+.++|.+|+..|||..+.|+.    |+|.|++..
T Consensus        48 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~   94 (99)
T 2div_A           48 TGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYS   94 (99)
T ss_dssp             SCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCC
T ss_pred             CCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCC
Confidence            8999999999999999999999999999999999    999998655

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.4e-15  Score=113.81  Aligned_cols=79  Identities=23%  Similarity=0.348  Sum_probs=71.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+||  .+|+++|+++|+.||.|.+|.+.      .++|||||+|.+.++|.+|++.|++..+.|+.|+|.
T Consensus        11 ~~~~~~~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           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3446789999996  89999999999999999999994      467999999999999999999999999999999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      ++..+..
T Consensus        83 ~a~~~~~   89 (97)
T 1x5p_A           83 IARKQPM   89 (97)
T ss_dssp             CCSSCCC
T ss_pred             ECCCCCC
Confidence            9987654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=8.7e-17  Score=125.86  Aligned_cols=81  Identities=17%  Similarity=0.199  Sum_probs=73.4

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCe----EEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPV----VNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i----~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      ....++|||+|||.++|+++|+++|+.||.|    ..|.|+.+. +|+++|||||+|.+.++|++|++. |+..+.||.|
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i   97 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEE
Confidence            3557899999999999999999999999986    689999885 899999999999999999999995 9999999999


Q ss_pred             EEeeCCC
Q psy3016         107 RVNKASS  113 (305)
Q Consensus       107 ~v~~~~~  113 (305)
                      .|..+..
T Consensus        98 ~V~~a~~  104 (123)
T 2dha_A           98 ELFRSTA  104 (123)
T ss_dssp             CCEEECH
T ss_pred             EEEECCH
Confidence            9887654

>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=99.65  E-value=1.4e-16  Score=125.09  Aligned_cols=82  Identities=21%  Similarity=0.294  Sum_probs=73.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeE--EEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVV--NVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~--~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .....++|||+|||+++|+++|+++|+.| .|.  .|+|+.++. |+++|||||+|.+.++|++|++ +++..+.||.|.
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEE
Confidence            44567899999999999999999999999 677  899999986 9999999999999999999999 478999999999


Q ss_pred             EeeCCCc
Q psy3016         108 VNKASSH  114 (305)
Q Consensus       108 v~~~~~~  114 (305)
                      |.++..+
T Consensus       115 V~~a~~~  121 (126)
T 2hgm_A          115 VFKSSQE  121 (126)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9887643

>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=99.65  E-value=3.8e-17  Score=130.59  Aligned_cols=83  Identities=19%  Similarity=0.203  Sum_probs=74.3

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||.++|+++|+++|+.|| |.+|+|+.++. ++++|||||+|.+.++|++|| .+|+..+.|+.|.|.
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~  118 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELF  118 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEE
Confidence            445678999999999999999999999999 67999999975 999999999999999999999 689999999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      ++....
T Consensus       119 ~a~~~~  124 (139)
T 2hgn_A          119 LNSTTG  124 (139)
T ss_dssp             ECCCSC
T ss_pred             ECCCCC
Confidence            887654

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.65  E-value=3.4e-16  Score=127.67  Aligned_cols=81  Identities=15%  Similarity=0.177  Sum_probs=72.5

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC--eeeEE
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG--KPIRV  108 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g--~~l~v  108 (305)
                      .....+|||+||+..+|+++|+++|++||.|.+|.+..+.    ++|||||+|.+.++|++|++.|||..|.|  +.|+|
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V  118 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  118 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEE
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEE
Confidence            3445689999999999999999999999999999996542    57999999999999999999999999966  99999


Q ss_pred             eeCCCcc
Q psy3016         109 NKASSHQ  115 (305)
Q Consensus       109 ~~~~~~~  115 (305)
                      +++..+.
T Consensus       119 ~~Ak~~~  125 (164)
T 1sjr_A          119 DFSKLTS  125 (164)
T ss_dssp             EECSSSS
T ss_pred             EEecCCc
Confidence            9998754

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=3.5e-16  Score=120.28  Aligned_cols=81  Identities=21%  Similarity=0.299  Sum_probs=71.1

Q ss_pred             cCCCCceEEE--cCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee-----C
Q psy3016          30 SGDGDATIYV--GGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL-----Y  102 (305)
Q Consensus        30 ~~~~~~~l~V--~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~-----~  102 (305)
                      .....++|||  |||+..+|+++|+++|++||.|..|.++.+      +|||||+|.+.++|++|++.|||..+     .
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~   94 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   94 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCC
Confidence            3345688999  889999999999999999999999988643      59999999999999999999999988     6


Q ss_pred             CeeeEEeeCCCccc
Q psy3016         103 GKPIRVNKASSHQK  116 (305)
Q Consensus       103 g~~l~v~~~~~~~~  116 (305)
                      |+.|.|.++.....
T Consensus        95 g~~l~v~~a~~~p~  108 (114)
T 2cq2_A           95 KITLYLNFVEKVQW  108 (114)
T ss_dssp             EEECEEEEESCCCC
T ss_pred             CcEEEEEecccCcc
Confidence            89999998875443

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=3.5e-16  Score=118.14  Aligned_cols=85  Identities=25%  Similarity=0.420  Sum_probs=75.7

Q ss_pred             cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      .....++|||+||+..+++++|+++|+.|+.+                                          .++.+.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~------------------------------------------~~~~~~   48 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSVRA------------------------------------------RIVTDR   48 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCSEE------------------------------------------EEEECS
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCeEE------------------------------------------EEEecC
Confidence            34457899999999999999999999988654                                          457777


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .++.++|||||+|.+.++|.+|+..||+..|.|+.|+|.|++.+...
T Consensus        49 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2fc8_A           49 ETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG   95 (102)
T ss_dssp             SSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCSS
T ss_pred             CCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCCC
Confidence            78999999999999999999999999999999999999999877654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=3.8e-16  Score=120.59  Aligned_cols=80  Identities=25%  Similarity=0.405  Sum_probs=70.0

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCC---CCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVT---QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~---~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      .....++|||+|||.++|+++|+++|++||.|. +.++.+..+   |+++|||||+|.+.++|++|++.|+  .++|+.+
T Consensus         4 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~   80 (114)
T 2dnl_A            4 GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLY   80 (114)
T ss_dssp             SSSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEE
Confidence            345678999999999999999999999999999 888888766   7899999999999999999999884  4778877


Q ss_pred             EEeeCC
Q psy3016         107 RVNKAS  112 (305)
Q Consensus       107 ~v~~~~  112 (305)
                      .+..+.
T Consensus        81 ~~~~~~   86 (114)
T 2dnl_A           81 LCVSSP   86 (114)
T ss_dssp             EEECCS
T ss_pred             EeccCC
Confidence            776544

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.65  E-value=6.9e-16  Score=121.30  Aligned_cols=80  Identities=14%  Similarity=0.215  Sum_probs=71.5

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceE-EEEEEcCHHHHHHHHHHhcCceeCC--eeeE
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGY-GFIEFMGEEDADYAIKIMNMIKLYG--KPIR  107 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~-afV~f~~~e~A~~Ai~~l~g~~~~g--~~l~  107 (305)
                      ...-.+|||+||++.+|+++|+++|++||.|.+|++..+     ++|| |||+|.+.++|.+|++.|||..|.|  +.|+
T Consensus        25 ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~Lr   99 (130)
T 3zzy_A           25 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR   99 (130)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEE
T ss_pred             CCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEE
Confidence            344557889999999999999999999999999998764     3577 9999999999999999999999998  8999


Q ss_pred             EeeCCCcc
Q psy3016         108 VNKASSHQ  115 (305)
Q Consensus       108 v~~~~~~~  115 (305)
                      |++++...
T Consensus       100 I~~ak~~~  107 (130)
T 3zzy_A          100 IDFSKLTS  107 (130)
T ss_dssp             EEECSCSS
T ss_pred             EEecCCCc
Confidence            99998654

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.65  E-value=2.4e-16  Score=117.41  Aligned_cols=81  Identities=31%  Similarity=0.580  Sum_probs=74.4

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||..+++++|+++|+.||.|..+                                       .++.|.. 
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~-   53 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKV---------------------------------------TICKDRE-   53 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECTT-
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEECCC-
Confidence            346899999999999999999999999999877                                       6677765 


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      +.++|||||+|.+.++|.+|+..||+..+.|+.|+|.|++.
T Consensus        54 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           54 GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            89999999999999999999999999999999999999853

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=2.9e-16  Score=121.50  Aligned_cols=84  Identities=24%  Similarity=0.386  Sum_probs=76.7

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+|+++|+++|+.||.|..+                                       .++.+..
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~   54 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEA---------------------------------------VVITDRQ   54 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEE---------------------------------------EESCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEE---------------------------------------EEEEcCC
Confidence            3456899999999999999999999999999877                                       6788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +++++|||||+|.+.++|.+|+..+|+ .|.|+.|+|.|+....
T Consensus        55 ~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~~   97 (116)
T 2cqd_A           55 TGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGA   97 (116)
T ss_dssp             SCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTC
T ss_pred             CCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcccCC
Confidence            899999999999999999999999998 8999999999986543

>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=99.65  E-value=1.3e-16  Score=120.81  Aligned_cols=84  Identities=26%  Similarity=0.497  Sum_probs=77.3

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+..+++++|+++|+.||.|..+                                       .++.+..+|
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~---------------------------------------~i~~~~~~g   47 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSF---------------------------------------RLVYDRETG   47 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEE---------------------------------------EEEEETTTT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEE---------------------------------------EEEeCCCCC
Confidence            35789999999999999999999999999877                                       678888889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..
T Consensus        48 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   90 (104)
T 1p1t_A           48 KPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKN   90 (104)
T ss_dssp             EEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTTH
T ss_pred             ccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCccc
Confidence            9999999999999999999999999999999999999876543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.65  E-value=1.5e-16  Score=129.87  Aligned_cols=83  Identities=18%  Similarity=0.328  Sum_probs=76.2

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcC--cccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFG--VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ..++|||+||+.++|+++|+++|+.||  .|..+                                       .++.|..
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v---------------------------------------~i~~d~~   94 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL---------------------------------------KFAENRA   94 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEE---------------------------------------EEEECTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEE---------------------------------------EEEecCC
Confidence            357899999999999999999999999  88776                                       7889989


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +|+++|||||+|.+.++|.+|+..|||..|+|+.|+|.++..+.
T Consensus        95 tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~~  138 (156)
T 3n9u_C           95 NGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQN  138 (156)
T ss_dssp             TCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCHHH
T ss_pred             CCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCCCc
Confidence            99999999999999999999999999999999999999997653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.65  E-value=1.8e-16  Score=112.87  Aligned_cols=75  Identities=23%  Similarity=0.413  Sum_probs=70.6

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      +|||+|||.++++++|+++|+.||.|..+                                       .++.+..++.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~~~~~   41 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDA---------------------------------------MLMFDKTTNRHR   41 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEE---------------------------------------CCCBCSSSTTSC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEecCCCCCcC
Confidence            48999999999999999999999999877                                       778888889999


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      |||||+|.+.++|.+|+. +|+..++|+.|+|.+|
T Consensus        42 g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           42 GFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             BEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             cEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            999999999999999998 9999999999999875

>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=99.65  E-value=1.3e-16  Score=130.61  Aligned_cols=81  Identities=22%  Similarity=0.480  Sum_probs=76.9

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||+|||..+|+++|+++|+.||.|..++++.+..+|.++|||||+|.+.++|.+|++ +++..+.|+.|.|.++.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            45699999999999999999999999999999999998889999999999999999999998 89999999999999987


Q ss_pred             Cc
Q psy3016         113 SH  114 (305)
Q Consensus       113 ~~  114 (305)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.65  E-value=7e-16  Score=113.82  Aligned_cols=78  Identities=19%  Similarity=0.436  Sum_probs=63.0

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCce--eCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIK--LYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~--~~g~~l~  107 (305)
                      ......+|||+|||.++|+++|+++|++||.|.+|+++.+     ++|||||+|.+.++|++    +++..  +.|+.|.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~   77 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVH   77 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEE
Confidence            4556789999999999999999999999999999999874     78999999999999983    45544  5599999


Q ss_pred             EeeCCCccc
Q psy3016         108 VNKASSHQK  116 (305)
Q Consensus       108 v~~~~~~~~  116 (305)
                      |.++.++..
T Consensus        78 v~~a~~k~~   86 (89)
T 3d2w_A           78 ISNAEPKHN   86 (89)
T ss_dssp             EEECC----
T ss_pred             EEEcCCCCc
Confidence            999886543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.64  E-value=7.2e-16  Score=131.45  Aligned_cols=85  Identities=28%  Similarity=0.488  Sum_probs=80.3

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ....++|||+|||..+|+++|+++|+.||.|..|+++.+..++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
T Consensus       122 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~  201 (216)
T 2qfj_A          122 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGK  201 (216)
T ss_dssp             HTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEE
T ss_pred             cCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEE
Confidence            34568999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             CCCcc
Q psy3016         111 ASSHQ  115 (305)
Q Consensus       111 ~~~~~  115 (305)
                      +....
T Consensus       202 a~~~~  206 (216)
T 2qfj_A          202 AVTPP  206 (216)
T ss_dssp             CSSCS
T ss_pred             ecCCC
Confidence            88764

>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=99.64  E-value=2e-16  Score=116.33  Aligned_cols=80  Identities=26%  Similarity=0.434  Sum_probs=74.6

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||.++++++|+++|+.||.|..+                                       .++.+..++.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~~~   46 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRV---------------------------------------TILCDKFSGH   46 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEE---------------------------------------EEEESCSSSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEE---------------------------------------EEEecCCCCC
Confidence            4789999999999999999999999999877                                       6788888899


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      ++|||||+|.+.++|.+|+ .|||..+.|+.|+|.+++.+
T Consensus        47 ~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A           47 PKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             CCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTT
T ss_pred             cceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCC
Confidence            9999999999999999999 89999999999999998653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=6.7e-16  Score=116.41  Aligned_cols=82  Identities=24%  Similarity=0.422  Sum_probs=73.2

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+|+++|+++|+.||.|.                                          ++.+ .
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~------------------------------------------~~~~-~   48 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFIK------------------------------------------VPQN-Q   48 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEEE------------------------------------------CCBC-S
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEE------------------------------------------EEEC-C
Confidence            34568999999999999999999999999883                                          3555 5


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +++++|||||+|.+.++|.+|+..||+..|.|+.|+|.|+..+..
T Consensus        49 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (101)
T 2fc9_A           49 NGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGS   93 (101)
T ss_dssp             SSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCC
T ss_pred             CCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCC
Confidence            688999999999999999999999999999999999999977643

>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=99.64  E-value=3.9e-16  Score=118.87  Aligned_cols=81  Identities=21%  Similarity=0.411  Sum_probs=75.1

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+|+++|+++|+.||.|..+                                       .++.+. 
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~-   65 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKA---------------------------------------AVHYDR-   65 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------EEEECT-
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEECC-
Confidence            3456899999999999999999999999999877                                       678887 


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      ++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+.
T Consensus        66 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           66 SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            89999999999999999999999999999999999999984

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.64  E-value=6.4e-16  Score=146.05  Aligned_cols=86  Identities=26%  Similarity=0.421  Sum_probs=80.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|.++|+.||.|..|.|+.+..++.++|||||+|.+.++|.+||+.|||..|.|+.|.|.
T Consensus        98 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~  177 (437)
T 3pgw_S           98 QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  177 (437)
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      ++....
T Consensus       178 ~a~~~~  183 (437)
T 3pgw_S          178 VERGRT  183 (437)
T ss_pred             EeCCCC
Confidence            988643

>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=99.64  E-value=1.1e-15  Score=124.81  Aligned_cols=81  Identities=35%  Similarity=0.462  Sum_probs=75.1

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee--eEE
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP--IRV  108 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~--l~v  108 (305)
                      ....++|||+|||..+|+++|+++|+.||.|..++++.+..+|.++|||||+|.+.++|.+|++.|||..+.|+.  |+|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEE
Confidence            345679999999999999999999999999999999999888999999999999999999999999999999975  888


Q ss_pred             eeC
Q psy3016         109 NKA  111 (305)
Q Consensus       109 ~~~  111 (305)
                      .||
T Consensus       165 ~~A  167 (167)
T 1fxl_A          165 KFA  167 (167)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            775

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=8.2e-16  Score=118.44  Aligned_cols=82  Identities=29%  Similarity=0.546  Sum_probs=75.0

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+++++|+++|..||.|..+                                       .++.+. +
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~---------------------------------------~i~~~~-~   52 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRA---------------------------------------DILEDK-D   52 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEE---------------------------------------EEEECT-T
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEECC-C
Confidence            346899999999999999999999999999876                                       667775 5


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +.++|||||+|.+.++|.+|+..||+..+.|+.|+|.|+...
T Consensus        53 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   94 (114)
T 2do0_A           53 GKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERA   94 (114)
T ss_dssp             CSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCC
T ss_pred             CCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccC
Confidence            899999999999999999999999999999999999998654

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=2.6e-16  Score=121.43  Aligned_cols=82  Identities=26%  Similarity=0.422  Sum_probs=76.1

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+..+++++|+++|+.||.|..+                                       .++.|..++
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~g   64 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDV---------------------------------------RIISDRNSR   64 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEE---------------------------------------EECCSCCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEE---------------------------------------EEEecCCCC
Confidence            35789999999999999999999999999877                                       678888889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .++|||||+|.+.++|.+|+ .||+..|.|+.|+|.|+..+.
T Consensus        65 ~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~  105 (114)
T 2cq4_A           65 RSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEK  105 (114)
T ss_dssp             SCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHHHH
T ss_pred             ccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCCCc
Confidence            99999999999999999999 999999999999999987654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.64  E-value=1.8e-16  Score=115.28  Aligned_cols=75  Identities=17%  Similarity=0.244  Sum_probs=67.7

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      +.-|||+||+..+|+++|+++|..||.|..+                                       .+..      
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~---------------------------------------~l~~------   41 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSF---------------------------------------HPYL------   41 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEE---------------------------------------EEET------
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEE---------------------------------------EEcC------
Confidence            4569999999999999999999999999976                                       2222      


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      ++|||||+|.+.++|.+|+++||+..+.|++|+|.+|.+.
T Consensus        42 ~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~e~   81 (89)
T 2wbr_A           42 NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSEN   81 (89)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCCHH
T ss_pred             CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECCHH
Confidence            6999999999999999999999999999999999999543

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=6.1e-16  Score=115.67  Aligned_cols=80  Identities=20%  Similarity=0.315  Sum_probs=72.5

Q ss_pred             ccccccccCCCchhcHHHHH----HHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         120 VGANIFIGNLDPEVDEKLLY----DTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      ..++|||+||+..+++++|+    ++|+.||.|..+                                       .++.|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v---------------------------------------~i~~~   48 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSV---------------------------------------ELSPH   48 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEE---------------------------------------EECSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEE---------------------------------------EEEeC
Confidence            35789999999999999999    999999999877                                       66777


Q ss_pred             CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         196 PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       196 ~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      ..+   +|||||+|.+.++|.+|+..|||..+.|+.|+|.+++...
T Consensus        49 ~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   91 (96)
T 2dgx_A           49 TDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGAS   91 (96)
T ss_dssp             CST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCSS
T ss_pred             CCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            654   8899999999999999999999999999999999996654

>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=99.64  E-value=8.4e-16  Score=117.53  Aligned_cols=83  Identities=18%  Similarity=0.382  Sum_probs=73.0

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+.++|+++|+++|+.||.|..+                                       .+..   +
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~---------------------------------------~i~~---~   57 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI---------------------------------------DLKN---R   57 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EECC---S
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEE---C
Confidence            346899999999999999999999999999876                                       3333   3


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      +.++|||||+|.+.++|.+|++.||+..|.|+.|+|.|++.+...
T Consensus        58 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~  102 (109)
T 1x4a_A           58 RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT  102 (109)
T ss_dssp             SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCCC
T ss_pred             CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCCCC
Confidence            568999999999999999999999999999999999999776543

>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=99.63  E-value=3.3e-16  Score=121.22  Aligned_cols=76  Identities=25%  Similarity=0.403  Sum_probs=66.6

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee-----e
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP-----I  106 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~-----l  106 (305)
                      ...++|||+|||.++|+++|+++|+.||.|..|.|+.+       |||||+|.+.++|++||+.||+..|.|+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            45689999999999999999999999999999999765       89999999999999999999999999998     6


Q ss_pred             EEeeCCCc
Q psy3016         107 RVNKASSH  114 (305)
Q Consensus       107 ~v~~~~~~  114 (305)
                      +|......
T Consensus        87 ~v~~~~~~   94 (115)
T 3beg_B           87 RVKVDGPR   94 (115)
T ss_dssp             EEEECC--
T ss_pred             EeccCCCC
Confidence            66665543

>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=99.63  E-value=5.4e-16  Score=113.61  Aligned_cols=80  Identities=30%  Similarity=0.502  Sum_probs=73.2

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+|||.++++++|+++|+.||.|..+                                       .++.+..
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~   48 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDC---------------------------------------TIKMDPN   48 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEE---------------------------------------EEEECTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEE---------------------------------------EEeecCC
Confidence            3456899999999999999999999999999887                                       6788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      ++.++|||||+|.+.++|.+|+. +++..+.|+.|.|.+|
T Consensus        49 ~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           49 TGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             TCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            89999999999999999999996 5888999999999875

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2.7e-16  Score=119.17  Aligned_cols=81  Identities=22%  Similarity=0.280  Sum_probs=70.8

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||+++|+++|+++|++||.|..+                                       .++.+   
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v---------------------------------------~i~~~---   51 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNL---------------------------------------LMLKG---   51 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEE---------------------------------------EEETT---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEcC---
Confidence            346889999999999999999999999999887                                       44543   


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcC--eeecCeeeEEEEeeecCCcC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHG--QYLCNRPISVSYAFKKDSKG  244 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~--~~~~g~~l~v~~a~~~~~~~  244 (305)
                         +|||||+|++.++|.+|+..|++  ..+.|++|+|.|++.+....
T Consensus        52 ---kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~~~   96 (105)
T 1sjq_A           52 ---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT   96 (105)
T ss_dssp             ---TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSCCC
T ss_pred             ---CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCCCc
Confidence               79999999999999999998864  78999999999998765543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=4.2e-16  Score=120.59  Aligned_cols=84  Identities=26%  Similarity=0.487  Sum_probs=77.6

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+..+|+++|+++|..||.|..+                                       .++.|..++
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~g   66 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDC---------------------------------------VVMRDPASK   66 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEE---------------------------------------EEECCTTTS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEECCCCC
Confidence            45889999999999999999999999999877                                       678888889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .++|||||+|.+.++|.+|+.. ++..|.|+.|+|.++..+...
T Consensus        67 ~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~~~  109 (116)
T 1x4b_A           67 RSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREES  109 (116)
T ss_dssp             SCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSCCCC
T ss_pred             CcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCCccC
Confidence            9999999999999999999998 999999999999999877554

>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=99.63  E-value=4.8e-16  Score=119.47  Aligned_cols=84  Identities=17%  Similarity=0.253  Sum_probs=74.7

Q ss_pred             ccccccccCCCchhcHHHHH---HHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLY---DTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~---~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      ..++|||+|||..+++++|.   ++|+.||.|..+                                       .++.+.
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v---------------------------------------~i~~~~   54 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKV---------------------------------------VINNST   54 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEE---------------------------------------EEECCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEE---------------------------------------EEecCC
Confidence            46789999999999999999   999999999877                                       556665


Q ss_pred             CCC---CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         197 DTG---NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       197 ~~~---~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++   .++|||||+|.+.++|.+|+..|||..++|+.|+|.|+..+..
T Consensus        55 ~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~~  103 (111)
T 2cpi_A           55 SYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC  103 (111)
T ss_dssp             SCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCSC
T ss_pred             CcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEecccccc
Confidence            543   5669999999999999999999999999999999999987753

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2.8e-16  Score=121.33  Aligned_cols=87  Identities=22%  Similarity=0.348  Sum_probs=75.1

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+|+++|+++|+.||.|..+                                       .+..+..+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~---------------------------------------~~~~~~~~   63 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGP---------------------------------------PIQFRMMT   63 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSS---------------------------------------CCEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccce---------------------------------------EEEEEcCC
Confidence            346899999999999999999999999999654                                       22233336


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCcC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKG  244 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~~  244 (305)
                      +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..+.
T Consensus        64 g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~  109 (115)
T 2cpx_A           64 GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRS  109 (115)
T ss_dssp             SSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCCC
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCCCCC
Confidence            8899999999999999999999999999999999999998776543

>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=99.63  E-value=6e-16  Score=113.20  Aligned_cols=72  Identities=24%  Similarity=0.574  Sum_probs=67.1

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccC----C-------CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCce
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQS----G-------PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIK  100 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~  100 (305)
                      ...++|||+|||.++|+++|+++|+.|    |       .|.++++..+      +|||||+|.+.++|.+|+ .||+..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            457899999999999999999999999    8       9999999754      599999999999999999 899999


Q ss_pred             eCCeeeEEee
Q psy3016         101 LYGKPIRVNK  110 (305)
Q Consensus       101 ~~g~~l~v~~  110 (305)
                      +.|+.|+|++
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999975

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=1.1e-15  Score=115.59  Aligned_cols=85  Identities=24%  Similarity=0.416  Sum_probs=76.7

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+++++|+++|+.||.|..+                                       .++.|..
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~   52 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMV---------------------------------------QVKKDLK   52 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECSS
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEE---------------------------------------EEEecCC
Confidence            3456889999999999999999999999999877                                       6788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ++.++|||||+|.+.++|.+|+.  ++..++|+.|+|.|+..+...
T Consensus        53 ~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cqg_A           53 TGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPNSKQSQ   96 (103)
T ss_dssp             SCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCCTTCCC
T ss_pred             CCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEecCCCCcC
Confidence            89999999999999999999999  578999999999999876543

>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=99.63  E-value=7e-16  Score=125.67  Aligned_cols=85  Identities=22%  Similarity=0.354  Sum_probs=78.7

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+|+++|.++|+.||.|..+                                       .++.+..+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~   77 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKI---------------------------------------IMGLDKMK   77 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECTTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEecCCC
Confidence            356899999999999999999999999999877                                       67888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +.++|||||+|.+.++|.+|+..||+..|.|+.|+|.|+.....
T Consensus        78 ~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  121 (156)
T 1h2v_Z           78 KTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE  121 (156)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCT
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            99999999999999999999999999999999999999976544

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.63  E-value=5.5e-16  Score=118.78  Aligned_cols=84  Identities=27%  Similarity=0.487  Sum_probs=75.0

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+.++|+++|+++|+.||.|..+                                       .++.|..+
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v---------------------------------------~i~~~~~t   63 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKEC---------------------------------------LVMRDPLT   63 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEE---------------------------------------EECCCTTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEE---------------------------------------EEEECCCC
Confidence            346899999999999999999999999999887                                       67888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      |.++|||||+|.+.++|.+|+..+ +..++|+.|+|.++..+..
T Consensus        64 g~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a~~~~~  106 (109)
T 2rs2_A           64 KRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVAFPRRA  106 (109)
T ss_dssp             CCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEECCCCCC
T ss_pred             CCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEccCCCC
Confidence            999999999999999999999976 5999999999999976643

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.63  E-value=5.4e-16  Score=114.76  Aligned_cols=83  Identities=28%  Similarity=0.427  Sum_probs=74.5

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||..+++++|+++|+.||.|..+                                       .++.+  +
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~---------------------------------------~i~~~--~   44 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYA---------------------------------------DIKME--N   44 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------EEEES--S
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEcc--C
Confidence            346789999999999999999999999999876                                       44543  6


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +.++|||||+|.+.++|.+|+..||+..+.|+.|+|.|++....
T Consensus        45 g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   88 (92)
T 2dgv_A           45 GKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASG   88 (92)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCSS
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCCC
Confidence            88999999999999999999999999999999999999976643

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.63  E-value=9.1e-16  Score=120.14  Aligned_cols=83  Identities=22%  Similarity=0.382  Sum_probs=76.4

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+++++|+++|+.||.|..+                                       .++.+. +
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v---------------------------------------~i~~~~-~   72 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA---------------------------------------AVDYDR-S   72 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEE---------------------------------------EEECCS-S
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEE---------------------------------------EEEECC-C
Confidence            456899999999999999999999999999877                                       677886 7


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      |.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+....
T Consensus        73 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  115 (124)
T 2kt5_A           73 GRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI  115 (124)
T ss_dssp             SSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCTT
T ss_pred             CCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCC
Confidence            9999999999999999999999999999999999999996553

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=3e-16  Score=119.03  Aligned_cols=79  Identities=14%  Similarity=0.240  Sum_probs=73.6

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||.++|+++|.++|+.||.|..+                                       .++.|.. +
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v---------------------------------------~i~~d~~-g   49 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNI---------------------------------------QMRRTLH-K   49 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEE---------------------------------------EEECCCT-T
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEE---------------------------------------EEEECCC-C
Confidence            35789999999999999999999999999877                                       6788877 9


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      .++|||||+|.+.++|.+|+. +++..+.|+.|.|.++..
T Consensus        50 ~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           50 AFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             SCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             CCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            999999999999999999999 999999999999999765

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.62  E-value=1.8e-16  Score=119.57  Aligned_cols=82  Identities=23%  Similarity=0.427  Sum_probs=73.3

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC-C
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP-D  197 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~-~  197 (305)
                      ...++|||+||+.++++++|+++|+.|| |..+                                       .++.+. .
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v---------------------------------------~i~~~~~~   56 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAV---------------------------------------RLPREPSN   56 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEE---------------------------------------ECSCCTTT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEE---------------------------------------EEEecCCc
Confidence            3468999999999999999999999999 8876                                       677777 5


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +|+++|||||+|.+.++|.+|+ .|||..+.|+.|+|.++..+.
T Consensus        57 ~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~~   99 (100)
T 2j76_E           57 PERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ   99 (100)
T ss_dssp             TCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECCCSC
T ss_pred             CCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEeccCCC
Confidence            8999999999999999999999 899999999999999997653

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=2.8e-16  Score=112.25  Aligned_cols=76  Identities=28%  Similarity=0.475  Sum_probs=71.4

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ++|||+|||.++++++|+++|+.||.|..+                                       .++.+..++.+
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v---------------------------------------~i~~~~~~~~~   41 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKEC---------------------------------------LVMRDPLTKRS   41 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCE---------------------------------------EEECCCCSSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEecCCCCCCc
Confidence            479999999999999999999999999876                                       67888888999


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      +|||||+|.+.++|.+|+..++ ..+.|+.|+|.++
T Consensus        42 ~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A           42 RGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             SSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            9999999999999999999999 9999999999987

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.62  E-value=4.4e-16  Score=121.87  Aligned_cols=83  Identities=28%  Similarity=0.402  Sum_probs=76.2

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+..+|+++|+++|+.||.|..+                                       .++.|..++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~~   75 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRI---------------------------------------TILCDKFSG   75 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEE---------------------------------------EEEEECTTS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEecCCCC
Confidence            35789999999999999999999999999877                                       678887889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++|||||+|.+.++|.+|+ .|||..|.|+.|+|.|++....
T Consensus        76 ~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~  117 (124)
T 2jwn_A           76 HPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMP  117 (124)
T ss_dssp             SCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCCCS
T ss_pred             CcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCCCC
Confidence            99999999999999999999 7999999999999999876543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.2e-15  Score=112.73  Aligned_cols=80  Identities=18%  Similarity=0.304  Sum_probs=73.5

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||.++++++|+++|+.| .|..+                                       .++.+ .+|
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v---------------------------------------~i~~~-~~g   47 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAI---------------------------------------RIVRN-AHG   47 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEE---------------------------------------EEEEC-TTS
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEE---------------------------------------EEEEC-CCC
Confidence            46789999999999999999999999 88766                                       67888 779


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .++|||||+|.+.++|.+|+. ||+..+.|+.|.|.++..+.
T Consensus        48 ~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~~   88 (91)
T 2dgw_A           48 NKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSGP   88 (91)
T ss_dssp             CEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSCC
T ss_pred             CCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcCC
Confidence            999999999999999999999 99999999999999997663

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=8.7e-16  Score=117.64  Aligned_cols=82  Identities=26%  Similarity=0.435  Sum_probs=73.6

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+.++++++|+++|+.||.|..+                                       .++.|. 
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~~~-   65 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV---------------------------------------EIIFNE-   65 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCE---------------------------------------EECCBT-
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEE---------------------------------------EEEECC-
Confidence            3456899999999999999999999999999876                                       556663 


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                       +.++|||||+|.+.++|.+|+..|||..++|+.|+|.++..+
T Consensus        66 -~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           66 -RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             -TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             -CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence             458999999999999999999999999999999999998765

>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=99.62  E-value=1.4e-16  Score=127.37  Aligned_cols=123  Identities=17%  Similarity=0.192  Sum_probs=72.9

Q ss_pred             eEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC-ccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhh
Q psy3016          77 GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS-HQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIM  155 (305)
Q Consensus        77 g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~-~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~  155 (305)
                      ++||.+|...+.+..++.++... ..|....-..... ........++|||+|||.++|+++|+++|+.|| +..+    
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v----   75 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRV----   75 (139)
T ss_dssp             --------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEE----
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEE----
Confidence            67888888888887777754332 2332221111111 112233467899999999999999999999999 5555    


Q ss_pred             hhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEE
Q psy3016         156 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS  235 (305)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~  235 (305)
                                                         .++.|.. ++++|||||+|++.++|.+|| .+|+..+.|+.|+|.
T Consensus        76 -----------------------------------~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~  118 (139)
T 2hgn_A           76 -----------------------------------HIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELF  118 (139)
T ss_dssp             -----------------------------------ECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCE
T ss_pred             -----------------------------------EEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEE
Confidence                                               6788865 999999999999999999999 789999999999999


Q ss_pred             EeeecCC
Q psy3016         236 YAFKKDS  242 (305)
Q Consensus       236 ~a~~~~~  242 (305)
                      .+.....
T Consensus       119 ~a~~~~~  125 (139)
T 2hgn_A          119 LNSTTGA  125 (139)
T ss_dssp             ECCCSCC
T ss_pred             ECCCCCC
Confidence            9876654

>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=99.62  E-value=6e-16  Score=116.97  Aligned_cols=80  Identities=21%  Similarity=0.292  Sum_probs=69.5

Q ss_pred             cccccccccccCCCc-hhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         117 NLDVGANIFIGNLDP-EVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      ..+..++|||+|||. .+|+++|+++|++||.|..+                                       .++.+
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v---------------------------------------~i~~~   51 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNH---------------------------------------LILNK   51 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEE---------------------------------------EECSS
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEE---------------------------------------EEEcC
Confidence            344678999999999 99999999999999999987                                       34443


Q ss_pred             CCCCCccceEEEEeCChHHHHHHHHHhcCe--eecCeeeEEEEeeecC
Q psy3016         196 PDTGNSKGFAFINYASFEASDASIDAMHGQ--YLCNRPISVSYAFKKD  241 (305)
Q Consensus       196 ~~~~~~~g~afV~f~~~~~A~~Al~~l~~~--~~~g~~l~v~~a~~~~  241 (305)
                            +|||||+|++.++|.+|+..||+.  .+.|++|+|.|++...
T Consensus        52 ------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~   93 (102)
T 1x4d_A           52 ------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   93 (102)
T ss_dssp             ------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             ------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCC
Confidence                  589999999999999999999864  5999999999997543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.62  E-value=1e-15  Score=122.12  Aligned_cols=80  Identities=35%  Similarity=0.556  Sum_probs=74.5

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||..+++++|+++|+.||.|..+                                       .++.|..+
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v---------------------------------------~i~~~~~~  101 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI---------------------------------------QIPLDYET  101 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------ECCCCTTT
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEeecCCC
Confidence            356899999999999999999999999999877                                       67888888


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      +.++|||||+|.+.++|.+|++.|||..+.|+.|+|.||
T Consensus       102 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A          102 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             CCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            999999999999999999999999999999999999985

>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=99.62  E-value=1e-16  Score=118.23  Aligned_cols=80  Identities=26%  Similarity=0.456  Sum_probs=72.3

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ++|||+||+.++++++|+++|+.||.|..+                                       .++.|..++.+
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~~~~   42 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNV---------------------------------------KLIYDRETKKP   42 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEE---------------------------------------EECCCSSSCCC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEEcCCCCCc
Confidence            479999999999999999999999999877                                       67888888999


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +|||||+|.+.+ |.+|+..|||..++|+.|+|.++....
T Consensus        43 ~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~   81 (90)
T 2ki2_A           43 KGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKK   81 (90)
T ss_dssp             CEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC----
T ss_pred             ceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            999999999999 999999999999999999999987654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=9.9e-17  Score=117.03  Aligned_cols=80  Identities=20%  Similarity=0.352  Sum_probs=74.1

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||..+++++|+++|+.||.|..+                                       .++.+..++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~---------------------------------------~i~~~~~~~   44 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVST---------------------------------------KAILDKTTN   44 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEE---------------------------------------EEECCSSSC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEecCCCC
Confidence            45789999999999999999999999999877                                       678888889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|+++++.
T Consensus        45 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           45 KCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             SCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            999999999999999999999999999999999888753

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.5e-15  Score=111.52  Aligned_cols=74  Identities=20%  Similarity=0.300  Sum_probs=66.0

Q ss_pred             CceEEEcCCCccccHHH----HHHHhccC-CCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          34 DATIYVGGLDDKVSETL----MWELFVQS-GPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~----L~~~F~~~-G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      .+.|||+|||.++++++    |+++|+.| |+|.+|       ++   |+|||.|.+.++|++|++.|+|..+.||.|+|
T Consensus         9 ~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v   78 (96)
T 2diu_A            9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIV   78 (96)
T ss_dssp             SEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             ceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEE
Confidence            34499999999999988    55899999 599998       23   99999999999999999999999999999999


Q ss_pred             eeCCCcccc
Q psy3016         109 NKASSHQKN  117 (305)
Q Consensus       109 ~~~~~~~~~  117 (305)
                      .++....+.
T Consensus        79 ~~A~~~sd~   87 (96)
T 2diu_A           79 SFTPKNREL   87 (96)
T ss_dssp             ESSCCSCCC
T ss_pred             EecCCCcce
Confidence            999876643

>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=99.62  E-value=1.3e-15  Score=115.07  Aligned_cols=82  Identities=24%  Similarity=0.274  Sum_probs=70.9

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+++++|+++|+.||.|..+                                       .++.+  
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v---------------------------------------~i~~~--   50 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNI---------------------------------------LMLKG--   50 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEE---------------------------------------EEETT--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEECC--
Confidence            3456899999999999999999999999999876                                       33433  


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhc--CeeecCeeeEEEEeeecCCcC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMH--GQYLCNRPISVSYAFKKDSKG  244 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~--~~~~~g~~l~v~~a~~~~~~~  244 (305)
                          +|||||+|++.++|.+|+..|+  +..+.|++|+|.|+..+..+.
T Consensus        51 ----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~~   95 (101)
T 2cq1_A           51 ----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKT   95 (101)
T ss_dssp             ----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSSCCC
T ss_pred             ----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcccCcC
Confidence                8999999999999999999874  678999999999998776554

>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=99.61  E-value=6.6e-16  Score=113.49  Aligned_cols=79  Identities=22%  Similarity=0.474  Sum_probs=67.7

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||..+|+++|+++|+.||.|.+|+++.+     ++|||||+|.+.++|++|+.  ....+.|+.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEec
Confidence            45789999999999999999999999999999999765     67999999999999986533  235668999999998


Q ss_pred             CCcccc
Q psy3016         112 SSHQKN  117 (305)
Q Consensus       112 ~~~~~~  117 (305)
                      .++...
T Consensus        76 ~~~~~~   81 (88)
T 1wf0_A           76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.61  E-value=8.3e-16  Score=118.69  Aligned_cols=82  Identities=16%  Similarity=0.166  Sum_probs=74.5

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcc-cchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVI-LQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ...++|||+|||.++|+++|+++|+.||.| ..+                                       .++.|. 
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v---------------------------------------~i~~d~-   52 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAV---------------------------------------HVLVDN-   52 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTE---------------------------------------EECCCT-
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeE---------------------------------------EEEECC-
Confidence            346889999999999999999999999999 655                                       678887 


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +++++|||||+|.+.++|.+|+.. |+..|.|+.|.|.++..+.
T Consensus        53 ~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~~~   95 (114)
T 2cpy_A           53 NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLED   95 (114)
T ss_dssp             TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEECHHH
T ss_pred             CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECCHHH
Confidence            899999999999999999999997 9999999999999997654

>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=99.61  E-value=3e-15  Score=123.58  Aligned_cols=96  Identities=18%  Similarity=0.239  Sum_probs=80.6

Q ss_pred             CCccceeecCccccccCcccccCCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEE
Q psy3016           3 LGREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIE   82 (305)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~   82 (305)
                      .|+.|.+..+.+...           ......++|||+|||..+|+++|+++|+.||.|..+     ..++.++|||||+
T Consensus        79 ~g~~l~v~~~~~~~~-----------~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~  142 (175)
T 1fje_B           79 FGNEIKLEKPKGRDS-----------KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIE  142 (175)
T ss_dssp             TTEEEEEECCCCSSC-----------STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEE
T ss_pred             CCeEEEEecCCCccc-----------cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEE
Confidence            366666666554321           223456899999999999999999999999988776     3467899999999


Q ss_pred             EcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          83 FMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        83 f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (305)
                      |.+.++|.+|++.|||..+.|+.|+|.++.++
T Consensus       143 f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          143 FKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             CSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             ECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            99999999999999999999999999998764

>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=99.61  E-value=9e-16  Score=117.27  Aligned_cols=84  Identities=19%  Similarity=0.323  Sum_probs=75.0

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCc-ccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcc-cCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGV-ILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIM-RDPD  197 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~-v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~-~d~~  197 (305)
                      ..++|||+||+..+|+++|+++|..||. |..+                                       .++ .|..
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v---------------------------------------~i~~~~~~   47 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDV---------------------------------------IVYASAAD   47 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEE---------------------------------------ECCSSSCT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEE---------------------------------------EEEccCCC
Confidence            3578999999999999999999999998 8876                                       455 7777


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhc--CeeecCeeeEEEEeeecCC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMH--GQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~--~~~~~g~~l~v~~a~~~~~  242 (305)
                      ++.++|||||+|.+.++|.+|+..||  +..+.|+.|+|.|+..+..
T Consensus        48 ~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~   94 (109)
T 2dis_A           48 KMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID   94 (109)
T ss_dssp             TTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCS
T ss_pred             CCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCC
Confidence            88999999999999999999999996  5899999999999976643

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.61  E-value=1e-15  Score=114.88  Aligned_cols=78  Identities=18%  Similarity=0.258  Sum_probs=68.6

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      .++++|||+|||.++|+++|+++|++||.|..+                                       .+++    
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v---------------------------------------~i~~----   55 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYV---------------------------------------VVMP----   55 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEET----
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEE---------------------------------------EEEc----
Confidence            457899999999999999999999999999876                                       3332    


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCee--ecCeeeEEEEeeecC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQY--LCNRPISVSYAFKKD  241 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~--~~g~~l~v~~a~~~~  241 (305)
                        .+|||||+|++.++|.+|+..|++..  +.|++|+|+|++.+.
T Consensus        56 --~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           56 --KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             --TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             --CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence              47999999999999999999999875  789999999997653

>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=99.61  E-value=6.2e-16  Score=123.13  Aligned_cols=82  Identities=13%  Similarity=0.169  Sum_probs=74.0

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCc---ccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGV---ILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      ...++|||+|||+++|+++|+++|+.||.   |..+                                       .+++|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v---------------------------------------~i~~d   82 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGV---------------------------------------HFIYT   82 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTE---------------------------------------EEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEE---------------------------------------EEEEC
Confidence            34678999999999999999999999999   6555                                       67888


Q ss_pred             CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         196 PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       196 ~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .. |+++|||||+|++.++|.+|+. +|+..++|+.|+|.++..++
T Consensus        83 ~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~~~e  126 (136)
T 2hgl_A           83 RE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRTE  126 (136)
T ss_dssp             SS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECCHHH
T ss_pred             CC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECChHH
Confidence            76 9999999999999999999999 99999999999999986543

>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=99.60  E-value=1.6e-15  Score=115.06  Aligned_cols=84  Identities=18%  Similarity=0.271  Sum_probs=74.8

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccc-hhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQ-TPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....+|||+|||.++|+++|+++|+.||.|.. +                                       .++.| .
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v---------------------------------------~i~~~-~   52 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGM---------------------------------------TLPVD-F   52 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEE---------------------------------------ECCBC-S
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeE---------------------------------------EEEEC-C
Confidence            45689999999999999999999999999875 4                                       45777 7


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      +++++|||||+|.+.++|.+|+.. |+..++|+.|.|.++..+...
T Consensus        53 ~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~~~~~   97 (104)
T 1wg5_A           53 QGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRAEVR   97 (104)
T ss_dssp             SSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECTTTSC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCHHHHH
Confidence            799999999999999999999997 999999999999998766543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.60  E-value=4.2e-16  Score=117.49  Aligned_cols=82  Identities=22%  Similarity=0.351  Sum_probs=74.0

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+.++|+++|+++|+.||.|..                                        .++.+..++
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~----------------------------------------~~~~~~~~g   55 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND----------------------------------------LAVVDVRTG   55 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT----------------------------------------CCCCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce----------------------------------------EEEecCCCC
Confidence            4679999999999999999999999999875                                        246676778


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++|||||+|.+.++|.+|+. |||..+.|+.|+|.++..+..
T Consensus        56 ~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~~~   97 (101)
T 1fj7_A           56 TNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDG   97 (101)
T ss_dssp             TTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSCCCC
T ss_pred             CcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCCCCC
Confidence            999999999999999999999 999999999999999976643

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.60  E-value=7.8e-16  Score=109.44  Aligned_cols=75  Identities=24%  Similarity=0.452  Sum_probs=70.0

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      +|||+|||.++++++|+++|+.||.|..+                                       .++.+..++.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~~~~~   41 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESI---------------------------------------ELPMDNKTNKRR   41 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEE---------------------------------------CCCCSCCCSSSC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEecCCCCCcC
Confidence            58999999999999999999999999877                                       678888889999


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      |||||+|.+.++|.+|+.. ++..+.|+.|+|.+|
T Consensus        42 g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           42 GFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            9999999999999999994 899999999999875

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.60  E-value=1.7e-15  Score=115.18  Aligned_cols=80  Identities=21%  Similarity=0.317  Sum_probs=72.0

Q ss_pred             ccccccccCCCchh------cHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcc
Q psy3016         120 VGANIFIGNLDPEV------DEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIM  193 (305)
Q Consensus       120 ~~~~l~v~nl~~~~------t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~  193 (305)
                      ..++|||+|||..+      |+++|+++|+.||.|..+                                       .++
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v---------------------------------------~i~   54 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITND---------------------------------------FYP   54 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEE---------------------------------------ECC
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEE---------------------------------------Eee
Confidence            36789999999999      889999999999999876                                       344


Q ss_pred             cCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCe-eeEEEEeeec
Q psy3016         194 RDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR-PISVSYAFKK  240 (305)
Q Consensus       194 ~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~-~l~v~~a~~~  240 (305)
                        ..+|.++|||||+|.+.++|.+|+..|||..+.|+ .|+|.++...
T Consensus        55 --~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~~  100 (105)
T 2nlw_A           55 --EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDF  100 (105)
T ss_dssp             --CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCCC
T ss_pred             --CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcchH
Confidence              36789999999999999999999999999999999 9999998654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.60  E-value=8.1e-15  Score=111.47  Aligned_cols=83  Identities=14%  Similarity=-0.019  Sum_probs=73.2

Q ss_pred             CCCCceEEEcCCCc-----cccHHHHHHHhccCCCeEEEEEcccCC-CCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe
Q psy3016          31 GDGDATIYVGGLDD-----KVSETLMWELFVQSGPVVNVHMPKDRV-TQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK  104 (305)
Q Consensus        31 ~~~~~~l~V~nLp~-----~~te~~L~~~F~~~G~i~~i~~~~~~~-~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~  104 (305)
                      ...+++|+|.||-.     .-++++|++.|++||.|.+|.|+.++. +++++|||||+|.+.++|.+|++.|||..+.||
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            34578999999963     237899999999999999999998864 368899999999999999999999999999999


Q ss_pred             eeEEeeCCC
Q psy3016         105 PIRVNKASS  113 (305)
Q Consensus       105 ~l~v~~~~~  113 (305)
                      .|.|.++..
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999864

>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=99.60  E-value=2e-15  Score=117.10  Aligned_cols=81  Identities=22%  Similarity=0.280  Sum_probs=71.0

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||+++|+++|+++|++||.|..+                                       .++.+   
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v---------------------------------------~i~~~---   66 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNL---------------------------------------LMLKG---   66 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEE---------------------------------------EEEGG---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEeCC---
Confidence            356889999999999999999999999999876                                       44443   


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcC--eeecCeeeEEEEeeecCCcC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHG--QYLCNRPISVSYAFKKDSKG  244 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~--~~~~g~~l~v~~a~~~~~~~  244 (305)
                         +|||||+|++.++|.+|+..|++  ..+.|++|+|.|++.+..+.
T Consensus        67 ---kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~~~  111 (119)
T 2ad9_A           67 ---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT  111 (119)
T ss_dssp             ---GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSCCC
T ss_pred             ---CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCCCc
Confidence               79999999999999999999884  68999999999998776543

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=9.9e-16  Score=120.02  Aligned_cols=82  Identities=23%  Similarity=0.350  Sum_probs=74.5

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...+|||+|||.++|+++|+++|+.||.|..+                                       .++.+..+|
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~---------------------------------------~~~~~~~~g   64 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDS---------------------------------------IYIAYGPNG   64 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTT---------------------------------------CEEEECTTS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccce---------------------------------------EEEEECCCC
Confidence            45799999999999999999999999999765                                       456666789


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +++|||||+|.+.++|.+||. ||+..|+|+.|.|.++..+.
T Consensus        65 ~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~~~  105 (124)
T 1wel_A           65 KATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKG  105 (124)
T ss_dssp             SEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECHHH
T ss_pred             CCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCHHH
Confidence            999999999999999999999 99999999999999997654

>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=99.59  E-value=1.7e-15  Score=116.68  Aligned_cols=82  Identities=28%  Similarity=0.541  Sum_probs=74.7

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||..+++++|+++|+.||.|..+                                       .++.|. +
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~---------------------------------------~i~~~~-~   62 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVIST---------------------------------------RILRDS-S   62 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEE---------------------------------------EEEECS-S
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEECC-C
Confidence            346789999999999999999999999999877                                       678886 7


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeee--------cCeeeEEEEeeec
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYL--------CNRPISVSYAFKK  240 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~--------~g~~l~v~~a~~~  240 (305)
                      +.++|||||+|.+.++|.+|+..|||..+        .+++|.|.|+.++
T Consensus        63 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           63 GTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             SCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCCS
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCCC
Confidence            99999999999999999999999999999        6888999998754

>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=99.59  E-value=3.1e-15  Score=114.30  Aligned_cols=78  Identities=14%  Similarity=0.205  Sum_probs=70.3

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||.++|+++|+++|+.||.|..+                                       .++.|    
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~---------------------------------------~i~~~----   50 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYA---------------------------------------DVYRD----   50 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEE---------------------------------------EEETT----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEE---------------------------------------EEecC----
Confidence            46889999999999999999999999999876                                       44444    


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecC-----eeeEEEEeeecCCc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCN-----RPISVSYAFKKDSK  243 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g-----~~l~v~~a~~~~~~  243 (305)
                         |||||+|.+.++|.+||+.||+..|.|     +.|+|.++..+...
T Consensus        51 ---g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~~~   96 (108)
T 1x4c_A           51 ---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPS   96 (108)
T ss_dssp             ---TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCSCC
T ss_pred             ---CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCCCC
Confidence               899999999999999999999999999     99999999876543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.37  E-value=9.7e-17  Score=124.26  Aligned_cols=93  Identities=27%  Similarity=0.411  Sum_probs=78.1

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+..+++++|+++|+.||.|..+..                               .......++.|..++
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~-------------------------------~~~~~v~i~~~~~~g   54 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKK-------------------------------TGQPMINLYTDRETG   54 (116)
Confidence            4678999999999999999999999999976200                               000001678888889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|+|.++..+...
T Consensus        55 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           55 KLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF   98 (116)
Confidence            99999999999999999999999999999999999999776543

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.59  E-value=2.6e-15  Score=115.04  Aligned_cols=94  Identities=21%  Similarity=0.451  Sum_probs=77.7

Q ss_pred             CCeeeEEeeCCCccc--cccccccccccCCCch-hcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCC
Q psy3016         102 YGKPIRVNKASSHQK--NLDVGANIFIGNLDPE-VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD  178 (305)
Q Consensus       102 ~g~~l~v~~~~~~~~--~~~~~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  178 (305)
                      .|..+.+..+.....  .....++|||+||+.. +++++|+++|+.||.|..+                           
T Consensus         6 ~g~~~~~~~s~~~~~~~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v---------------------------   58 (110)
T 1wf1_A            6 SGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGC---------------------------   58 (110)
T ss_dssp             CSCCCCCCCCCSCCSCCCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEE---------------------------
T ss_pred             CCcccccccCCCCCCCCCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEE---------------------------
Confidence            456666666543322  2234579999999999 9999999999999999876                           


Q ss_pred             CcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       179 ~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                                  .+        ++|||||+|.+.++|.+|+..||+..++|+.|+|.|+.....
T Consensus        59 ------------~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~  102 (110)
T 1wf1_A           59 ------------SV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKP  102 (110)
T ss_dssp             ------------EE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCCS
T ss_pred             ------------EE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCCC
Confidence                        22        589999999999999999999999999999999999975543

>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=99.58  E-value=4.7e-15  Score=121.97  Aligned_cols=80  Identities=21%  Similarity=0.352  Sum_probs=73.6

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC---CeeeEE
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY---GKPIRV  108 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~---g~~l~v  108 (305)
                      ...++|||+|||..+|+++|+++|+.||.|.++.++.+. +|.++|||||+|.+.++|.+|++.|||..+.   |+.|.|
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V  171 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV  171 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEE
Confidence            356799999999999999999999999999999999986 5889999999999999999999999998776   499999


Q ss_pred             eeCC
Q psy3016         109 NKAS  112 (305)
Q Consensus       109 ~~~~  112 (305)
                      .++.
T Consensus       172 ~~ad  175 (175)
T 3nmr_A          172 KFAD  175 (175)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9873

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.58  E-value=2.1e-15  Score=117.25  Aligned_cols=80  Identities=14%  Similarity=0.170  Sum_probs=72.6

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCc---ccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGV---ILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      ..++|||+||+.++|+++|+++|+.||.   |..+                                       .++.|.
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v---------------------------------------~i~~~~   56 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGV---------------------------------------HFIYTR   56 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGE---------------------------------------EEEECS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeE---------------------------------------EEEECC
Confidence            4678999999999999999999999999   5555                                       677786


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      . |+++|||||+|.+.++|.+|+. +|+..++|+.|+|.++..+
T Consensus        57 ~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~~   98 (118)
T 2db1_A           57 E-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRT   98 (118)
T ss_dssp             S-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEEECHH
T ss_pred             C-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECCHH
Confidence            6 9999999999999999999999 9999999999999998654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=3.6e-15  Score=109.94  Aligned_cols=78  Identities=26%  Similarity=0.434  Sum_probs=69.9

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+.++++++|+++|+.||.|..+                                       .++     
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~~~-----   41 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLEC---------------------------------------DII-----   41 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEE---------------------------------------EEE-----
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEE---------------------------------------EEE-----
Confidence            346889999999999999999999999999876                                       222     


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                         +|||||+|.+.++|.+|+..||+..+.|+.|+|.|+..+...
T Consensus        42 ---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   83 (90)
T 2dnq_A           42 ---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKA   83 (90)
T ss_dssp             ---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCCC
T ss_pred             ---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCCC
Confidence               689999999999999999999999999999999999776543

>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=99.58  E-value=3.1e-15  Score=111.88  Aligned_cols=78  Identities=27%  Similarity=0.497  Sum_probs=69.3

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+.++|+++|+++|+.||.|..+                                       .++.+   
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v---------------------------------------~~~~~---   52 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTI---------------------------------------DHVKG---   52 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEE---------------------------------------EECSS---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEE---------------------------------------EEeCC---
Confidence            346889999999999999999999999999876                                       23322   


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeec--CeeeEEEEeeecC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLC--NRPISVSYAFKKD  241 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~--g~~l~v~~a~~~~  241 (305)
                         +|||||+|.+.++|.+|++.||+..+.  |+.|+|.|++.+.
T Consensus        53 ---~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           53 ---DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             ---SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             ---CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence               789999999999999999999999999  9999999997764

>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=99.58  E-value=3e-15  Score=113.68  Aligned_cols=80  Identities=18%  Similarity=0.293  Sum_probs=69.0

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+++++|+++|++||.|..+                                       .++.   
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v---------------------------------------~i~~---   49 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYV---------------------------------------MMMP---   49 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEE---------------------------------------EEET---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEE---------------------------------------EEEC---
Confidence            3456899999999999999999999999999876                                       3333   


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCe--eecCeeeEEEEeeecCC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQ--YLCNRPISVSYAFKKDS  242 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~--~~~g~~l~v~~a~~~~~  242 (305)
                         .+|||||+|++.++|.+|+..|++.  .+.|++|+|.|+..+..
T Consensus        50 ---~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~   93 (104)
T 1wex_A           50 ---FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             ---TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSC
T ss_pred             ---CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCccc
Confidence               2799999999999999999998764  58999999999976654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.58  E-value=1.9e-15  Score=113.84  Aligned_cols=76  Identities=21%  Similarity=0.485  Sum_probs=69.3

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ++|||+|||.++|+++|+++|+.||.|..+                                       .++.+     +
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~-----~   36 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTV---------------------------------------WIARN-----P   36 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEE---------------------------------------EEESS-----S
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEeeC-----C
Confidence            479999999999999999999999999876                                       44544     6


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+.
T Consensus        37 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A           37 PGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            8999999999999999999999999999999999997765

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=5.4e-15  Score=111.00  Aligned_cols=77  Identities=21%  Similarity=0.404  Sum_probs=68.8

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhc--CcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAF--GVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~--g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      ...++|||+||+..+|+++|+++|+.|  |.|..+                                             
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~---------------------------------------------   47 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV---------------------------------------------   47 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE---------------------------------------------
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEE---------------------------------------------
Confidence            456899999999999999999999999  888765                                             


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                        ...+|||||+|.+.++|.+|+..|||..+.|+.|+|.|++.+..
T Consensus        48 --~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpd_A           48 --KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   91 (99)
T ss_dssp             --EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             --EEeCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence              12377999999999999999999999999999999999987654

>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=99.58  E-value=1.7e-15  Score=114.65  Aligned_cols=82  Identities=18%  Similarity=0.282  Sum_probs=72.7

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ....+|||+|||.++|+++|+++|+.||.+ .+                                       .++.|. +
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v---------------------------------------~i~~d~-~   51 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RV---------------------------------------HIEIGP-D   51 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EE---------------------------------------EEEESS-S
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EE---------------------------------------EEEECC-C
Confidence            346789999999999999999999999954 55                                       678886 7


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      ++++|||||+|.+.++|.+||. +|+..+.++.|+|.++.....
T Consensus        52 g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~~~~   94 (102)
T 1wez_A           52 GRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGT   94 (102)
T ss_dssp             SCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCC
T ss_pred             CCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCCCCC
Confidence            9999999999999999999995 799999999999999876553

>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=99.58  E-value=4.5e-15  Score=111.43  Aligned_cols=81  Identities=22%  Similarity=0.424  Sum_probs=71.3

Q ss_pred             cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..+                                       .++.  
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~~~~--   49 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEV---------------------------------------FIHK--   49 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEE---------------------------------------EEET--
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEE---------------------------------------EEec--
Confidence            34456899999999999999999999999999876                                       3332  


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                          .+|||||+|.+.++|.+|++.|||..+.|+.|+|.|+..+..
T Consensus        50 ----~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpj_A           50 ----DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS   91 (99)
T ss_dssp             ----TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSC
T ss_pred             ----CCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCC
Confidence                379999999999999999999999999999999999977643

>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=99.58  E-value=3.9e-15  Score=113.86  Aligned_cols=78  Identities=18%  Similarity=0.509  Sum_probs=70.7

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+..+++++|+++|+.||.|..+                                       .++.+    
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~----   60 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEI---------------------------------------RVFPE----   60 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEE---------------------------------------EEETT----
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEeCC----
Confidence            46789999999999999999999999999876                                       44444    


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                        +|||||+|.+.++|.+|+..|||..+.|+.|+|.|++.+..
T Consensus        61 --~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           61 --KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             --TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             --CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence              79999999999999999999999999999999999977654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.58  E-value=7.8e-16  Score=111.33  Aligned_cols=73  Identities=23%  Similarity=0.366  Sum_probs=65.7

Q ss_pred             ccccccCCCchh------cHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         122 ANIFIGNLDPEV------DEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       122 ~~l~v~nl~~~~------t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      ++|||+|||..+      ++++|+++|+.||.|..+                                       .++  
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~--   40 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITND---------------------------------------FYP--   40 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEE---------------------------------------ECC--
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEE---------------------------------------Eec--
Confidence            689999999999      789999999999999876                                       333  


Q ss_pred             CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCe-eeEEE
Q psy3016         196 PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR-PISVS  235 (305)
Q Consensus       196 ~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~-~l~v~  235 (305)
                      ..+|+++|||||+|.+.++|.+|+..|||..++|+ +|+|+
T Consensus        41 ~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V~   81 (81)
T 2krb_A           41 EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN   81 (81)
T ss_dssp             CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCCC
T ss_pred             CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEeC
Confidence            35789999999999999999999999999999999 88763

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=9.2e-15  Score=108.21  Aligned_cols=77  Identities=17%  Similarity=0.416  Sum_probs=69.0

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+++++|+++|+.||.|..+                                       .++     
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v---------------------------------------~~~-----   43 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIEC---------------------------------------DIV-----   43 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEE---------------------------------------EEC-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEE-----
Confidence            456899999999999999999999999999876                                       233     


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                         ++||||+|.+.++|.+|+..||+..+.|+.|+|.|+..+..
T Consensus        44 ---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   84 (92)
T 2dgt_A           44 ---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR   84 (92)
T ss_dssp             ---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCS
T ss_pred             ---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCC
Confidence               44999999999999999999999999999999999977654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.57  E-value=3.6e-15  Score=114.52  Aligned_cols=78  Identities=13%  Similarity=0.035  Sum_probs=68.3

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcC-cccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFG-VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...+|||+|||.++++++|+++|+.|| .|..+                                       .+..    
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v---------------------------------------~i~~----   63 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFS---------------------------------------SVNT----   63 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEE---------------------------------------ECSS----
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEE---------------------------------------EEEc----
Confidence            457899999999999999999999999 88765                                       2221    


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++...
T Consensus        64 ~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           64 RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            347999999999999999999999999999999999998543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.57  E-value=2.8e-15  Score=117.99  Aligned_cols=82  Identities=24%  Similarity=0.397  Sum_probs=71.3

Q ss_pred             cccccccccCCCchhcHHHHH----HHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc
Q psy3016         119 DVGANIFIGNLDPEVDEKLLY----DTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR  194 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  194 (305)
                      ...++|||+||+..+++++|+    ++|+.||.|..+                                       .+. 
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v---------------------------------------~i~-   66 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDI---------------------------------------VVD-   66 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEE---------------------------------------EEC-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEE---------------------------------------Eec-
Confidence            346789999999999998865    799999999765                                       222 


Q ss_pred             CCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       195 d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                        .+++++|||||+|.+.++|.+|+..|||..+.|+.|+|.|++.+..
T Consensus        67 --~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~~~  112 (127)
T 2a3j_A           67 --LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS  112 (127)
T ss_dssp             --CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCCCH
T ss_pred             --cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCcch
Confidence              3578899999999999999999999999999999999999977654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=4.9e-15  Score=110.86  Aligned_cols=79  Identities=18%  Similarity=0.358  Sum_probs=69.8

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+++++|+++|+.||.|. +                                       .++.    
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~---------------------------------------~~~~----   52 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-L---------------------------------------RLTW----   52 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-S---------------------------------------EEEE----
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-E---------------------------------------EEEc----
Confidence            3468999999999999999999999999985 3                                       2232    


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++..+.
T Consensus        53 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           53 QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            4679999999999999999999999999999999999997653

>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=99.57  E-value=8.6e-15  Score=123.56  Aligned_cols=81  Identities=16%  Similarity=0.205  Sum_probs=73.4

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||+|||..+|+++|+++|+.||.|..|++..+. ++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.+..
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKD  185 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhH
Confidence            35899999999999999999999999999999999986 5889999999999999999999855 569999999999887


Q ss_pred             Ccc
Q psy3016         113 SHQ  115 (305)
Q Consensus       113 ~~~  115 (305)
                      ...
T Consensus       186 ~y~  188 (193)
T 2voo_A          186 DYF  188 (193)
T ss_dssp             TC-
T ss_pred             HHH
Confidence            644

>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=99.57  E-value=8.1e-15  Score=110.90  Aligned_cols=78  Identities=27%  Similarity=0.468  Sum_probs=69.7

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+.++|+++|+++|+.||.|..+                                       .++     
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v---------------------------------------~~~-----   44 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERV---------------------------------------KKL-----   44 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEE---------------------------------------EEC-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEE-----
Confidence            346889999999999999999999999999876                                       222     


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                         ++||||+|.+.++|.+|+..||+..|.|+.|+|.|+..+...
T Consensus        45 ---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A           45 ---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             ---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             ---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence               569999999999999999999999999999999999876554

>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=99.57  E-value=6.7e-15  Score=109.13  Aligned_cols=78  Identities=23%  Similarity=0.433  Sum_probs=68.2

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCc-ccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGV-ILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~-v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ..++|||+||+.++|+++|+++|+.||. |..+                                        ++     
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~----------------------------------------~~-----   41 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQ----------------------------------------VL-----   41 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSC----------------------------------------EE-----
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEE----------------------------------------EE-----
Confidence            4578999999999999999999999999 4432                                        11     


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcC-eeecCeeeEEEEeeecCCc
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHG-QYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~-~~~~g~~l~v~~a~~~~~~  243 (305)
                       .++|||||+|.+.++|.+|+..||| ..++|+.|+|.|+..+..+
T Consensus        42 -~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~~   86 (93)
T 2cqh_A           42 -LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   86 (93)
T ss_dssp             -EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             -cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcccc
Confidence             2589999999999999999999999 9999999999999876543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.56  E-value=3.5e-15  Score=111.32  Aligned_cols=81  Identities=22%  Similarity=0.363  Sum_probs=71.9

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ....++|||+||+..+++++|+++|+.||.|..                                          +  ..
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~------------------------------------------~--~~   48 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRL------------------------------------------V--SQ   48 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECC------------------------------------------E--EE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEE------------------------------------------e--CC
Confidence            345689999999999999999999999998853                                          2  34


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      ++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..
T Consensus        49 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           49 DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            688999999999999999999999999999999999999976543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.56  E-value=3.2e-15  Score=112.62  Aligned_cols=76  Identities=25%  Similarity=0.371  Sum_probs=68.4

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+.++++++|+++|+.||.|..+                                       .++      
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~---------------------------------------~~~------   60 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDF---------------------------------------KHY------   60 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEE---------------------------------------EEE------
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEE---------------------------------------EEe------
Confidence            35789999999999999999999999999876                                       233      


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|+|.|++++
T Consensus        61 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           61 PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            45899999999999999999999999999999999998653

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.56  E-value=2.1e-15  Score=115.05  Aligned_cols=81  Identities=19%  Similarity=0.165  Sum_probs=73.4

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCc---ccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGV---ILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      ...++|||+||+.++|+++|+++|+.||.   |..+                                       .++.|
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v---------------------------------------~i~~~   49 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGI---------------------------------------HFLLN   49 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTE---------------------------------------ECCCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceE---------------------------------------EEEEC
Confidence            45678999999999999999999999998   6655                                       67888


Q ss_pred             CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         196 PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       196 ~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      .. |+++|||||+|.+.++|.+|+. +|+..++|+.|+|.++..+
T Consensus        50 ~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~~   92 (107)
T 2lmi_A           50 RD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEINNE   92 (107)
T ss_dssp             TT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEECCHH
T ss_pred             CC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEECCHH
Confidence            77 9999999999999999999999 9999999999999998654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=9.4e-15  Score=107.70  Aligned_cols=77  Identities=21%  Similarity=0.397  Sum_probs=68.9

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+|+++|+++|+.||.|..+                                       .++     
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~---------------------------------------~~~-----   42 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIEC---------------------------------------DVV-----   42 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEE---------------------------------------EEC-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEE---------------------------------------EEE-----
Confidence            456889999999999999999999999999876                                       233     


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                         ++||||+|.+.++|.+|+..|||..+.|+.|+|.|+.....
T Consensus        43 ---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   83 (90)
T 2dnp_A           43 ---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK   83 (90)
T ss_dssp             ---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             ---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCC
Confidence               44999999999999999999999999999999999977644

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.56  E-value=4.2e-15  Score=114.64  Aligned_cols=82  Identities=23%  Similarity=0.410  Sum_probs=73.2

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||..+|+++|+++|+.||.|..+                                       .++.+   +
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v---------------------------------------~i~~~---~   44 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQI---------------------------------------RVGNT---P   44 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------EEECS---T
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEeeC---C
Confidence            46789999999999999999999999999876                                       44544   5


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|.|.|+..+...
T Consensus        45 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   88 (115)
T 3lqv_A           45 ETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAF   88 (115)
T ss_dssp             TTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHHHT
T ss_pred             CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCChhh
Confidence            56999999999999999999999999999999999999875543

>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=99.56  E-value=2.5e-15  Score=120.58  Aligned_cols=88  Identities=24%  Similarity=0.368  Sum_probs=73.5

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchh--hhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP--KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      ...++|||+||+..+|+++|+++|+.||.|..+.  .+                                 +  . +...
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~---------------------------------~--d-i~~~   86 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIM---------------------------------F--D-IRLM   86 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHH---------------------------------C--E-EEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccce---------------------------------e--e-EEec
Confidence            3467899999999999999999999999998651  11                                 0  0 1112


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.....
T Consensus        87 ~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~  132 (143)
T 3egn_A           87 KEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARP  132 (143)
T ss_dssp             EETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEEEECCCSCC
T ss_pred             cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            4688999999999999999999999999999999999999976543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.56  E-value=8e-15  Score=127.10  Aligned_cols=80  Identities=24%  Similarity=0.413  Sum_probs=71.4

Q ss_pred             cCCCCceEEEcCCCccc---------cHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCce
Q psy3016          30 SGDGDATIYVGGLDDKV---------SETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIK  100 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~---------te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~  100 (305)
                      .....++||||||+..+         ++++|+++|++||+|.+|+|+.      ++|||||+|.+.++|+.|++.|+|..
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            45568899999999998         7999999999999999999986      46999999999999999999999999


Q ss_pred             e------------CCeeeEEeeCCCcc
Q psy3016         101 L------------YGKPIRVNKASSHQ  115 (305)
Q Consensus       101 ~------------~g~~l~v~~~~~~~  115 (305)
                      +            .|+.|.|+|+....
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             EeccccccccccCCCCEEEEEEccCCC
Confidence            9            89999999998653

>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=99.56  E-value=4.5e-15  Score=113.89  Aligned_cols=81  Identities=21%  Similarity=0.253  Sum_probs=69.4

Q ss_pred             ccccccccccCCCch-hcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         118 LDVGANIFIGNLDPE-VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      ....++|||+||+.+ +++++|+++|++||.|..+                                       .++   
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v---------------------------------------~i~---   59 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNY---------------------------------------ILM---   59 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEE---------------------------------------EEE---
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEE---------------------------------------EEe---
Confidence            345789999999998 9999999999999999876                                       333   


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcC--eeecCeeeEEEEeeecCCc
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHG--QYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~--~~~~g~~l~v~~a~~~~~~  243 (305)
                         +++|||||+|++.++|.+|+..||+  ..+.|++|+|.|+..+...
T Consensus        60 ---~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~~  105 (112)
T 1x4f_A           60 ---RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKL  105 (112)
T ss_dssp             ---TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSSS
T ss_pred             ---cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcccccc
Confidence               2489999999999999999998864  5699999999999766543

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=6.6e-15  Score=107.18  Aligned_cols=75  Identities=20%  Similarity=0.394  Sum_probs=67.5

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||..+++++|+++|+.||.|..+                                       .++.    
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~---------------------------------------~~~~----   46 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTI---------------------------------------TVVQ----   46 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEE---------------------------------------EEEG----
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEE---------------------------------------EEEC----
Confidence            456899999999999999999999999999876                                       3333    


Q ss_pred             CCccceEEEEeCChHHHHHHHHHh-cCeeecCeeeEEEEee
Q psy3016         199 GNSKGFAFINYASFEASDASIDAM-HGQYLCNRPISVSYAF  238 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l-~~~~~~g~~l~v~~a~  238 (305)
                        ++|||||+|.+.++|.+|+..| |+..+.|+.|+|.|++
T Consensus        47 --~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           47 --RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             --GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             --CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence              3799999999999999999999 9999999999999974

>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=99.55  E-value=3.5e-15  Score=111.42  Aligned_cols=82  Identities=23%  Similarity=0.458  Sum_probs=72.4

Q ss_pred             cccccccccCCCchhcHHHHH----HHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc
Q psy3016         119 DVGANIFIGNLDPEVDEKLLY----DTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR  194 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  194 (305)
                      ...++|||+||+.++++++|+    ++|+.||.|..+                                       .++ 
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v---------------------------------------~i~-   45 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---------------------------------------LVS-   45 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEE---------------------------------------ECC-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEE---------------------------------------EEE-
Confidence            346789999999999999999    999999999876                                       233 


Q ss_pred             CCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       195 d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                        .++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..
T Consensus        46 --~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (97)
T 1nu4_A           46 --RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   91 (97)
T ss_dssp             --HHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCCT
T ss_pred             --cCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCCCc
Confidence              2467899999999999999999999999999999999999977643

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.55  E-value=7.9e-15  Score=112.12  Aligned_cols=77  Identities=26%  Similarity=0.561  Sum_probs=69.1

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+|+++|+++|+.||.|..+                                       .++     
T Consensus        29 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v---------------------------------------~i~-----   64 (108)
T 2jvo_A           29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEV---------------------------------------KIL-----   64 (108)
T ss_dssp             CSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEE---------------------------------------EEE-----
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEE-----
Confidence            356899999999999999999999999999876                                       233     


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                         +|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..
T Consensus        65 ---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  105 (108)
T 2jvo_A           65 ---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK  105 (108)
T ss_dssp             ---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC-
T ss_pred             ---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCCC
Confidence               78999999999999999999999999999999999976543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=7.1e-15  Score=112.52  Aligned_cols=78  Identities=14%  Similarity=0.207  Sum_probs=70.4

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ..+|||+|||.++|+++|+++|+.| .|..+                                       .++.|.. |+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v---------------------------------------~i~~d~~-g~   54 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAV---------------------------------------HLLKDHV-GR   54 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEE---------------------------------------EECCCTT-CC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEE---------------------------------------EEEECCC-CC
Confidence            4789999999999999999999999 77665                                       6778865 99


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      ++|||||+|.+.++|.+|+ .+|+..++||.|.|..+..+
T Consensus        55 ~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           55 NNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             CCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            9999999999999999999 69999999999999888544

>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=99.55  E-value=9.8e-15  Score=112.14  Aligned_cols=78  Identities=14%  Similarity=0.109  Sum_probs=69.5

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+..+++++|+++|+.||.|..+                                       .++      
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v---------------------------------------~i~------   43 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRV---------------------------------------LLP------   43 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECC------
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEe------
Confidence            35789999999999999999999999999876                                       222      


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|.|.|+.....
T Consensus        44 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   86 (111)
T 1whx_A           44 EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVF   86 (111)
T ss_dssp             SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTTT
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCcc
Confidence            2578999999999999999999999999999999999976544

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.54  E-value=4.9e-15  Score=110.68  Aligned_cols=78  Identities=22%  Similarity=0.413  Sum_probs=69.2

Q ss_pred             cccccccccCCCc-hhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         119 DVGANIFIGNLDP-EVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       119 ~~~~~l~v~nl~~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ...++|||+|||. .+++++|+++|+.||.|..+                                       .+     
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v---------------------------------------~i-----   43 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI---------------------------------------NI-----   43 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEE---------------------------------------EE-----
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEE---------------------------------------EE-----
Confidence            4568999999998 99999999999999999876                                       22     


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                         ++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+...
T Consensus        44 ---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   86 (96)
T 2kvi_A           44 ---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARP   86 (96)
T ss_dssp             ---ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC-
T ss_pred             ---eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCCC
Confidence               3789999999999999999999999999999999999776543

>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=99.54  E-value=1.4e-14  Score=111.25  Aligned_cols=81  Identities=16%  Similarity=0.273  Sum_probs=69.5

Q ss_pred             cccccccc--cCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         119 DVGANIFI--GNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       119 ~~~~~l~v--~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      ...++|||  +||+.++++++|+++|++||.|..+                                       .++.  
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v---------------------------------------~i~~--   61 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDAL---------------------------------------LMPP--   61 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEE---------------------------------------ECCT--
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEeC--
Confidence            34678999  7799999999999999999999875                                       2222  


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeee-----cCeeeEEEEeeecCCcC
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYL-----CNRPISVSYAFKKDSKG  244 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~-----~g~~l~v~~a~~~~~~~  244 (305)
                          .+|||||+|++.++|.+|+..|||+++     .|++|.|.|+....+..
T Consensus        62 ----~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~p~~~  110 (114)
T 2cq2_A           62 ----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWSG  110 (114)
T ss_dssp             ----TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCCCCSS
T ss_pred             ----CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccCcccC
Confidence                378999999999999999999999998     78999999997665543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.53  E-value=1.2e-14  Score=121.03  Aligned_cols=83  Identities=22%  Similarity=0.382  Sum_probs=76.2

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+||+..+++++|+++|+.||.|..+                                       .+..|. +
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v---------------------------------------~i~~d~-~  125 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA---------------------------------------AVDYDR-S  125 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEE---------------------------------------EECCCT-T
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEECC-C
Confidence            346899999999999999999999999999877                                       677776 7


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +.++|||||+|.+.++|.+|+..|||..++|+.|+|.|+....
T Consensus       126 g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~~~  168 (177)
T 2f3j_A          126 GRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI  168 (177)
T ss_dssp             SSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESSGG
T ss_pred             CCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            9999999999999999999999999999999999999996553

>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=99.53  E-value=1.3e-14  Score=108.72  Aligned_cols=75  Identities=23%  Similarity=0.449  Sum_probs=67.9

Q ss_pred             cccccccccCCCc-hhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         119 DVGANIFIGNLDP-EVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       119 ~~~~~l~v~nl~~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ...++|||+||+. .+++++|+++|+.||.|..+                                       .+     
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v---------------------------------------~i-----   55 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI---------------------------------------NI-----   55 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEE---------------------------------------EE-----
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEE---------------------------------------EE-----
Confidence            3568999999998 99999999999999999876                                       22     


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                         .+|||||+|.+.++|.+|+..|||..++|+.|+|.|++.+
T Consensus        56 ---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           56 ---KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             ---CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             ---eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence               3799999999999999999999999999999999998654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=2.2e-14  Score=107.24  Aligned_cols=80  Identities=21%  Similarity=0.413  Sum_probs=69.5

Q ss_pred             cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      .....++|||+|+  ++|+++|+++|+.||.|..+                                       .+    
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v---------------------------------------~i----   45 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDL---------------------------------------SM----   45 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEE---------------------------------------EE----
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEE---------------------------------------Ee----
Confidence            3345689999996  89999999999999999876                                       22    


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                        +.++|||||+|.+.++|.+|+..||+..+.|+.|+|.|+..+...
T Consensus        46 --~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~   90 (97)
T 1x5p_A           46 --DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPML   90 (97)
T ss_dssp             --ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCCC
T ss_pred             --cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCCC
Confidence              256899999999999999999999999999999999999776543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=1.4e-14  Score=107.76  Aligned_cols=78  Identities=23%  Similarity=0.326  Sum_probs=68.8

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+.++|+++|+++|+.||.|..+                                         +.+..++
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v-----------------------------------------~~~~~~g   45 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-----------------------------------------VMDKDKG   45 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE-----------------------------------------EECSSSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE-----------------------------------------EEcCCCC
Confidence            45789999999999999999999999999854                                         5665555


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .   ||||+|.+.++|.+|+. |||..+.|+.|+|.++..+..
T Consensus        46 ~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A           46 V---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEF   84 (94)
T ss_dssp             C---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCC
T ss_pred             c---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCC
Confidence            5   99999999999999999 999999999999998865543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.53  E-value=7.9e-15  Score=110.64  Aligned_cols=81  Identities=21%  Similarity=0.466  Sum_probs=74.1

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+..+++++|+++|+.||.|..+                                       .++.|. ++
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~~~-~g   47 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEV---------------------------------------KIITDR-TG   47 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECT-TS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEE---------------------------------------EEEECC-CC
Confidence            35789999999999999999999999999877                                       678887 89


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++|||||+|.+.++|.+|+.  ++..+.|+.|.|.++..+..
T Consensus        48 ~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~~~~   88 (102)
T 2xs2_A           48 VSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRKQN   88 (102)
T ss_dssp             CEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEECC-
T ss_pred             CccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCcCcc
Confidence            999999999999999999999  99999999999999977643

>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=99.52  E-value=1.1e-14  Score=118.70  Aligned_cols=79  Identities=22%  Similarity=0.278  Sum_probs=68.7

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ...|||+||++.+|+++|+++|++||.|..+                                       .+..    ..
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V---------------------------------------~i~~----k~   82 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKI---------------------------------------ITFT----KN   82 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEE---------------------------------------EEEE----SS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEe----CC
Confidence            4569999999999999999999999999876                                       2222    23


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecC--eeeEEEEeeecCC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCN--RPISVSYAFKKDS  242 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g--~~l~v~~a~~~~~  242 (305)
                      ++|||||+|++.++|.+|++.|||..|.|  +.|+|.|++.+..
T Consensus        83 ~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~l  126 (164)
T 1sjr_A           83 NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  126 (164)
T ss_dssp             SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSSC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCcc
Confidence            57899999999999999999999999965  9999999987653

>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=99.52  E-value=7.1e-14  Score=123.28  Aligned_cols=82  Identities=27%  Similarity=0.335  Sum_probs=74.6

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc-CceeC---CeeeEEe
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN-MIKLY---GKPIRVN  109 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~-g~~~~---g~~l~v~  109 (305)
                      .++|||+|||..+|+++|+++|+.||.|..|.++.+ .+|.++|||||+|.+.++|.+|++.|+ +..+.   ++.|.|.
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~  174 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            569999999999999999999999999999999999 488999999999999999999999995 55555   9999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      ++.....
T Consensus       175 ~~~~~~~  181 (261)
T 3sde_A          175 PMEQFDD  181 (261)
T ss_dssp             ECCCEES
T ss_pred             eccccCc
Confidence            9887643

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=2.2e-14  Score=105.35  Aligned_cols=74  Identities=20%  Similarity=0.276  Sum_probs=65.2

Q ss_pred             ccc-ccccCCCchhcHHH----HHHHHhhcC-cccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc
Q psy3016         121 GAN-IFIGNLDPEVDEKL----LYDTFSAFG-VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR  194 (305)
Q Consensus       121 ~~~-l~v~nl~~~~t~~~----l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  194 (305)
                      ..+ |||+||+..+++++    |+++|+.|| .|..+                                           
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------------------------------------------   44 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------------------------------------------   44 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------------------------------------------
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------------------------------------------
Confidence            444 99999999999988    668999995 99753                                           


Q ss_pred             CCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       195 d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                         ++   |+|||+|.+.++|.+|++.|||..+.||+|+|+||+.+.+-
T Consensus        45 ---tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~sd~   87 (96)
T 2diu_A           45 ---TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNREL   87 (96)
T ss_dssp             ---CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSCCC
T ss_pred             ---ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCcce
Confidence               23   99999999999999999999999999999999999887654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.52  E-value=9.9e-15  Score=113.23  Aligned_cols=77  Identities=17%  Similarity=0.298  Sum_probs=69.7

Q ss_pred             ccccccCC----CchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         122 ANIFIGNL----DPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       122 ~~l~v~nl----~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ..|||+||    ++.+++++|+++|+.||+|..+                                       .++.|+.
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~---------------------------------------~li~Dp~   43 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHF---------------------------------------EAFNDPN   43 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEE---------------------------------------EEEECTT
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEEecCC
Confidence            47999999    9999999999999999999988                                       7899999


Q ss_pred             CCCccceEEEEeCC----hHH----HHHHHH--HhcCeeecCeeeEEEEe
Q psy3016         198 TGNSKGFAFINYAS----FEA----SDASID--AMHGQYLCNRPISVSYA  237 (305)
Q Consensus       198 ~~~~~g~afV~f~~----~~~----A~~Al~--~l~~~~~~g~~l~v~~a  237 (305)
                      ||.++|||||+|.+    .++    |.+|+.  .+||..|+|++|+|.+.
T Consensus        44 Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln   93 (136)
T 2j8a_A           44 SALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILN   93 (136)
T ss_dssp             TCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEEC
T ss_pred             CCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEEC
Confidence            99999999999996    333    788888  78999999999999985

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=2.1e-14  Score=106.97  Aligned_cols=80  Identities=20%  Similarity=0.328  Sum_probs=69.3

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||..+++++|+++|+.||.|..+.                                      .++.+..+ 
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~--------------------------------------~i~~~~~~-   54 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCE--------------------------------------QVNTDSET-   54 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEE--------------------------------------EECCSSSS-
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEE--------------------------------------EeecCCCC-
Confidence            467899999999999999999999999998751                                      13555443 


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                         +.|||+|.+.++|.+|+..|||..+.|+.|+|.|+.+++
T Consensus        55 ---~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           55 ---AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             ---EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             ---CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence               339999999999999999999999999999999998764

>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=6.3e-14  Score=118.05  Aligned_cols=76  Identities=22%  Similarity=0.222  Sum_probs=70.9

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCC-CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC-CeeeEEee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY-GKPIRVNK  110 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~-g~~l~v~~  110 (305)
                      ..++|||+|||..+|+++|+++|+.|| .|.+|+++.+     .+|||||+|.+.++|.+|++.|||..+. |+.|+|.+
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  193 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  193 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEe
Confidence            478999999999999999999999999 9999999764     3699999999999999999999999999 99999999


Q ss_pred             CCC
Q psy3016         111 ASS  113 (305)
Q Consensus       111 ~~~  113 (305)
                      +.+
T Consensus       194 a~~  196 (198)
T 1qm9_A          194 SKS  196 (198)
T ss_dssp             ECC
T ss_pred             ecc
Confidence            875

>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=99.51  E-value=1.3e-13  Score=105.93  Aligned_cols=82  Identities=15%  Similarity=0.195  Sum_probs=70.3

Q ss_pred             cCCCCceEEEcCCCccc-----------cHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcC
Q psy3016          30 SGDGDATIYVGGLDDKV-----------SETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM   98 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~-----------te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g   98 (305)
                      ....+++|+|.||-...           ++++|+++|++||.|.+|.| .+.   .++|||||+|.+.++|.+|++.|||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            44568899999994332           26899999999999999966 443   3789999999999999999999999


Q ss_pred             ceeCCeeeEEeeCCCcc
Q psy3016          99 IKLYGKPIRVNKASSHQ  115 (305)
Q Consensus        99 ~~~~g~~l~v~~~~~~~  115 (305)
                      ..+.|+.|.|.++.+..
T Consensus        87 ~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             CEECCcEEEEEEeCCCC
Confidence            99999999999987654

>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=99.50  E-value=8.7e-14  Score=123.71  Aligned_cols=78  Identities=19%  Similarity=0.299  Sum_probs=72.0

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC-CeeeEE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY-GKPIRV  108 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~-g~~l~v  108 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|+++.++     +|||||+|.+.++|.+|++.|||..+. |+.|+|
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  277 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKI  277 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEE
Confidence            44467899999999999999999999999999999998653     589999999999999999999999999 999999


Q ss_pred             eeCC
Q psy3016         109 NKAS  112 (305)
Q Consensus       109 ~~~~  112 (305)
                      .|++
T Consensus       278 ~~ak  281 (282)
T 3pgw_A          278 SFAK  281 (282)
T ss_pred             EEec
Confidence            9975

>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=99.50  E-value=2.5e-14  Score=105.00  Aligned_cols=75  Identities=16%  Similarity=0.234  Sum_probs=67.1

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||..+++++|+++|+.| .|..+                                       .+  +    +
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~---------------------------------------~i--~----~   38 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQEVHDLLKDY-DLKYC---------------------------------------YV--D----R   38 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCE---------------------------------------EE--E----G
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEE---------------------------------------EE--e----C
Confidence            5789999999999999999999999 88765                                       22  2    5


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      ++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+.
T Consensus        39 ~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A           39 NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             GGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            79999999999999999999999999999999999986553

>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=99.50  E-value=1.3e-13  Score=119.24  Aligned_cols=77  Identities=22%  Similarity=0.218  Sum_probs=71.2

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCC-CeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC-CeeeEEee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY-GKPIRVNK  110 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~-g~~l~v~~  110 (305)
                      ..++|||+|||..+|+++|+++|+.|| .|..|+++.+     ++|||||+|.+.++|.+|++.|+|..+. |+.|+|.+
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~  224 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  224 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEE
Confidence            468999999999999999999999999 9999999663     3689999999999999999999999999 99999999


Q ss_pred             CCCc
Q psy3016         111 ASSH  114 (305)
Q Consensus       111 ~~~~  114 (305)
                      +.+.
T Consensus       225 a~~~  228 (229)
T 2adc_A          225 SKST  228 (229)
T ss_dssp             CSSC
T ss_pred             ecCC
Confidence            8753

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=7.4e-15  Score=114.83  Aligned_cols=81  Identities=16%  Similarity=0.142  Sum_probs=71.2

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCccc----chhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVIL----QTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      ...+|||+|||+++|+++|+++|+.||.|.    .+                                       .++.|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v---------------------------------------~i~~d   62 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGI---------------------------------------LFVTY   62 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGE---------------------------------------EEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceE---------------------------------------EEEEC
Confidence            357899999999999999999999999863    33                                       56777


Q ss_pred             CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         196 PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       196 ~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                       .+|+++|||||+|.+.++|.+|+.. |+..+.|+.|.|..+..++
T Consensus        63 -~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a~~~e  106 (123)
T 2dha_A           63 -PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRSTAAE  106 (123)
T ss_dssp             -TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEEECHHH
T ss_pred             -CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEECCHHH
Confidence             5799999999999999999999996 9999999999999886543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.50  E-value=1.8e-14  Score=113.14  Aligned_cols=78  Identities=22%  Similarity=0.345  Sum_probs=67.9

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      -.|||+||+..+|+++|+++|++||.|..+                                       .+..+     .
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V---------------------------------------~i~~~-----~   64 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKI---------------------------------------ITFTK-----N   64 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEE---------------------------------------EEEEE-----T
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEE---------------------------------------EEEcC-----C
Confidence            468899999999999999999999999876                                       22322     3


Q ss_pred             cce-EEEEeCChHHHHHHHHHhcCeeecC--eeeEEEEeeecCCc
Q psy3016         202 KGF-AFINYASFEASDASIDAMHGQYLCN--RPISVSYAFKKDSK  243 (305)
Q Consensus       202 ~g~-afV~f~~~~~A~~Al~~l~~~~~~g--~~l~v~~a~~~~~~  243 (305)
                      +|+ |||+|.+.++|.+|++.|||..|.|  +.|+|.|++.+.-.
T Consensus        65 ~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l~  109 (130)
T 3zzy_A           65 NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLN  109 (130)
T ss_dssp             TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSCC
T ss_pred             CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCcee
Confidence            677 9999999999999999999999988  99999999877543

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.49  E-value=1.2e-14  Score=113.98  Aligned_cols=81  Identities=21%  Similarity=0.314  Sum_probs=70.9

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCccc--chhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVIL--QTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      ....+|||+|||+++|+++|+++|+.| .|.  .+                                       .++.|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v---------------------------------------~i~~d~   79 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGI---------------------------------------TLPVDP   79 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEE---------------------------------------ECCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEE---------------------------------------EEEECC
Confidence            346789999999999999999999999 454  44                                       678887


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      . |+++|||||+|++.++|.+|+.. ++..++||.|.|..+..++
T Consensus        80 ~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~a~~~e  122 (126)
T 2hgm_A           80 E-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKSSQEE  122 (126)
T ss_dssp             S-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEECHHH
T ss_pred             C-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEECCHHH
Confidence            6 99999999999999999999994 7899999999999886554

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.49  E-value=3.3e-14  Score=107.90  Aligned_cols=72  Identities=26%  Similarity=0.363  Sum_probs=65.1

Q ss_pred             EcCCCccccHHHHHHHh------------ccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          39 VGGLDDKVSETLMWELF------------VQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        39 V~nLp~~~te~~L~~~F------------~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (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 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            67888888888887766            999999999999886 47899999999999999999999999999999999


Q ss_pred             EEeeC
Q psy3016         107 RVNKA  111 (305)
Q Consensus       107 ~v~~~  111 (305)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99876

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.48  E-value=4.8e-14  Score=107.19  Aligned_cols=83  Identities=13%  Similarity=0.219  Sum_probs=70.6

Q ss_pred             ccccccccCCCc-----hhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc
Q psy3016         120 VGANIFIGNLDP-----EVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR  194 (305)
Q Consensus       120 ~~~~l~v~nl~~-----~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  194 (305)
                      .+++|+|.|+-.     +.++++|++.|++||.|..+                                       .|+.
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v---------------------------------------~i~~   47 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKC---------------------------------------VIFE   47 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEE---------------------------------------EEEE
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEE---------------------------------------EEec
Confidence            467888888852     34789999999999999987                                       5666


Q ss_pred             CCCC-CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         195 DPDT-GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       195 d~~~-~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      ++.+ ++++|||||+|.+.++|.+|+..|||++++||.|+|.|+....
T Consensus        48 ~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~~~   95 (105)
T 2pe8_A           48 IPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLDK   95 (105)
T ss_dssp             CSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHH
T ss_pred             CCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCHHH
Confidence            6543 6889999999999999999999999999999999999997644

>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=99.48  E-value=1.6e-13  Score=104.22  Aligned_cols=82  Identities=12%  Similarity=0.133  Sum_probs=70.8

Q ss_pred             CCCceEEEcCC--Cccc--------cHHHHHHHhccCCCeEEEEEcccCCC--CCcceEEEEEEcCHHHHHHHHHHhcCc
Q psy3016          32 DGDATIYVGGL--DDKV--------SETLMWELFVQSGPVVNVHMPKDRVT--QTHQGYGFIEFMGEEDADYAIKIMNMI   99 (305)
Q Consensus        32 ~~~~~l~V~nL--p~~~--------te~~L~~~F~~~G~i~~i~~~~~~~~--~~~~g~afV~f~~~e~A~~Ai~~l~g~   99 (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            35778999998  3333        34789999999999999999988754  367899999999999999999999999


Q ss_pred             eeCCeeeEEeeCCC
Q psy3016         100 KLYGKPIRVNKASS  113 (305)
Q Consensus       100 ~~~g~~l~v~~~~~  113 (305)
                      .+.||.|++.++..
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999998754

>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=99.47  E-value=4.3e-14  Score=109.21  Aligned_cols=74  Identities=15%  Similarity=0.217  Sum_probs=63.2

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+||+.++++++|+++|+.||.|..+                                       .++.|    
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~---------------------------------------~i~~~----   51 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYA---------------------------------------DVYRD----   51 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEE---------------------------------------EECTT----
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEE---------------------------------------EEecC----
Confidence            35789999999999999999999999999876                                       34443    


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCee-----eEEEEeee
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRP-----ISVSYAFK  239 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~-----l~v~~a~~  239 (305)
                         |||||+|.+.++|.+||+.|||..|+|+.     |+|..+..
T Consensus        52 ---g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~   93 (115)
T 3beg_B           52 ---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP   93 (115)
T ss_dssp             ---SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC-
T ss_pred             ---CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCC
Confidence               89999999999999999999999999999     55555544

>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=99.47  E-value=1.1e-13  Score=116.79  Aligned_cols=114  Identities=11%  Similarity=0.153  Sum_probs=90.6

Q ss_pred             CHHHHHHHHHHh--cCceeCCeeeEEeeCCCccc--------cccccccccccCCCchhcHHHHHHHHhhcCcccchhhh
Q psy3016          85 GEEDADYAIKIM--NMIKLYGKPIRVNKASSHQK--------NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI  154 (305)
Q Consensus        85 ~~e~A~~Ai~~l--~g~~~~g~~l~v~~~~~~~~--------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~  154 (305)
                      +.+.+..|++..  ....+.+....+.+......        .....++|||+|||.++|+++|.++|+.||.|..+   
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v---  139 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNI---  139 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEE---
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEE---
Confidence            667788888866  55677776677766532111        11235789999999999999999999999999877   


Q ss_pred             hhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEE
Q psy3016         155 MNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV  234 (305)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v  234 (305)
                                                          .+.++. ++.++|||||+|++.++|.+|+..++ ..+.|+.|.|
T Consensus       140 ------------------------------------~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V  181 (193)
T 2voo_A          140 ------------------------------------QMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLI  181 (193)
T ss_dssp             ------------------------------------EEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEE
T ss_pred             ------------------------------------EEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEE
Confidence                                                556664 48899999999999999999998655 5899999999


Q ss_pred             EEeee
Q psy3016         235 SYAFK  239 (305)
Q Consensus       235 ~~a~~  239 (305)
                      .++..
T Consensus       182 ~~~~~  186 (193)
T 2voo_A          182 LFKDD  186 (193)
T ss_dssp             EETTT
T ss_pred             EEhHH
Confidence            98754

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.45  E-value=9.6e-14  Score=118.21  Aligned_cols=76  Identities=14%  Similarity=0.202  Sum_probs=67.6

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCe--EEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe----ee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPV--VNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK----PI  106 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i--~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~----~l  106 (305)
                      ..++|||+|||..+|+++|+++|+.||.|  .+++++.+.  +.++|||||+|.+.++|.+|+..|||..+.|+    .+
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~  199 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY  199 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcce
Confidence            46789999999999999999999999999  899998875  44569999999999999999999999999886    45


Q ss_pred             EEee
Q psy3016         107 RVNK  110 (305)
Q Consensus       107 ~v~~  110 (305)
                      .|++
T Consensus       200 ~vk~  203 (205)
T 3tyt_A          200 TLKL  203 (205)
T ss_dssp             ECEE
T ss_pred             EEEe
Confidence            5554

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=2.2e-13  Score=104.96  Aligned_cols=76  Identities=22%  Similarity=0.378  Sum_probs=64.7

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC-
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT-  198 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~-  198 (305)
                      ..++|||+||+.++|+++|+++|+.||.|. +                                       .++.+..+ 
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~---------------------------------------~~~~~~~~~   46 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-V---------------------------------------DWPHKAESK   46 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-E---------------------------------------ECTTSSSSC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-E---------------------------------------EEeecCCCC
Confidence            467899999999999999999999999998 4                                       45666665 


Q ss_pred             --CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         199 --GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       199 --~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                        |+++|||||+|.+.++|.+|++.|+  .++|+.+.+..+
T Consensus        47 ~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~~~   85 (114)
T 2dnl_A           47 SYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCVSS   85 (114)
T ss_dssp             CCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEECC
T ss_pred             CCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEeccC
Confidence              7999999999999999999999984  367777766654

>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=99.44  E-value=3.8e-13  Score=104.29  Aligned_cols=81  Identities=16%  Similarity=0.128  Sum_probs=71.0

Q ss_pred             CCceEEEcCCCc--cc---cHHHHHHHhccCCCeEEEEEcccCC----CCCcceEEEEEEcCHHHHHHHHHHhcCceeCC
Q psy3016          33 GDATIYVGGLDD--KV---SETLMWELFVQSGPVVNVHMPKDRV----TQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG  103 (305)
Q Consensus        33 ~~~~l~V~nLp~--~~---te~~L~~~F~~~G~i~~i~~~~~~~----~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g  103 (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            578999999943  22   3689999999999999999998864    45788999999999999999999999999999


Q ss_pred             eeeEEeeCCC
Q psy3016         104 KPIRVNKASS  113 (305)
Q Consensus       104 ~~l~v~~~~~  113 (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            9999998754

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.44  E-value=1.1e-13  Score=108.05  Aligned_cols=76  Identities=17%  Similarity=0.282  Sum_probs=65.5

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      -.|||+||++.+|+++|+++|+.||.|..+                                       .++.  .    
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v---------------------------------------~i~~--~----   60 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRI---------------------------------------VIFK--R----   60 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEE---------------------------------------EEEE--S----
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEE---------------------------------------EEEe--C----
Confidence            347899999999999999999999999876                                       3322  1    


Q ss_pred             cce-EEEEeCChHHHHHHHHHhcCeeecC--eeeEEEEeeecCC
Q psy3016         202 KGF-AFINYASFEASDASIDAMHGQYLCN--RPISVSYAFKKDS  242 (305)
Q Consensus       202 ~g~-afV~f~~~~~A~~Al~~l~~~~~~g--~~l~v~~a~~~~~  242 (305)
                      .|| |||+|++.++|.+|+.+|||..|.|  +.|+|.|++.+..
T Consensus        61 ~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           61 NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            275 9999999999999999999999987  6999999987753

>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=99.43  E-value=2e-13  Score=100.50  Aligned_cols=75  Identities=20%  Similarity=0.416  Sum_probs=60.7

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...+|||+||+.++|+++|+++|+.||.|..+                                       .++.+    
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v---------------------------------------~i~~~----   46 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDV---------------------------------------FIPKP----   46 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTTSCEEEE---------------------------------------ECCSS----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCEEEE---------------------------------------EEeeC----
Confidence            45789999999999999999999999999887                                       44543    


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCee--ecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQY--LCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~--~~g~~l~v~~a~~~~~  242 (305)
                       ++|||||+|++.++|.+    +++..  +.|+.|.|.++.++..
T Consensus        47 -srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k~~   86 (89)
T 3d2w_A           47 -FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPKHN   86 (89)
T ss_dssp             -CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC----
T ss_pred             -CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCCCc
Confidence             79999999999999873    56655  4699999999976643

>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=99.40  E-value=1.8e-13  Score=100.27  Aligned_cols=78  Identities=19%  Similarity=0.337  Sum_probs=63.5

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||.++++++|+++|+.||.|..+                                       .++.+    
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~~----   40 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDV---------------------------------------FIPKP----   40 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEE---------------------------------------ECCSS----
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEE---------------------------------------EEecC----
Confidence            35789999999999999999999999999876                                       34433    


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                       ++|||||+|.+.++|.+|+..  ...+.|+.|.|.++..+...
T Consensus        41 -~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A           41 -FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             -CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCCCC
T ss_pred             -CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCCCC
Confidence             689999999999999754321  34559999999999776543

>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=99.40  E-value=2.5e-13  Score=99.13  Aligned_cols=71  Identities=23%  Similarity=0.504  Sum_probs=61.7

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhc----C-------cccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAF----G-------VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNL  188 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~----g-------~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  188 (305)
                      ..++|||+|||.++++++|+++|+.|    |       .|..+                                     
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~-------------------------------------   47 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAV-------------------------------------   47 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEE-------------------------------------
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEE-------------------------------------
Confidence            35789999999999999999999999    7       55544                                     


Q ss_pred             CCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEE
Q psy3016         189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY  236 (305)
Q Consensus       189 ~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~  236 (305)
                        .+..      .+|||||+|.+.++|.+|+ .|||..+.|+.|+|+.
T Consensus        48 --~~~~------~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           48 --QINQ------DKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             --EECS------SSSEEEEEESSHHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             --EecC------CCcEEEEEcCCHHHHHHHH-hcCCCEECCeEEEEeC
Confidence              2232      3899999999999999999 9999999999999974

>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=99.36  E-value=1.1e-12  Score=99.67  Aligned_cols=82  Identities=20%  Similarity=0.277  Sum_probs=66.9

Q ss_pred             cccccccCC--Cch--------hcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCC
Q psy3016         121 GANIFIGNL--DPE--------VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDP  190 (305)
Q Consensus       121 ~~~l~v~nl--~~~--------~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  190 (305)
                      +++|.+.|+  +..        ..+++|++.|++||.|..+                                       
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v---------------------------------------   45 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSI---------------------------------------   45 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEE---------------------------------------
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEE---------------------------------------
Confidence            456666665  222        3457899999999999987                                       


Q ss_pred             CcccCCCC--CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         191 EIMRDPDT--GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       191 ~i~~d~~~--~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .|+++..+  +.++|+|||+|++.++|.+|+.+|||++++||.|+|.|+....
T Consensus        46 ~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~~~~   98 (105)
T 3v4m_A           46 EIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDS   98 (105)
T ss_dssp             ECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECHHH
T ss_pred             EEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeCHHH
Confidence            56666543  4689999999999999999999999999999999999986654

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.36  E-value=8.1e-13  Score=114.49  Aligned_cols=101  Identities=17%  Similarity=0.258  Sum_probs=75.5

Q ss_pred             cCceeCCeeeEEeeCCCcc---ccccccccccccCCCchh---------cHHHHHHHHhhcCcccchhhhhhhhhhcCcc
Q psy3016          97 NMIKLYGKPIRVNKASSHQ---KNLDVGANIFIGNLDPEV---------DEKLLYDTFSAFGVILQTPKIMNMIKLYGKP  164 (305)
Q Consensus        97 ~g~~~~g~~l~v~~~~~~~---~~~~~~~~l~v~nl~~~~---------t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~  164 (305)
                      +...+.|+.....+.....   ......++|||+||+..+         ++++|+++|+.||.|..+             
T Consensus       107 ~~~D~fGr~k~~~~~d~~~g~gs~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v-------------  173 (240)
T 3u1l_A          107 EVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRI-------------  173 (240)
T ss_dssp             SSBCTTSSBCGGGTC---------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEE-------------
T ss_pred             cCcccccchhcccchhcccCcCccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEE-------------
Confidence            3455557654433322211   122346899999999998         899999999999999976             


Q ss_pred             eeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeee------------cCeee
Q psy3016         165 IRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL------------CNRPI  232 (305)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~------------~g~~l  232 (305)
                                                .++.      ++|||||+|.+.++|..|+.+|+|..+            .|+.|
T Consensus       174 --------------------------~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L  221 (240)
T 3u1l_A          174 --------------------------RYVE------SKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGL  221 (240)
T ss_dssp             --------------------------EEEG------GGTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCC
T ss_pred             --------------------------EEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEE
Confidence                                      3342      489999999999999999999999999            89999


Q ss_pred             EEEEeeecCC
Q psy3016         233 SVSYAFKKDS  242 (305)
Q Consensus       233 ~v~~a~~~~~  242 (305)
                      .|.||+.+..
T Consensus       222 ~V~wA~~~pn  231 (240)
T 3u1l_A          222 LVKWANEDPD  231 (240)
T ss_dssp             EEEECC----
T ss_pred             EEEEccCCCC
Confidence            9999976543

>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=99.36  E-value=4.8e-13  Score=101.43  Aligned_cols=72  Identities=10%  Similarity=0.328  Sum_probs=61.9

Q ss_pred             ccCCCchhcHHHHHHHH------------hhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcc
Q psy3016         126 IGNLDPEVDEKLLYDTF------------SAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIM  193 (305)
Q Consensus       126 v~nl~~~~t~~~l~~~f------------~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~  193 (305)
                      +.+|+..+++++|.+.|            ++||.|..+                                       .++
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v---------------------------------------~i~   60 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEM---------------------------------------NVC   60 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEE---------------------------------------EEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEE---------------------------------------EEE
Confidence            56777788887777666            999999987                                       566


Q ss_pred             cCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         194 RDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       194 ~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      .+.. ++++|||||+|.+.++|.+|+..|||++++||.|+|.|+
T Consensus        61 ~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           61 DNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             CSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             eCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            6643 789999999999999999999999999999999999986

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=6.1e-12  Score=94.49  Aligned_cols=76  Identities=16%  Similarity=0.267  Sum_probs=63.6

Q ss_pred             CceEEEcCCC-------ccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          34 DATIYVGGLD-------DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        34 ~~~l~V~nLp-------~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      ..+|.|.-..       ..+|+++|+++|++||.|.+|.|+     +.++|||||+|.+.++|.+|++.++  .+.|+.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeE
Confidence            4466665544       458999999999999999999997     3578999999999999999999754  4679999


Q ss_pred             EEeeCCCccc
Q psy3016         107 RVNKASSHQK  116 (305)
Q Consensus       107 ~v~~~~~~~~  116 (305)
                      +|.|+.....
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999887654

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.35  E-value=3.8e-12  Score=97.64  Aligned_cols=83  Identities=19%  Similarity=0.229  Sum_probs=68.2

Q ss_pred             cccccccccccCCCchh-----------cHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEe
Q psy3016         117 NLDVGANIFIGNLDPEV-----------DEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFI  185 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~~-----------t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  185 (305)
                      .....++|+|.||-...           ++++|+++|++||.|..+                                  
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v----------------------------------   56 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKL----------------------------------   56 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEE----------------------------------
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEE----------------------------------
Confidence            34457889999994322           368999999999999876                                  


Q ss_pred             ccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         186 GNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       186 ~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                           . +.|   ..++|||||+|.+.++|.+|+..|||.+++|+.|+|.|+..+..
T Consensus        57 -----~-i~~---~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           57 -----L-LFD---RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             -----E-EET---TCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCC
T ss_pred             -----E-Eec---CCCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCC
Confidence                 2 233   23799999999999999999999999999999999999976543

>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=99.33  E-value=3.1e-12  Score=116.55  Aligned_cols=76  Identities=20%  Similarity=0.329  Sum_probs=65.8

Q ss_pred             CCCCceEEEcC--CCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC---Ce-
Q psy3016          31 GDGDATIYVGG--LDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY---GK-  104 (305)
Q Consensus        31 ~~~~~~l~V~n--Lp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~---g~-  104 (305)
                      ...+++|||||  |+..+|+++|+++|++||+|.+|.+..      +||||||+|.+.++|++|++.|||..+.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            45577999999  578999999999999999999998854      4699999999999999999999998883   45 


Q ss_pred             -eeEEeeCC
Q psy3016         105 -PIRVNKAS  112 (305)
Q Consensus       105 -~l~v~~~~  112 (305)
                       .|.+.++.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             57777765

>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=99.31  E-value=1.5e-12  Score=100.90  Aligned_cols=83  Identities=12%  Similarity=0.226  Sum_probs=67.6

Q ss_pred             ccccccccCCCc--h---hcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc
Q psy3016         120 VGANIFIGNLDP--E---VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR  194 (305)
Q Consensus       120 ~~~~l~v~nl~~--~---~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  194 (305)
                      .+++|++.|+-.  +   -.+++|++.|++||.|..+                                       .|+.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v---------------------------------------~I~~   59 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRV---------------------------------------IIYQ   59 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEE---------------------------------------EEEE
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEE---------------------------------------EEee
Confidence            456777777632  1   2468999999999999987                                       4555


Q ss_pred             CCC----CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         195 DPD----TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       195 d~~----~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +..    +++++|++||+|.+.++|.+|+.+|||++|+||.|+|.|+....
T Consensus        60 ~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~~~~  110 (118)
T 3ue2_A           60 EKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQER  110 (118)
T ss_dssp             EEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECHHH
T ss_pred             cCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcChHh
Confidence            533    46788999999999999999999999999999999999986543

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.29  E-value=1.5e-11  Score=94.67  Aligned_cols=78  Identities=14%  Similarity=0.091  Sum_probs=65.9

Q ss_pred             CCCceEEEcCCCcc----------ccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee
Q psy3016          32 DGDATIYVGGLDDK----------VSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL  101 (305)
Q Consensus        32 ~~~~~l~V~nLp~~----------~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~  101 (305)
                      ..++.|.+.|+=..          --++||++.|++||.|.+|.|.++.    ++|||||+|.+.++|.+|++.|||..+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            34667888887332          1246889999999999999997663    589999999999999999999999999


Q ss_pred             CCeeeEEeeCCC
Q psy3016         102 YGKPIRVNKASS  113 (305)
Q Consensus       102 ~g~~l~v~~~~~  113 (305)
                      .||.|++.++..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999998753

>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=99.13  E-value=6.7e-11  Score=90.93  Aligned_cols=66  Identities=15%  Similarity=0.353  Sum_probs=56.2

Q ss_pred             hcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCCh
Q psy3016         133 VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF  212 (305)
Q Consensus       133 ~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~  212 (305)
                      -.+++|++.|++||.|..+                                       .+.++    .++|+|||+|++.
T Consensus        29 el~edl~~~f~kfG~V~~v---------------------------------------~i~~~----~~~G~~fV~f~~~   65 (114)
T 3s6e_A           29 EIKDDVIEECNKHGGVIHI---------------------------------------YVDKN----SAQGNVYVKCPSI   65 (114)
T ss_dssp             HHHHHHHHHHTTTTCCSEE---------------------------------------EECTT----CTTCCEEEECSSH
T ss_pred             HHHHHHHHHHhccCCEEEE---------------------------------------EEecC----CCcEEEEEEECCH
Confidence            3467899999999999876                                       33333    2589999999999


Q ss_pred             HHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         213 EASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       213 ~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      ++|.+|+..|||++|+||.|+|.|+....
T Consensus        66 e~A~~Ai~~lnG~~f~GR~i~v~~~~~~~   94 (114)
T 3s6e_A           66 AAAIAAVNALHGRWFAGKMITAAYVPLPT   94 (114)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEEECHHH
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEEEcHHH
Confidence            99999999999999999999999986554

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=7.8e-11  Score=88.41  Aligned_cols=83  Identities=13%  Similarity=0.324  Sum_probs=64.4

Q ss_pred             CeeeEEeeCCCccccccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcce
Q psy3016         103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN  182 (305)
Q Consensus       103 g~~l~v~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  182 (305)
                      .++|.|.|......           ..+..+++++|+++|+.||.|..+                               
T Consensus        10 ~~~~~v~w~~~~~~-----------~~~~~~te~~L~~~F~~~G~V~~v-------------------------------   47 (100)
T 2d9o_A           10 TPKLKLKWKCKKED-----------ESKGGYSKDVLLRLLQKYGEVLNL-------------------------------   47 (100)
T ss_dssp             SCEEEEECCCCSSC-----------SCCCSCCHHHHHHHHHTTSCEEEE-------------------------------
T ss_pred             cceEEEeeeccCcc-----------CcCCCCCHHHHHHHHHhcCCEEEE-------------------------------
Confidence            45677777543210           113578999999999999999876                               


Q ss_pred             eEeccCCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       183 ~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                              .++     ++++|||||+|++.++|.+|+..+++  +.|+.|+|.|+..+..
T Consensus        48 --------~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           48 --------VLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             --------EEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             --------EEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence                    333     46899999999999999999998555  6899999999876643

>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=99.11  E-value=8e-11  Score=107.23  Aligned_cols=75  Identities=16%  Similarity=0.328  Sum_probs=63.0

Q ss_pred             cccccccccC--CCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         119 DVGANIFIGN--LDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       119 ~~~~~l~v~n--l~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      .+.++|||+|  |+..+|+++|+++|++||.|..+                                         ..+.
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v-----------------------------------------~~~~   54 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDAL-----------------------------------------LMPP   54 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEE-----------------------------------------ECCT
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEE-----------------------------------------EEeC
Confidence            3568999999  57889999999999999999865                                         2221


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeee---cCe--eeEEEEee
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYL---CNR--PISVSYAF  238 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~---~g~--~l~v~~a~  238 (305)
                          +||||||+|++.++|.+|+++|||+++   .|+  .|.+.|+.
T Consensus        55 ----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           55 ----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE   97 (345)
T ss_dssp             ----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECS
T ss_pred             ----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEee
Confidence                479999999999999999999999988   244  68888874

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.07  E-value=8.2e-10  Score=85.28  Aligned_cols=82  Identities=17%  Similarity=0.147  Sum_probs=70.9

Q ss_pred             CCCcCCCCceEEEcCCCcc-ccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcC-HHHHHHHHHHhc--CceeC
Q psy3016          27 GGESGDGDATIYVGGLDDK-VSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG-EEDADYAIKIMN--MIKLY  102 (305)
Q Consensus        27 ~~~~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~-~e~A~~Ai~~l~--g~~~~  102 (305)
                      ..-.-...+.|+|+||+.. ++.++|+++|+.||+|..|.++.+.      ..|||.|.+ .++|..|++.|+  +..|.
T Consensus        11 ~~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~------~tgfVrf~~~~~~A~~av~~ln~~~~~i~   84 (121)
T 1owx_A           11 GSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAKEALGKAKDANNGNLQLR   84 (121)
T ss_dssp             CCCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC------SEEEEEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             CcccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC------CEEEEEECCChHHHHHHHHHhhcCCcEEe
Confidence            3345566889999999999 9999999999999999999998876      359999999 899999999995  78899


Q ss_pred             CeeeEEeeCCCc
Q psy3016         103 GKPIRVNKASSH  114 (305)
Q Consensus       103 g~~l~v~~~~~~  114 (305)
                      |..++++.....
T Consensus        85 g~~~~~evL~Ge   96 (121)
T 1owx_A           85 NKEVTWEVLEGE   96 (121)
T ss_dssp             SSSEEEEECCHH
T ss_pred             CcEEEEEECCCH
Confidence            998888876543

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.02  E-value=1.1e-09  Score=79.62  Aligned_cols=72  Identities=17%  Similarity=0.276  Sum_probs=61.3

Q ss_pred             CCceEEEcCCCc----cccH----HHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe
Q psy3016          33 GDATIYVGGLDD----KVSE----TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK  104 (305)
Q Consensus        33 ~~~~l~V~nLp~----~~te----~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~  104 (305)
                      ...||+|.-.+.    .+-.    .+|.+.|+.||+|..++++.++        +||+|.+.++|.+|++ |||..+.||
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCe
Confidence            345888877662    3333    5789999999999999998875        8999999999999999 999999999


Q ss_pred             eeEEeeCCC
Q psy3016         105 PIRVNKASS  113 (305)
Q Consensus       105 ~l~v~~~~~  113 (305)
                      .|+|+.+.+
T Consensus        77 ~LkV~lkt~   85 (91)
T 2dnr_A           77 TITIALKSP   85 (91)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEeCCC
Confidence            999998775

>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=98.89  E-value=4.1e-09  Score=90.31  Aligned_cols=68  Identities=18%  Similarity=0.082  Sum_probs=60.8

Q ss_pred             ccHHHHHHHhccCCCeEEEEEcccC----CCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          46 VSETLMWELFVQSGPVVNVHMPKDR----VTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        46 ~te~~L~~~F~~~G~i~~i~~~~~~----~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (305)
                      -.+++|++.|++||.|.++.|..+.    .+++++|++||+|.+.++|.+|++.|||..+.||.|.+.++..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            3567899999999999999998544    3458999999999999999999999999999999999998763

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.83  E-value=4.8e-09  Score=76.58  Aligned_cols=71  Identities=18%  Similarity=0.250  Sum_probs=60.5

Q ss_pred             CCceEEEcCCCcc-----ccH----HHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC
Q psy3016          33 GDATIYVGGLDDK-----VSE----TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG  103 (305)
Q Consensus        33 ~~~~l~V~nLp~~-----~te----~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g  103 (305)
                      ...||+|.-++..     +-.    .+|.+.|+.||+|..++++.++        +||+|.+.++|.+||+ |||..+.|
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeCC
Confidence            3568999877632     322    5688999999999999998875        9999999999999999 99999999


Q ss_pred             eeeEEeeCC
Q psy3016         104 KPIRVNKAS  112 (305)
Q Consensus       104 ~~l~v~~~~  112 (305)
                      |.|+|++-.
T Consensus        85 r~L~V~~k~   93 (95)
T 1ufw_A           85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEeccC
Confidence            999998754

>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=98.76  E-value=7.9e-09  Score=88.49  Aligned_cols=71  Identities=13%  Similarity=0.215  Sum_probs=60.1

Q ss_pred             hcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcc----cCCCCCCccceEEEE
Q psy3016         133 VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIM----RDPDTGNSKGFAFIN  208 (305)
Q Consensus       133 ~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~----~d~~~~~~~g~afV~  208 (305)
                      -.+++|.+.|++||.|..+                                       .|.    .+..++.++|++||+
T Consensus       141 e~~~dl~~e~~~~G~v~~~---------------------------------------~v~~~~~~~~~~~~~~G~~fv~  181 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRV---------------------------------------IIYQEKQGEEEDAEIIVKIFVE  181 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEE---------------------------------------EEEEEECCSSTTCCEEEEEEEE
T ss_pred             HHHHHHHHHHHccCCeEEE---------------------------------------EEecCCCCcccCcCceeEEEEE
Confidence            4567899999999999876                                       333    233456899999999


Q ss_pred             eCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         209 YASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       209 f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      |.+.++|.+|+..|||++++||.|.+.|......
T Consensus       182 f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~~f  215 (222)
T 3dxb_A          182 FSIASETHKAIQALNGRWFAGRKVVAEVYDQERF  215 (222)
T ss_dssp             ESSHHHHHHHHHHHTTCBSSSSBCEEEECCHHHH
T ss_pred             ECCHHHHHHHHHHhcCceECCeEEEEEEcCHHHh
Confidence            9999999999999999999999999999865543

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.75  E-value=9.8e-09  Score=79.21  Aligned_cols=77  Identities=13%  Similarity=0.063  Sum_probs=65.7

Q ss_pred             ccccccccccCCCch-hcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         118 LDVGANIFIGNLDPE-VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      ....+.|||+||+.. ++.++|+++|+.||.|.+|                                       +++.+.
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~V---------------------------------------d~~~g~   55 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWI---------------------------------------DFVRGA   55 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEE---------------------------------------ECCTTC
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEE---------------------------------------EEecCC
Confidence            445788999999999 9999999999999999987                                       556554


Q ss_pred             CCCCccceEEEEeCC-hHHHHHHHHHhc--CeeecCeeeEEEEeee
Q psy3016         197 DTGNSKGFAFINYAS-FEASDASIDAMH--GQYLCNRPISVSYAFK  239 (305)
Q Consensus       197 ~~~~~~g~afV~f~~-~~~A~~Al~~l~--~~~~~g~~l~v~~a~~  239 (305)
                      .      .|||+|.+ .++|..|+.++|  +..|+|..+++....-
T Consensus        56 ~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~G   95 (121)
T 1owx_A           56 K------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEG   95 (121)
T ss_dssp             S------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCH
T ss_pred             C------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECCC
Confidence            3      59999999 899999999995  6788999888887643

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.69  E-value=1.6e-08  Score=73.37  Aligned_cols=57  Identities=18%  Similarity=0.377  Sum_probs=49.4

Q ss_pred             HHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEEeCChHHH
Q psy3016         136 KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEAS  215 (305)
Q Consensus       136 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~f~~~~~A  215 (305)
                      .+|.+.|..||.|..+                                       ++..|        .+||+|.+.++|
T Consensus        30 ~~L~~~F~~~G~Vi~v---------------------------------------r~~~d--------~~fVtF~d~~sA   62 (91)
T 2dnr_A           30 DELLQQFASFGEVILI---------------------------------------RFVED--------KMWVTFLEGSSA   62 (91)
T ss_dssp             HHHHHHHHTTCCEEEE---------------------------------------EECSS--------SEEEEESSHHHH
T ss_pred             HHHHHHHHhCCCeEEE---------------------------------------EEecC--------CEEEEECChHHH
Confidence            5689999999998876                                       44544        289999999999


Q ss_pred             HHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         216 DASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       216 ~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      .+|+. |||..++||.|+|+++.+.
T Consensus        63 laAi~-mnG~~v~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           63 LNVLS-LNGKELLNRTITIALKSPS   86 (91)
T ss_dssp             HHGGG-GTTCEETTEEEEEEECCCS
T ss_pred             HHHHh-cCCeEeCCeEEEEEeCCCC
Confidence            99999 9999999999999998654

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.58  E-value=2.9e-07  Score=68.55  Aligned_cols=75  Identities=24%  Similarity=0.268  Sum_probs=69.1

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccC-----CCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQS-----GPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK  104 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~-----G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~  104 (305)
                      ..+..++|-+-|||..+++..|+.+++++     |.|..|.+..|-      +=|+|+|.+...|.+|.=.|+|.+|.|+
T Consensus        17 ~~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr   90 (117)
T 2l9w_A           17 SKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGK   90 (117)
T ss_dssp             TTTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTE
T ss_pred             CccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCe
Confidence            45568899999999999999999999999     999999999886      5699999999999999988999999999


Q ss_pred             eeEEee
Q psy3016         105 PIRVNK  110 (305)
Q Consensus       105 ~l~v~~  110 (305)
                      +|++.-
T Consensus        91 ~Lr~gT   96 (117)
T 2l9w_A           91 VIRSGT   96 (117)
T ss_dssp             EEEEEC
T ss_pred             EEEecC
Confidence            999974

>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=98.52  E-value=8.8e-08  Score=69.89  Aligned_cols=71  Identities=17%  Similarity=0.305  Sum_probs=56.2

Q ss_pred             ccccccccCCCc-----hhcH----HHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCC
Q psy3016         120 VGANIFIGNLDP-----EVDE----KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDP  190 (305)
Q Consensus       120 ~~~~l~v~nl~~-----~~t~----~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  190 (305)
                      +..+|+|..++.     ++.+    .+|.+.|..||.|..+                                       
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilv---------------------------------------   54 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLV---------------------------------------   54 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEE---------------------------------------
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEE---------------------------------------
Confidence            456777776652     2323    5588899999988766                                       


Q ss_pred             CcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         191 EIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       191 ~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      ++..|.        +||+|.+.++|.+||. |||..++||.|+|++..
T Consensus        55 r~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           55 RINQGQ--------MLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             EEETTE--------EEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             EEecCc--------EEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence            455552        9999999999999999 99999999999999753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.24  E-value=3.5e-06  Score=62.76  Aligned_cols=73  Identities=14%  Similarity=0.084  Sum_probs=62.4

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhc-----CcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAF-----GVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR  194 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~-----g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  194 (305)
                      ..++|-+-|||..+++..|+.+.+++     |.+..+                                         ..
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI-----------------------------------------~L   58 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKI-----------------------------------------LL   58 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEE-----------------------------------------EE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEE-----------------------------------------EE
Confidence            35789999999999999999999999     776633                                         33


Q ss_pred             CCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       195 d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      .++    .+-|+|+|.+..+|.+|.-+|+|.+|.|++|+|.-.
T Consensus        59 ~pD----H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           59 VSD----FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             ETT----TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEECH
T ss_pred             ecC----CCceEEEEccchhhHHHHhhcCCeeecCeEEEecCH
Confidence            333    557999999999999999999999999999998754

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.13  E-value=2.5e-05  Score=57.60  Aligned_cols=89  Identities=22%  Similarity=0.347  Sum_probs=73.1

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhcc-----CCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQ-----SGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~-----~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      ...++|.|.|||..++++.|.-+|+.     =|+|..+....        +-|+|+|.+.+.|++.++. ....+++..|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEE
Confidence            45679999999999999999999997     25999998744        4589999999999999983 3678899999


Q ss_pred             EEeeCCCccccccccccccccCCCchhc
Q psy3016         107 RVNKASSHQKNLDVGANIFIGNLDPEVD  134 (305)
Q Consensus       107 ~v~~~~~~~~~~~~~~~l~v~nl~~~~t  134 (305)
                      .|.......     ..++++.+|++.++
T Consensus        77 sV~P~~~~~-----~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           77 SLRPAPPRA-----PARLLLQGLPPGTS   99 (104)
T ss_dssp             EEEECCCCC-----CCCCCCCSCCCCCC
T ss_pred             EEEcCCCCC-----cceEeeecCCCCCC
Confidence            998765543     35789999988764

>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=97.71  E-value=0.00011  Score=54.35  Aligned_cols=76  Identities=20%  Similarity=0.144  Sum_probs=64.3

Q ss_pred             CCCceEEEcCCCccc-cH----HHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          32 DGDATIYVGGLDDKV-SE----TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~-te----~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      +...+|+|.||+..+ +.    +.++.+|..|+++......+.-      +-..|.|.+.++|.+|...|++..+.|+.+
T Consensus         3 ~~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~   76 (104)
T 1wey_A            3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCcee
Confidence            346789999999866 32    5678999999999888876653      346899999999999999999999999999


Q ss_pred             EEeeCCC
Q psy3016         107 RVNKASS  113 (305)
Q Consensus       107 ~v~~~~~  113 (305)
                      +|.++..
T Consensus        77 r~YFgq~   83 (104)
T 1wey_A           77 KLYFAQT   83 (104)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9998774

>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=97.50  E-value=0.00035  Score=50.70  Aligned_cols=69  Identities=9%  Similarity=0.065  Sum_probs=57.3

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCC--CcceEEEEEEcCHHHHHHHHHHhcCceeCC
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQ--THQGYGFIEFMGEEDADYAIKIMNMIKLYG  103 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~--~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g  103 (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            478999999999999999999999988777776655332  223569999999999999999999987764

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.45  E-value=0.00038  Score=50.74  Aligned_cols=65  Identities=15%  Similarity=0.251  Sum_probs=52.0

Q ss_pred             cCCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc
Q psy3016          24 LEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN   97 (305)
Q Consensus        24 ~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~   97 (305)
                      +.++.........++| ++|+.+...||.++|+.||- ..|+.+.|       .-|||.|.+.+.|..|+..+.
T Consensus         6 l~g~d~~p~r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidD-------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A            6 SGGPDLQPKRDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSCCCCCCCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            4455555555556666 99999999999999999994 55777777       469999999999999999753

>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=97.14  E-value=0.00054  Score=50.69  Aligned_cols=73  Identities=10%  Similarity=0.080  Sum_probs=58.1

Q ss_pred             cccccccCCCchhc-----HHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         121 GANIFIGNLDPEVD-----EKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       121 ~~~l~v~nl~~~~t-----~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      -++|+|+||+.++-     .+.++++|..|+.+...                                       ..+  
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF---------------------------------------~~l--   43 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTF---------------------------------------QYF--   43 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEE---------------------------------------EEE--
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcce---------------------------------------eec--
Confidence            46799999988652     25678899999877653                                       111  


Q ss_pred             CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         196 PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       196 ~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                          ++-.-..|.|.+.++|.+|-..||+..|.|+.++|=|+.
T Consensus        44 ----kSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq   82 (104)
T 1wey_A           44 ----KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             ----TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             ----CcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecC
Confidence                123357899999999999999999999999999999986

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.95  E-value=0.0053  Score=46.60  Aligned_cols=75  Identities=16%  Similarity=0.123  Sum_probs=61.0

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC-eeeEEe
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG-KPIRVN  109 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g-~~l~v~  109 (305)
                      ....+.|.|-+.|... ...+.+.|++||+|.+....      ....+-.|.|.+..+|++|+. .||..+.| -.|-|.
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~   92 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVK   92 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEE
Confidence            4457789999999985 56778889999999988872      134789999999999999999 59999984 778887


Q ss_pred             eCCC
Q psy3016         110 KASS  113 (305)
Q Consensus       110 ~~~~  113 (305)
                      +...
T Consensus        93 p~~d   96 (119)
T 1wwh_A           93 PCID   96 (119)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            7543

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.66  E-value=0.0029  Score=46.19  Aligned_cols=70  Identities=7%  Similarity=0.013  Sum_probs=52.0

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCC--CcceEEEEEEcCHHHHHHHHHHhcCceeCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQ--THQGYGFIEFMGEEDADYAIKIMNMIKLYG  103 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~--~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g  103 (305)
                      +-+|-|..||+.+||+++.+.+..+-++.....+..+.+.  ..-.-|||.|.+.++.....+.++|..+.+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            4579999999999999999888876554433333322221  122458999999999999999999987754

>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=96.61  E-value=0.0024  Score=46.66  Aligned_cols=54  Identities=13%  Similarity=0.242  Sum_probs=46.1

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN   97 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~   97 (305)
                      .||+-++|+.+...||.++|+.|| -..|+.+.|       .-|||.|.+.+.|..|+..+.
T Consensus         7 HV~~l~FP~ewKt~Di~~lFs~fg-gv~I~WidD-------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHVTFPKEWKTSDLYQLFSAFG-NIQISWIDD-------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEECCTTCCHHHHHHHTTTSE-EEEEEEEET-------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEEeCChhhhhHHHHHHHhccC-CEEEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            344449999999999999999999 566888777       369999999999999999764

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.25  E-value=0.011  Score=42.85  Aligned_cols=68  Identities=16%  Similarity=0.155  Sum_probs=49.8

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      +|.|.+||+.+|++++.+.++....+...                               -|+.   .++..+   -...
T Consensus         3 KvVIRrLPP~LteeeF~~~l~~~~~~d~~-------------------------------~fv~---G~~s~~---~~~~   45 (91)
T 1uw4_A            3 KVVIRRLPPTLTKEQLQEHLQPMPEHDYF-------------------------------EFFS---NDTSLY---PHMY   45 (91)
T ss_dssp             EEEEEEECTTCCHHHHHHHHCSCCCEEEE-------------------------------EEEE---SCCSST---TCCC
T ss_pred             EEEEeCCCCCCCHHHHHHHhcCcccceEE-------------------------------EEeC---CccCCC---CCcc
Confidence            58899999999999999999987655432                               0110   011111   1234


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeee
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYL  227 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~  227 (305)
                      ..|||.|.+.++...-...++|..|
T Consensus        46 SRaYi~f~~~e~v~~f~~~~~g~~F   70 (91)
T 1uw4_A           46 ARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             EEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             eEEEEEeCCHHHHHHHHHHhCCcEE
Confidence            5699999999999999999999887

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.91  E-value=0.01  Score=45.63  Aligned_cols=79  Identities=16%  Similarity=0.206  Sum_probs=56.6

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEE-EEEcccCC--------CC-----CcceEEEEEEcCHHHHHHHHHHhcC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRV--------TQ-----THQGYGFIEFMGEEDADYAIKIMNM   98 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~-i~~~~~~~--------~~-----~~~g~afV~f~~~e~A~~Ai~~l~g   98 (305)
                      +...|.|-+.|...+ ..+-+.|++||.|.+ +.......        ..     ....+-.|+|++..+|.+|+. .||
T Consensus         6 ~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENG   83 (132)
T ss_dssp             --CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTT
T ss_pred             CceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCC
Confidence            456788889987765 456678899999876 22211000        00     124678999999999999999 599


Q ss_pred             ceeCCeeeEEeeCCC
Q psy3016          99 IKLYGKPIRVNKASS  113 (305)
Q Consensus        99 ~~~~g~~l~v~~~~~  113 (305)
                      ..+.|..|-|.+...
T Consensus        84 ~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           84 AVFNGVLLGVIPYTK   98 (132)
T ss_dssp             CEETTEECEEEECCH
T ss_pred             eEeCcEEEEEEECCH
Confidence            999999999988764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.52  E-value=0.0056  Score=57.52  Aligned_cols=56  Identities=21%  Similarity=0.306  Sum_probs=43.0

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHH
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK   94 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~   94 (305)
                      ..+.|+|. .|..+++++|.++|++||+|.++.+..+.     .-||.|+|.+.+.+..++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            45799997 79999999999999999999999887653     2799999999999987765

>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=95.30  E-value=0.033  Score=40.53  Aligned_cols=56  Identities=23%  Similarity=0.332  Sum_probs=44.8

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ....+++ +.|..+-..+|.++|+.||-|.-                                        +++-|    
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv~I----------------------------------------~WidD----   49 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNIQI----------------------------------------SWIDD----   49 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSCCC----------------------------------------EEEET----
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCEEE----------------------------------------EEEcC----
Confidence            3456666 99999999999999999996542                                        23333    


Q ss_pred             CccceEEEEeCChHHHHHHHHHhc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMH  223 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~  223 (305)
                         ..|||-|.+.+.|..|++.+.
T Consensus        50 ---TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           50 ---TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             ---TEEEEECSCHHHHHHHHHHHH
T ss_pred             ---CeEEEEecCHHHHHHHHHhcc
Confidence               369999999999999999774

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.27  E-value=0.038  Score=40.64  Aligned_cols=74  Identities=18%  Similarity=0.192  Sum_probs=56.2

Q ss_pred             cccccccCCCchhcHHHHHHHHhhc-----CcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAF-----GVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~-----g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      ..+|.|.|||..+.++.|.-.|+.-     |.|..+                                         .++
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v-----------------------------------------~~~   46 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW-----------------------------------------QRL   46 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEE-----------------------------------------EEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEE-----------------------------------------EEc
Confidence            4689999999999999999999862     455433                                         222


Q ss_pred             CCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         196 PDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       196 ~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                            .+-|+|+|.+.+.|.+.++ -..+.+.+..|.|.-..+++.
T Consensus        47 ------~~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV~P~~~~~~   86 (104)
T 2dhx_A           47 ------GCGGVLTFREPADAERVLA-QADHELHGAQLSLRPAPPRAP   86 (104)
T ss_dssp             ------TTEEEEEESSHHHHHHHHT-CSCCBSSSSBCEEEECCCCCC
T ss_pred             ------CCcEEEEEcChHHHHHHhc-CCcceecCeEEEEEcCCCCCc
Confidence                  1578999999999988887 236678889999976555543

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.96  E-value=0.048  Score=39.71  Aligned_cols=69  Identities=13%  Similarity=0.108  Sum_probs=47.9

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      -+|.|..||+.+|++++.+.++..-++.+.                                  .....++...   ...
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~----------------------------------~fv~G~~s~~---~~~   52 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYF----------------------------------EFFAADLSLY---PHL   52 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEEC----------------------------------CCCCCCSSSC---CSC
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceE----------------------------------EEeCCccCCC---CCc
Confidence            468899999999999998887764433221                                  1111111111   123


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeee
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYL  227 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~  227 (305)
                      ...|||.|.+.++...-...++|..|
T Consensus        53 ~SRAYI~F~~~edv~~F~~~f~g~~F   78 (97)
T 2l08_A           53 YSRAYINFRNPDDILLFRDRFDGYIF   78 (97)
T ss_dssp             CCCCEEEESCHHHHHHHHHHSTTEEE
T ss_pred             ceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            34599999999999999999999887

>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=94.44  E-value=0.097  Score=39.61  Aligned_cols=73  Identities=16%  Similarity=0.251  Sum_probs=55.8

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ...|.|.+.+... ...|...|+.||.|...                                         ..    -.
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~-----------------------------------------~~----~~   57 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKH-----------------------------------------VM----SN   57 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEE-----------------------------------------EE----CS
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEe-----------------------------------------cc----CC
Confidence            4678888898875 56677889999999863                                         11    12


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecC-eeeEEEEeeec
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCN-RPISVSYAFKK  240 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g-~~l~v~~a~~~  240 (305)
                      ..+...|+|++..+|.+||. .||..++| -.|-|..+.++
T Consensus        58 ~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~d~   97 (119)
T 1wwh_A           58 TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   97 (119)
T ss_dssp             SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECCCH
Confidence            35688999999999999999 69999975 56667776433

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.21  E-value=0.31  Score=37.39  Aligned_cols=38  Identities=13%  Similarity=0.107  Sum_probs=32.8

Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      .+...|+|++..+|.+||. -||..|.|.-|=|..+.+.
T Consensus        62 ~NWikItYds~~~A~rAL~-~NG~ii~G~mIGV~Py~~~   99 (132)
T 3p3d_A           62 NSWTKITYDNPASAVDALL-ENGAVFNGVLLGVIPYTKD   99 (132)
T ss_dssp             TTEEEEEBSSHHHHHHHHT-TTTCEETTEECEEEECCHH
T ss_pred             CcEEEEEcCCHHHHHHHHH-hCCeEeCcEEEEEEECCHH
Confidence            5678999999999999999 7999999998888887543

>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=93.11  E-value=0.044  Score=39.97  Aligned_cols=54  Identities=24%  Similarity=0.353  Sum_probs=43.4

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ..+++ +.|..+-..+|.++|+.||.|.-                                        +++-|      
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~I----------------------------------------~WidD------   39 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQI----------------------------------------SWIDD------   39 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEEE----------------------------------------EEEET------
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEEE----------------------------------------EEEcC------
Confidence            45666 99999999999999999995542                                        22333      


Q ss_pred             cceEEEEeCChHHHHHHHHHhc
Q psy3016         202 KGFAFINYASFEASDASIDAMH  223 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~  223 (305)
                       ..|||-|.+.+.|..|+..+.
T Consensus        40 -TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A           40 -TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             -TEEEEEEEEECHHHHHHHHHT
T ss_pred             -CeEEEEecCHHHHHHHHHhcc
Confidence             369999999999999999874

>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=92.26  E-value=0.34  Score=46.12  Aligned_cols=65  Identities=18%  Similarity=0.305  Sum_probs=50.6

Q ss_pred             cCCCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc
Q psy3016          24 LEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN   97 (305)
Q Consensus        24 ~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~   97 (305)
                      ++++.........++|+ +|..+...+|.++|+.||. ..|+.+.+       ..|||.|.+.+.|..++..+.
T Consensus       430 l~g~d~~~~R~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          430 LEGPDLQPKRDHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             SSSCCCCCCGGGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            44444444445577776 9999999999999999995 45666555       469999999999999999875

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=89.50  E-value=0.13  Score=48.27  Aligned_cols=57  Identities=16%  Similarity=0.246  Sum_probs=40.0

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...+.|+|. .+..+++.+|.+.|..||.|..+                                         ..+...
T Consensus        51 qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~-----------------------------------------~~~~~~   88 (464)
T 3pq1_A           51 QAQRTVLIH-CPEKISENKFLKYLSQFGPINNH-----------------------------------------FFYESF   88 (464)
T ss_dssp             HHHTEEEEE-ECCC---CHHHHHHGGGSCCCCE-----------------------------------------EEECSS
T ss_pred             HhcceEEEE-cCCCCCHHHHHHHHHhcCCcceE-----------------------------------------EEEccC
Confidence            345789997 78889999999999999999864                                         444333


Q ss_pred             CCccceEEEEeCChHHHHHHHH
Q psy3016         199 GNSKGFAFINYASFEASDASID  220 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~  220 (305)
                      |   .||.|+|.+.+++..++.
T Consensus        89 g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           89 G---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             S---EEEEEECC---CCHHHHS
T ss_pred             C---eEEEEEeCCHHHHHHHHh
Confidence            3   799999999988886654

>2v8f_C MDIA1, profilin IIA; alternative splicing, protein-binding, cytoplasm, acetylation, cytoskeleton, actin-binding; 1.1A {Mus musculus}

Probab=86.69  E-value=0.72  Score=24.14  Aligned_cols=7  Identities=71%  Similarity=1.958  Sum_probs=2.8

Q ss_pred             CCCCCCC
Q psy3016         291 GLPPPPP  297 (305)
Q Consensus       291 ~~ppppp  297 (305)
                      +.|||||
T Consensus        12 giPpPpp   18 (26)
T 2v8f_C           12 SIPPPPP   18 (26)
T ss_pred             CCCCCCC
Confidence            3444333

---

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
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-21
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-14
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-21
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-21
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	7e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-19
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-19
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-18
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-18
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-18
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-09
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	9e-18
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-17
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-17
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-17
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	7e-17
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-17
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-16
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	8e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-16
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-15
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-16
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-16
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-16
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-07
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-16
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	4e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	5e-16
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-16
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-08
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	7e-16
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	8e-16
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	9e-16
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	9e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-15
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-15
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-15
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-15
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	7e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-15
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	9e-09
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-15
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	4e-15
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	7e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-15
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	8e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-14
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-14
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-14
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-06
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-14
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	8e-14
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-13
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-13
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-13
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-06
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-13
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-13
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	9e-13
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-12
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	4e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-12
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	5e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	0.002
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-12
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	8e-12
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	8e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	9e-12
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.001
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-11
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	4e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	4e-11
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-11
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	7e-11
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	7e-11
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	7e-11
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.004
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-10
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	7e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-06
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:) 3e-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:) 3e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-10
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-09
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	6e-05
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-09
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-09
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-09
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	1e-08
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	0.001
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-08
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	0.001
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-08
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-08
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-08
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	4e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	6e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-07
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	4e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	4e-07
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	2e-05
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	2e-06
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-06
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.001
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	7e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-05
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002

>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 = 84.6 bits (209), Expect = 1e-21
 Identities = 25/77 (32%), Positives = 48/77 (62%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           A++YVG L   V+E +++E F  +GP++++ + +D +T+   GY ++ F    DA+ A+ 
Sbjct: 1   ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 60

Query: 95  IMNMIKLYGKPIRVNKA 111
            MN   + GKP+R+  +
Sbjct: 61  TMNFDVIKGKPVRIMWS 77

>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 = 65.3 bits (159), Expect = 2e-14
 Identities = 24/120 (20%), Positives = 50/120 (41%), Gaps = 40/120 (33%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
           A++++G+L P+V E +LY+ FS  G IL                                
Sbjct: 1   ASLYVGDLHPDVTEAMLYEKFSPAGPIL-------------------------------- 28

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                     + RD  T  S G+A++N+     ++ ++D M+   +  +P+ + ++ ++D
Sbjct: 29  -------SIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS-QRD 80

>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 = 87.7 bits (216), Expect = 1e-21
 Identities = 38/209 (18%), Positives = 71/209 (33%), Gaps = 44/209 (21%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +++GGL  + ++  +   F Q G + +  + +D  T+  +G+GF+ +   E+ D A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 96  MN----MIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQT 151
                    +  K     + S           IF+G +  + +E  L D F  +G I   
Sbjct: 68  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--- 124

Query: 152 PKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYAS 211
                                                  EIM D  +G  +GFAF+ +  
Sbjct: 125 ------------------------------------EVIEIMTDRGSGKKRGFAFVTFDD 148

Query: 212 FEASDASIDAMHGQYLCNRPISVSYAFKK 240
            ++ D  +       +      V  A  K
Sbjct: 149 HDSVDKIV-IQKYHTVNGHNCEVRKALSK 176

>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 = 64.6 bits (156), Expect = 3e-13
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
             I+VGG+ +   E  + + F Q G +  + +  DR +   +G+ F+ F   +  D  + 
Sbjct: 98  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157

Query: 95  IMNMIKLYGKPIRVNKASSHQK 116
                 + G    V KA S Q+
Sbjct: 158 -QKYHTVNGHNCEVRKALSKQE 178

>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 = 83.5 bits (206), Expect = 5e-21
 Identities = 70/87 (80%), Positives = 80/87 (91%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           + DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT  HQGYGF+EF+ EEDADY
Sbjct: 7   NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 66

Query: 92  AIKIMNMIKLYGKPIRVNKASSHQKNL 118
           AIKIM+MIKLYGKPIRVNKAS+H KNL
Sbjct: 67  AIKIMDMIKLYGKPIRVNKASAHNKNL 93

>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 = 52.7 bits (126), Expect = 7e-10
 Identities = 25/120 (20%), Positives = 44/120 (36%), Gaps = 39/120 (32%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
           A +++G LD +V E LL++ F   G                                   
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAG----------------------------------- 34

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                 ++  + +D  TG  +G+ F+ + S E +D +I  M    L  +PI V+ A   +
Sbjct: 35  ----PVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN 90

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.8 bits (194), Expect = 3e-19
 Identities = 24/82 (29%), Positives = 47/82 (57%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+YVG L    +E  ++ELF +SG +  + M  D++ +T  G+ F+E+    DA+ A++ 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 96  MNMIKLYGKPIRVNKASSHQKN 117
           +N  +L  + IR +  +  ++ 
Sbjct: 69  INGTRLDDRIIRTDWDAGFKEG 90

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.1 bits (135), Expect = 5e-11
 Identities = 20/123 (16%), Positives = 38/123 (30%), Gaps = 39/123 (31%)

Query: 115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQ 174
           +K L     +++GNL     E+ +Y+ FS  G                            
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSG---------------------------- 32

Query: 175 KNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
                            +  D     + GF F+ Y S   ++ ++  ++G  L +R I  
Sbjct: 33  -----------DIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT 81

Query: 235 SYA 237
            + 
Sbjct: 82  DWD 84

>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 = 78.1 bits (192), Expect = 5e-19
 Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDR-VTQTHQGYGFIEFMGEEDADYAI 93
           + I V  +  + ++  + ELF   G +  V +PK    T  H+G+GF++F+ ++DA  A 
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 94  KIM-NMIKLYGKPIRVNKASS 113
             + +   LYG+ + +  A S
Sbjct: 69  NALCHSTHLYGRRLVLEWADS 89

>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 = 60.3 bits (146), Expect = 2e-12
 Identities = 16/124 (12%), Positives = 44/124 (35%), Gaps = 41/124 (33%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
           + I + N+  + +++ + + FS FG +                                 
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVR----------------------------- 39

Query: 182 NIFIGNLDPEIMRDPD-TGNSKGFAFINYASFEASDASIDAM-HGQYLCNRPISVSYAFK 239
                     + +    TG  +GF F+++ + + +  + +A+ H  +L  R + + +A  
Sbjct: 40  ----------LPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 89

Query: 240 KDSK 243
           + + 
Sbjct: 90  EVTV 93

>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 = 76.5 bits (188), Expect = 2e-18
 Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           + + V GL  K +E  + E F   G V+ V + KD  T   +G+GF+ F   E     + 
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 95  IMNMIKLYGKPIRVNKASSHQ 115
             +MI   G+       +S Q
Sbjct: 69  QRHMID--GRWCDCKLPNSKQ 87

>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 = 55.7 bits (134), Expect = 6e-11
 Identities = 20/129 (15%), Positives = 40/129 (31%), Gaps = 41/129 (31%)

Query: 115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQ 174
           ++ +   +++ +  L  +  E+ L + FS F                             
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTF----------------------------- 32

Query: 175 KNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
                        L  ++ +D  TG+SKGF F+ +  +E     +   H   +  R    
Sbjct: 33  ----------GEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHM--IDGRWCDC 80

Query: 235 SYAFKKDSK 243
                K S+
Sbjct: 81  KLPNSKQSQ 89

>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 = 76.1 bits (187), Expect = 2e-18
 Identities = 22/86 (25%), Positives = 44/86 (51%), Gaps = 3/86 (3%)

Query: 28  GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           GES   D  +YV  L   +++  +  +F + G +V  ++ +D++T   +G  F+ +   E
Sbjct: 1   GESIK-DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 59

Query: 88  DADYAIKIMN--MIKLYGKPIRVNKA 111
           +A  AI  +N  + +   +P+ V  A
Sbjct: 60  EAQEAISALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 59.2 bits (143), Expect = 3e-12
 Identities = 21/119 (17%), Positives = 39/119 (32%), Gaps = 41/119 (34%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
             N+++ NL   + +  L   F  +G I+Q   + +                        
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK----------------------- 42

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL--CNRPISVSYA 237
                            TG  +G AF+ Y   E +  +I A++       ++P+SV  A
Sbjct: 43  ----------------LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 85

>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 = 74.7 bits (183), Expect = 7e-18
 Identities = 25/81 (30%), Positives = 44/81 (54%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL + +++  + EL    GP+   ++ KD  T   +GY F E++     D AI  +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 97  NMIKLYGKPIRVNKASSHQKN 117
           N ++L  K + V +AS   KN
Sbjct: 64  NGMQLGDKKLLVQRASVGAKN 84

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 7e-09
 Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 20/79 (25%)

Query: 183 IFIGNLDPEI--------------------MRDPDTGNSKGFAFINYASFEASDASIDAM 222
           +FIG L   +                    ++D  TG SKG+AF  Y     +D +I  +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 223 HGQYLCNRPISVSYAFKKD 241
           +G  L ++ + V  A    
Sbjct: 64  NGMQLGDKKLLVQRASVGA 82

>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 = 74.2 bits (182), Expect = 9e-18
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL  + ++  + E F Q G V    + +D +T+  +G+GF+ FM +   D  +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 97  NMIKLYGKPIRVNKA 111
           +  +L  K I    A
Sbjct: 62  SRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.8 bits (134), Expect = 5e-11
 Identities = 23/115 (20%), Positives = 36/115 (31%), Gaps = 40/115 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FIG L  +  ++ L + F  FG                                     
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFG------------------------------------- 25

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
                +  +MRDP T  S+GF F+ +      D  + A     L ++ I    AF
Sbjct: 26  --EVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKVAF 77

>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 = 73.5 bits (180), Expect = 5e-17
 Identities = 18/118 (15%), Positives = 47/118 (39%), Gaps = 12/118 (10%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +Y+  L  K++   M+++F + GP+  + +         +G  ++ +    DA  A   
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNACDH 65

Query: 96  MNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
           ++   +  + + V   ++++             +D +  E+ L      +G+    PK
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAF---------QKMDTKKKEEQLKLLKEKYGINTDPPK 114

>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 = 58.1 bits (140), Expect = 2e-11
 Identities = 22/130 (16%), Positives = 41/130 (31%), Gaps = 42/130 (32%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           ++I NL  ++  + +YD F  +G I Q                                 
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQ--------------------------------- 36

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                    +R  +T  ++G A++ Y     +  + D + G  +CNR + V Y     + 
Sbjct: 37  ---------IRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAF 87

Query: 244 GDRHGSAAER 253
                   E 
Sbjct: 88  QKMDTKKKEE 97

>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 = 72.4 bits (177), Expect = 5e-17
 Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 2/80 (2%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           DA +YV GL   +++  + +LF Q G ++   +  D+VT   +G GFI F    +A+ AI
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 94  KIMNMIKLYG--KPIRVNKA 111
           K +N  K  G  +PI V  A
Sbjct: 66  KGLNGQKPSGATEPITVKFA 85

>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 = 57.4 bits (138), Expect = 2e-11
 Identities = 23/119 (19%), Positives = 40/119 (33%), Gaps = 41/119 (34%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
            AN+++  L   + +K L   FS +G                                  
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYG---------------------------------- 31

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL--CNRPISVSYA 237
                  +   I+ D  TG S+G  FI +     ++ +I  ++GQ       PI+V +A
Sbjct: 32  -----RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 85

>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 = 71.9 bits (176), Expect = 6e-17
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +++GGL    ++  + + F + G VV+  +  D +T   +G+GF+ F   E  D  +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 97  NMIKLYGKPIRVNKA 111
              KL GK I   +A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.4 bits (115), Expect = 2e-08
 Identities = 25/114 (21%), Positives = 36/114 (31%), Gaps = 40/114 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FIG L  +  +K L D FS                                        
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSK--------------------------------------- 22

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           F   +D  +  DP TG S+GF F+ +   E+ D  +D      L  + I    A
Sbjct: 23  FGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA 75

>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 = 72.0 bits (176), Expect = 7e-17
 Identities = 30/76 (39%), Positives = 48/76 (63%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +YVGGL ++V + ++   F+  G + ++ +P D  T+ H+G+ F+EF   EDA  AI  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 96  MNMIKLYGKPIRVNKA 111
           MN  +L+G+ IRVN A
Sbjct: 67  MNESELFGRTIRVNLA 82

>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 = 50.8 bits (121), Expect = 4e-09
 Identities = 30/120 (25%), Positives = 45/120 (37%), Gaps = 39/120 (32%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++G L  EVD+K+L+  F  FG I                                   
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDIT---------------------------------- 33

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                D +I  D +T   +GFAF+ +   E + A+ID M+   L  R I V+ A     K
Sbjct: 34  -----DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK 88

>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 = 72.2 bits (177), Expect = 9e-17
 Identities = 20/96 (20%), Positives = 47/96 (48%), Gaps = 14/96 (14%)

Query: 28  GESGDGD-----ATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFI 81
           G SG  D     + +++G L+   V ++ +  +F + G +V   +        H+G+ F+
Sbjct: 4   GSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFV 55

Query: 82  EFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
           +++ E +A  A+   +   + G+ + +N A+  + N
Sbjct: 56  QYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVN 91

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.0 bits (135), Expect = 6e-11
 Identities = 19/132 (14%), Positives = 39/132 (29%), Gaps = 48/132 (36%)

Query: 119 DVGANIFIGNLDPE-VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNL 177
            + + +FIGNL+   V +  +   FS +G I+                            
Sbjct: 13  SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK---------------------- 50

Query: 178 DVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                                    GFAF+ Y +   + A++    G+ +  + + ++ A
Sbjct: 51  -------------------------GFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA 85

Query: 238 FKKDSKGDRHGS 249
            +         S
Sbjct: 86  AEPKVNRSGPSS 97

>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 = 71.1 bits (174), Expect = 1e-16
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           + V  LD  VS+  + ELF + G +    +  DR +    G   + F  + DA  A+K  
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 97  NMIKLYGKPIRVNKASS 113
           N + L G+P+ +   +S
Sbjct: 62  NGVPLDGRPMNIQLVTS 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 = 49.5 bits (118), Expect = 8e-09
 Identities = 15/114 (13%), Positives = 35/114 (30%), Gaps = 40/114 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           + + NLD  V +  + + F+ FG + +     +                           
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-------------------------- 36

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                         +G S G A +++     +  ++   +G  L  RP+++   
Sbjct: 37  --------------SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 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 = 71.3 bits (174), Expect = 1e-16
 Identities = 75/121 (61%), Positives = 83/121 (68%), Gaps = 38/121 (31%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IFIGNLDPE+DEKLLYDTFSAFGVILQTPKIM                            
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIM---------------------------- 32

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                     RDPDTGNSKG+AFIN+ASF+ASDA+I+AM+GQYLCNRPI+VSYAFKKDSK
Sbjct: 33  ----------RDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK 82

Query: 244 G 244
           G
Sbjct: 83  G 83

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.1 bits (163), Expect = 4e-15
 Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVH-MPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           I++G LD ++ E L+++ F   G ++    + +D  T   +GY FI F   + +D AI+ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 96  MNMIKLYGKPIRVNKA 111
           MN   L  +PI V+ A
Sbjct: 61  MNGQYLCNRPITVSYA 76

>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 = 70.5 bits (172), Expect = 2e-16
 Identities = 24/83 (28%), Positives = 45/83 (54%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G   + D +  + V GL    +E  + E+F + GP+ +V +  D+ ++  +G+ F+ F  
Sbjct: 1   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 86  EEDADYAIKIMNMIKLYGKPIRV 108
            +DA  A +  N ++L G+ IRV
Sbjct: 61  VDDAKEAKERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 1e-07
 Identities = 21/120 (17%), Positives = 38/120 (31%), Gaps = 39/120 (32%)

Query: 115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQ 174
           + N D    + +  L     E+ L + FS +G                            
Sbjct: 3   RANPDPNCCLGVFGLSLYTTERDLREVFSKYG---------------------------- 34

Query: 175 KNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
                         D  I+ D  +  S+GFAF+ + + + +  + +  +G  L  R I V
Sbjct: 35  -----------PIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

>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 = 70.5 bits (172), Expect = 4e-16
 Identities = 20/90 (22%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 28  GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           G +G+ D  IYVG L   +    + ++F + G + ++ +      +    + F+EF    
Sbjct: 8   GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPR 64

Query: 88  DADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
           DA+ A+   +     G  +RV    S +  
Sbjct: 65  DAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 94

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 2e-07
 Identities = 16/121 (13%), Positives = 32/121 (26%), Gaps = 42/121 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           I++GNL P++  K + D F  +G I                                   
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAI----------------------------------- 41

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                    +   +      FAF+ +     ++ ++    G       + V +       
Sbjct: 42  -------RDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 94

Query: 244 G 244
           G
Sbjct: 95  G 95

>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 = 70.5 bits (172), Expect = 4e-16
 Identities = 23/90 (25%), Positives = 42/90 (46%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           G     G   ++V  L    SE  + +LF   GP+  +H P D +T+  +G+ F+ FM  
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKASSHQK 116
           E A  A   ++     G+ + V  ++  ++
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPSTIKKE 90

>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 = 44.7 bits (105), Expect = 7e-07
 Identities = 22/128 (17%), Positives = 38/128 (29%), Gaps = 39/128 (30%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            +F+ NL     E+ L   FSA+G + +    ++                          
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPID-------------------------- 43

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
                          T   KGFAF+ +   E +  +   + GQ    R + V  +  K  
Sbjct: 44  -------------SLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE 90

Query: 243 KGDRHGSA 250
                 S+
Sbjct: 91  ASQSGPSS 98

>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 = 69.6 bits (170), Expect = 5e-16
 Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VGGL     E  + E F   G V ++ +P D  T   +G+ FI F  EE     ++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 97  NMIKLYGKPIRVNKA 111
               +      +  A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 4e-08
 Identities = 18/114 (15%), Positives = 32/114 (28%), Gaps = 40/114 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+G L P+  E+ + + F  FG +                                   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVES--------------------------------- 28

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                  E+  D  T   +GF FI +   E     ++  +   +      +  A
Sbjct: 29  ------IELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY-HNVGLSKCEIKVA 75

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.7 bits (170), Expect = 5e-16
 Identities = 26/80 (32%), Positives = 39/80 (48%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D +ATI V  L +   ET + ELF   G +  +++ KD+ T   +G+ FI F   EDA  
Sbjct: 6   DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 92  AIKIMNMIKLYGKPIRVNKA 111
           AI  ++        + V  A
Sbjct: 66  AIAGVSGFGYDHLILNVEWA 85

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 3e-08
 Identities = 24/123 (19%), Positives = 39/123 (31%), Gaps = 39/123 (31%)

Query: 115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQ 174
            +  D  A I + NL  +  E  L + F  F                             
Sbjct: 2   NRRADDNATIRVTNLSEDTRETDLQELFRPF----------------------------- 32

Query: 175 KNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
                            + +D  TG SKGFAFI++   E +  +I  + G    +  ++V
Sbjct: 33  ----------GSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV 82

Query: 235 SYA 237
            +A
Sbjct: 83  EWA 85

>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 = 69.3 bits (169), Expect = 6e-16
 Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +++GGL  + ++  +   F Q G + +  + +D  T+  +G+GF+ +   E+ D A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66

Query: 96  MNMIKLYGKPIRVNKASS 113
               K+ G+ +   +A S
Sbjct: 67  ARPHKVDGRVVEPKRAVS 84

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 24/114 (21%), Positives = 38/114 (33%), Gaps = 40/114 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FIG L  E  ++ L   F                                         
Sbjct: 9   LFIGGLSFETTDESLRSHFEQ--------------------------------------- 29

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
           +    D  +MRDP+T  S+GF F+ YA+ E  DA+++      +  R +    A
Sbjct: 30  WGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA 82

>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 = 69.0 bits (168), Expect = 7e-16
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I+VGGL    +   +   F Q G V +  +  D+ T  H+G+GF+ F  E+  +   + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 97  NMIKLYGKPIRVNKA 111
           +  ++  K +   KA
Sbjct: 61  HFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.2 bits (101), Expect = 2e-06
 Identities = 17/114 (14%), Positives = 31/114 (27%), Gaps = 40/114 (35%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           IF+G L      + +   F  FG +                                   
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDD--------------------------------- 28

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                   +M D  T   +GF F+ + S +  +     +H   + N+ +    A
Sbjct: 29  ------AMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHFHEINNKMVECKKA 75

>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 = 69.3 bits (169), Expect = 8e-16
 Identities = 22/78 (28%), Positives = 41/78 (52%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           +  + V  L   +++  ++ LF   GP+    + +D  T    GY F++F  E D+  AI
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 94  KIMNMIKLYGKPIRVNKA 111
           K++N I +  K ++V+ A
Sbjct: 62  KVLNGITVRNKRLKVSYA 79

>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 = 53.5 bits (128), Expect = 4e-10
 Identities = 23/115 (20%), Positives = 41/115 (35%), Gaps = 39/115 (33%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           N+ +  L  ++ ++ LY  F A G I     + +                          
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY------------------------- 38

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                          TG S G+AF+++ S   S  +I  ++G  + N+ + VSYA
Sbjct: 39  --------------KTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA 79

>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 = 69.7 bits (170), Expect = 9e-16
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T++   L  ++    + + F   G V +V +  DR ++  +G  ++EF   +    AI  
Sbjct: 20  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG- 78

Query: 96  MNMIKLYGKPIRVNKASSHQKN 117
           +   +L G PI V  + + +KN
Sbjct: 79  LTGQRLLGVPIIVQASQA-EKN 99

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 9e-09
 Identities = 25/139 (17%), Positives = 46/139 (33%), Gaps = 41/139 (29%)

Query: 105 PIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKP 164
           P+R    +   +  D    +F   L   +  + L D FSA G +                
Sbjct: 3   PVREPVDNLSPEERD-ARTVFCMQLAARIRPRDLEDFFSAVGKVR--------------- 46

Query: 165 IRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHG 224
                                   D  I+ D ++  SKG A++ +   ++   +I  + G
Sbjct: 47  ------------------------DVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTG 81

Query: 225 QYLCNRPISVSYAFKKDSK 243
           Q L   PI V  +  + ++
Sbjct: 82  QRLLGVPIIVQASQAEKNR 100

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.3 bits (169), Expect = 1e-15
 Identities = 18/101 (17%), Positives = 47/101 (46%), Gaps = 1/101 (0%)

Query: 17  QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
           ++L    LE      +    +++GGL  + +E  +   + Q G + +  + +D  ++  +
Sbjct: 3   KTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSR 62

Query: 77  GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
           G+GF+ F    + D A+       + G+ +   +A + +++
Sbjct: 63  GFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREES 102

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.4 bits (138), Expect = 2e-11
 Identities = 24/141 (17%), Positives = 46/141 (32%), Gaps = 40/141 (28%)

Query: 104 KPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGK 163
           K +        ++  +    +FIG L  E  E+ L + +  +G +               
Sbjct: 3   KTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTD------------- 49

Query: 164 PIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMH 223
                                       +MRDP +  S+GF F+ ++S    DA++ A  
Sbjct: 50  --------------------------CVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AAR 82

Query: 224 GQYLCNRPISVSYAFKKDSKG 244
              +  R +    A  ++  G
Sbjct: 83  PHSIDGRVVEPKRAVAREESG 103

>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 = 68.5 bits (167), Expect = 1e-15
 Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+YVG L   V+E L+ +LF Q GP  +  M  +    ++  Y F+EF    DA  A+  
Sbjct: 10  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALAA 67

Query: 96  MNMIKLYGKPIRVNKASS 113
           MN  K+ GK ++VN A++
Sbjct: 68  MNGRKILGKEVKVNWATT 85

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 17/120 (14%), Positives = 39/120 (32%), Gaps = 41/120 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++GNL  +V E L+   FS  G                                     
Sbjct: 11  LYVGNLSRDVTEVLILQLFSQIGPCK---------------------------------- 36

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
                        +  ++  + F+ +     + A++ AM+G+ +  + + V++A    S+
Sbjct: 37  -------SCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ 89

>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 = 68.5 bits (167), Expect = 2e-15
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 6/87 (6%)

Query: 27  GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
           G ++    + ++VG L   ++E  M +LF + G    V +         +G+GFI     
Sbjct: 1   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETR 54

Query: 87  EDADYAIKIMNMIKLYGKPIRVNKASS 113
             A+ A   ++ + L GK +RV  A  
Sbjct: 55  TLAEIAKVELDNMPLRGKQLRVRFACH 81

>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 = 45.3 bits (107), Expect = 3e-07
 Identities = 15/120 (12%), Positives = 32/120 (26%), Gaps = 45/120 (37%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            +F+GNL P++ E+ +   F  +G   +     +                          
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------------------------ 45

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
                                F FI   +   ++ +   +    L  + + V +A    S
Sbjct: 46  ---------------------FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS 84

>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 = 67.8 bits (165), Expect = 2e-15
 Identities = 21/76 (27%), Positives = 41/76 (53%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            + V  L   +++     LF   G + +  + +D++T    GYGF+ ++  +DA+ AI  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 96  MNMIKLYGKPIRVNKA 111
           +N ++L  K I+V+ A
Sbjct: 64  LNGLRLQTKTIKVSYA 79

>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 = 49.7 bits (118), Expect = 7e-09
 Identities = 20/115 (17%), Positives = 38/115 (33%), Gaps = 39/115 (33%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           N+ +  L   + ++     F + G I     + +                          
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK------------------------- 38

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                          TG S G+ F+NY   + ++ +I+ ++G  L  + I VSYA
Sbjct: 39  --------------ITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA 79

>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 = 67.8 bits (165), Expect = 3e-15
 Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           G   I++  LD  +    +++ F   G +++  +         +GYGF+ F  +E A+ A
Sbjct: 7   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQEAAERA 64

Query: 93  IKIMNMIKLYGKPIRVNKASS 113
           I+ MN + L  + + V +  S
Sbjct: 65  IEKMNGMLLNDRKVFVGRFKS 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 = 49.6 bits (118), Expect = 9e-09
 Identities = 32/122 (26%), Positives = 49/122 (40%), Gaps = 41/122 (33%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
            NIFI NLD  +D K LYDTFSAFG IL    + +                         
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG---------------------- 46

Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                              SKG+ F+++ + EA++ +I+ M+G  L +R + V     + 
Sbjct: 47  -------------------SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 87

Query: 242 SK 243
            +
Sbjct: 88  ER 89

>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 = 67.5 bits (164), Expect = 3e-15
 Identities = 12/78 (15%), Positives = 32/78 (41%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           + T+++       ++  + +L      V            T + + +I+   +EDA Y +
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 94  KIMNMIKLYGKPIRVNKA 111
           + +N +K+ G  +    +
Sbjct: 61  EKLNGLKIEGYTLVTKVS 78

>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 = 42.1 bits (98), Expect = 3e-06
 Identities = 11/114 (9%), Positives = 34/114 (29%), Gaps = 39/114 (34%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++ N  P   ++ + D      V+  + ++ ++                          
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF------------------------ 39

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                            S+ FA+I+  S E +   ++ ++G  +    +    +
Sbjct: 40  ---------------NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS 78

>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 = 67.8 bits (165), Expect = 4e-15
 Identities = 22/101 (21%), Positives = 47/101 (46%), Gaps = 2/101 (1%)

Query: 19  LSQTKLEGGGESGDG--DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
           L+Q  +   G   +G   A +++  L  +  +  + ++F+  G VV+  +  D+ T   +
Sbjct: 1   LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 60

Query: 77  GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
            +GF+ +     A  AI+ MN  ++  K ++V    S   +
Sbjct: 61  CFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 101

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 7e-10
 Identities = 29/134 (21%), Positives = 48/134 (35%), Gaps = 40/134 (29%)

Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
           A+  QK    GAN+FI +L  E  ++ L   F                            
Sbjct: 8   AAGSQKEGPEGANLFIYHLPQEFGDQDLLQMF---------------------------- 39

Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
                        F   +  ++  D  T  SK F F++Y +  ++ A+I +M+G  +  +
Sbjct: 40  -----------MPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMK 88

Query: 231 PISVSYAF-KKDSK 243
            + V     K DSK
Sbjct: 89  RLKVQLKRSKNDSK 102

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 67.0 bits (163), Expect = 4e-15
 Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 3/83 (3%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVN---VHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           +++  L+   +E  +  +F + G + +                G+GF+E+   E A  A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 94  KIMNMIKLYGKPIRVNKASSHQK 116
           K +    + G  + V  +    K
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 = 53.9 bits (129), Expect = 3e-10
 Identities = 18/118 (15%), Positives = 30/118 (25%), Gaps = 36/118 (30%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FI NL+    E+ L   FS  G I                                   
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKK-------------------------- 34

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
                            S GF F+ Y   E +  ++  + G  +    + V  + +  
Sbjct: 35  ----------NKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERAT 82

>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 = 66.9 bits (163), Expect = 6e-15
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
           +S   + T+Y GG+   +++ LM + F   G ++ + +         +GY F+ F   E 
Sbjct: 13  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP------EKGYSFVRFSTHES 66

Query: 89  ADYAIKIMNMIKLYGKPIRVNKA 111
           A +AI  +N   + G  ++    
Sbjct: 67  AAHAIVSVNGTTIEGHVVKCYWG 89

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 8e-08
 Identities = 11/117 (9%), Positives = 37/117 (31%), Gaps = 45/117 (38%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
              ++ G +   + ++L+  TFS FG                                  
Sbjct: 18  NCTVYCGGIASGLTDQLMRQTFSPFG---------------------------------- 43

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                  ++  +  +        ++F+ +++ E++  +I +++G  +    +   + 
Sbjct: 44  -----QIMEIRVFPEKG------YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG 89

>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 = 66.3 bits (161), Expect = 1e-14
 Identities = 19/76 (25%), Positives = 39/76 (51%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            ++V  + ++  E  + E F   G + N+H+  DR T   +GY  +E+   + A  A + 
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 96  MNMIKLYGKPIRVNKA 111
           +N  ++ G+ I+V+  
Sbjct: 69  LNGAEIMGQTIQVDWC 84

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 48.2 bits (114), Expect = 3e-08
 Identities = 21/120 (17%), Positives = 42/120 (35%), Gaps = 39/120 (32%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
           G  +F+ ++  E  E  + + F  +G                                  
Sbjct: 7   GWILFVTSIHEEAQEDEIQEKFCDYG---------------------------------- 32

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                   +  +  D  TG SKG+A + Y + + + A+ +A++G  +  + I V + F K
Sbjct: 33  -----EIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 87

>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 = 65.5 bits (159), Expect = 2e-14
 Identities = 28/84 (33%), Positives = 47/84 (55%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           +  ++VGGL    +E  + ++F + G +  V + KDR TQ  +G+GF+ F   +DA  A+
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 94  KIMNMIKLYGKPIRVNKASSHQKN 117
             MN   + G+ IRV++A     N
Sbjct: 65  MAMNGKSVDGRQIRVDQAGKSSDN 88

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 6e-08
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 20/81 (24%)

Query: 183 IFIGNLDPEI--------------------MRDPDTGNSKGFAFINYASFEASDASIDAM 222
           +F+G L  +                     ++D +T  S+GF F+ + + + +  ++ AM
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 223 HGQYLCNRPISVSYAFKKDSK 243
           +G+ +  R I V  A K    
Sbjct: 68  NGKSVDGRQIRVDQAGKSSDN 88

>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 = 64.7 bits (157), Expect = 3e-14
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            I+VGG+ +   E  + + F Q G +  + +  DR +   +G+ F+ F   +  D  +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 96  MNMIKLYGKPIRVNKA 111
                + G    V KA
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 2e-06
 Identities = 14/75 (18%), Positives = 24/75 (32%), Gaps = 21/75 (28%)

Query: 183 IFIGNLDPEI--------------------MRDPDTGNSKGFAFINYASFEASDASIDAM 222
           IF+G +  +                     M D  +G  +GFAF+ +   ++ D  I   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK-IVIQ 63

Query: 223 HGQYLCNRPISVSYA 237
               +      V  A
Sbjct: 64  KYHTVNGHNCEVRKA 78

>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 = 65.1 bits (158), Expect = 3e-14
 Identities = 21/88 (23%), Positives = 45/88 (51%), Gaps = 2/88 (2%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G  ES      ++V  +  +  +  + ++F Q G +++V +  +   +  +G+GF+ F  
Sbjct: 3   GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFEN 60

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASS 113
             DAD A + ++   + G+ I VN A++
Sbjct: 61  SADADRAREKLHGTVVEGRKIEVNNATA 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 = 49.7 bits (118), Expect = 1e-08
 Identities = 19/130 (14%), Positives = 40/130 (30%), Gaps = 41/130 (31%)

Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
           +S + ++      + + N+     +  L   F  FG I                      
Sbjct: 1   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKI---------------------- 38

Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
                               ++    +   SKGF F+ + +   +D + + +HG  +  R
Sbjct: 39  -------------------LDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGR 79

Query: 231 PISVSYAFKK 240
            I V+ A  +
Sbjct: 80  KIEVNNATAR 89

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 64.7 bits (157), Expect = 5e-14
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+    L   ++E  + E+F        + +         +G  +IEF  E DA+  ++ 
Sbjct: 18  TLLAKNLSFNITEDELKEVFED-----ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 96  MNMIKLYGKPIRVNKA 111
               ++ G+ + +   
Sbjct: 73  KQGAEIDGRSVSLYYT 88

>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 = 52.0 bits (124), Expect = 2e-09
 Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 15/84 (17%)

Query: 175 KNLDVGANIFIGNLDPEI---------------MRDPDTGNSKGFAFINYASFEASDASI 219
           K +     +   NL   I                     G SKG A+I + S   ++ ++
Sbjct: 11  KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNL 70

Query: 220 DAMHGQYLCNRPISVSYAFKKDSK 243
           +   G  +  R +S+ Y  +K   
Sbjct: 71  EEKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 64.4 bits (156), Expect = 8e-14
 Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 1/81 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            I+VGGL    ++  + + F   G +    +  DR T   +GYGF+       A+ A K 
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 96  MNMIKLYGKPIRVNKASSHQK 116
            N I + G+   VN A    K
Sbjct: 72  PNPI-IDGRKANVNLAYLGAK 91

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 4e-06
 Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 22/90 (24%)

Query: 182 NIFIGNLDPEI--------------------MRDPDTGNSKGFAFINYASFEASDASIDA 221
            IF+G L                        + D  TG S+G+ F+  A   A++ +   
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 222 MHGQYLCNRPISVSYAFKKDS-KGDRHGSA 250
            +   +  R  +V+ A+     +  + G A
Sbjct: 72  PNP-IIDGRKANVNLAYLGAKPRSLQTGFA 100

>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 = 64.0 bits (155), Expect = 1e-13
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 8/86 (9%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPV--------VNVHMPKDRVTQTHQGYGFIEFMG 85
           ++ IYV GL+D V+   + + F Q G V          +H+  D+ T   +G   + +  
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKA 111
              A  A++  +     G  ++V+ A
Sbjct: 68  PPTAKAAVEWFDGKDFQGSKLKVSLA 93

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.6 bits (128), Expect = 6e-10
 Identities = 22/120 (18%), Positives = 38/120 (31%), Gaps = 31/120 (25%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
            + I++  L+  V    L D F   GV+    +    +                      
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHI------------------- 48

Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
                         D +TG  KG A ++Y     + A+++   G+      + VS A KK
Sbjct: 49  ------------YLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>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 = 63.6 bits (154), Expect = 1e-13
 Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 4/80 (5%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVN--VHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
            +++GG+        + E   +    V   +          ++G+ F+E+     A  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 94  KIMNM--IKLYGKPIRVNKA 111
           + +    I+L+G  I V+ A
Sbjct: 63  RKLMPGRIQLWGHQIAVDWA 82

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 2e-08
 Identities = 15/122 (12%), Positives = 32/122 (26%), Gaps = 39/122 (31%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +FIG +      + + +  +     +    +                             
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYAS-------------------------- 37

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY--LCNRPISVSYAFKKD 241
                        D   ++GFAF+ Y S  A+  +   +      L    I+V +A  + 
Sbjct: 38  -----------AADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEI 86

Query: 242 SK 243
             
Sbjct: 87  DV 88

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 2e-13
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 36  TIYVGGLDDKVSE-TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           TIY+  L++K+ +  L   L         +       +   +G  F+ F     A  A++
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 95  IMNMIKLYGKPIRVNKASS 113
            M     Y KP+R+  A +
Sbjct: 65  SMQGFPFYDKPMRIQYAKT 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 = 50.8 bits (121), Expect = 3e-09
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 22/82 (26%)

Query: 183 IFIGNLDPEI---------------------MRDPDTGNSKGFAFINYASFEASDASIDA 221
           I+I NL+ +I                     +    +   +G AF+ +    ++  ++ +
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 65

Query: 222 MHGQYLCNRPISVSYAFKKDSK 243
           M G    ++P+ + YA K DS 
Sbjct: 66  MQGFPFYDKPMRIQYA-KTDSD 86

>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 = 63.3 bits (153), Expect = 2e-13
 Identities = 21/88 (23%), Positives = 41/88 (46%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
             G+ +  +Y+  L  +V+E  +  LF +        +    +T   +G  FI F  +E 
Sbjct: 13  NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 72

Query: 89  ADYAIKIMNMIKLYGKPIRVNKASSHQK 116
           A  A+ ++N  KLYGK + +    + ++
Sbjct: 73  AWQALHLVNGYKLYGKILVIEFGKNKKQ 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 = 43.6 bits (102), Expect = 2e-06
 Identities = 14/92 (15%), Positives = 33/92 (35%), Gaps = 23/92 (25%)

Query: 175 KNLDVGA---NIFIGNLDPEI--------------------MRDPDTGNSKGFAFINYAS 211
            + + G     +++ NL P +                         TG  +G AFI + +
Sbjct: 10  SSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPN 69

Query: 212 FEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
            E +  ++  ++G  L  + + + +   K  +
Sbjct: 70  KEIAWQALHLVNGYKLYGKILVIEFGKNKKQR 101

>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 = 62.8 bits (152), Expect = 2e-13
 Identities = 13/86 (15%), Positives = 27/86 (31%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G      G   I V  +   VS   + + F     +      K        G   + F  
Sbjct: 1   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKA 111
            ++A  A+  +N   +  + +++   
Sbjct: 61  RDEATAAVIDLNDRPIGSRKVKLVLG 86

>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 = 53.5 bits (128), Expect = 4e-10
 Identities = 8/76 (10%), Positives = 26/76 (34%), Gaps = 20/76 (26%)

Query: 182 NIFIGNLDPE--------------------IMRDPDTGNSKGFAFINYASFEASDASIDA 221
            I + N+                        ++  + G   G A + + S + + A++  
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 222 MHGQYLCNRPISVSYA 237
           ++ + + +R + +   
Sbjct: 71  LNDRPIGSRKVKLVLG 86

>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 = 62.5 bits (151), Expect = 4e-13
 Identities = 29/94 (30%), Positives = 55/94 (58%), Gaps = 5/94 (5%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           +++VG +  + +E  + ++F + GPVV+  +  DR T   +GYGF E+  +E A  A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 96  MNMIKLYGKPIRVNKASSHQ-----KNLDVGANI 124
           +N  +  G+ +RV+ A+S +     K+L  GA +
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKSLGTGAPV 103

>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 = 43.6 bits (102), Expect = 2e-06
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 20/85 (23%)

Query: 182 NIFIGNLDPEI--------------------MRDPDTGNSKGFAFINYASFEASDASIDA 221
           ++F+GN+  E                     + D +TG  KG+ F  Y   E + +++  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 222 MHGQYLCNRPISVSYAFKKDSKGDR 246
           ++G+    R + V  A  + +K + 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEEL 94

>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 = 61.3 bits (148), Expect = 7e-13
 Identities = 13/85 (15%), Positives = 33/85 (38%), Gaps = 6/85 (7%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPK-----DRVTQTHQGYGFIEFMGEEDAD 90
            +YVG +   ++E  M + F     +  +                + + F+EF   ++  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 91  YAIKIMNMIKLYGKPIRVNKASSHQ 115
            A+   + I   G+ +++ +   +Q
Sbjct: 63  QAM-AFDGIIFQGQSLKIRRPHDYQ 86

>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 = 44.4 bits (104), Expect = 7e-07
 Identities = 13/112 (11%), Positives = 35/112 (31%), Gaps = 35/112 (31%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +++GN+   + E+ + D F+A   +                  + +A  +          
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRL----------------GGLTQAPGNP--------- 38

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS 235
                    +        K FAF+ + S + +  ++    G     + + + 
Sbjct: 39  ---------VLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR 80

>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 = 60.8 bits (147), Expect = 9e-13
 Identities = 16/86 (18%), Positives = 37/86 (43%), Gaps = 7/86 (8%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
            G + ++VG     ++E  + E F Q G V++V +P     +  + + F+ F  ++ A  
Sbjct: 3   SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQS 57

Query: 92  AIKIMNMIKLYGKPIRVNKASSHQKN 117
                  + + G  + ++ A     +
Sbjct: 58  L--CGEDLIIKGISVHISNAEPKHNS 81

>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 = 41.2 bits (96), Expect = 1e-05
 Identities = 10/76 (13%), Positives = 24/76 (31%), Gaps = 21/76 (27%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFG----------------VILQTPK-----IMNMIKL 160
           + +F+G    ++ E  L + FS +G                V     +         + +
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLII 65

Query: 161 YGKPIRVNKASSHQKN 176
            G  + ++ A     +
Sbjct: 66  KGISVHISNAEPKHNS 81

>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 = 40.0 bits (93), Expect = 3e-05
 Identities = 11/84 (13%), Positives = 26/84 (30%), Gaps = 17/84 (20%)

Query: 181 ANIFIGNLDPEI---------------MRDPDTGNSKGFAFINYASFEASDASIDAMHGQ 225
           + +F+G    ++               M        + FAF+ +A  + + +        
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLC--GEDL 63

Query: 226 YLCNRPISVSYAFKKDSKGDRHGS 249
            +    + +S A  K +      S
Sbjct: 64  IIKGISVHISNAEPKHNSNSGPSS 87

>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 = 60.2 bits (145), Expect = 2e-12
 Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+++  L     E  + E+  Q G +  V +     T+  +G  F +FM +E A   +  
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 96  MNM------IKLYGKPIRVNKASSHQK 116
            ++      +KL G+ ++V+ A +  +
Sbjct: 70  ASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.2 bits (93), Expect = 3e-05
 Identities = 22/88 (25%), Positives = 32/88 (36%), Gaps = 26/88 (29%)

Query: 180 GANIFIGNLDPEI--------------------MRDPDTGNSKGFAFINYASFEASDASI 219
           G  +FI NL  +                     +  PDT +SKG AF  + + EA+   +
Sbjct: 8   GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 67

Query: 220 DAMH------GQYLCNRPISVSYAFKKD 241
            A        G  L  R + V  A  +D
Sbjct: 68  AAASLEAEGGGLKLDGRQLKVDLAVTRD 95

>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 = 60.2 bits (145), Expect = 2e-12
 Identities = 11/90 (12%), Positives = 30/90 (33%), Gaps = 1/90 (1%)

Query: 28  GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           G+        ++  +   +++  + +         N             G   ++F  E+
Sbjct: 2   GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 61

Query: 88  DADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
           DA  + + ++  KL G+   V+  +     
Sbjct: 62  DARKSER-LHRKKLNGREAFVHVVTLEDMR 90

>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 = 59.7 bits (144), Expect = 3e-12
 Identities = 24/76 (31%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +YV  L    SE ++ + F    P     + K R       Y F+ F   EDA  A+K 
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD------YAFVHFSNREDAVEAMKA 63

Query: 96  MNMIKLYGKPIRVNKA 111
           +N   L G PI V  A
Sbjct: 64  LNGKVLDGSPIEVTLA 79

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 4e-09
 Identities = 13/73 (17%), Positives = 30/73 (41%), Gaps = 14/73 (19%)

Query: 183 IFIGNLDPEI--------------MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
           +++ NL                           + +AF+++++ E +  ++ A++G+ L 
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLD 70

Query: 229 NRPISVSYAFKKD 241
             PI V+ A   D
Sbjct: 71  GSPIEVTLAKPVD 83

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 3e-12
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 8/76 (10%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+YV G D  ++ TL+   F   G ++++ M         +   F+ +   E AD A+  
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAE 58

Query: 96  MNMIKLYGKPIRVNKA 111
           +N  ++    ++VN A
Sbjct: 59  LNGTQVESVQLKVNIA 74

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 5e-08
 Identities = 12/73 (16%), Positives = 29/73 (39%), Gaps = 12/73 (16%)

Query: 180 GANIFIGNLD------------PEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
           G  +++   D               + D      +  AF+ Y   E++D ++  ++G  +
Sbjct: 5   GNTLYVYGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV 64

Query: 228 CNRPISVSYAFKK 240
            +  + V+ A K+
Sbjct: 65  ESVQLKVNIARKQ 77

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 13/72 (18%), Positives = 23/72 (31%), Gaps = 24/72 (33%)

Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTP----------------------KIMNMI 158
           G  +++   D  +   LL   FS FG I+                           +N  
Sbjct: 5   GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGT 62

Query: 159 KLYGKPIRVNKA 170
           ++    ++VN A
Sbjct: 63  QVESVQLKVNIA 74

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 4e-12
 Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +Y+G L   V+   + +LF      +   +          GY F+++  +  A  AI+ 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVDYPDQNWAIRAIET 56

Query: 96  MN-MIKLYGKPIRVNKA 111
           ++  ++L+GK + V+ +
Sbjct: 57  LSGKVELHGKIMEVDYS 73

>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 = 47.8 bits (113), Expect = 4e-08
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 15/76 (19%)

Query: 183 IFIGNLDPEI--------------MRDPDTGNSKGFAFINYASFEASDASIDAMHGQY-L 227
           ++IGNL P +                        G+AF++Y     +  +I+ + G+  L
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVEL 63

Query: 228 CNRPISVSYAFKKDSK 243
             + + V Y+  K  +
Sbjct: 64  HGKIMEVDYSVSKKLR 79

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.3 bits (140), Expect = 8e-12
 Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 36  TIYVGGLDDKVSET---LMWELFVQSGPVVNVHMPKDRVTQTHQ---GYGFIEFMGEEDA 89
            ++V GL  ++++       E F + G +  V +         Q      ++ ++  EDA
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 90  DYAIKIMNMIKLYGKPIRV 108
             AI+ +N + + G+ ++ 
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.0 bits (108), Expect = 2e-07
 Identities = 19/124 (15%), Positives = 34/124 (27%), Gaps = 44/124 (35%)

Query: 115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQ 174
           QKNL     +F+  L   + +  +      FG              +GK  +V       
Sbjct: 7   QKNL-----VFVVGLSQRLADPEVLKRPEYFGK-------------FGKIHKVV------ 42

Query: 175 KNLDVGANIFIGNLDPEIMRDPDTGNS---KGFAFINYASFEASDASIDAMHGQYLCNRP 231
                            I        S      A++ Y   E +  +I  ++   +  R 
Sbjct: 43  -----------------INNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT 85

Query: 232 ISVS 235
           +  S
Sbjct: 86  LKAS 89

>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 = 58.6 bits (141), Expect = 8e-12
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T ++G L   V+E  + E F            +    +  +G+G+ EF   +    A+  
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 75

Query: 96  MNMIKLYGKPIRVNKASSHQKN 117
           +N   L  K IRV+ A   Q  
Sbjct: 76  LNEESLGNKRIRVDVADQAQDK 97

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 3e-05
 Identities = 16/120 (13%), Positives = 34/120 (28%), Gaps = 40/120 (33%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
            F+GNL  +V E+ + + F                                         
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGL-------------------------------------- 39

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
              +         +    KGF +  +   ++  +   +++ + L N+ I V  A +   K
Sbjct: 40  -NISAVRLPREPSNPERLKGFGYAEFEDLDSLLS-ALSLNEESLGNKRIRVDVADQAQDK 97

>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 = 57.6 bits (138), Expect = 9e-12
 Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           T+ V  L    ++  +++ F   GP+++V +           +  IEF   + A  AI  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR--FARIEFARYDGALAAITK 59

Query: 96  MNMIKLYGKPIRVNKAS 112
            +   +    I V+  +
Sbjct: 60  THK-VVGQNEIIVSHLT 75

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 34.4 bits (78), Expect = 0.001
 Identities = 8/74 (10%), Positives = 19/74 (25%), Gaps = 25/74 (33%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMI------------------------ 158
            + + NL    ++  +Y  F   G I+      ++                         
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 61

Query: 159 -KLYGKPIRVNKAS 171
             +    I V+  +
Sbjct: 62  KVVGQNEIIVSHLT 75

>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 = 57.7 bits (139), Expect = 2e-11
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 4/87 (4%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I V  L   V+  ++ ++F + G V+ +          +Q    +++     A +A   +
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 65

Query: 97  NMIKLYGKPIRVNKASSHQKNLDVGAN 123
           +   +Y     +    S   +L+V  N
Sbjct: 66  DGQNIYNACCTLRIDFSKLTSLNVKYN 92

>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 = 42.7 bits (100), Expect = 4e-06
 Identities = 17/129 (13%), Positives = 35/129 (27%), Gaps = 45/129 (34%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
            I + NL   V   +L+  FS FG +L+                                
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-------------------------- 42

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQ--YLCNRPISVSYAFKK 240
                            N++  A + YA   ++  +  ++ GQ  Y     + + ++   
Sbjct: 43  -----------------NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 85

Query: 241 DSKGDRHGS 249
                 +  
Sbjct: 86  SLNVKYNND 94

>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 = 56.3 bits (135), Expect = 4e-11
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 35  ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
           AT+++  +   VSE  +  LF  +G VV          Q  +    I+    E+A  A+ 
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK----FFQKDRKMALIQMGSVEEAVQALI 66

Query: 95  IMNMIKLY-GKPIRVNKASS 113
            ++   L     +RV+ + S
Sbjct: 67  DLHNHDLGENHHLRVSFSKS 86

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.3 bits (135), Expect = 6e-11
 Identities = 17/87 (19%), Positives = 38/87 (43%), Gaps = 6/87 (6%)

Query: 33  GDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           G++ + V  L+ ++V+   ++ LF          + + ++    +    ++      A  
Sbjct: 1   GNSVLLVSNLNPERVTPQSLFILFGV-----YGDVQRVKILFNKKENALVQMADGNQAQL 55

Query: 92  AIKIMNMIKLYGKPIRVNKASSHQKNL 118
           A+  +N  KL+GKPIR+  +      L
Sbjct: 56  AMSHLNGHKLHGKPIRITLSKHQNVQL 82

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 4e-07
 Identities = 15/88 (17%), Positives = 33/88 (37%), Gaps = 16/88 (18%)

Query: 183 IFIGNLDPEIMRDPD----------------TGNSKGFAFINYASFEASDASIDAMHGQY 226
           + + NL+PE +                      N K  A +  A    +  ++  ++G  
Sbjct: 5   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 64

Query: 227 LCNRPISVSYAFKKDSKGDRHGSAAERL 254
           L  +PI ++ +  ++ +  R G   + L
Sbjct: 65  LHGKPIRITLSKHQNVQLPREGQEDQGL 92

>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 = 55.2 bits (132), Expect = 7e-11
 Identities = 15/71 (21%), Positives = 32/71 (45%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           +Y+ GL    ++  + +L    G +V+     D+ T   +GYGF++F     A  A+  +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 97  NMIKLYGKPIR 107
               +  +  +
Sbjct: 61  KASGVQAQMAK 71

>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 = 56.1 bits (135), Expect = 7e-11
 Identities = 10/66 (15%), Positives = 21/66 (31%), Gaps = 4/66 (6%)

Query: 51  MWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK 110
           +     + G +  + +          G   + F   E+ADY I+ ++     G+ I    
Sbjct: 36  LRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 91

Query: 111 ASSHQK 116
                 
Sbjct: 92  WDGTTD 97

>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 = 46.8 bits (111), Expect = 1e-07
 Identities = 8/43 (18%), Positives = 17/43 (39%)

Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
                +  G A +++   E +D  I  + G++   R I+    
Sbjct: 50  LLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 55.7 bits (133), Expect = 7e-11
 Identities = 16/86 (18%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 28  GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           G        +++G L+   S   +     +     ++ +   R T T++ +G+++F   E
Sbjct: 7   GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAE 65

Query: 88  DADYAIKIMNMIKLYGKPIRVNKASS 113
           D + A+  +  +K++G  I++ K   
Sbjct: 66  DLEKAL-ELTGLKVFGNEIKLEKPKG 90

>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 = 33.8 bits (76), Expect = 0.004
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 20/78 (25%)

Query: 182 NIFIGNLDPEIMRD-------------------PDTGNSKGFAFINYASFEASDASIDAM 222
           N+FIGNL+P                          TG ++ F ++++ S E  + +++ +
Sbjct: 15  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73

Query: 223 HGQYLCNRPISVSYAFKK 240
            G  +    I +     +
Sbjct: 74  TGLKVFGNEIKLEKPKGR 91

>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 = 55.6 bits (133), Expect = 1e-10
 Identities = 13/90 (14%), Positives = 24/90 (26%), Gaps = 11/90 (12%)

Query: 33  GDATIYVGGLDDKV-----SETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           G + +     +D V     +      LF            K            I F    
Sbjct: 4   GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPL 57

Query: 88  DADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
            A  A   ++  +  GK +++  A +    
Sbjct: 58  SAADARLRLHKTEFLGKEMKLYFAQTLHIG 87

>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 = 40.9 bits (95), Expect = 2e-05
 Identities = 6/84 (7%), Positives = 23/84 (27%), Gaps = 19/84 (22%)

Query: 182 NIFIGNLDPEIMRDPDT-------------------GNSKGFAFINYASFEASDASIDAM 222
            +     + ++  + +T                     S     IN+++  ++  +   +
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRL 66

Query: 223 HGQYLCNRPISVSYAFKKDSKGDR 246
           H      + + + +A         
Sbjct: 67  HKTEFLGKEMKLYFAQTLHIGSSH 90

>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 = 54.7 bits (131), Expect = 1e-10
 Identities = 13/84 (15%), Positives = 26/84 (30%), Gaps = 7/84 (8%)

Query: 33  GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
           G + I V  L    +   + +L                    ++   F+  +  E A  A
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR-------NKRTAFVTLLNGEQAQNA 56

Query: 93  IKIMNMIKLYGKPIRVNKASSHQK 116
           I++ +     GK + V    +   
Sbjct: 57  IQMFHQYSFRGKDLIVQLQPTDAL 80

>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 = 40.1 bits (93), Expect = 2e-05
 Identities = 11/76 (14%), Positives = 24/76 (31%), Gaps = 14/76 (18%)

Query: 181 ANIFIGNLDPEI-------------MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
           + I + NL  +              ++      +K  AF+   + E +  +I   H    
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF 65

Query: 228 CNRPISVSYAFKKDSK 243
             + + V      D+ 
Sbjct: 66  RGKDLIVQLQ-PTDAL 80

>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 = 7/75 (9%), Positives = 21/75 (28%), Gaps = 21/75 (28%)

Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTP---------------------KIMNMIKL 160
           + I + NL  + + + ++D    + +                          ++ +    
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF 65

Query: 161 YGKPIRVNKASSHQK 175
            GK + V    +   
Sbjct: 66  RGKDLIVQLQPTDAL 80

>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 = 55.7 bits (133), Expect = 2e-10
 Identities = 26/100 (26%), Positives = 47/100 (47%), Gaps = 5/100 (5%)

Query: 32  DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
           D    + V  +   V E  + +LF + GP+ +V +  DR T+  +GYGF++F     A  
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 92  AIKIMNMIKLYGKPIRVNKASSHQKNLDV-----GANIFI 126
           AI  +N   +  K ++V  A+S  +   +       N ++
Sbjct: 100 AIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 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 = 44.1 bits (103), Expect = 2e-06
 Identities = 15/96 (15%), Positives = 37/96 (38%), Gaps = 20/96 (20%)

Query: 178 DVGANIFIGNLDPEI--------------------MRDPDTGNSKGFAFINYASFEASDA 217
           DV  N+ +  +   +                    + D +T  S+G+ F+ + S  ++  
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 218 SIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAER 253
           +I  ++G  + N+ + V+ A     +    G+  + 
Sbjct: 100 AIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDG 135

>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 = 54.0 bits (129), Expect = 3e-10
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 3/78 (3%)

Query: 36  TIYVGGLD-DKVSETLMWELFVQ-SGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
            I +  L  + + E L+ E F               +    +    F+ F  ++ A+ A+
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 94  KIMNMIKLYGKPIRVNKA 111
           + MN   L  + I V+ A
Sbjct: 66  Q-MNRSLLGNREISVSLA 82

>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 = 43.6 bits (102), Expect = 1e-06
 Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 23/83 (27%)

Query: 180 GANIFIGNLDPEI----------------------MRDPDTGNSKGFAFINYASFEASDA 217
           G  I I NL  E+                          +   +   AF+ + + ++++ 
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 218 SIDAMHGQYLCNRPISVSYAFKK 240
           ++  M+   L NR ISVS A KK
Sbjct: 64  AL-QMNRSLLGNREISVSLADKK 85

>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 = 54.3 bits (130), Expect = 3e-10
 Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           + +    D+  E +  E+  + G V  +++  +       G  +++F  EEDA+ A+  +
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 97  NMIKLYGKPIRVN 109
           N     G+PI   
Sbjct: 89  NNRWFNGQPIHAE 101

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 3e-05
 Identities = 8/114 (7%), Positives = 30/114 (26%), Gaps = 40/114 (35%)

Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
           ++ +     E  E++  +    +G + +                                
Sbjct: 29  DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVC---------------------------- 60

Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
                       D    +  G  ++ +   E ++ ++  ++ ++   +PI    
Sbjct: 61  ------------DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>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 = 53.8 bits (128), Expect = 6e-10
 Identities = 17/90 (18%), Positives = 30/90 (33%), Gaps = 6/90 (6%)

Query: 28  GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
           G SG     I    L        + E F + G +  V +P+            +EF+   
Sbjct: 4   GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPL 57

Query: 88  DADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
           +A  A + +   K +  P+ +  A      
Sbjct: 58  EARKAFRHLAYSKFHHVPLYLEWAPIGVFG 87

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (91), Expect = 7e-05
 Identities = 6/78 (7%), Positives = 16/78 (20%), Gaps = 14/78 (17%)

Query: 182 NIFIGNLDPEI--------------MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
            I   NL                  +           A + +     +  +   +     
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKF 71

Query: 228 CNRPISVSYAFKKDSKGD 245
            + P+ + +A        
Sbjct: 72  HHVPLYLEWAPIGVFGAA 89

>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 = 51.3 bits (122), Expect = 3e-09
 Identities = 15/92 (16%), Positives = 32/92 (34%), Gaps = 7/92 (7%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           GG  +   D  + V GL    S   + +   +                   G G +E++ 
Sbjct: 7   GGPPTRRSDFRVLVSGLPPSGSWQDLKDHMRE-------AGDVCYADVQKDGMGMVEYLR 59

Query: 86  EEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
           +ED +YA++ ++  K        +    + + 
Sbjct: 60  KEDMEYALRKLDDTKFRSHEGETSYIRVYPER 91

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 10/81 (12%), Positives = 20/81 (24%), Gaps = 15/81 (18%)

Query: 183 IFIGNLDPEIMRD-------------PDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
           + +  L P                         G   + Y   E  + ++  +      +
Sbjct: 18  VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYLRKEDMEYALRKLDDTKFRS 77

Query: 230 RPISVSYA--FKKDSKGDRHG 248
                SY   + + S G   G
Sbjct: 78  HEGETSYIRVYPERSSGPSSG 98

>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 = 51.2 bits (122), Expect = 3e-09
 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 8/80 (10%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            ++VGGL    S   +   F + G +  +             + +I++   + A  A   
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDH------VKGDSFAYIQYESLDAAQAACAK 72

Query: 96  MNMIKLYG--KPIRVNKASS 113
           M    L G  + +RV+ A S
Sbjct: 73  MRGFPLGGPDRRLRVDFAKS 92

>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 = 38.9 bits (90), Expect = 6e-05
 Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 16/79 (20%)

Query: 182 NIFIGNLDPEI--------------MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
            +++G L P                +R  D      FA+I Y S +A+ A+   M G  L
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPL 78

Query: 228 --CNRPISVSYAFKKDSKG 244
              +R + V +A    S G
Sbjct: 79  GGPDRRLRVDFAKSGPSSG 97

>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 = 50.9 bits (121), Expect = 4e-09
 Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 1/76 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +Y+  L   + E  +  +    G V++  + +D      +G GF      E  +  I  
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGT-SRGVGFARMESTEKCEAVIGH 78

Query: 96  MNMIKLYGKPIRVNKA 111
            N   +   P      
Sbjct: 79  FNGKFIKTPPGVSAPT 94

>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 = 37.8 bits (87), Expect = 2e-04
 Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 19/75 (25%)

Query: 182 NIFIGNLDPEI-------------------MRDPDTGNSKGFAFINYASFEASDASIDAM 222
           N++I NL   +                   +    +G S+G  F    S E  +A I   
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 223 HGQYLCNRPISVSYA 237
           +G+++   P   +  
Sbjct: 80  NGKFIKTPPGVSAPT 94

>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 = 51.0 bits (121), Expect = 5e-09
 Identities = 16/100 (16%), Positives = 33/100 (33%), Gaps = 8/100 (8%)

Query: 26  GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
           G          ++V GL + V E  + E   + G +  V M         +    +EF  
Sbjct: 7   GSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFEN 60

Query: 86  EEDADYAIKIMNM--IKLYGKPIRVNKASSHQKNLDVGAN 123
            + A   +       + + G+    N ++S +      + 
Sbjct: 61  IDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSG 100

>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 = 36.7 bits (84), Expect = 5e-04
 Identities = 8/90 (8%), Positives = 25/90 (27%), Gaps = 16/90 (17%)

Query: 170 ASSHQKNLDVGANIFIGNLDPEI--------------MRDPDTGNSKGFAFINYASFEAS 215
           +S     + V   + +  L   +              +        K  A + + + +++
Sbjct: 5   SSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSA 64

Query: 216 DASIDAMHGQ--YLCNRPISVSYAFKKDSK 243
              +        Y+  +    +Y+  K   
Sbjct: 65  KECVTFAADVPVYIAGQQAFFNYSTSKRIT 94

>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 = 50.5 bits (120), Expect = 5e-09
 Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 2/76 (2%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
           ++Y+ G     +   + E     G V+N+ M +    +  +G  F+ F   E A   ++ 
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE- 65

Query: 96  MNMIKLYGKPIRVNKA 111
               K     + +   
Sbjct: 66  TPGQKYKETDLLILFK 81

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 7e-09
 Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 11/94 (11%)

Query: 28  GESGDGDA--------TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYG 79
           G SG   +         +++ GL  + +E  ++  F    P+               G  
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEA 58

Query: 80  FIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
            +EF   EDA  A+   +   +  + + +   S+
Sbjct: 59  DVEFATHEDAVAAMA-KDKANMQHRYVELFLNST 91

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.3 bits (119), Expect = 1e-08
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +Y+ GL  +     + + F +   V +             G GF+EF  E D   A+  
Sbjct: 20  CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC- 78

Query: 96  MNMIKLYGKPIRVNKAS 112
            +   +  + I+V+  +
Sbjct: 79  RHKQYMGNRFIQVHPIT 95

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.6 bits (81), Expect = 0.001
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 193 MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
           +     G + G  F+ + +     A++   H QY+ NR I V    KK 
Sbjct: 51  IAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKG 98

>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 = 49.8 bits (118), Expect = 1e-08
 Identities = 17/82 (20%), Positives = 27/82 (32%), Gaps = 7/82 (8%)

Query: 29  ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE-E 87
           E   G    + G LDD+     +  LF   G +  +   +          G I F  + +
Sbjct: 6   EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR------GAKEGIILFKEKAK 59

Query: 88  DADYAIKIMNMIKLYGKPIRVN 109
           +A    K  N   L  +   V 
Sbjct: 60  EALGKAKDANNGNLQLRNKEVT 81

>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 = 35.9 bits (82), Expect = 0.001
 Identities = 12/93 (12%), Positives = 28/93 (30%), Gaps = 18/93 (19%)

Query: 182 NIFIGNLDPEI--------------MRDPDTGNSKGFAFINYAS-FEASDASIDAMHGQY 226
             F G+LD +               ++  D         I +    + +       +   
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGN 72

Query: 227 LCNRPISVSYAFKKDSKGDRHGSAAERLLAAQN 259
           L  R   V++      +G+    A ++++  Q 
Sbjct: 73  LQLRNKEVTWEVL---EGEVEKEALKKIIEDQQ 102

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 1e-08
 Identities = 10/64 (15%), Positives = 23/64 (35%), Gaps = 2/64 (3%)

Query: 51  MWELFVQSGPVVNVHMPKDRVTQTHQGYGF--IEFMGEEDADYAIKIMNMIKLYGKPIRV 108
           + +   + G V ++ +P+        G G   +EF    D   A++ +   K   + +  
Sbjct: 31  VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 90

Query: 109 NKAS 112
               
Sbjct: 91  KYCD 94

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.1 bits (109), Expect = 2e-07
 Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 2/52 (3%)

Query: 188 LDPEIMRDPDTGN--SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
              EI R  D       G  F+ + S      ++  + G+   NR +   Y 
Sbjct: 42  KSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYC 93

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.9 bits (116), Expect = 2e-08
 Identities = 16/90 (17%), Positives = 33/90 (36%), Gaps = 9/90 (10%)

Query: 30  SGDGDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
             +    +++      K     + +L    G + N  +             FIE    ED
Sbjct: 4   RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI------LNKINEAFIEMATTED 57

Query: 89  ADYAIKIMNM--IKLYGKPIRVNKASSHQK 116
           A  A+         ++GKP+RV+ +  +++
Sbjct: 58  AQAAVDYYTTTPALVFGKPVRVHLSQKYKR 87

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.3 bits (114), Expect = 2e-08
 Identities = 13/82 (15%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +++  L  +V+ET +  L +            + +    +   F+E   EE A   +  
Sbjct: 10  VLHIRKLPGEVTETEVIALGLP------FGKVTNILMLKGKNQAFLELATEEAAITMVNY 63

Query: 96  MNM--IKLYGKPIRVNKASSHQ 115
            +     L  +PI +  ++  +
Sbjct: 64  YSAVTPHLRNQPIYIQYSNHKE 85

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.7 bits (84), Expect = 4e-04
 Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 16/78 (20%)

Query: 182 NIFIGNLDPEIMRD--------------PDTGNSKGFAFINYASFEASDASIDAMH--GQ 225
            + I  L  E+                       K  AF+  A+ EA+   ++       
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTP 69

Query: 226 YLCNRPISVSYAFKKDSK 243
           +L N+PI + Y+  K+ K
Sbjct: 70  HLRNQPIYIQYSNHKELK 87

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 6e-08
 Identities = 13/84 (15%), Positives = 32/84 (38%), Gaps = 7/84 (8%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +  GGL + VS   +  +  + G V  + M        ++ Y F  +   E++  A   
Sbjct: 22  VVANGGLGNGVSRNQLLPVLEKCGLVDALLM------PPNKPYSFARYRTTEESKRAYVT 75

Query: 96  MNMIKLY-GKPIRVNKASSHQKNL 118
           +N  ++      ++    +  + +
Sbjct: 76  LNGKEVVDDLGQKITLYLNFVEKV 99

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 3e-04
 Identities = 12/121 (9%), Positives = 27/121 (22%), Gaps = 50/121 (41%)

Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
           +  G L   V    L       G++       N                           
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------------------------- 57

Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC-----NRPISVSYAF 238
                               ++F  Y + E S  +   ++G+ +         + +++  
Sbjct: 58  --------------------YSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE 97

Query: 239 K 239
           K
Sbjct: 98  K 98

>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 = 46.0 bits (108), Expect = 2e-07
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 36  TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
            +++  L ++ +E ++  LF Q      V +             F+EF  E  ++ A + 
Sbjct: 10  ILFLTNLPEETNEMMLSMLFNQFPGFKEVRLV-----PNRHDIAFVEFTTELQSNAAKEA 64

Query: 96  MNMIKLY-GKPIRVNKA 111
           +   K+     +++  A
Sbjct: 65  LQGFKITPTHAMKITFA 81

>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 = 36.4 bits (83), Expect = 4e-04
 Identities = 13/73 (17%), Positives = 27/73 (36%), Gaps = 16/73 (21%)

Query: 183 IFIGNLDPEIMRD---------------PDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
           +F+ NL  E                       N    AF+ + +   S+A+ +A+ G  +
Sbjct: 11  LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKI 70

Query: 228 C-NRPISVSYAFK 239
                + +++A K
Sbjct: 71  TPTHAMKITFAKK 83

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.9 bits (105), Expect = 4e-07
 Identities = 13/75 (17%), Positives = 24/75 (32%), Gaps = 7/75 (9%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           + V GL    S   + +   +                   G G +EF+ +ED  YA++ +
Sbjct: 3   VVVSGLPPSGSWQDLKDHMRE-------AGDVCYADVYRDGTGVVEFVRKEDMTYAVRKL 55

Query: 97  NMIKLYGKPIRVNKA 111
           +  K           
Sbjct: 56  DNTKFRSHEGETAYI 70

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (94), Expect = 2e-05
 Identities = 7/84 (8%), Positives = 16/84 (19%), Gaps = 13/84 (15%)

Query: 183 IFIGNLDPEIMRD-------------PDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
           + +  L P                         G   + +   E    ++  +      +
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRS 62

Query: 230 RPISVSYAFKKDSKGDRHGSAAER 253
                +Y   K            R
Sbjct: 63  HEGETAYIRVKVDGPRSPSYGRSR 86

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.8 bits (102), Expect = 2e-06
 Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 9/84 (10%)

Query: 36  TIYVGGLDD-KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
            I++  L     S++ + +L    G + N  +         +   FIE    EDA   + 
Sbjct: 20  VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL------MRMKSQAFIEMETREDAMAMVD 73

Query: 95  IMNM--IKLYGKPIRVNKASSHQK 116
                 +   G+ ++V+ +  ++K
Sbjct: 74  HCLKKALWFQGRCVKVDLSEKYKK 97

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.6 bits (100), Expect = 2e-06
 Identities = 10/73 (13%), Positives = 22/73 (30%), Gaps = 8/73 (10%)

Query: 34  DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
           D  + V G     +  ++   F Q G ++   M           +  I +  +  A  A+
Sbjct: 4   DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKAL 56

Query: 94  KIMNMIKLYGKPI 106
              +        +
Sbjct: 57  S-KDGRIFGESIM 68

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 8/75 (10%), Positives = 19/75 (25%), Gaps = 15/75 (20%)

Query: 181 ANIFIGNLDPEI-------------MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
             + +                    +      N+  +  I Y S   +  ++ +  G+  
Sbjct: 5   TWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKAL-SKDGRIF 63

Query: 228 CNRP-ISVSYAFKKD 241
                I V     K+
Sbjct: 64  GESIMIGVKPCIDKN 78

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.1 bits (95), Expect = 7e-06
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 14/73 (19%)

Query: 183 IFIGNLDPEI-------------MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
           I I  L  ++             ++       KG AF+   + E ++A+I+  H   L  
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRE 60

Query: 230 RPISVSYAFKKDS 242
           R +SV      D+
Sbjct: 61  RELSVQLQ-PTDA 72

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.9 bits (92), Expect = 2e-05
 Identities = 14/77 (18%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 37  IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
           I + GL   V+   + +L             K      ++G  F+  +  E A+ AI   
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYEL-------KYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 97  NMIKLYGKPIRVNKASS 113
           +  +L  + + V    +
Sbjct: 54  HQSRLRERELSVQLQPT 70

>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 = 35.2 bits (80), Expect = 0.002
 Identities = 11/51 (21%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 193 MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
           +     G S G AF+ +AS E ++ ++   H + + +R I +  + + + +
Sbjct: 48  LPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVR 97

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	99.98
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.86
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	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
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.84
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.83
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.83
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.83
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.83
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.82
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.82
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.81
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.81
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.81
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.81
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.81
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.81
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.81
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.8
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.8
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.78
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.78
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.78
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.78
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.78
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.78
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.77
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.77
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.77
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.77
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.76
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.76
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.76
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.76
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.75
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.75
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.75
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.75
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.75
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.75
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.75
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.75
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.74
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.74
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.74
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.74
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.73
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.73
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.73
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.73
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.73
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.73
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.73
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.72
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.72
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.72
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.71
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.71
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.71
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.71
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.71
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.71
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.71
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.71
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.7
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.7
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.7
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.7
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.7
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.7
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.69
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.69
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.69
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.69
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.69
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.68
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.68
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.68
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.67
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.66
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.66
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.66
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.66
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.66
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.65
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.64
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.64
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.64
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.63
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.63
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.63
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.63
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.63
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.62
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.62
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.62
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.61
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.61
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.61
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.61
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.61
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.61
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.6
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.6
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.59
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.58
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.58
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.57
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	99.57
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.56
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.56
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.54
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.53
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.53
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.52
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.52
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.51
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.51
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.5
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.5
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	99.5
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.49
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.48
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.47
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.44
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.41
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.3
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.29
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.25
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.24
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.23
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.15
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.53
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.36
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.17
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.06
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.6
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.43
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.42
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	85.91

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.98  E-value=5.1e-32  Score=225.43  Aligned_cols=168  Identities=24%  Similarity=0.427  Sum_probs=150.9

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||||||+.+|+++|+++|++||.|.+++++.+..++.++|||||+|.+.++|.+|+. +++..+.++.+.+.+..
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhh
Confidence            45899999999999999999999999999999999998899999999999999999999998 56777888888888766


Q ss_pred             Cccc-----cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEecc
Q psy3016         113 SHQK-----NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGN  187 (305)
Q Consensus       113 ~~~~-----~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  187 (305)
                      ....     .....++|||+|||..+|+++|+++|+.||.|..+                                    
T Consensus        84 ~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~------------------------------------  127 (183)
T d1u1qa_          84 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI------------------------------------  127 (183)
T ss_dssp             CTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEE------------------------------------
T ss_pred             hcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeee------------------------------------
Confidence            5432     22346789999999999999999999999999876                                    


Q ss_pred             CCCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         188 LDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       188 l~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                         .++.|..++.++|||||+|.+.++|.+|+. +++..+.|+.|+|.+|.++.
T Consensus       128 ---~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k~  177 (183)
T d1u1qa_         128 ---EIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQ  177 (183)
T ss_dssp             ---EEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCHH
T ss_pred             ---eeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCcc
Confidence               678888889999999999999999999997 78999999999999987653

>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=99.87  E-value=4e-22  Score=147.05  Aligned_cols=90  Identities=76%  Similarity=1.231  Sum_probs=83.6

Q ss_pred             CCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        27 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      |.......++|||+|||..+|+++|+++|++||.|.+|+|+.++.+|.++|||||+|.+.++|++|++.|||..+.|+.|
T Consensus         2 P~~~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   81 (93)
T d1x5ua1           2 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   81 (93)
T ss_dssp             CCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CCCcCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34455667899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCCCccc
Q psy3016         107 RVNKASSHQK  116 (305)
Q Consensus       107 ~v~~~~~~~~  116 (305)
                      +|+++.++.+
T Consensus        82 ~V~~A~~~~~   91 (93)
T d1x5ua1          82 RVNKASAHNK   91 (93)
T ss_dssp             EEEETTTTSC
T ss_pred             EEEEcCCCCC
Confidence            9999987654

>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=99.86  E-value=8.7e-22  Score=144.36  Aligned_cols=88  Identities=30%  Similarity=0.377  Sum_probs=82.4

Q ss_pred             CCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        28 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      ....+..++|||+|||..+|+++|+++|+.||.|.+|+++.+..+|.++|||||+|.+.++|.+|++.|||..+.|+.|+
T Consensus         2 ~~~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~   81 (90)
T d2cq0a1           2 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   81 (90)
T ss_dssp             CCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            44566778999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EeeCCCcc
Q psy3016         108 VNKASSHQ  115 (305)
Q Consensus       108 v~~~~~~~  115 (305)
                      |+|+.++.
T Consensus        82 v~~akp~~   89 (90)
T d2cq0a1          82 VEWAKPST   89 (90)
T ss_dssp             EEESSCCC
T ss_pred             EEeeeCCC
Confidence            99998653

>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=99.86  E-value=9.9e-22  Score=141.47  Aligned_cols=80  Identities=28%  Similarity=0.494  Sum_probs=77.2

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (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~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            57899999999999999999999999999999999988999999999999999999999999999999999999999864

>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=99.85  E-value=2.4e-21  Score=141.37  Aligned_cols=83  Identities=23%  Similarity=0.366  Sum_probs=78.4

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (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~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35679999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             CCc
Q psy3016         112 SSH  114 (305)
Q Consensus       112 ~~~  114 (305)
                      ..+
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            754

>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=1.4e-21  Score=143.00  Aligned_cols=84  Identities=36%  Similarity=0.659  Sum_probs=79.6

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||.++|+++|+++|+.||+|.+|+++.+..+|.++|||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34679999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             CCcc
Q psy3016         112 SSHQ  115 (305)
Q Consensus       112 ~~~~  115 (305)
                      .++.
T Consensus        83 ~p~~   86 (89)
T d2cqba1          83 KPMR   86 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=3.7e-21  Score=141.82  Aligned_cols=83  Identities=29%  Similarity=0.514  Sum_probs=79.2

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ..+++|||+|||.++|+++|+++|+.||.|.+|.++.++.++.++|||||+|.+.++|..|++.|||..+.|+.|+|+|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCc
Q psy3016         112 SSH  114 (305)
Q Consensus       112 ~~~  114 (305)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=99.85  E-value=4.1e-21  Score=138.15  Aligned_cols=80  Identities=26%  Similarity=0.495  Sum_probs=76.6

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (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~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            35799999999999999999999999999999999988899999999999999999999999999999999999999865

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=4.5e-21  Score=143.79  Aligned_cols=85  Identities=21%  Similarity=0.339  Sum_probs=80.2

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+|||.++|+++|+++|+.||.|.+++++.+..+|.++|||||+|.+.++|+.|++.|||..+.|+.|+|+++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccc
Q psy3016         112 SSHQK  116 (305)
Q Consensus       112 ~~~~~  116 (305)
                      .++.+
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            87654

>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=99.85  E-value=3.7e-21  Score=138.80  Aligned_cols=80  Identities=29%  Similarity=0.437  Sum_probs=75.3

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      +.....++|||+|||.++|+++|+++|++||.|.+|+++.++.++.++|||||+|.+.++|.+|++.||+..+.|+.|+|
T Consensus         4 ~~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           4 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            34455789999999999999999999999999999999999988999999999999999999999999999999999986

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=3.7e-21  Score=137.77  Aligned_cols=78  Identities=31%  Similarity=0.670  Sum_probs=75.4

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (305)
                      .|||||||..+|+++|+++|+.||+|.+|+|+.++.+|+++|||||+|.+.++|.+|++.|||..+.|+.|+|.|+..
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            699999999999999999999999999999999998999999999999999999999999999999999999999853

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=7.4e-21  Score=141.81  Aligned_cols=86  Identities=26%  Similarity=0.419  Sum_probs=81.0

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ..+.++|||+|||..+|+++|+++|++||.|.+|+++.++.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35577899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             CCCccc
Q psy3016         111 ASSHQK  116 (305)
Q Consensus       111 ~~~~~~  116 (305)
                      +..+..
T Consensus        85 a~~~~~   90 (99)
T d1whwa_          85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             CCCCCc
Confidence            987654

>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=1.1e-20  Score=149.69  Aligned_cols=88  Identities=28%  Similarity=0.436  Sum_probs=81.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ..+..++|||+|||.++|+++|+++|+.||.|.+|+|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~  117 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34455789999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             eCCCcccc
Q psy3016         110 KASSHQKN  117 (305)
Q Consensus       110 ~~~~~~~~  117 (305)
                      ++.....+
T Consensus       118 ~a~~~~~~  125 (139)
T d1u6fa1         118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             EcCCCCCC
Confidence            99765543

>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=141.61  Aligned_cols=86  Identities=27%  Similarity=0.353  Sum_probs=78.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|.+|+++.++.+|.++|||||+|.+.++|.+|++.+++ .+.|+.|.|+
T Consensus         6 ~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~   84 (103)
T d2cqda1           6 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   84 (103)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEE
Confidence            344557899999999999999999999999999999999998999999999999999999999998876 7999999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      ++....+
T Consensus        85 ~a~~~~~   91 (103)
T d2cqda1          85 LAYLGAK   91 (103)
T ss_dssp             ESTTTCC
T ss_pred             EcCCCCC
Confidence            9876543

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=3.4e-21  Score=139.60  Aligned_cols=81  Identities=28%  Similarity=0.463  Sum_probs=77.8

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (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~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             c
Q psy3016         115 Q  115 (305)
Q Consensus       115 ~  115 (305)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.2e-20  Score=136.25  Aligned_cols=80  Identities=21%  Similarity=0.424  Sum_probs=75.7

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      +..++|||+|||..+|+++|+++|+.||.|.+++|+.|+.+|.++|||||+|.+.++|++|++ +++..+.|+.|+|++|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            445799999999999999999999999999999999999999999999999999999999998 6999999999999987


Q ss_pred             C
Q psy3016         112 S  112 (305)
Q Consensus       112 ~  112 (305)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=1.1e-20  Score=136.76  Aligned_cols=79  Identities=37%  Similarity=0.519  Sum_probs=74.2

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe--eeEEee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK--PIRVNK  110 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~--~l~v~~  110 (305)
                      ..++|||+|||..+|+++|+++|++||+|.+++++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+  +|+|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            357899999999999999999999999999999999988899999999999999999999999999999984  588887


Q ss_pred             C
Q psy3016         111 A  111 (305)
Q Consensus       111 ~  111 (305)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=2.2e-20  Score=136.79  Aligned_cols=84  Identities=35%  Similarity=0.560  Sum_probs=76.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||.++|+++|+++|+.||+|.+|+++.+..+  .+|||||+|.+.++|.+|++.|+|..+.|+.|+|.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3455789999999999999999999999999999999998754  47999999999999999999999999999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      |+.+..
T Consensus        82 ~a~~~~   87 (90)
T d2cqia1          82 WATTPS   87 (90)
T ss_dssp             ECCCTT
T ss_pred             EcCCCC
Confidence            998654

>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=1.6e-20  Score=135.99  Aligned_cols=79  Identities=25%  Similarity=0.473  Sum_probs=74.9

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC--eeeEEee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG--KPIRVNK  110 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g--~~l~v~~  110 (305)
                      ..++|||+|||.++|+++|+++|++||.|.+++++.++.+|.++|||||+|.+.++|.+|++.||+..+.|  +.|+|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            45689999999999999999999999999999999998899999999999999999999999999999987  8899998


Q ss_pred             C
Q psy3016         111 A  111 (305)
Q Consensus       111 ~  111 (305)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=3e-20  Score=135.89  Aligned_cols=84  Identities=25%  Similarity=0.279  Sum_probs=77.1

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ..+..++|||+|||.++|+++|+++|+.||.|.+|+|+.|+.+|.++|||||+|.+.++|++|++.  +..+.|+.|.|+
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~   81 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEE
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEE
Confidence            344568999999999999999999999999999999999998999999999999999999999984  558999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      ++.++.
T Consensus        82 ~a~~k~   87 (90)
T d2cqga1          82 LPNSKQ   87 (90)
T ss_dssp             CCCTTC
T ss_pred             eCCCCC
Confidence            988754

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=1.8e-20  Score=138.34  Aligned_cols=85  Identities=27%  Similarity=0.490  Sum_probs=78.4

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccC-CCCCcceEEEEEEcCHHHHHHHHHHh-cCceeCCeeeEE
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDR-VTQTHQGYGFIEFMGEEDADYAIKIM-NMIKLYGKPIRV  108 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~-~~~~~~g~afV~f~~~e~A~~Ai~~l-~g~~~~g~~l~v  108 (305)
                      ....++|||+|||..+++++|+++|+.||.|.+|+|+.+. .+|.++|||||+|.+.++|.+|++.| |+..+.|+.|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            4456789999999999999999999999999999998875 37899999999999999999999998 899999999999


Q ss_pred             eeCCCcc
Q psy3016         109 NKASSHQ  115 (305)
Q Consensus       109 ~~~~~~~  115 (305)
                      +|+..+.
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998754

>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=99.82  E-value=5e-20  Score=135.62  Aligned_cols=88  Identities=24%  Similarity=0.392  Sum_probs=80.0

Q ss_pred             CCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        26 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      +..+.....++|||+|||..+|+++|+++|+.||+|.+|+++.+..  .++|||||+|.+.++|.+|++.||+..+.|+.
T Consensus         3 g~~~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~   80 (93)
T d2cq3a1           3 GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRK   80 (93)
T ss_dssp             CCSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            3455667788999999999999999999999999999999998863  36899999999999999999999999999999


Q ss_pred             eEEeeCCCcc
Q psy3016         106 IRVNKASSHQ  115 (305)
Q Consensus       106 l~v~~~~~~~  115 (305)
                      |+|+++.++.
T Consensus        81 l~V~~A~~r~   90 (93)
T d2cq3a1          81 IEVNNATARV   90 (93)
T ss_dssp             CEEEECCSSC
T ss_pred             EEEEecCcCC
Confidence            9999998754

>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=99.82  E-value=8.4e-21  Score=138.99  Aligned_cols=85  Identities=32%  Similarity=0.540  Sum_probs=79.6

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      .+.++|||+|||.++|+++|+++|+.||.|..+.++.+..++.++|||||+|.++++|++|++.|||..+.|+.|+|+++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            45678999999999999999999999999999999998889999999999999999999999999999999999999998


Q ss_pred             CCccc
Q psy3016         112 SSHQK  116 (305)
Q Consensus       112 ~~~~~  116 (305)
                      ..+..
T Consensus        83 ~~~~~   87 (90)
T d1x5sa1          83 GKSSD   87 (90)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            76543

>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=1.2e-20  Score=135.38  Aligned_cols=80  Identities=15%  Similarity=0.271  Sum_probs=70.0

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (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~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            47999999999999999999999999999998888888899999999999999999999999999999999999999875

>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=99.82  E-value=8.7e-21  Score=138.63  Aligned_cols=83  Identities=25%  Similarity=0.492  Sum_probs=76.2

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      .++..+|||+|||.++|+++|+++|+.||.|.+++|+.+.  +.++|||||+|.+.++|++|++.|||..+.|+.|.|.+
T Consensus         5 ~s~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~   82 (89)
T d1cvja2           5 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR   82 (89)
T ss_dssp             HTTTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999999986  34789999999999999999999999999999999999


Q ss_pred             CCCcc
Q psy3016         111 ASSHQ  115 (305)
Q Consensus       111 ~~~~~  115 (305)
                      +..+.
T Consensus        83 a~~~~   87 (89)
T d1cvja2          83 FKSRK   87 (89)
T ss_dssp             CCCTT
T ss_pred             CCCCC
Confidence            98654

>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=99.82  E-value=3.3e-20  Score=132.06  Aligned_cols=76  Identities=28%  Similarity=0.375  Sum_probs=73.2

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (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~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999986 78899999999999999999999999999999999999875

>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=1.4e-20  Score=140.70  Aligned_cols=81  Identities=22%  Similarity=0.394  Sum_probs=76.3

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||+|||..+|+++|+++|+.||.|.+|+++.+..+|.++|||||+|.+.++|.+|++ |||..|.|+.|.|.++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            35799999999999999999999999999999999999899999999999999999999996 99999999999999875


Q ss_pred             Cc
Q psy3016         113 SH  114 (305)
Q Consensus       113 ~~  114 (305)
                      ++
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            43

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=2.4e-20  Score=139.90  Aligned_cols=84  Identities=18%  Similarity=0.412  Sum_probs=78.2

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      +..++|||+|||.++|+++|+++|++||.|..+.|..+..++.++|||||+|.+.++|.+|++ +++..|.|+.|.|+++
T Consensus        18 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a   96 (103)
T d1x4ba1          18 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRA   96 (103)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            345799999999999999999999999999999999999889999999999999999999997 7999999999999998


Q ss_pred             CCccc
Q psy3016         112 SSHQK  116 (305)
Q Consensus       112 ~~~~~  116 (305)
                      .++..
T Consensus        97 ~~ke~  101 (103)
T d1x4ba1          97 VAREE  101 (103)
T ss_dssp             SSCCC
T ss_pred             cccCC
Confidence            87653

>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=99.81  E-value=1.9e-20  Score=140.85  Aligned_cols=82  Identities=30%  Similarity=0.555  Sum_probs=78.0

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (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~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46899999999999999999999999999999999998999999999999999999999999999999999999999876


Q ss_pred             cc
Q psy3016         114 HQ  115 (305)
Q Consensus       114 ~~  115 (305)
                      ..
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=8e-21  Score=134.92  Aligned_cols=76  Identities=26%  Similarity=0.457  Sum_probs=73.3

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      |+|||+|||.++|+++|+++|++||.|.+++++.|+.+|+++|||||+|.+.++|++|++ +++..++|+.|.|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            689999999999999999999999999999999999999999999999999999999998 7999999999999876

>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=2.6e-20  Score=134.21  Aligned_cols=79  Identities=32%  Similarity=0.563  Sum_probs=74.4

Q ss_pred             EEEcCCCccccHHHHHHHhccCCCeEEE-EEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCcc
Q psy3016          37 IYVGGLDDKVSETLMWELFVQSGPVVNV-HMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQ  115 (305)
Q Consensus        37 l~V~nLp~~~te~~L~~~F~~~G~i~~i-~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~~  115 (305)
                      |||+|||.++|+++|+++|+.||.|.++ +++.+..+|+++|||||+|.+.++|.+|++.|+|..+.|+.|+|+++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999999764 788898889999999999999999999999999999999999999988654

>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=3.3e-20  Score=131.02  Aligned_cols=75  Identities=28%  Similarity=0.496  Sum_probs=71.7

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      +|||+|||.++|+++|+++|++||+|.+++++.++.+++++|||||+|.+.++|++|++ +++..+.|+.|.|++|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            59999999999999999999999999999999999999999999999999999999998 7999999999999764

>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=99.81  E-value=1.1e-19  Score=138.83  Aligned_cols=106  Identities=15%  Similarity=0.275  Sum_probs=89.1

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      .+.+++|||+|||.++|+++|+++|+.||.|.+|++..+   +.++|||||+|.+.++|..|++.|||..+.|+.|+|.+
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   80 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY   80 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345789999999999999999999999999999999765   45789999999999999999999999999999999999


Q ss_pred             CCCccccccccccccccCCCchhcHHHHHHHHhhcCcc
Q psy3016         111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVI  148 (305)
Q Consensus       111 ~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v  148 (305)
                      +......         ........++++..+.+.+|.-
T Consensus        81 a~~~~~~---------~~~~~~~~~~~~~~~~~~~g~~  109 (114)
T d2f9da1          81 YNANRAF---------QKMDTKKKEEQLKLLKEKYGIN  109 (114)
T ss_dssp             CCHHHHT---------TTSCHHHHHHHHHHHHHHHCCC
T ss_pred             cCCCchh---------hhhHHHHHHHHHHHHHHHhCCC
Confidence            8654322         2233445677788888887754

>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=99.80  E-value=1e-19  Score=129.80  Aligned_cols=77  Identities=23%  Similarity=0.449  Sum_probs=73.7

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      .++|||||||.++|+++|+++|+.||.|..+++..++.++.++|||||+|.+.++|.+|++ ++|..|.|+.|.|++|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            4799999999999999999999999999999999999999999999999999999999996 8999999999999876

>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=99.80  E-value=7.7e-20  Score=132.32  Aligned_cols=78  Identities=19%  Similarity=0.390  Sum_probs=72.5

Q ss_pred             EEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCC---CcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQ---THQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        37 l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~---~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (305)
                      |||+|||.++|+++|+++|+.||.|.+++|+.++.++   .++|||||+|.+.++|.+|++.|||..+.|+.|.|+++..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999999876554   4689999999999999999999999999999999999865


Q ss_pred             c
Q psy3016         114 H  114 (305)
Q Consensus       114 ~  114 (305)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.80  E-value=1.7e-19  Score=133.99  Aligned_cols=85  Identities=22%  Similarity=0.327  Sum_probs=78.6

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc------CceeCCe
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN------MIKLYGK  104 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~------g~~~~g~  104 (305)
                      .+..++|||+|||.++|+++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|.+|++.|+      |..+.|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3456899999999999999999999999999999999999889999999999999999999999886      6788999


Q ss_pred             eeEEeeCCCcc
Q psy3016         105 PIRVNKASSHQ  115 (305)
Q Consensus       105 ~l~v~~~~~~~  115 (305)
                      .|+|.++.++.
T Consensus        85 ~l~v~~a~~k~   95 (98)
T d1x4ha1          85 QLKVDLAVTRD   95 (98)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999998754

>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=99.78  E-value=1.5e-19  Score=130.99  Aligned_cols=81  Identities=22%  Similarity=0.355  Sum_probs=71.1

Q ss_pred             CCceEEEcCCCcccc-HHHHHHHhccCCCeEEEEEccc-CCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          33 GDATIYVGGLDDKVS-ETLMWELFVQSGPVVNVHMPKD-RVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        33 ~~~~l~V~nLp~~~t-e~~L~~~F~~~G~i~~i~~~~~-~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (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~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            468999999999876 6679999999999999998764 4678999999999999999999997 999999999999999


Q ss_pred             CCCc
Q psy3016         111 ASSH  114 (305)
Q Consensus       111 ~~~~  114 (305)
                      +..+
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8754

>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=99.78  E-value=3.9e-19  Score=132.75  Aligned_cols=86  Identities=23%  Similarity=0.364  Sum_probs=77.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeE--------EEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVV--------NVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL  101 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~--------~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~  101 (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            344578999999999999999999999999874        567777878899999999999999999999999999999


Q ss_pred             CCeeeEEeeCCCcc
Q psy3016         102 YGKPIRVNKASSHQ  115 (305)
Q Consensus       102 ~g~~l~v~~~~~~~  115 (305)
                      .|+.|+|+++..+.
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999998754

>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=99.78  E-value=1.3e-19  Score=127.85  Aligned_cols=75  Identities=27%  Similarity=0.461  Sum_probs=72.2

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      +|||||||.++|+++|+++|+.||.|..+.++.++.++.+++||||+|.+.++|++|++ +|+..+.|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            59999999999999999999999999999999999889999999999999999999997 9999999999999875

>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=99.78  E-value=7.6e-20  Score=129.04  Aligned_cols=75  Identities=27%  Similarity=0.418  Sum_probs=70.8

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (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-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999998 4778899999998764

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.5e-19  Score=130.70  Aligned_cols=82  Identities=34%  Similarity=0.519  Sum_probs=77.1

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||.++|+++|+++|+.||.|..+                                       .++.|..+|.
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~d~~~~~   45 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDI---------------------------------------QIPLDYETEK   45 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCE---------------------------------------ECCCCSSSCC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEec---------------------------------------cccccccccc
Confidence            5789999999999999999999999999877                                       7788989999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      ++|||||+|.+.++|.+|+..|||..++|+.|+|.|+.++.
T Consensus        46 ~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~~   86 (89)
T d2cqba1          46 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR   86 (89)
T ss_dssp             CSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             ccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            99999999999999999999999999999999999997653

>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=99.78  E-value=3.4e-19  Score=133.13  Aligned_cols=83  Identities=17%  Similarity=0.257  Sum_probs=75.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||.++|+++|+++|+.||.|..+.+..+. ++.++|||||+|.+.++|.+|++.|||..+.|+.+.+.
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~   92 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   92 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccC
Confidence            33456799999999999999999999999999999998885 78899999999999999999999999999999999887


Q ss_pred             eCCC
Q psy3016         110 KASS  113 (305)
Q Consensus       110 ~~~~  113 (305)
                      ++.+
T Consensus        93 ~~~P   96 (101)
T d1x5oa1          93 PTEP   96 (101)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            7654

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.78  E-value=2.6e-19  Score=130.34  Aligned_cols=82  Identities=27%  Similarity=0.499  Sum_probs=77.0

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...+|||+||+.++|+++|+++|+.||.|..+                                       +++.|..+|
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v---------------------------------------~i~~d~~tg   46 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNI---------------------------------------HLNLDRRTG   46 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECTTTS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccc---------------------------------------ccccccccc
Confidence            35789999999999999999999999999877                                       778898999


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +++|||||+|.+.++|.+|+..|||..+.|+.|+|+||..+
T Consensus        47 ~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          47 FSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK   87 (88)
T ss_dssp             SEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             ccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecCC
Confidence            99999999999999999999999999999999999999875

>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=5.2e-19  Score=130.82  Aligned_cols=76  Identities=24%  Similarity=0.478  Sum_probs=71.5

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||+|||..+|+++|+++|+.||.|.+|+++.+      +|||||+|.+.++|.+|++.|||..+.|+.|+|.|+.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4579999999999999999999999999999999876      4899999999999999999999999999999999987


Q ss_pred             Cc
Q psy3016         113 SH  114 (305)
Q Consensus       113 ~~  114 (305)
                      ..
T Consensus        91 ~~   92 (96)
T d1x4ga1          91 ES   92 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.1e-18  Score=128.73  Aligned_cols=82  Identities=23%  Similarity=0.402  Sum_probs=74.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ..+.+++|||+|||.++|+++|+++|+.||.|..+.+..+   +.+++||||+|.+.++|++||+.||+..+.|+.|+|+
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999998655   3568999999999999999999999999999999999


Q ss_pred             eCCCc
Q psy3016         110 KASSH  114 (305)
Q Consensus       110 ~~~~~  114 (305)
                      ++...
T Consensus        87 ~a~~~   91 (95)
T d1x4aa1          87 FPRSG   91 (95)
T ss_dssp             CCCCC
T ss_pred             eccCC
Confidence            98753

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=4.2e-19  Score=132.87  Aligned_cols=86  Identities=28%  Similarity=0.460  Sum_probs=79.5

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      +..++|||+|||.++++++|+++|+.||.|..+                                       .++.+..+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~---------------------------------------~~~~~~~~   56 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSA---------------------------------------KVFIDKQT   56 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEE---------------------------------------EEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhcccccc---------------------------------------ceeeeccc
Confidence            346789999999999999999999999999877                                       67888889


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      |.++|||||+|.+.++|.+|++.|||..|.|+.|+|+|+..+...
T Consensus        57 g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~~  101 (102)
T d2cpza1          57 NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS  101 (102)
T ss_dssp             CSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCC
T ss_pred             CCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCCCC
Confidence            999999999999999999999999999999999999999877653

>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=99.77  E-value=2.8e-19  Score=128.41  Aligned_cols=80  Identities=34%  Similarity=0.554  Sum_probs=75.1

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||.++|+++|+++|+.||.|..+                                       ++.+|..+|.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~---------------------------------------~i~~~~~~g~   42 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTC---------------------------------------RIMRDYKTGY   42 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCEETTTTE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccee---------------------------------------eeeeecccCC
Confidence            3579999999999999999999999999877                                       6788888899


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      ++|||||+|.+.++|.+|++.|||..+.|+.|+|+|+++
T Consensus        43 ~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          43 SYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             ECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            999999999999999999999999999999999999864

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=2.6e-19  Score=130.90  Aligned_cols=85  Identities=31%  Similarity=0.418  Sum_probs=78.4

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      .+..++|||+|||.++++++|+++|+.||.|..+                                       .++.|..
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v---------------------------------------~i~~d~~   45 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRI---------------------------------------YLAKDKT   45 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEE---------------------------------------EEEECSS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccc---------------------------------------ccccccc
Confidence            3456789999999999999999999999999877                                       6788888


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+||+++.
T Consensus        46 t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~~   89 (90)
T d2cq0a1          46 TGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   89 (90)
T ss_dssp             SCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             ccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCCC
Confidence            89999999999999999999999999999999999999997653

>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=99.76  E-value=1.1e-18  Score=126.08  Aligned_cols=78  Identities=17%  Similarity=0.238  Sum_probs=72.8

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||+|||.++|+++|+++|+.||.|..|++..+. ++.++|||||+|.+.++|.+|++ +++..+.|+.|.|.+..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            35799999999999999999999999999999998875 78899999999999999999997 79999999999999854

>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=99.76  E-value=7.1e-20  Score=134.19  Aligned_cols=82  Identities=17%  Similarity=0.343  Sum_probs=75.0

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||.++|+++|+++|+.||.|..++++.+ .+|+++|||||+|.+.++|++|++ ||+..+.|+.|+|.
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            3445679999999999999999999999999999988765 478999999999999999999996 99999999999999


Q ss_pred             eCCC
Q psy3016         110 KASS  113 (305)
Q Consensus       110 ~~~~  113 (305)
                      ++..
T Consensus        87 ~ak~   90 (91)
T d1fjeb1          87 KPKG   90 (91)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9875

>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=99.76  E-value=1.4e-19  Score=135.39  Aligned_cols=85  Identities=24%  Similarity=0.334  Sum_probs=79.4

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      +.+++|||+|||.++|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|+|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45689999999999999999999999999999999888778899999999999999999999999999999999999999


Q ss_pred             CCccc
Q psy3016         112 SSHQK  116 (305)
Q Consensus       112 ~~~~~  116 (305)
                      ..+..
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87653

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.7e-19  Score=127.89  Aligned_cols=78  Identities=28%  Similarity=0.628  Sum_probs=74.2

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      .|||+|||..+|+++|+++|+.||.|..+                                       ++++|..+|.++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~d~~tg~~~   42 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSI---------------------------------------RVCRDMITRRSL   42 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECTTTCCEE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEE---------------------------------------EEEecccccCCC
Confidence            59999999999999999999999999887                                       789999999999


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      |||||+|.+.++|.+|++.|||.++.|+.|+|+|++.
T Consensus        43 g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1          43 GYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             CceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            9999999999999999999999999999999999853

>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=99.76  E-value=5.7e-19  Score=129.88  Aligned_cols=83  Identities=31%  Similarity=0.549  Sum_probs=77.9

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||..+|+++|+++|+.||.|..+                                       .+++|..+|
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v---------------------------------------~~~~d~~tg   48 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNT---------------------------------------HMPKDRVTG   48 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCBCSSSC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCcccc---------------------------------------ceeeccccc
Confidence            35789999999999999999999999999877                                       778999999


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .++|||||+|.+.++|.+|++.|||..+.|+.|+|+||..+.
T Consensus        49 ~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          49 QHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   90 (93)
T ss_dssp             SBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             ccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            999999999999999999999999999999999999997664

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.76  E-value=1e-18  Score=129.31  Aligned_cols=82  Identities=17%  Similarity=0.241  Sum_probs=73.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ..+..++|||+|||.++|+++|+++|+.||.|..++.     ++.++|||||+|.+.++|.+|++.||+..+.|+.|+|.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3345689999999999999999999999998877653     56789999999999999999999999999999999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      |+.++..
T Consensus        87 ~a~~k~~   93 (96)
T d1fjca_          87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EeCCCCC
Confidence            9987653

>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=6.5e-19  Score=126.74  Aligned_cols=82  Identities=89%  Similarity=1.424  Sum_probs=74.7

Q ss_pred             ccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccc
Q psy3016         124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKG  203 (305)
Q Consensus       124 l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g  203 (305)
                      |||+|||.++|+++|+++|+.||.|..+.                                      .+++|..+|+++|
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~--------------------------------------~i~~~~~~g~~~g   42 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTP--------------------------------------KIMRDPDTGNSKG   42 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCC--------------------------------------EECCCTTTCSCCS
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeE--------------------------------------EEEeeccccccCc
Confidence            79999999999999999999999986541                                      4588888999999


Q ss_pred             eEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         204 FAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       204 ~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ||||+|.+.++|.+|++.|||..+.|++|+|+|+.++..+
T Consensus        43 ~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~~k   82 (83)
T d1x5ta1          43 YAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK   82 (83)
T ss_dssp             EEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCC
T ss_pred             eEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCCcC
Confidence            9999999999999999999999999999999999876543

>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=99.76  E-value=1.1e-18  Score=126.36  Aligned_cols=77  Identities=30%  Similarity=0.469  Sum_probs=71.5

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      +.++|||+|||.++++++|+++|+.||.|.+|++.++      +|||||+|.+.++|.+|++.|||..+.|+.|+|+|+.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            4568999999999999999999999999999999765      4899999999999999999999999999999999987


Q ss_pred             Ccc
Q psy3016         113 SHQ  115 (305)
Q Consensus       113 ~~~  115 (305)
                      ...
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            653

>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=99.76  E-value=9.8e-19  Score=128.58  Aligned_cols=83  Identities=23%  Similarity=0.360  Sum_probs=77.4

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ..+++|||+|||.++|+++|+++|+.||.|..+                                       .++.|..+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~   45 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKI---------------------------------------IMGLDKMK   45 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECTTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccee---------------------------------------cccccccc
Confidence            356899999999999999999999999999887                                       77888889


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +.++|||||+|.+.++|..|++.|||..++|+.|+|.|+...
T Consensus        46 ~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~~   87 (93)
T d1h2vz_          46 KTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGF   87 (93)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCC
T ss_pred             ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            999999999999999999999999999999999999998644

>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=99.75  E-value=3.5e-19  Score=124.68  Aligned_cols=71  Identities=21%  Similarity=0.416  Sum_probs=68.5

Q ss_pred             EEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        37 l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (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            79999999999999999999999999999999998999999999999999999999999999999998764

>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=99.75  E-value=8.8e-19  Score=125.72  Aligned_cols=79  Identities=28%  Similarity=0.512  Sum_probs=74.4

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      .+|||+|||.++++++|+++|+.||.|..+                                       .+.+|..++.+
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v---------------------------------------~i~~~~~~~~~   43 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESC---------------------------------------KLVRDKITGQS   43 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------EEEECTTTCCE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccc---------------------------------------cceeeccCCCc
Confidence            469999999999999999999999999877                                       67788888999


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      +|||||+|.+.++|.+|++.|||..+.|+.|+|.||++
T Consensus        44 ~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          44 LGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            99999999999999999999999999999999999864

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.2e-18  Score=128.96  Aligned_cols=83  Identities=19%  Similarity=0.366  Sum_probs=74.3

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCC-eEEEEEcccC-CCCCcceEEEEEEcCHHHHHHHHHHhcC--ceeCCeeeEEe
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGP-VVNVHMPKDR-VTQTHQGYGFIEFMGEEDADYAIKIMNM--IKLYGKPIRVN  109 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~-i~~i~~~~~~-~~~~~~g~afV~f~~~e~A~~Ai~~l~g--~~~~g~~l~v~  109 (305)
                      +|+|||||||..+|+++|+++|+.||+ |.+++++.+. .+++++|||||+|.++++|..|++.|++  ..+.|+.|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            478999999999999999999999996 9999999875 4688999999999999999999999864  56679999999


Q ss_pred             eCCCccc
Q psy3016         110 KASSHQK  116 (305)
Q Consensus       110 ~~~~~~~  116 (305)
                      |+.++..
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9987543

>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=99.75  E-value=1.9e-18  Score=128.57  Aligned_cols=84  Identities=26%  Similarity=0.316  Sum_probs=77.9

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||.++|+++|+++|+.||.|..+                                       .++.|..++
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v---------------------------------------~i~~d~~tg   47 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSEL---------------------------------------HYPIDSLTK   47 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCCCTTTC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceee---------------------------------------eeccccccc
Confidence            35679999999999999999999999999877                                       678888899


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++|||||+|.+.++|.+|+..||+..|.|+.|+|.++..+..
T Consensus        48 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~   90 (99)
T d1whwa_          48 KPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             CCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCST
T ss_pred             ccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCc
Confidence            9999999999999999999999999999999999999987643

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=3.8e-18  Score=128.01  Aligned_cols=84  Identities=26%  Similarity=0.394  Sum_probs=74.1

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccC-CCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDR-VTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~-~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ...++|||+|||.++|+++|+++|+.|| +.++.++.+. .++.++|||||+|.+.++|++|++ ||+..|.|+.|+|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            3468999999999999999999999999 7788877765 468899999999999999987775 999999999999999


Q ss_pred             CCCcccc
Q psy3016         111 ASSHQKN  117 (305)
Q Consensus       111 ~~~~~~~  117 (305)
                      +..+...
T Consensus        91 a~~~~~~   97 (104)
T d1wi8a_          91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8876543

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.8e-18  Score=127.31  Aligned_cols=78  Identities=19%  Similarity=0.416  Sum_probs=70.2

Q ss_pred             cCCCCceEEEcCCC-ccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          30 SGDGDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        30 ~~~~~~~l~V~nLp-~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      .....++|||+||+ ..+++++|+++|++||.|.+|++        ++|||||+|.+.++|.+|++.|||..+.|+.|+|
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V   82 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI   82 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999997 57889999999999999999998        4699999999999999999999999999999999


Q ss_pred             eeCCCcc
Q psy3016         109 NKASSHQ  115 (305)
Q Consensus       109 ~~~~~~~  115 (305)
                      +++....
T Consensus        83 ~~a~~~~   89 (98)
T d1wf2a_          83 NLAAEPK   89 (98)
T ss_dssp             EETTSCC
T ss_pred             EECCCCC
Confidence            9997543

>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=99.75  E-value=1.1e-18  Score=127.20  Aligned_cols=76  Identities=18%  Similarity=0.354  Sum_probs=69.4

Q ss_pred             CceEEEcCCCccccHHHH---HHHhccCCCeEEEEEcccCCCCCc---ceEEEEEEcCHHHHHHHHHHhcCceeCCeeeE
Q psy3016          34 DATIYVGGLDDKVSETLM---WELFVQSGPVVNVHMPKDRVTQTH---QGYGFIEFMGEEDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L---~~~F~~~G~i~~i~~~~~~~~~~~---~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      .++|||+|||+++++++|   +++|++||.|.+|.+++++.++.+   +|||||+|.+.++|.+|++.|||..+.|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            457999999999999999   778999999999999998766544   48999999999999999999999999999999


Q ss_pred             Ee
Q psy3016         108 VN  109 (305)
Q Consensus       108 v~  109 (305)
                      ++
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            84

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.75  E-value=3.4e-18  Score=122.90  Aligned_cols=75  Identities=17%  Similarity=0.307  Sum_probs=69.0

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC-CeeeEEeeC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY-GKPIRVNKA  111 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~-g~~l~v~~~  111 (305)
                      .+++|||+|||.++|+++|+++|+.||.|.+|+++++     .+|||||+|.+.++|..|++.|+|..+. |+.|+|.|+
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            4689999999999999999999999999999999765     3589999999999999999999998884 689999998


Q ss_pred             C
Q psy3016         112 S  112 (305)
Q Consensus       112 ~  112 (305)
                      +
T Consensus        82 k   82 (83)
T d2b0ga1          82 K   82 (83)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.75  E-value=2e-18  Score=130.63  Aligned_cols=77  Identities=25%  Similarity=0.433  Sum_probs=70.9

Q ss_pred             CCceEEEcCCCc-cccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          33 GDATIYVGGLDD-KVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        33 ~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ++++|||+||++ .+|+++|+++|+.||.|.+|+|+.++     +|||||+|.+.++|.+|++.|||..+.|+.|+|+++
T Consensus         1 g~~~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           1 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   75 (109)
T ss_dssp             CCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            478999999965 69999999999999999999998873     689999999999999999999999999999999998


Q ss_pred             CCc
Q psy3016         112 SSH  114 (305)
Q Consensus       112 ~~~  114 (305)
                      ...
T Consensus        76 ~~~   78 (109)
T d2adca1          76 KHQ   78 (109)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            644

>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=99.75  E-value=1.5e-18  Score=125.61  Aligned_cols=82  Identities=15%  Similarity=0.129  Sum_probs=71.8

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      ......+|||+|||.+++++||+++|+.||.+....++.+..++.++|||||+|.+.++|++|++.||+..+.||.|+|.
T Consensus         5 g~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~   84 (86)
T d2cqpa1           5 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   84 (86)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEE
Confidence            44456789999999999999999999999998764333444578999999999999999999999999999999999998


Q ss_pred             eC
Q psy3016         110 KA  111 (305)
Q Consensus       110 ~~  111 (305)
                      ++
T Consensus        85 l~   86 (86)
T d2cqpa1          85 LG   86 (86)
T ss_dssp             ES
T ss_pred             EC
Confidence            64

>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=99.74  E-value=1.2e-18  Score=124.65  Aligned_cols=79  Identities=14%  Similarity=0.264  Sum_probs=67.2

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ++|||+|||.++|+++|+++|+.||.|..+                                       .++.+..+|.+
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~---------------------------------------~~~~~~~~~~~   42 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALS---------------------------------------IRLPSLRFNTS   42 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCE---------------------------------------EECC-------
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEee---------------------------------------eeecccccccc
Confidence            689999999999999999999999999765                                       45666677999


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      +|||||+|.+.++|.+|++.|||..++|++|+|+++++
T Consensus        43 ~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          43 RRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            99999999999999999999999999999999999864

>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=99.74  E-value=9.1e-19  Score=126.57  Aligned_cols=81  Identities=26%  Similarity=0.503  Sum_probs=76.2

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      .+|||+|||.++|+++|+++|+.||.|..+                                       ++++|..+|.+
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v---------------------------------------~i~~d~~tg~~   42 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAF---------------------------------------NLVKDSATGLS   42 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEE---------------------------------------EEECCCSSSCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceE---------------------------------------Eeecccccccc
Confidence            469999999999999999999999999887                                       78899999999


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      +|||||+|.+.++|.+|+..|||..+.|+.|+|.|+....
T Consensus        43 rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_          43 KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             CCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             ceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            9999999999999999999999999999999999996543

>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=99.74  E-value=2.8e-18  Score=126.33  Aligned_cols=84  Identities=19%  Similarity=0.446  Sum_probs=75.4

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC-
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD-  197 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~-  197 (305)
                      ....+|||+|||.++++++|+++|+.||.|..+                                       .++.|.. 
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~   46 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTV---------------------------------------RLPKKMTG   46 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEE---------------------------------------EEEecccc
Confidence            346789999999999999999999999999876                                       5666643 


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHh-cCeeecCeeeEEEEeeecC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAM-HGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l-~~~~~~g~~l~v~~a~~~~  241 (305)
                      +|.++|||||+|.+.++|.+|+..| ||..++|++|.|.||..+.
T Consensus        47 ~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~   91 (94)
T d2cpha1          47 TGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV   91 (94)
T ss_dssp             SCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCC
T ss_pred             CCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCCC
Confidence            7899999999999999999999998 8999999999999997664

>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=6.8e-18  Score=122.14  Aligned_cols=78  Identities=29%  Similarity=0.342  Sum_probs=71.0

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS  112 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~  112 (305)
                      ..++|||+|||.++|+++|+++|+.||.|..+++.      .++|||||+|.+.++|.+|+..|||..+.|+.|.|+|+.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            45799999999999999999999999999888773      356999999999999999999999999999999999998


Q ss_pred             Cccc
Q psy3016         113 SHQK  116 (305)
Q Consensus       113 ~~~~  116 (305)
                      +..+
T Consensus        81 P~~~   84 (86)
T d2cpda1          81 PVDK   84 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6553

>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=99.74  E-value=1.1e-18  Score=132.58  Aligned_cols=79  Identities=20%  Similarity=0.239  Sum_probs=71.5

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||+|..|.|..      ++|||||+|.+.++|.+|++.|||..|.|+.|.|+
T Consensus         6 ~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~   79 (111)
T d1whxa_           6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEE
Confidence            344567999999999999999999999999999999843      56999999999999999999999999999999999


Q ss_pred             eCCCc
Q psy3016         110 KASSH  114 (305)
Q Consensus       110 ~~~~~  114 (305)
                      |+...
T Consensus        80 ~a~~~   84 (111)
T d1whxa_          80 WAPIG   84 (111)
T ss_dssp             EEETT
T ss_pred             ECCCC
Confidence            97643

>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=99.74  E-value=2.2e-18  Score=123.94  Aligned_cols=77  Identities=26%  Similarity=0.406  Sum_probs=72.5

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      +..++|||+|||.++|+++|+++|+.||.|..+                                       .+++|..+
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~   47 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADV---------------------------------------SIVYDQQS   47 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEE---------------------------------------EEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccc---------------------------------------cccccccc
Confidence            456789999999999999999999999999877                                       67888889


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEE
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV  234 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v  234 (305)
                      ++++|||||+|.+.++|.+|+..|||..|+|+.|+|
T Consensus        48 ~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          48 RRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             cccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            999999999999999999999999999999999987

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=3.4e-18  Score=121.75  Aligned_cols=75  Identities=25%  Similarity=0.393  Sum_probs=68.9

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ...++|||+||+  +|+++|+++|++||.|.+|++.++      +|||||+|.+.++|.+|++.|||..+.|+.|+|.|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456799999996  899999999999999999999654      489999999999999999999999999999999999


Q ss_pred             CCc
Q psy3016         112 SSH  114 (305)
Q Consensus       112 ~~~  114 (305)
                      .++
T Consensus        75 ~~~   77 (79)
T d2bz2a1          75 RKQ   77 (79)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            754

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=2.8e-18  Score=125.28  Aligned_cols=84  Identities=27%  Similarity=0.534  Sum_probs=77.0

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ..+|||+|||.++|+++|.++|+.||.|..+                                       .++.+..++.
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~---------------------------------------~~~~~~~~~~   45 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEV---------------------------------------VVVKDRETQR   45 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEE---------------------------------------EECCCSSSCS
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccce---------------------------------------eecccccccc
Confidence            4679999999999999999999999999876                                       5677778899


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ++|||||+|.+.++|.+|+..|||..|+|+.|+|.++..+..+
T Consensus        46 ~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~~   88 (90)
T d1x5sa1          46 SRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN   88 (90)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCC
T ss_pred             ccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCCC
Confidence            9999999999999999999999999999999999999776553

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1.7e-18  Score=123.69  Aligned_cols=76  Identities=22%  Similarity=0.339  Sum_probs=68.6

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCc-eeCCeeeEEeeCCC
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMI-KLYGKPIRVNKASS  113 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~-~~~g~~l~v~~~~~  113 (305)
                      .+|||+|||.++|+++|+++|++||.|..+++..      ++|||||+|.+.++|.+|++.|||. .+.|+.|+|+++.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            3799999999999999999999999988777654      4599999999999999999999985 69999999999987


Q ss_pred             ccc
Q psy3016         114 HQK  116 (305)
Q Consensus       114 ~~~  116 (305)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            654

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=2.5e-18  Score=124.25  Aligned_cols=78  Identities=31%  Similarity=0.566  Sum_probs=72.6

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||..+|+++|+++|+.||.|..+                                       +++.|..+|.
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v---------------------------------------~i~~d~~~g~   46 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITS---------------------------------------RILVDQVTGV   46 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECTTTCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcccc---------------------------------------cccccccccc
Confidence            4679999999999999999999999999987                                       7788888899


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecC--eeeEEEEe
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCN--RPISVSYA  237 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g--~~l~v~~a  237 (305)
                      ++|||||+|.+.++|.+|++.|||..+.|  ++|+|+||
T Consensus        47 ~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          47 SRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             EEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            99999999999999999999999999987  55999986

>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=99.73  E-value=4.9e-18  Score=123.47  Aligned_cols=77  Identities=17%  Similarity=0.283  Sum_probs=67.1

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      .++++|||+|||.+++++||+++|+.|| +..+.+      +.++|||||+|.+.++|++|++.||+..+.|+.|+|+++
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a   75 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3567999999999999999999999999 333333      346799999999999999999999999999999999998


Q ss_pred             CCcc
Q psy3016         112 SSHQ  115 (305)
Q Consensus       112 ~~~~  115 (305)
                      ..+.
T Consensus        76 ~~~~   79 (88)
T d1wg1a_          76 PTDA   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.73  E-value=4.9e-18  Score=124.28  Aligned_cols=80  Identities=23%  Similarity=0.492  Sum_probs=72.0

Q ss_pred             CCceEEEcCCCccccHHHHHH----HhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEE
Q psy3016          33 GDATIYVGGLDDKVSETLMWE----LFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV  108 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~----~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v  108 (305)
                      .+++|||+|||..+|++||++    +|+.||+|.+|++..+   +.++|||||+|.+.++|.+|++.+||..+.|+.|+|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~---~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS---LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH---HHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeee---ccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            368999999999999999864    6899999999998653   567899999999999999999999999999999999


Q ss_pred             eeCCCcc
Q psy3016         109 NKASSHQ  115 (305)
Q Consensus       109 ~~~~~~~  115 (305)
                      .|+..+.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9998654

>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=99.73  E-value=6.8e-18  Score=122.68  Aligned_cols=77  Identities=23%  Similarity=0.200  Sum_probs=69.5

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee-CCeeeEEeeC
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL-YGKPIRVNKA  111 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~-~g~~l~v~~~  111 (305)
                      .+++|||+|||.++|+++|+++|+.||.|..+.+...    +++|||||+|.+.++|.+|+..|+|..+ .|+.|+|+++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            3679999999999999999999999999988877554    3578999999999999999999999888 5899999998


Q ss_pred             CC
Q psy3016         112 SS  113 (305)
Q Consensus       112 ~~  113 (305)
                      +.
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            75

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.73  E-value=4.1e-18  Score=134.59  Aligned_cols=84  Identities=25%  Similarity=0.442  Sum_probs=77.7

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||.++|+++|+++|+.||.|..+                                       .++.|..++
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~d~~t~   81 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESV---------------------------------------KIVCDRETR   81 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEE---------------------------------------EEEEETTTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhcccccc---------------------------------------ccccccccc
Confidence            34679999999999999999999999999877                                       778888899


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++|||||+|.+.++|.+|+..|||.+|+|+.|+|.|+..+..
T Consensus        82 ~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~~  124 (139)
T d1u6fa1          82 QSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ  124 (139)
T ss_dssp             EEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCC
T ss_pred             cccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            9999999999999999999999999999999999999976543

>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=7.9e-18  Score=118.57  Aligned_cols=74  Identities=20%  Similarity=0.284  Sum_probs=68.2

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            48999999999999999999999999999999988643  45899999999999999996 8999999999999865

>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=99.72  E-value=3.7e-18  Score=123.30  Aligned_cols=78  Identities=31%  Similarity=0.563  Sum_probs=72.8

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ..+|||+|||.++++++|+++|+.||.|..+                                       ++++|..+|+
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~---------------------------------------~~~~d~~~g~   46 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQK---------------------------------------NILRDKLTGR   46 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEE---------------------------------------EEEECTTTCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEeee---------------------------------------eeeccccccc
Confidence            4579999999999999999999999999877                                       6788888999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecC--eeeEEEEe
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCN--RPISVSYA  237 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g--~~l~v~~a  237 (305)
                      ++|||||+|.+.++|.+|++.|||..+.|  ++|+|+||
T Consensus        47 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          47 PRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             EEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            99999999999999999999999999976  88999986

>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=99.72  E-value=5.3e-18  Score=120.41  Aligned_cols=76  Identities=21%  Similarity=0.388  Sum_probs=71.0

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      +|||+|||.++++++|+++|+.||.|..+                                       ++..|. +++++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~---------------------------------------~i~~~~-~g~~~   41 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKA---------------------------------------AVHYDR-SGRSL   41 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEE---------------------------------------EESCSS-CCCSC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEE---------------------------------------EEEEee-ccccc
Confidence            59999999999999999999999999877                                       667774 69999


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      |||||+|.+.++|.+|++.|||..+.|+.|+|+++.
T Consensus        42 g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_          42 GTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             eeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            999999999999999999999999999999999984

>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=99.72  E-value=4.7e-18  Score=123.56  Aligned_cols=78  Identities=22%  Similarity=0.480  Sum_probs=70.2

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ..+++|||+|||..+|+++|+++|++||.|.+|++..     .+++||||+|.+.++|++|+.  ++..+.|+.|.|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            4578999999999999999999999999999998754     367999999999999999986  788999999999999


Q ss_pred             CCccc
Q psy3016         112 SSHQK  116 (305)
Q Consensus       112 ~~~~~  116 (305)
                      .++..
T Consensus        76 ~~k~~   80 (88)
T d1wf0a_          76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76554

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.7e-17  Score=124.38  Aligned_cols=90  Identities=20%  Similarity=0.199  Sum_probs=78.6

Q ss_pred             CCCCcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCee
Q psy3016          26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKP  105 (305)
Q Consensus        26 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~  105 (305)
                      +.........+|||+|||+++|++||+++|+.+|.|..+.++.+..++.++|||||+|.+.++|++|++ +|+..|.||.
T Consensus         7 ~~~~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~   85 (104)
T d1wg5a_           7 GNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRY   85 (104)
T ss_dssp             CCCSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSC
T ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceE
Confidence            334455566789999999999999999999999999886666666788999999999999999999997 8999999999


Q ss_pred             eEEeeCCCccc
Q psy3016         106 IRVNKASSHQK  116 (305)
Q Consensus       106 l~v~~~~~~~~  116 (305)
                      |.|.++.....
T Consensus        86 i~V~~~~~~~~   96 (104)
T d1wg5a_          86 IEIFKSSRAEV   96 (104)
T ss_dssp             CEEEEECTTTS
T ss_pred             EEEEECCHHHh
Confidence            99999887653

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.1e-17  Score=126.23  Aligned_cols=81  Identities=14%  Similarity=0.126  Sum_probs=72.6

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCcee--CCeeeEE
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKL--YGKPIRV  108 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~--~g~~l~v  108 (305)
                      .....+|||+|||..+|+++|+++|++||.|.+|+++.++    ++|||||+|.+.++|++|++.|||..+  .|+.|++
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            3456789999999999999999999999999999998774    579999999999999999999999988  4788999


Q ss_pred             eeCCCcc
Q psy3016         109 NKASSHQ  115 (305)
Q Consensus       109 ~~~~~~~  115 (305)
                      .++....
T Consensus        80 ~~s~~~~   86 (108)
T d2adba1          80 DFSKLTS   86 (108)
T ss_dssp             EECSSCS
T ss_pred             EecCCcc
Confidence            9887643

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=8.8e-18  Score=122.54  Aligned_cols=82  Identities=24%  Similarity=0.408  Sum_probs=74.7

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...+|||+|||.++|+++|+++|+.||.|..+                                       .++.|..+|
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~d~~tg   47 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMV---------------------------------------QVKKDLKTG   47 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECSSSC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhccccee---------------------------------------eeccCCCCc
Confidence            45789999999999999999999999999887                                       789999999


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++|||||+|.+.++|.+||+.  +..++|+.|.|.++..+..
T Consensus        48 ~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~~k~~   88 (90)
T d2cqga1          48 HSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPNSKQS   88 (90)
T ss_dssp             SEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCCTTCC
T ss_pred             ccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCCCCCC
Confidence            9999999999999999999984  4589999999999977643

>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=99.71  E-value=3.4e-18  Score=128.26  Aligned_cols=81  Identities=27%  Similarity=0.514  Sum_probs=75.8

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+||+.++|+++|+++|+.||.|..+                                       .++.|..+|+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v---------------------------------------~i~~~~~tg~   48 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSF---------------------------------------RLVYDRETGK   48 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEE---------------------------------------EEEEETTTTE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhcccccccc---------------------------------------ccccccceec
Confidence            3679999999999999999999999999877                                       6788888999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      ++|||||+|.+.++|.+|++.|||..|.|+.|+|.|+..+
T Consensus        49 ~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_          49 PKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             EEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             cCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            9999999999999999999999999999999999998654

>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=99.71  E-value=3.6e-18  Score=120.97  Aligned_cols=76  Identities=28%  Similarity=0.470  Sum_probs=71.7

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ++|||+|||.++|+++|+++|+.||.|..+                                       .++.|..+|++
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~d~~tg~~   41 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKEC---------------------------------------LVMRDPLTKRS   41 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCE---------------------------------------EEECCCCSSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCccee---------------------------------------eeecccCCCCc
Confidence            579999999999999999999999999876                                       77899999999


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      +|||||+|.+.++|.+|+. +|+..++|+.|.|..|
T Consensus        42 kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          42 RGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             SSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             cceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            9999999999999999997 7999999999999987

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.3e-17  Score=124.34  Aligned_cols=92  Identities=26%  Similarity=0.325  Sum_probs=77.6

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...+|||+|||..+|+++|.++|+.||.|..+.                               +.......+..|..++
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~-------------------------------~~~~~~~~~~~d~~~~   55 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNK-------------------------------RTGQPMIHIYLDKETG   55 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCS-------------------------------SSCCBSEECCBCTTTC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEee-------------------------------ecccceeEEeeccccc
Confidence            457899999999999999999999999986431                               0111122467777889


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +++|||||+|.+.++|.+|++.|||..|.|+.|+|+|++.+..
T Consensus        56 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          56 KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP   98 (101)
T ss_dssp             SBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCC
T ss_pred             cccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            9999999999999999999999999999999999999976643

>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=99.71  E-value=2.1e-17  Score=116.33  Aligned_cols=71  Identities=18%  Similarity=0.346  Sum_probs=64.5

Q ss_pred             EEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        37 l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (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-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 555555      346799999999999999999999999999999999998654

>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=99.71  E-value=8.2e-18  Score=125.92  Aligned_cols=81  Identities=25%  Similarity=0.416  Sum_probs=74.3

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||..+|+++|+++|+.||.|..+                                       .++.|..+|+
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~d~~tg~   50 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEA---------------------------------------VVITDRQTGK   50 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEE---------------------------------------EESCCSSSCC
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccce---------------------------------------eccccccccc
Confidence            4679999999999999999999999999877                                       7788988999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      ++|||||+|.+.++|.+|++.+|+ .+.|+.|+|.++..+.
T Consensus        51 ~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~~~   90 (103)
T d2cqda1          51 SRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGA   90 (103)
T ss_dssp             CCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTC
T ss_pred             cCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCCCC
Confidence            999999999999999999998876 7999999999986553

>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=99.71  E-value=1.7e-17  Score=123.01  Aligned_cols=78  Identities=21%  Similarity=0.315  Sum_probs=71.1

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      ....++|||+|||..+++++|+++|+.||.|.++++..       +|||||+|.+.++|++||+.||+..+.|+.|+|.+
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~   84 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSY   84 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            34567899999999999999999999999999999854       48999999999999999999999999999999998


Q ss_pred             CCCcc
Q psy3016         111 ASSHQ  115 (305)
Q Consensus       111 ~~~~~  115 (305)
                      ...+.
T Consensus        85 ~~~~~   89 (98)
T d1wg4a_          85 IRVYP   89 (98)
T ss_dssp             EEEEC
T ss_pred             EecCC
Confidence            76544

>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=99.71  E-value=1.7e-17  Score=121.10  Aligned_cols=81  Identities=21%  Similarity=0.479  Sum_probs=72.3

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||.++|+++|+++|+.||.|..+                                       .+..|..+  
T Consensus         8 ~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~d~~~--   46 (90)
T d2cqia1           8 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSC---------------------------------------KMITEHTS--   46 (90)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEE---------------------------------------EEECCCCS--
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCceee---------------------------------------eeecccCc--
Confidence            5689999999999999999999999999876                                       56666543  


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .+|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..
T Consensus        47 ~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~   88 (90)
T d2cqia1          47 NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS   88 (90)
T ss_dssp             SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTC
T ss_pred             cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            488999999999999999999999999999999999976543

>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=99.70  E-value=3.9e-17  Score=120.81  Aligned_cols=76  Identities=24%  Similarity=0.356  Sum_probs=69.7

Q ss_pred             CCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCC--eeeEEee
Q psy3016          33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG--KPIRVNK  110 (305)
Q Consensus        33 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g--~~l~v~~  110 (305)
                      ..++|||+|||.++|+++|+++|++||.|..|++.++      ++||||+|.+.++|.+|++.||+..+.|  +.|+|+|
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            4689999999999999999999999999999999764      4899999999999999999999999986  5899999


Q ss_pred             CCCc
Q psy3016         111 ASSH  114 (305)
Q Consensus       111 ~~~~  114 (305)
                      +...
T Consensus        90 ak~~   93 (97)
T d1whya_          90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>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=99.70  E-value=5.6e-17  Score=117.74  Aligned_cols=80  Identities=24%  Similarity=0.300  Sum_probs=71.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHh--cCceeCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM--NMIKLYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l--~g~~~~g~~l~  107 (305)
                      ....+++|||+|||.++|+++|+++|+.||.|.++++.++      ++||||+|.+.++|.+|++.+  ++..+.|+.|+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            4557889999999999999999999999999999999765      389999999999999999865  57899999999


Q ss_pred             EeeCCCcc
Q psy3016         108 VNKASSHQ  115 (305)
Q Consensus       108 v~~~~~~~  115 (305)
                      |+++..+.
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99987654

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.4e-17  Score=121.00  Aligned_cols=83  Identities=25%  Similarity=0.427  Sum_probs=73.8

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||.++++++|+++|+.||.|..+                                       .++.|.  
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v---------------------------------------~~~~~~--   47 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV---------------------------------------EIIFNE--   47 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEE---------------------------------------EEECCT--
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeec---------------------------------------cccccc--
Confidence            345789999999999999999999999999877                                       556664  


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +.++|||||+|.+.++|.+|+..|||..++|+.|+|.||.++..
T Consensus        48 ~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~~   91 (93)
T d2cq3a1          48 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM   91 (93)
T ss_dssp             TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCC
T ss_pred             cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCCC
Confidence            34699999999999999999999999999999999999987643

>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=99.70  E-value=3.9e-18  Score=123.73  Aligned_cols=72  Identities=22%  Similarity=0.321  Sum_probs=67.1

Q ss_pred             eEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCCc
Q psy3016          36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSH  114 (305)
Q Consensus        36 ~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~~  114 (305)
                      +|||+|||..+|+++|+++|+.||.|.+++++.+       |||||+|.+.++|++||+.|||..+.|+.|.|.++..+
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            6999999999999999999999999999998654       89999999999999999999999999999999876543

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=8.7e-18  Score=125.26  Aligned_cols=79  Identities=27%  Similarity=0.441  Sum_probs=73.9

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+||+.++|+++|+++|+.||.|..+                                       .+++|..+|+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v---------------------------------------~i~~d~~tg~   58 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDV---------------------------------------RIISDRNSRR   58 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEE---------------------------------------EECCSCCSSS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEE---------------------------------------EeeecCCCcc
Confidence            4679999999999999999999999999877                                       7889989999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      ++|||||+|.+.++|.+|+. |||..|.|+.|+|.++..
T Consensus        59 ~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          59 SKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             CCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             ccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            99999999999999999995 999999999999999754

>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=6.2e-18  Score=126.30  Aligned_cols=84  Identities=23%  Similarity=0.337  Sum_probs=77.5

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      +.++|||+|||.++++++|+++|..||.|..+                                       .++.+..+|
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~---------------------------------------~~~~~~~~g   57 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGP---------------------------------------PIQFRMMTG   57 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSS---------------------------------------CCEEEEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeE---------------------------------------Eeecccccc
Confidence            46789999999999999999999999999876                                       667777789


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++|||||+|.+.++|.+|+..|||..|.|+.|+|+|++.+..
T Consensus        58 ~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~~  100 (102)
T d2cpxa1          58 RMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ  100 (102)
T ss_dssp             SSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             cccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCccc
Confidence            9999999999999999999999999999999999999987654

>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=99.69  E-value=7.4e-18  Score=126.07  Aligned_cols=83  Identities=25%  Similarity=0.486  Sum_probs=76.4

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||.++|+++|+++|..||.|..+                                       .|..|..++.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~---------------------------------------~i~~d~~~~~   60 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDC---------------------------------------VVMRDPASKR   60 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEE---------------------------------------EEECCTTTSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccce---------------------------------------eecccccCCC
Confidence            4789999999999999999999999999877                                       6788888899


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      ++|||||+|.+.++|.+|+. +++..|.|+.|.|.+|.+++..
T Consensus        61 ~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~ke~~  102 (103)
T d1x4ba1          61 SRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREES  102 (103)
T ss_dssp             CCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSCCCC
T ss_pred             ccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcccCCC
Confidence            99999999999999999996 7999999999999999877653

>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=99.69  E-value=9e-18  Score=121.20  Aligned_cols=78  Identities=24%  Similarity=0.426  Sum_probs=69.4

Q ss_pred             ccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC---C
Q psy3016         124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG---N  200 (305)
Q Consensus       124 l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~---~  200 (305)
                      |||+|||.++|+++|+++|+.||.|..+                                       .++.|..++   .
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v---------------------------------------~i~~~~~~~~~~~   41 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSC---------------------------------------TISKKKNKAGVLL   41 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------EEEEEECTTCCEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCcccc---------------------------------------ceecccccccccc
Confidence            7999999999999999999999999877                                       455554443   5


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      ++|||||+|.+.++|.+|++.|||..++|+.|.|.|+...
T Consensus        42 ~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~~   81 (85)
T d2cpfa1          42 SMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERA   81 (85)
T ss_dssp             EEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCS
T ss_pred             cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            7999999999999999999999999999999999998543

>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=99.69  E-value=2e-17  Score=119.06  Aligned_cols=78  Identities=31%  Similarity=0.552  Sum_probs=72.9

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||.++|+++|.++|+.||.|..+                                       .++.|..+|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v---------------------------------------~i~~d~~tg~   46 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDC---------------------------------------VVMRDPNTKR   46 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECTTTCC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccce---------------------------------------eecccccCCC
Confidence            4689999999999999999999999999887                                       7789999999


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      ++|||||+|.+.++|.+|++ +++..+.|+.|+|..|.
T Consensus        47 ~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          47 SRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             EEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             cccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            99999999999999999997 69999999999998874

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=7.9e-18  Score=122.62  Aligned_cols=81  Identities=41%  Similarity=0.681  Sum_probs=72.5

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ..+|||+|||.++|+++|+++|+.||.|..+                                       .++.|.  +.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~---------------------------------------~i~~~~--~~   46 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSC---------------------------------------KVVCDE--NG   46 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEE---------------------------------------EECCBT--TB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEE---------------------------------------EEEeec--CC
Confidence            4579999999999999999999999999876                                       556664  44


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      ++|||||+|++.++|.+|++.|||..++|+.|+|.++..+..
T Consensus        47 ~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~~   88 (89)
T d1cvja2          47 SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE   88 (89)
T ss_dssp             CCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTTT
T ss_pred             CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            789999999999999999999999999999999999976643

>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=99.69  E-value=1.9e-17  Score=123.88  Aligned_cols=81  Identities=12%  Similarity=0.103  Sum_probs=72.1

Q ss_pred             CCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      +...+|||+|||.++|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|++|++ +|+..|.|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            345689999999999999999999999999875555555688999999999999999999997 8999999999999887


Q ss_pred             CC
Q psy3016         112 SS  113 (305)
Q Consensus       112 ~~  113 (305)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            54

>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=99.69  E-value=1.5e-17  Score=117.10  Aligned_cols=75  Identities=33%  Similarity=0.528  Sum_probs=69.9

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      +|||+|||.++|+++|+++|+.||.|..+                                       .++.|..+++++
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~---------------------------------------~i~~d~~t~~~k   41 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDC---------------------------------------TLKLDPITGRSR   41 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCCBTTTTBCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhcccccc---------------------------------------ccccCCCCCCcC
Confidence            48999999999999999999999999887                                       778999999999


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      |||||+|.+.++|.+|+. +++..+.|+.|.|..|
T Consensus        42 g~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          42 GFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             SEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             ceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            999999999999999997 7999999999998653

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=4e-17  Score=120.84  Aligned_cols=83  Identities=31%  Similarity=0.500  Sum_probs=75.1

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||.++|+++|+++|+.||.|..+                                       .++.+..++
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~---------------------------------------~~~~~~~~~   47 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYV---------------------------------------RVVLHPDTE   47 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------ECCBCSSSC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceee---------------------------------------eeccccccc
Confidence            45789999999999999999999999999876                                       567777888


Q ss_pred             CccceEEEEeCChHHHHHHHHHhc------CeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMH------GQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~------~~~~~g~~l~v~~a~~~~  241 (305)
                      .++|||||+|.+.++|.+|+..||      |..+.|+.|+|.|+.++.
T Consensus        48 ~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          48 HSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD   95 (98)
T ss_dssp             CBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCC
T ss_pred             cccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCC
Confidence            999999999999999999999986      678899999999997764

>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=99.68  E-value=7.7e-17  Score=117.22  Aligned_cols=79  Identities=19%  Similarity=0.241  Sum_probs=71.1

Q ss_pred             cCCCCceEEEcCCCcc-ccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHh--cCceeCCeee
Q psy3016          30 SGDGDATIYVGGLDDK-VSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM--NMIKLYGKPI  106 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l--~g~~~~g~~l  106 (305)
                      ..+.+++|||+|||.. +|++||+++|+.||.|.+|.++.++      ++|||+|.+.++|..|++.|  ++..+.|+.|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            4567899999999986 8999999999999999999997654      79999999999999999966  5789999999


Q ss_pred             EEeeCCCc
Q psy3016         107 RVNKASSH  114 (305)
Q Consensus       107 ~v~~~~~~  114 (305)
                      +|.++...
T Consensus        78 ~V~~s~~~   85 (89)
T d1x4da1          78 RVHLSQKY   85 (89)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCc
Confidence            99998754

>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=99.68  E-value=3.4e-17  Score=115.15  Aligned_cols=75  Identities=23%  Similarity=0.413  Sum_probs=69.9

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      +|||+|||.++|+++|+++|+.||.+..+                                       .++.+..++.++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~---------------------------------------~~~~~~~~~~~~   41 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDA---------------------------------------MLMFDKTTNRHR   41 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEE---------------------------------------CCBCCTTCTTSC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCccee---------------------------------------eeeeeccccccC
Confidence            48999999999999999999999999876                                       667787889999


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      |||||+|.+.++|.+|++ +||..|+|+.|+|++|
T Consensus        42 ~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          42 GFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             ceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            999999999999999996 9999999999999875

>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=3.6e-17  Score=122.16  Aligned_cols=83  Identities=18%  Similarity=0.252  Sum_probs=73.1

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEee
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNK  110 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~  110 (305)
                      .....+|||+|||+++|++||+++|+.||. ..+.++.+. ++.++|||||+|.+.++|++|++ +|+..|.||.|+|.+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            344569999999999999999999999984 567777775 57899999999999999999997 899999999999999


Q ss_pred             CCCccc
Q psy3016         111 ASSHQK  116 (305)
Q Consensus       111 ~~~~~~  116 (305)
                      +.....
T Consensus        89 s~~~~~   94 (102)
T d1weza_          89 NSTAGT   94 (102)
T ss_dssp             ECCCCC
T ss_pred             cCCCCC
Confidence            886543

>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=99.68  E-value=2.1e-16  Score=118.29  Aligned_cols=80  Identities=19%  Similarity=0.199  Sum_probs=71.4

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHh--cCceeCCeeeE
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM--NMIKLYGKPIR  107 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l--~g~~~~g~~l~  107 (305)
                      ....+++|||+|||..+|+++|+++|+.||.|.++.+.++      +++|||+|.+.++|++|++.+  ++..+.|+.|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            4456789999999999999999999999999999999654      489999999999999999977  46678899999


Q ss_pred             EeeCCCcc
Q psy3016         108 VNKASSHQ  115 (305)
Q Consensus       108 v~~~~~~~  115 (305)
                      |.++..+.
T Consensus        85 v~~s~~~~   92 (104)
T d1wexa_          85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEcCCCc
Confidence            99997654

>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=99.67  E-value=8e-17  Score=119.52  Aligned_cols=80  Identities=18%  Similarity=0.239  Sum_probs=70.7

Q ss_pred             cCCCCceEEEcCCCcc-ccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHH--HhcCceeCCeee
Q psy3016          30 SGDGDATIYVGGLDDK-VSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK--IMNMIKLYGKPI  106 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~--~l~g~~~~g~~l  106 (305)
                      ....+++|||+|||.. +|+++|+++|+.||.|.++.++++      +|||||+|.+.++|.+|++  .+++..+.|+.|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            4456789999999985 899999999999999999999765      4899999999999999998  467889999999


Q ss_pred             EEeeCCCcc
Q psy3016         107 RVNKASSHQ  115 (305)
Q Consensus       107 ~v~~~~~~~  115 (305)
                      +|.++..+.
T Consensus        88 ~V~~s~~~~   96 (99)
T d1x4fa1          88 KVDLSEKYK   96 (99)
T ss_dssp             EEEEECSCS
T ss_pred             EEEEcCCcc
Confidence            999987543

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.66  E-value=3.5e-17  Score=118.35  Aligned_cols=80  Identities=34%  Similarity=0.494  Sum_probs=67.7

Q ss_pred             cccccccCCCchhc-HHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc-CCCC
Q psy3016         121 GANIFIGNLDPEVD-EKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR-DPDT  198 (305)
Q Consensus       121 ~~~l~v~nl~~~~t-~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~-d~~~  198 (305)
                      .++|||+|||.++| +++|+++|+.||.|..+                                       .+.. +..+
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v---------------------------------------~i~~~~~~~   44 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKI---------------------------------------NIPAGQKEH   44 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEE---------------------------------------ECCSCCC--
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccce---------------------------------------eeecccCCc
Confidence            57899999999986 55699999999999876                                       4433 4567


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +.++|||||+|.+.++|.+|++ |||..++|+.|+|+|+..+
T Consensus        45 ~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a~~k   85 (86)
T d2ghpa3          45 SFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADKK   85 (86)
T ss_dssp             -CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEECCCC
T ss_pred             cccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEcCCC
Confidence            8999999999999999999996 9999999999999998754

>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=99.66  E-value=3.1e-17  Score=124.62  Aligned_cols=84  Identities=18%  Similarity=0.217  Sum_probs=74.3

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||+.+|+++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|.+|++ +|+..|.||.|.|.
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~   92 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   92 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEE
Confidence            44567799999999999999999999999998776666665689999999999999999999997 89999999999998


Q ss_pred             eCCCc
Q psy3016         110 KASSH  114 (305)
Q Consensus       110 ~~~~~  114 (305)
                      .+...
T Consensus        93 ~~~~~   97 (112)
T d1wela1          93 PITKK   97 (112)
T ss_dssp             EECHH
T ss_pred             EcChH
Confidence            77543

>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=99.66  E-value=2.9e-17  Score=120.05  Aligned_cols=80  Identities=20%  Similarity=0.348  Sum_probs=71.5

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...+|||+|||.++|+++|+++|+.||.|..+                                       .++. ..+|
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~---------------------------------------~v~~-~~~g   51 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDL---------------------------------------AVVD-VRTG   51 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC---------------------------------------CCCE-EEEE
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEe---------------------------------------eeee-cCCC
Confidence            45689999999999999999999999999865                                       4544 3679


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +++|||||+|.+.++|.+||+ |||..+.|+.|+|.+++.+
T Consensus        52 ~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~k   91 (91)
T d1fjeb1          52 TNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR   91 (91)
T ss_dssp             TTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCS
T ss_pred             CccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCCC
Confidence            999999999999999999996 9999999999999998653

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2.6e-17  Score=115.83  Aligned_cols=75  Identities=24%  Similarity=0.447  Sum_probs=69.5

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      +|||+|||.++|+++|+++|+.||.|..+                                       .++.|..+++++
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v---------------------------------------~i~~d~~t~~~r   41 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESI---------------------------------------ELPMDNKTNKRR   41 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEE---------------------------------------ECCCCTTTCCTT
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccc---------------------------------------cccccccccccc
Confidence            48999999999999999999999999877                                       788999999999


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      |||||+|.+.++|.+|++ .++..++|+.|.|..|
T Consensus        42 G~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          42 GFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             cEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            999999999999999997 5778899999999864

>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=99.66  E-value=6.8e-17  Score=114.80  Aligned_cols=76  Identities=28%  Similarity=0.503  Sum_probs=70.5

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ++|||+|||.++|+++|+++|+.||.|..+                                       .+..|..++.+
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~---------------------------------------~~~~~~~~~~~   43 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVI---------------------------------------EIMTDRGSGKK   43 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEE---------------------------------------EEEECTTTCCE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhcccccc---------------------------------------ccccCCCCccc
Confidence            679999999999999999999999999877                                       67888888999


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      +|||||+|.+.++|.+|+. +||..|+|+.|+|..|
T Consensus        44 ~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          44 RGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             EEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             ccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            9999999999998888885 8999999999999876

>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=99.66  E-value=5.1e-17  Score=115.81  Aligned_cols=76  Identities=25%  Similarity=0.449  Sum_probs=66.9

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ++|||+|||.++|+++|+++|+.||.|..+                                       .+      ...
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~---------------------------------------~~------~~~   36 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAG---------------------------------------QV------LLK   36 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSS---------------------------------------CE------EEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEe---------------------------------------EE------ecc
Confidence            369999999999999999999999988754                                       22      335


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCe-eecCeeeEEEEeeecCC
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQ-YLCNRPISVSYAFKKDS  242 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~-~~~g~~l~v~~a~~~~~  242 (305)
                      +|||||+|.+.++|.+|++.|||. .+.|+.|+|.|+.++..
T Consensus        37 rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1          37 SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            899999999999999999999996 69999999999987654

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=8.4e-17  Score=116.27  Aligned_cols=77  Identities=19%  Similarity=0.320  Sum_probs=68.7

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||.++|+++|+++|+.||.+..+                                             ..+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~---------------------------------------------~~~   41 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVE---------------------------------------------RVK   41 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEE---------------------------------------------EEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeE---------------------------------------------EEc
Confidence            45789999999999999999999999988653                                             124


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .++|||||+|.+.++|.+|+..|||..+.|+.|+|+|+++++
T Consensus        42 ~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1          42 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            568999999999999999999999999999999999997664

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.2e-16  Score=117.56  Aligned_cols=80  Identities=19%  Similarity=0.395  Sum_probs=70.0

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||.++|+++|+++|+.||.|..+                                       .+..   +
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~---------------------------------------~~~~---~   49 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI---------------------------------------DLKN---R   49 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------------------------------------EECC---S
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEE---------------------------------------Eecc---c
Confidence            345689999999999999999999999999865                                       2222   3


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +.+++||||+|.+.++|.+|++.|||..|.|++|+|+|++..
T Consensus        50 ~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          50 RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            557899999999999999999999999999999999998654

>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=99.65  E-value=8.5e-17  Score=122.47  Aligned_cols=80  Identities=26%  Similarity=0.470  Sum_probs=71.2

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||..+|+++|+++|+.||.|..+                                       .+..   ++
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i---------------------------------------~~~~---~~   43 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQI---------------------------------------RVGN---TP   43 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------EEEC---ST
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEee---------------------------------------cccc---cC
Confidence            35789999999999999999999999999876                                       3333   36


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .++|||||+|.+.++|..|+..|||..|+|+.|+|.|+....
T Consensus        44 ~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   85 (114)
T d2f9da1          44 ETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANR   85 (114)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHH
T ss_pred             CcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            679999999999999999999999999999999999987543

>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=99.64  E-value=1.1e-16  Score=118.15  Aligned_cols=80  Identities=23%  Similarity=0.346  Sum_probs=71.3

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ...++|||+|||.++|+++|+++|+.||.|..+                                         .   .+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~-----------------------------------------~---~~   49 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----------------------------------------S---QD   49 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----------------------------------------E---ET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceee-----------------------------------------e---ec
Confidence            346889999999999999999999999988643                                         1   34


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+.++..
T Consensus        50 ~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          50 GKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             TEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            78899999999999999999999999999999999999977654

>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=99.64  E-value=1.6e-16  Score=114.78  Aligned_cols=77  Identities=22%  Similarity=0.426  Sum_probs=68.5

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||.++++++|+++|+.||.|..+                                       .+..     
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i---------------------------------------~~~~-----   42 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEV---------------------------------------FIHK-----   42 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEE---------------------------------------EEET-----
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEe---------------------------------------eeec-----
Confidence            34679999999999999999999999999876                                       3333     


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                       .+|||||+|++.++|.+|+..|||..|.|+.|+|+||..+.
T Consensus        43 -~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1          43 -DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             -TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             -ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence             37899999999999999999999999999999999997653

>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=99.64  E-value=1.7e-16  Score=117.08  Aligned_cols=75  Identities=19%  Similarity=0.538  Sum_probs=68.6

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+||+..+++++|+++|+.||.|..+                                       +++.|     
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v---------------------------------------~i~~~-----   53 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEI---------------------------------------RVFPE-----   53 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEE---------------------------------------EEETT-----
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEE---------------------------------------EEEec-----
Confidence            4689999999999999999999999999876                                       44544     


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                       +|||||+|.+.++|.+|+..|||..+.|+.|+|+|++.+
T Consensus        54 -kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          54 -KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             -TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             -ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence             789999999999999999999999999999999998664

>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=99.63  E-value=2.3e-16  Score=114.47  Aligned_cols=75  Identities=15%  Similarity=0.216  Sum_probs=65.7

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ..+|||+|||.++++++|+++|++||... +                                             ..+.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G~~~-~---------------------------------------------~~~~   38 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYDLKY-C---------------------------------------------YVDR   38 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSCCCC-E---------------------------------------------EEEG
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcCcee-e---------------------------------------------eeec
Confidence            46899999999999999999999999321 1                                             1245


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .+|||||+|.+.++|.+|++.||+..+.|+.|+|+|+..+.
T Consensus        39 ~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_          39 NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             GGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             cCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            68999999999999999999999999999999999996554

>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=99.63  E-value=2.8e-16  Score=113.43  Aligned_cols=79  Identities=16%  Similarity=0.240  Sum_probs=70.4

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ....|||+|||.++++++|+++|+.||.+...                                       .++.+..++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~---------------------------------------~~~~~~~~g   48 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGS---------------------------------------VCLKYNEKG   48 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTT---------------------------------------CEEEECSSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeE---------------------------------------EEEEeCCCC
Confidence            34679999999999999999999999998653                                       234555679


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      +++|+|||+|.+.++|.+|++.||+..+.|+.|+|+++
T Consensus        49 ~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          49 MPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            99999999999999999999999999999999999875

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=9.7e-17  Score=116.69  Aligned_cols=76  Identities=17%  Similarity=0.277  Sum_probs=67.3

Q ss_pred             cccccccCCCchhcHHHH---HHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         121 GANIFIGNLDPEVDEKLL---YDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l---~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      .++|||+|||.++++++|   +++|++||.|..+                                       .++.|..
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v---------------------------------------~i~~~~~   48 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKV---------------------------------------VINNSTS   48 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEE---------------------------------------EEECCSS
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEE---------------------------------------EEeeccC
Confidence            467999999999999999   7789999999987                                       5666765


Q ss_pred             CCC---ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEE
Q psy3016         198 TGN---SKGFAFINYASFEASDASIDAMHGQYLCNRPISVS  235 (305)
Q Consensus       198 ~~~---~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~  235 (305)
                      ++.   .+|||||+|++.++|.+|+..|||..++|+.|+|+
T Consensus        49 ~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          49 YAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             CCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            554   45899999999999999999999999999999986

>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=99.63  E-value=3.2e-16  Score=118.55  Aligned_cols=78  Identities=14%  Similarity=0.112  Sum_probs=69.3

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||..+++++|+++|+.||.|..+                                       .+      .
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v---------------------------------------~l------~   43 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRV---------------------------------------LL------P   43 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEE---------------------------------------EC------C
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEE---------------------------------------Ee------e
Confidence            34689999999999999999999999999876                                       22      2


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      ..+|||||+|.+.++|.+|+..|||..|.|++|.|.|+.....
T Consensus        44 ~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~~   86 (111)
T d1whxa_          44 EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVF   86 (111)
T ss_dssp             SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTTT
T ss_pred             ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCcc
Confidence            3579999999999999999999999999999999999976543

>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=99.63  E-value=2.4e-16  Score=114.32  Aligned_cols=79  Identities=23%  Similarity=0.304  Sum_probs=67.9

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      +++++|||+|||.++|+++|+++|+.||.|..+                                       .++    .
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~---------------------------------------~~~----~   44 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKG---------------------------------------FKF----F   44 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEE---------------------------------------EEE----C
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEE---------------------------------------EEe----e
Confidence            346789999999999999999999999999764                                       111    2


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeee-cCeeeEEEEeeec
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYL-CNRPISVSYAFKK  240 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~-~g~~l~v~~a~~~  240 (305)
                      ++.+|||||+|++.++|.+|+..|||..+ +|+.|+|+|++..
T Consensus        45 ~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2          45 QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            34588999999999999999999999988 6899999998653

>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=99.62  E-value=6.2e-17  Score=112.93  Aligned_cols=71  Identities=21%  Similarity=0.430  Sum_probs=66.5

Q ss_pred             ccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccc
Q psy3016         124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKG  203 (305)
Q Consensus       124 l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g  203 (305)
                      |||+|||.++|+++|+++|+.||.|..+                                       ++..+..++.++|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~---------------------------------------~~~~~~~~~~~~g   41 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVST---------------------------------------KAILDKTTNKCKG   41 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEE---------------------------------------EEECCSSSCSCCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhcccccc---------------------------------------ccccccccccccc
Confidence            7999999999999999999999999876                                       5677888899999


Q ss_pred             eEEEEeCChHHHHHHHHHhcCeeecCeeeE
Q psy3016         204 FAFINYASFEASDASIDAMHGQYLCNRPIS  233 (305)
Q Consensus       204 ~afV~f~~~~~A~~Al~~l~~~~~~g~~l~  233 (305)
                      ||||+|.+.++|.+|+..|||..|.|+.|+
T Consensus        42 ~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1          42 YGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             eeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            999999999999999999999999999874

>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=99.62  E-value=9.8e-16  Score=125.83  Aligned_cols=85  Identities=24%  Similarity=0.399  Sum_probs=78.9

Q ss_pred             cCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        30 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (305)
                      .....++|||+|||..+|+++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|.+|++ +++..+.|+.|.|.
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVR  171 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEE
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEE
Confidence            34566899999999999999999999999999999999998889999999999999999999998 79999999999999


Q ss_pred             eCCCcc
Q psy3016         110 KASSHQ  115 (305)
Q Consensus       110 ~~~~~~  115 (305)
                      ++.++.
T Consensus       172 ~A~~k~  177 (183)
T d1u1qa_         172 KALSKQ  177 (183)
T ss_dssp             ECCCHH
T ss_pred             ecCCcc
Confidence            987654

>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=99.62  E-value=7.7e-16  Score=115.13  Aligned_cols=82  Identities=20%  Similarity=0.374  Sum_probs=68.8

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc-CCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR-DPDT  198 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~-d~~~  198 (305)
                      +.++|||+|||.++|+++|+++|+.||.+ .+                                       .++. +..+
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g~~-~~---------------------------------------~~~~~~~~~   53 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLNIS-AV---------------------------------------RLPREPSNP   53 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSCEE-EE---------------------------------------ECCBCSSCT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhccc-cc---------------------------------------eeeeeeccC
Confidence            45789999999999999999999999944 33                                       2333 3356


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +.++|||||+|.+.++|.+|+ .||+..|.|+.|+|.|+..+..
T Consensus        54 g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a~~~~~   96 (104)
T d1wi8a_          54 ERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD   96 (104)
T ss_dssp             TSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCC
T ss_pred             CCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEECCCCCC
Confidence            889999999999999998666 5999999999999999976644

>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=99.62  E-value=1.2e-16  Score=118.97  Aligned_cols=79  Identities=29%  Similarity=0.508  Sum_probs=70.7

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||.++++++|+++|+.||.|..+                                       .+..+ .++.
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~---------------------------------------~~~~~-~~~~   57 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVIST---------------------------------------RILRD-SSGT   57 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEE---------------------------------------EEEEC-SSSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccce---------------------------------------eeecc-cccc
Confidence            4689999999999999999999999999765                                       44555 4688


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK  239 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~  239 (305)
                      ++|||||+|.+.++|.+|++.|||..|.|+++.|.++.+
T Consensus        58 ~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          58 SRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             EEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             cccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            999999999999999999999999999999998877654

>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=99.61  E-value=2.2e-16  Score=116.90  Aligned_cols=76  Identities=25%  Similarity=0.513  Sum_probs=66.7

Q ss_pred             cccccccccCCC-chhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         119 DVGANIFIGNLD-PEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       119 ~~~~~l~v~nl~-~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ...++|||+||+ ..+++++|+++|++||.|..+                                       .+     
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~---------------------------------------~i-----   48 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGC---------------------------------------SV-----   48 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEE---------------------------------------EE-----
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEE---------------------------------------EE-----
Confidence            345789999997 567888999999999999876                                       22     


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                         ++|||||+|++.++|.+|+..|||.++.|+.|+|.|+..+.
T Consensus        49 ---~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          49 ---HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             ---ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             ---eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence               47999999999999999999999999999999999986543

>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=99.61  E-value=3.5e-16  Score=109.92  Aligned_cols=72  Identities=25%  Similarity=0.331  Sum_probs=63.5

Q ss_pred             ccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccc
Q psy3016         124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKG  203 (305)
Q Consensus       124 l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g  203 (305)
                      |||+|||.++++++|+++|++||.+. +                                             ..++++|
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g~~~-~---------------------------------------------~~~~~~g   34 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYELKY-C---------------------------------------------FVDKYKG   34 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSCEEE-E---------------------------------------------EEETTTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhcccccc-e---------------------------------------------eecccce
Confidence            79999999999999999999999332 1                                             1255789


Q ss_pred             eEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         204 FAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       204 ~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      ||||+|.+.++|.+|+..|||..+.|++|+|+|+..+.
T Consensus        35 ~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1          35 TAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             eEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            99999999999999999999999999999999996553

>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=99.61  E-value=4e-16  Score=110.81  Aligned_cols=74  Identities=24%  Similarity=0.473  Sum_probs=65.4

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|++  +|+++|+++|+.||.|..+                                       .+.      
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v---------------------------------------~~~------   36 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDL---------------------------------------SMD------   36 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCE---------------------------------------EEE------
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCcccee---------------------------------------eec------
Confidence            35789999986  8999999999999999875                                       222      


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      +.+|||||+|.+.++|.+|+..|||..++|+.|+|.|++++
T Consensus        37 ~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1          37 PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             cCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            34789999999999999999999999999999999999654

>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=99.61  E-value=4.2e-16  Score=114.90  Aligned_cols=82  Identities=20%  Similarity=0.346  Sum_probs=70.3

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCc-ccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC-CCC
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGV-ILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP-DTG  199 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~-v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~-~~~  199 (305)
                      ++|||+|||.++|+++|+++|+.||. |..+                                       .++.|. .++
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v---------------------------------------~~~~~~~~~~   42 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDV---------------------------------------IVYASAADKM   42 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEE---------------------------------------ECCSSSCTTT
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEE---------------------------------------EEeeeccccc
Confidence            57999999999999999999999996 6654                                       556664 358


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCe--eecCeeeEEEEeeecCC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQ--YLCNRPISVSYAFKKDS  242 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~--~~~g~~l~v~~a~~~~~  242 (305)
                      +++|||||+|.+.++|.+|++.|++.  .+.|+.|+|.||.++..
T Consensus        43 ~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~   87 (96)
T d2disa1          43 KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID   87 (96)
T ss_dssp             TTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCS
T ss_pred             cCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCCC
Confidence            89999999999999999999999754  45899999999976554

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.61  E-value=5.8e-16  Score=111.00  Aligned_cols=77  Identities=19%  Similarity=0.352  Sum_probs=67.5

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      .++.++|||+|||.++|+++|.++|+.||.|..+                                       +++.+  
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v---------------------------------------~~~~~--   43 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEV---------------------------------------RLVPN--   43 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEE---------------------------------------EECTT--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEe---------------------------------------eeecc--
Confidence            3456899999999999999999999999999876                                       33333  


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeee-cCeeeEEEEee
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYL-CNRPISVSYAF  238 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~-~g~~l~v~~a~  238 (305)
                         .+|||||+|.+.++|..|++.|||..+ +|+.|+|+||+
T Consensus        44 ---~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          44 ---RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             ---TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             ---cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence               378999999999999999999999998 57899999985

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=4.5e-16  Score=116.36  Aligned_cols=78  Identities=19%  Similarity=0.137  Sum_probs=69.5

Q ss_pred             CCCceEEEcCCCccc-cH----HHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeee
Q psy3016          32 DGDATIYVGGLDDKV-SE----TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPI  106 (305)
Q Consensus        32 ~~~~~l~V~nLp~~~-te----~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l  106 (305)
                      .+.++|||+||+..+ ++    ++|+++|+.||.|.++++++      +++||||+|.+.++|.+|++.|||..+.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            467899999999987 33    56999999999999999975      45899999999999999999999999999999


Q ss_pred             EEeeCCCcc
Q psy3016         107 RVNKASSHQ  115 (305)
Q Consensus       107 ~v~~~~~~~  115 (305)
                      +|.|+....
T Consensus        77 ~v~~a~~~~   85 (104)
T d1weya_          77 KLYFAQTLH   85 (104)
T ss_dssp             EEECCCCSS
T ss_pred             EEeecccCC
Confidence            999997654

>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=99.60  E-value=5.7e-16  Score=116.78  Aligned_cols=77  Identities=19%  Similarity=0.441  Sum_probs=68.3

Q ss_pred             cccccccCCCc-hhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         121 GANIFIGNLDP-EVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       121 ~~~l~v~nl~~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      .++|||+||++ .+|+++|+++|+.||.|..+                                       .++.|    
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v---------------------------------------~i~~~----   38 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRV---------------------------------------KILFN----   38 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEE---------------------------------------EECCT----
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceE---------------------------------------EEEec----
Confidence            46899999965 59999999999999999987                                       45555    


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                       .+|||||+|++.++|.+|+..|||..|.|+.|+|.|++...
T Consensus        39 -~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1          39 -KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             -TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             -ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence             37899999999999999999999999999999999986543

>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=6.1e-18  Score=123.45  Aligned_cols=78  Identities=15%  Similarity=0.362  Sum_probs=68.6

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcc-----cCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEe
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPK-----DRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN  109 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~-----~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~  109 (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            7899999999999999999999999887766542     33456789999999999999999996 99999999999998


Q ss_pred             eCCC
Q psy3016         110 KASS  113 (305)
Q Consensus       110 ~~~~  113 (305)
                      ++..
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6554

>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=99.60  E-value=3.4e-16  Score=114.22  Aligned_cols=80  Identities=24%  Similarity=0.482  Sum_probs=69.0

Q ss_pred             cccccccCCCchhcHHHHHH----HHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYD----TFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~----~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      .++|||+|||.++++++|++    +|+.||.|..+                                       .+.   
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i---------------------------------------~~~---   40 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---------------------------------------LVS---   40 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEE---------------------------------------ECC---
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccce---------------------------------------EEe---
Confidence            57899999999999998864    57999999875                                       222   


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      .++.++|||||+|.+.++|.+|+..+||..+.|+.|+|.|++.+..
T Consensus        41 ~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~~~   86 (91)
T d1nu4a_          41 RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   86 (91)
T ss_dssp             HHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCCT
T ss_pred             eeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCCCch
Confidence            2466899999999999999999999999999999999999976643

>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=99.60  E-value=5.3e-16  Score=111.71  Aligned_cols=77  Identities=14%  Similarity=0.241  Sum_probs=69.6

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .++|||+|||.++|+++|+++|+.||.|..+                                       .+..+ .++.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v---------------------------------------~l~~~-~~~~   45 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNI---------------------------------------QMRRT-LHKA   45 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEE---------------------------------------EEEEC-TTCC
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccc---------------------------------------eeeee-ccCC
Confidence            4689999999999999999999999999876                                       45555 4689


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      ++|||||+|.+.++|.+|++ +++..+.|+.|+|.|+.
T Consensus        46 ~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          46 FKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             EEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            99999999999999999996 79999999999999863

>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=99.59  E-value=1.3e-16  Score=115.47  Aligned_cols=75  Identities=13%  Similarity=0.201  Sum_probs=66.5

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ++|||+|||.++++++|+++|+.||.|..+                                       .++.       
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~---------------------------------------~i~~-------   34 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYA---------------------------------------DVYR-------   34 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEE---------------------------------------EECT-------
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccc---------------------------------------cccc-------
Confidence            369999999999999999999999999876                                       3332       


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCC
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~  242 (305)
                      +|||||+|.+.++|.+|+..|||..|.|+.|+|.++..+..
T Consensus        35 ~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~~   75 (87)
T d3begb1          35 DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   75 (87)
T ss_dssp             TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEEC
T ss_pred             cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCcC
Confidence            48999999999999999999999999999999999866543

>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=99.58  E-value=1.2e-15  Score=113.83  Aligned_cols=81  Identities=14%  Similarity=0.112  Sum_probs=71.0

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...||||+|||.++|+++|.++|..||.+..+                                       .++.+..+|
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~---------------------------------------~~~~~~~~g   47 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENA---------------------------------------VHVLVDNNG   47 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTT---------------------------------------EEECCCTTS
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEE---------------------------------------EEEEeCCCC
Confidence            35689999999999999999999999988753                                       234555679


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                      .++|||||+|.+.++|.+|+. +|+..|.|+.|.|.++...
T Consensus        48 ~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~~   87 (103)
T d2cpya1          48 QGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLE   87 (103)
T ss_dssp             SCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECHH
T ss_pred             CcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCHH
Confidence            999999999999999999996 9999999999999987543

>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=99.58  E-value=2.1e-15  Score=112.74  Aligned_cols=85  Identities=16%  Similarity=0.234  Sum_probs=73.3

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ....+|||+|||+++|+++|+++|..+|.+...                                       .++.+..+
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~---------------------------------------v~~~~~~~   53 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG---------------------------------------MTLPVDFQ   53 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEE---------------------------------------EECCBCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEE---------------------------------------EEEEeCCC
Confidence            345679999999999999999999999988753                                       23445567


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      +.++|||||+|.+.++|.+|++ +|+..|.||.|.|.++..+...
T Consensus        54 ~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~~~~~~   97 (104)
T d1wg5a_          54 GRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVR   97 (104)
T ss_dssp             SCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEECTTTSC
T ss_pred             CCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECCHHHhc
Confidence            8999999999999999999996 8999999999999999776553

>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=99.57  E-value=1e-15  Score=115.22  Aligned_cols=79  Identities=20%  Similarity=0.265  Sum_probs=68.9

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      ..+|||+||+.++|+++|+++|+.||.|..+                                       .++.+    +
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~---------------------------------------~i~~~----~   43 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKI---------------------------------------ITFTK----N   43 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEE---------------------------------------EEEEE----T
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEE---------------------------------------EEEee----C
Confidence            4679999999999999999999999999876                                       44444    3


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeee--cCeeeEEEEeeecCC
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYL--CNRPISVSYAFKKDS  242 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~--~g~~l~v~~a~~~~~  242 (305)
                      .+|||||+|++.++|.+|+..|||..+  .++.|++.|++.+..
T Consensus        44 ~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~~   87 (108)
T d2adba1          44 NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL   87 (108)
T ss_dssp             TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCSC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCccc
Confidence            489999999999999999999999998  678999999876543

>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=99.57  E-value=4.8e-16  Score=116.17  Aligned_cols=76  Identities=21%  Similarity=0.262  Sum_probs=71.4

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeC
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA  111 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~  111 (305)
                      ..++|.++...++|++|+++|++||.|.+|+|+++. ++.++|||||+|.+.++|.+|++.|||..+.||.|.|+++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            468899999999999999999999999999998774 7899999999999999999999999999999999999875

>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=99.56  E-value=1.1e-15  Score=110.82  Aligned_cols=78  Identities=19%  Similarity=0.321  Sum_probs=67.4

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..++|||+|||.++|+++|+++|+.||.|..+                                       .++     .
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v---------------------------------------~~~-----~   39 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDV---------------------------------------FIP-----K   39 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEE---------------------------------------ECC-----S
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEE---------------------------------------EEe-----e
Confidence            35789999999999999999999999999865                                       222     3


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      .++|||||+|++.++|.+|+.  ++..|+|+.|.|.++.++...
T Consensus        40 ~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~~   81 (88)
T d1wf0a_          40 PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCCC
Confidence            468999999999999999986  788999999999999766543

>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=99.56  E-value=5e-15  Score=109.37  Aligned_cols=78  Identities=13%  Similarity=0.206  Sum_probs=69.4

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...+|||+|||.++++++|+++|+.||.|..+                                       .+.      
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~---------------------------------------~i~------   48 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYA---------------------------------------DVQ------   48 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEE---------------------------------------EEE------
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccc---------------------------------------ccc------
Confidence            45679999999999999999999999999876                                       222      


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                       .+|||||+|.+.++|.+||+.|||..|.|+.|+|.|++.+..+
T Consensus        49 -~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~~   91 (98)
T d1wg4a_          49 -KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPER   91 (98)
T ss_dssp             -TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECCC
T ss_pred             -ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCCC
Confidence             3689999999999999999999999999999999999876543

>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=99.54  E-value=5.6e-15  Score=108.94  Aligned_cols=76  Identities=28%  Similarity=0.497  Sum_probs=66.9

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      +.++|||+||+.++++++|+++|+.||.|..+                                       ++.+     
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~---------------------------------------~~~~-----   51 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTI---------------------------------------DHVK-----   51 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEE---------------------------------------EECS-----
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceE---------------------------------------eeec-----
Confidence            46899999999999999999999999999876                                       2332     


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecC--eeeEEEEeeec
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCN--RPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g--~~l~v~~a~~~  240 (305)
                       .++||||+|.+.++|.+|++.||+.+|.|  ++|+|+|++..
T Consensus        52 -~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          52 -GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             -SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             -cccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence             37899999999999999999999999976  58999998754

>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=99.53  E-value=7.6e-15  Score=106.22  Aligned_cols=79  Identities=24%  Similarity=0.278  Sum_probs=68.2

Q ss_pred             ccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         118 LDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       118 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      .+++++|||+|||.++++++|+++|+.||.|..+                                       .++.   
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v---------------------------------------~~~~---   42 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNI---------------------------------------LMLK---   42 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEE---------------------------------------EEET---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccc---------------------------------------cccc---
Confidence            4467899999999999999999999999999876                                       2332   


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHh--cCeeecCeeeEEEEeeecC
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAM--HGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l--~~~~~~g~~l~v~~a~~~~  241 (305)
                         .++||||+|.+.++|.+|+..+  ++..+.|+.|+|.|++.+.
T Consensus        43 ---~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          43 ---GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             ---TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             ---cceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence               3689999999999999999865  5678999999999997654

>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=99.53  E-value=4.9e-15  Score=110.30  Aligned_cols=83  Identities=17%  Similarity=0.231  Sum_probs=70.7

Q ss_pred             cccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCC
Q psy3016         119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT  198 (305)
Q Consensus       119 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~  198 (305)
                      ....+|||+|||+++|+++|+++|..+|.+. +                                       .++.+ .+
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~-v---------------------------------------~~~~~-~~   51 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNPMR-V---------------------------------------HIEIG-PD   51 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCSE-E---------------------------------------EEEES-SS
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCcce-e---------------------------------------eeEEe-cC
Confidence            3457899999999999999999999998553 3                                       34555 34


Q ss_pred             CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecCCc
Q psy3016         199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK  243 (305)
Q Consensus       199 ~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~~~  243 (305)
                      +..+|||||+|.+.++|.+|++ +|+..|.||.|+|.++......
T Consensus        52 g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~~~   95 (102)
T d1weza_          52 GRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTS   95 (102)
T ss_dssp             SCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCCC
T ss_pred             CcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCCCCC
Confidence            8899999999999999999986 8999999999999998776543

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=1.7e-14  Score=107.72  Aligned_cols=81  Identities=17%  Similarity=0.285  Sum_probs=68.6

Q ss_pred             cccccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCC
Q psy3016         117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDP  196 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~  196 (305)
                      ....+++|||+|||..+|+++|.++|+.||.|..+                                       .+.   
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~---------------------------------------~~~---   48 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYV---------------------------------------MMM---   48 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEE---------------------------------------EEE---
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEE---------------------------------------EEE---
Confidence            34467899999999999999999999999999876                                       222   


Q ss_pred             CCCCccceEEEEeCChHHHHHHHHHhc--CeeecCeeeEEEEeeecCC
Q psy3016         197 DTGNSKGFAFINYASFEASDASIDAMH--GQYLCNRPISVSYAFKKDS  242 (305)
Q Consensus       197 ~~~~~~g~afV~f~~~~~A~~Al~~l~--~~~~~g~~l~v~~a~~~~~  242 (305)
                         +.+++|||+|++.++|.+|+..++  +..+.|++|+|.|++.+..
T Consensus        49 ---~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~~   93 (104)
T d1wexa_          49 ---PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             ---TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSC
T ss_pred             ---ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCcc
Confidence               247899999999999999999884  5578999999999976543

>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=99.52  E-value=7.5e-15  Score=109.58  Aligned_cols=77  Identities=9%  Similarity=0.054  Sum_probs=66.1

Q ss_pred             ccccccccCCCchhcH-----HHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCccc
Q psy3016         120 VGANIFIGNLDPEVDE-----KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR  194 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~-----~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  194 (305)
                      ..++|||+||+.++..     ++|.++|+.||.|..+                                       +++ 
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~---------------------------------------~~~-   43 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTF---------------------------------------QYF-   43 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEE---------------------------------------EEE-
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEE---------------------------------------EEe-
Confidence            4578999999998633     5699999999999876                                       233 


Q ss_pred             CCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       195 d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                           ++++||||+|.+.++|.+|+..|||..|.|+.|+|.|++...
T Consensus        44 -----k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~   85 (104)
T d1weya_          44 -----KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLH   85 (104)
T ss_dssp             -----TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSS
T ss_pred             -----cCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccCC
Confidence                 358899999999999999999999999999999999996553

>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=1.1e-14  Score=105.53  Aligned_cols=78  Identities=22%  Similarity=0.294  Sum_probs=67.1

Q ss_pred             cccccccccccCCCch-hcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccC
Q psy3016         117 NLDVGANIFIGNLDPE-VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRD  195 (305)
Q Consensus       117 ~~~~~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d  195 (305)
                      ..+.+++|||+||+.. +|+++|.++|++||.|..+                                       .++.+
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i---------------------------------------~i~~~   44 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNH---------------------------------------LILNK   44 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEE---------------------------------------EECSS
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEE---------------------------------------Eeecc
Confidence            3456789999999986 8899999999999999976                                       33333


Q ss_pred             CCCCCccceEEEEeCChHHHHHHHHHh--cCeeecCeeeEEEEeee
Q psy3016         196 PDTGNSKGFAFINYASFEASDASIDAM--HGQYLCNRPISVSYAFK  239 (305)
Q Consensus       196 ~~~~~~~g~afV~f~~~~~A~~Al~~l--~~~~~~g~~l~v~~a~~  239 (305)
                            +++|||+|++.++|.+|+..+  ++..+.|++|+|+|++.
T Consensus        45 ------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1          45 ------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             ------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             ------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence                  679999999999999999966  67789999999999864

>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=99.51  E-value=8.6e-15  Score=102.66  Aligned_cols=74  Identities=20%  Similarity=0.349  Sum_probs=64.9

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      .+|||+|||.++++++|+++|+.||.|..+                                       .+..+..  ..
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v---------------------------------------~~~~~~~--~~   39 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHV---------------------------------------DVADSLK--KN   39 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEE---------------------------------------EEEECTT--SS
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEE---------------------------------------EEEeecc--cc
Confidence            369999999999999999999999999876                                       4556643  34


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      ++||||+|++.++|.+|+. +|+..|+|+.|.|+.+
T Consensus        40 ~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          40 FRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             SEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             ceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            5799999999999999986 8999999999999865

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=9.3e-15  Score=110.64  Aligned_cols=82  Identities=23%  Similarity=0.350  Sum_probs=72.2

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...+|||+|||+++|+++|.++|+.+|.+..+                                       .++.+..+|
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~---------------------------------------~~~~~~~~g   57 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDS---------------------------------------IYIAYGPNG   57 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTT---------------------------------------CEEEECTTS
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccc---------------------------------------eeeecCccc
Confidence            45689999999999999999999999998754                                       345566779


Q ss_pred             CccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeecC
Q psy3016         200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD  241 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~~  241 (305)
                      .++|||||+|.+.++|.+|+. +||..|+|+.|.|..+....
T Consensus        58 ~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~~~~   98 (112)
T d1wela1          58 KATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKG   98 (112)
T ss_dssp             SEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECHHH
T ss_pred             ceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcChHH
Confidence            999999999999999999996 99999999999999885543

>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=2.4e-14  Score=106.25  Aligned_cols=66  Identities=23%  Similarity=0.386  Sum_probs=58.7

Q ss_pred             CCCCceEEE--cCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeC
Q psy3016          31 GDGDATIYV--GGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY  102 (305)
Q Consensus        31 ~~~~~~l~V--~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~  102 (305)
                      .....+|||  ||||..+|+++|+++|++||.|..|+++.+      ++||||+|.+.++|.+|++.|||..+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            345678888  559999999999999999999999999765      489999999999999999999998773

>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=99.50  E-value=4.4e-15  Score=110.85  Aligned_cols=76  Identities=9%  Similarity=0.250  Sum_probs=70.2

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ..++|.++...+++++|.++|++||.|..+                                       .|+.+ .++++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v---------------------------------------~I~~~-~~~~~   67 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEM---------------------------------------NVCDN-LGDHL   67 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEE---------------------------------------EECCS-SSSSS
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEE---------------------------------------EeecC-CCCCE
Confidence            568999999999999999999999999987                                       56655 57999


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      +|||||+|.+.++|.+|+..|||++++|++|+|.|+
T Consensus        68 ~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          68 VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             EEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             eeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            999999999999999999999999999999999985

>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=99.49  E-value=3.4e-14  Score=107.63  Aligned_cols=79  Identities=22%  Similarity=0.168  Sum_probs=67.7

Q ss_pred             CcCCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCH-HHHHHHHHHhcCceeCCeeeE
Q psy3016          29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE-EDADYAIKIMNMIKLYGKPIR  107 (305)
Q Consensus        29 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~-e~A~~Ai~~l~g~~~~g~~l~  107 (305)
                      +.+.+-..+||||||..+|+++|+++|+.||+|.+|+|+.+      +|||||.|.+. ++|..|+..+++..+.++.+.
T Consensus         6 ~~~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~   79 (113)
T d1owxa_           6 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKE   79 (113)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             CCCCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceE
Confidence            44556667799999999999999999999999999999865      49999999985 789999999999888877777


Q ss_pred             EeeCCC
Q psy3016         108 VNKASS  113 (305)
Q Consensus       108 v~~~~~  113 (305)
                      |.+...
T Consensus        80 v~~~~~   85 (113)
T d1owxa_          80 VTWEVL   85 (113)
T ss_dssp             EEEEEC
T ss_pred             EEEeec
Confidence            766543

>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=99.48  E-value=2e-14  Score=106.34  Aligned_cols=77  Identities=23%  Similarity=0.312  Sum_probs=66.4

Q ss_pred             cccccccccCCCch-hcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         119 DVGANIFIGNLDPE-VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       119 ~~~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      ..+++|||+|||.+ +|+++|.++|+.||.|..+                                       .++.   
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v---------------------------------------~~~~---   53 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNY---------------------------------------ILMR---   53 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEE---------------------------------------EEET---
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEE---------------------------------------EEee---
Confidence            34678999999975 8999999999999999876                                       3333   


Q ss_pred             CCCccceEEEEeCChHHHHHHHH--HhcCeeecCeeeEEEEeeec
Q psy3016         198 TGNSKGFAFINYASFEASDASID--AMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~--~l~~~~~~g~~l~v~~a~~~  240 (305)
                         .+|+|||+|.+.++|.+|+.  .+++..+.|+.|+|+|++.+
T Consensus        54 ---~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~   95 (99)
T d1x4fa1          54 ---MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY   95 (99)
T ss_dssp             ---TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             ---cCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCc
Confidence               37899999999999999998  57888999999999999654

>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=99.47  E-value=1.3e-15  Score=110.86  Aligned_cols=80  Identities=15%  Similarity=0.311  Sum_probs=66.6

Q ss_pred             ccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCc
Q psy3016         122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNS  201 (305)
Q Consensus       122 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~  201 (305)
                      ++|||+|||..+|+++|+++|+.||.+..+...                                  ......+..++.+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~----------------------------------~~~~~~~~~~~~~   47 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA----------------------------------PGNPVLAVQINQD   47 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCS----------------------------------SSCSEEECCEETT
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEe----------------------------------ccceeeecccCCC
Confidence            579999999999999999999999988764100                                  1122344566788


Q ss_pred             cceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEE
Q psy3016         202 KGFAFINYASFEASDASIDAMHGQYLCNRPISVSY  236 (305)
Q Consensus       202 ~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~  236 (305)
                      +|||||+|++.++|.+|+. |||..+.|+.|+|+.
T Consensus        48 kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_          48 KNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRR   81 (90)
T ss_dssp             TTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCBC
T ss_pred             ceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEECC
Confidence            9999999999999999985 999999999999974

>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=99.44  E-value=2.7e-13  Score=100.06  Aligned_cols=82  Identities=12%  Similarity=0.168  Sum_probs=70.5

Q ss_pred             cCCCCceEEEcCC--Ccccc---------HHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcC
Q psy3016          30 SGDGDATIYVGGL--DDKVS---------ETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNM   98 (305)
Q Consensus        30 ~~~~~~~l~V~nL--p~~~t---------e~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g   98 (305)
                      ....+++|+|.||  |..+.         ++||++.|++||.|..|++..+.    .+|||||+|.+.++|.+|+..|||
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~----~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC----TTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC----CccEEEEEECCHHHHHHHHHHhCC
Confidence            4466889999999  55432         36899999999999999986653    679999999999999999999999


Q ss_pred             ceeCCeeeEEeeCCCcc
Q psy3016          99 IKLYGKPIRVNKASSHQ  115 (305)
Q Consensus        99 ~~~~g~~l~v~~~~~~~  115 (305)
                      ..+.||.|.|.++.++.
T Consensus        80 ~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          80 RWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             cEECCEEEEEEEeCCcC
Confidence            99999999999987653

>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=2.6e-13  Score=96.24  Aligned_cols=73  Identities=16%  Similarity=0.170  Sum_probs=62.7

Q ss_pred             CceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe-eeEEeeCC
Q psy3016          34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK-PIRVNKAS  112 (305)
Q Consensus        34 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~-~l~v~~~~  112 (305)
                      .+.|+|+++|++.+++.| +.|++||+|.++++.      ++++||||+|.+.++|++|++ +||..+.|+ .|.|.++.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            568999999999997655 579999999999884      346999999999999999997 899999997 46788776


Q ss_pred             Cc
Q psy3016         113 SH  114 (305)
Q Consensus       113 ~~  114 (305)
                      .+
T Consensus        76 ~k   77 (81)
T d1wwha1          76 DK   77 (81)
T ss_dssp             CH
T ss_pred             Ch
Confidence            54

>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=99.30  E-value=3e-12  Score=95.18  Aligned_cols=81  Identities=12%  Similarity=0.118  Sum_probs=68.5

Q ss_pred             CCceEEEcCC--Ccc--------ccHHHHHHHhccCCCeEEEEEcccCCC--CCcceEEEEEEcCHHHHHHHHHHhcCce
Q psy3016          33 GDATIYVGGL--DDK--------VSETLMWELFVQSGPVVNVHMPKDRVT--QTHQGYGFIEFMGEEDADYAIKIMNMIK  100 (305)
Q Consensus        33 ~~~~l~V~nL--p~~--------~te~~L~~~F~~~G~i~~i~~~~~~~~--~~~~g~afV~f~~~e~A~~Ai~~l~g~~  100 (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            4778999999  332        234679999999999999999876543  3456899999999999999999999999


Q ss_pred             eCCeeeEEeeCCC
Q psy3016         101 LYGKPIRVNKASS  113 (305)
Q Consensus       101 ~~g~~l~v~~~~~  113 (305)
                      +.||.|.+.++..
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999998753

>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=99.29  E-value=2.1e-12  Score=95.47  Aligned_cols=63  Identities=16%  Similarity=0.297  Sum_probs=54.3

Q ss_pred             cccccccc--CCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCC
Q psy3016         120 VGANIFIG--NLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPD  197 (305)
Q Consensus       120 ~~~~l~v~--nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~  197 (305)
                      +..+|+|.  +|+.++|+++|+++|++||.|..+                                       .++.   
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i---------------------------------------~~~~---   54 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDAL---------------------------------------LMPP---   54 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEE---------------------------------------ECCT---
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEE---------------------------------------eecc---
Confidence            45678885  599999999999999999999875                                       2232   


Q ss_pred             CCCccceEEEEeCChHHHHHHHHHhcCeee
Q psy3016         198 TGNSKGFAFINYASFEASDASIDAMHGQYL  227 (305)
Q Consensus       198 ~~~~~g~afV~f~~~~~A~~Al~~l~~~~~  227 (305)
                         .++||||+|.+.++|.+|+..|||+.+
T Consensus        55 ---~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          55 ---NKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             ---TCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             ---CccEEEEEECCHHHHHHHHHHhCCCCC
Confidence               367999999999999999999999987

>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=99.25  E-value=2.8e-12  Score=96.79  Aligned_cols=76  Identities=18%  Similarity=0.133  Sum_probs=64.4

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ..-.+||+||+..+|+++|+++|+.||.|..+                                       .++.     
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v---------------------------------------~i~~-----   45 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWI---------------------------------------DFVR-----   45 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEE---------------------------------------ECCT-----
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCChheE---------------------------------------EEec-----
Confidence            34456999999999999999999999999987                                       4443     


Q ss_pred             CccceEEEEeCCh-HHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         200 NSKGFAFINYASF-EASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       200 ~~~g~afV~f~~~-~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                       .+|||||+|.+. ++|..|+..+|+..+.++.+.|.++...
T Consensus        46 -~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          46 -GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             -TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             -CCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeecc
Confidence             379999999985 7899999999999998888888876543

>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=99.24  E-value=9.7e-12  Score=91.47  Aligned_cols=78  Identities=19%  Similarity=0.247  Sum_probs=63.8

Q ss_pred             ccccccccCC--Cchh---------cHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccC
Q psy3016         120 VGANIFIGNL--DPEV---------DEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNL  188 (305)
Q Consensus       120 ~~~~l~v~nl--~~~~---------t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  188 (305)
                      .+++|+|.|+  +.++         .+++|++.|++||.|..+                                     
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v-------------------------------------   49 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKL-------------------------------------   49 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEE-------------------------------------
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEE-------------------------------------
Confidence            4678999998  4432         246899999999999865                                     


Q ss_pred             CCCcccCCCCCCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         189 DPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       189 ~~~i~~d~~~~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                        .+..    +..+|+|||+|++.++|.+|+..|||++|+||.|+|.|...+
T Consensus        50 --~~~~----~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          50 --LLFD----RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGT   95 (99)
T ss_dssp             --EEET----TCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSC
T ss_pred             --eccC----CCCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCc
Confidence              2222    346799999999999999999999999999999999998654

>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=99.23  E-value=5.6e-12  Score=93.68  Aligned_cols=82  Identities=20%  Similarity=0.267  Sum_probs=65.6

Q ss_pred             ccccccccCC--Cc--------hhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCC
Q psy3016         120 VGANIFIGNL--DP--------EVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLD  189 (305)
Q Consensus       120 ~~~~l~v~nl--~~--------~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  189 (305)
                      ++++|.+.|+  +.        ....++|++.|++||.|..+                                      
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v--------------------------------------   44 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSI--------------------------------------   44 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEE--------------------------------------
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEE--------------------------------------
Confidence            3567788887  22        23456799999999999987                                      


Q ss_pred             CCcccCCCC--CCccceEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEeeec
Q psy3016         190 PEIMRDPDT--GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK  240 (305)
Q Consensus       190 ~~i~~d~~~--~~~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~~~  240 (305)
                       .|.++..+  ....|++||+|.+.++|.+|+..|||++++||.|.+.|....
T Consensus        45 -~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~~~   96 (104)
T d1o0pa_          45 -EIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPD   96 (104)
T ss_dssp             -ECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEECHH
T ss_pred             -EEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcCHH
Confidence             44444433  345789999999999999999999999999999999998654

>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=99.15  E-value=2e-11  Score=86.25  Aligned_cols=73  Identities=18%  Similarity=0.253  Sum_probs=60.5

Q ss_pred             cccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCC
Q psy3016         121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN  200 (305)
Q Consensus       121 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~  200 (305)
                      .+.|+|+++|++.+++.| +.|+.||.|..+                                             ..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~---------------------------------------------~~~~   37 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKH---------------------------------------------VMSN   37 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEE---------------------------------------------EECS
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheE---------------------------------------------EecC
Confidence            356999999999987655 579999999875                                             1245


Q ss_pred             ccceEEEEeCChHHHHHHHHHhcCeeecCee-eEEEEeeec
Q psy3016         201 SKGFAFINYASFEASDASIDAMHGQYLCNRP-ISVSYAFKK  240 (305)
Q Consensus       201 ~~g~afV~f~~~~~A~~Al~~l~~~~~~g~~-l~v~~a~~~  240 (305)
                      .+|||||+|++.++|.+||. +||..++|+. |.|..+.++
T Consensus        38 ~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1          38 TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCCh
Confidence            58999999999999999996 9999999985 568887654

>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=97.53  E-value=0.00015  Score=50.84  Aligned_cols=69  Identities=9%  Similarity=0.057  Sum_probs=58.2

Q ss_pred             ceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCC--cceEEEEEEcCHHHHHHHHHHhcCceeCC
Q psy3016          35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQT--HQGYGFIEFMGEEDADYAIKIMNMIKLYG  103 (305)
Q Consensus        35 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~--~~g~afV~f~~~e~A~~Ai~~l~g~~~~g  103 (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            4789999999999999999999999998887776554322  22569999999999999999999987754

>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=97.36  E-value=0.00013  Score=50.42  Aligned_cols=69  Identities=19%  Similarity=0.320  Sum_probs=55.1

Q ss_pred             CceEEEcCCCccccH---------HHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCe
Q psy3016          34 DATIYVGGLDDKVSE---------TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGK  104 (305)
Q Consensus        34 ~~~l~V~nLp~~~te---------~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~  104 (305)
                      ..||.|.=...+..+         .+|.+.|..||+|.=++++.+.        .+|+|.+-+.|.+|+. +++..+.|+
T Consensus        15 DgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~--------mwVTF~dG~SAL~al~-l~g~~v~G~   85 (95)
T d1ufwa_          15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKGR   85 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETTE
T ss_pred             CcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCe--------EEEEECCcHHHHHHhc-cCCeEEcce
Confidence            457777444322222         3577889999999999997764        7999999999999999 899999999


Q ss_pred             eeEEeeC
Q psy3016         105 PIRVNKA  111 (305)
Q Consensus       105 ~l~v~~~  111 (305)
                      .|+|...
T Consensus        86 ~l~It~~   92 (95)
T d1ufwa_          86 AVKISGP   92 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEecC
Confidence            9999754

>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=97.17  E-value=0.0011  Score=43.37  Aligned_cols=62  Identities=24%  Similarity=0.255  Sum_probs=52.7

Q ss_pred             HHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhcCceeCCeeeEEeeCCC
Q psy3016          49 TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS  113 (305)
Q Consensus        49 ~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~l~v~~~~~  113 (305)
                      +-|.+.|.++|.|.++.+.... .  ..-.|-|...+.++|..|+..|+...+++++|.|.++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-d--g~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-D--YQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-S--TTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-C--CcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            3456789999999999997653 2  335799999999999999999999999999999998753

>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=97.06  E-value=0.0012  Score=43.28  Aligned_cols=68  Identities=18%  Similarity=0.266  Sum_probs=52.3

Q ss_pred             CCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCccceEEEE
Q psy3016         129 LDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFIN  208 (305)
Q Consensus       129 l~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~g~afV~  208 (305)
                      |+..--.+.|.+.|.+++.|..+                                       .+...   ....-.|-|.
T Consensus         4 L~~kelqq~L~~~f~~h~~V~sv---------------------------------------~l~~~---~dg~~~A~V~   41 (73)
T d2dgxa1           4 LSRKELQQLLQEAFARHGKVKSV---------------------------------------ELSPH---TDYQLKAVVQ   41 (73)
T ss_dssp             SCHHHHHHHHHHHHHHHSCEEEE---------------------------------------EECSC---CSTTCCEEEE
T ss_pred             CCHHHHHHHHHHHHHhheeEEEE---------------------------------------EEEec---cCCcEEEEEE
Confidence            33334456688889999999875                                       22222   1223358999


Q ss_pred             eCChHHHHHHHHHhcCeeecCeeeEEEEee
Q psy3016         209 YASFEASDASIDAMHGQYLCNRPISVSYAF  238 (305)
Q Consensus       209 f~~~~~A~~Al~~l~~~~~~g~~l~v~~a~  238 (305)
                      ..+..+|.-|+..||.+.+++++|.|+++.
T Consensus        42 v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          42 MENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             ESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            999999999999999999999999999974

>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=96.60  E-value=0.0019  Score=44.53  Aligned_cols=33  Identities=15%  Similarity=0.288  Sum_probs=30.2

Q ss_pred             eEEEEeCChHHHHHHHHHhcCeeecCeeeEEEEe
Q psy3016         204 FAFINYASFEASDASIDAMHGQYLCNRPISVSYA  237 (305)
Q Consensus       204 ~afV~f~~~~~A~~Al~~l~~~~~~g~~l~v~~a  237 (305)
                      -..|.|.+-++|.+|+. ++|.+++|+.|+++..
T Consensus        60 ~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          60 QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            46999999999999999 9999999999999853

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.43  E-value=0.0031  Score=43.84  Aligned_cols=68  Identities=18%  Similarity=0.178  Sum_probs=50.5

Q ss_pred             cccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCCCcc
Q psy3016         123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSK  202 (305)
Q Consensus       123 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~~~~  202 (305)
                      +|.|..||+.+|++++.+.++..|.+.+.                               -|...   +....   ....
T Consensus         3 KvVvRrLPP~Lte~~F~~~l~~~~~~d~~-------------------------------~f~~G---k~s~~---~~~~   45 (91)
T d1uw4a_           3 KVVIRRLPPTLTKEQLQEHLQPMPEHDYF-------------------------------EFFSN---DTSLY---PHMY   45 (91)
T ss_dssp             EEEEEEECTTCCHHHHHHHHCSCCCEEEE-------------------------------EEEES---CCSST---TCCC
T ss_pred             eEEEecCCCCCCHHHHHHHhCCcCceEEE-------------------------------EEeCC---CcCCC---CCcc
Confidence            58899999999999999999987776543                               00100   11111   1234


Q ss_pred             ceEEEEeCChHHHHHHHHHhcCeee
Q psy3016         203 GFAFINYASFEASDASIDAMHGQYL  227 (305)
Q Consensus       203 g~afV~f~~~~~A~~Al~~l~~~~~  227 (305)
                      ..|||.|.+.++...-.+.++|..|
T Consensus        46 SRAYi~F~~~~~v~~F~~~f~g~~F   70 (91)
T d1uw4a_          46 ARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             EEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             eEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            5699999999999999999999887

>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=94.42  E-value=0.071  Score=36.97  Aligned_cols=59  Identities=12%  Similarity=0.200  Sum_probs=47.3

Q ss_pred             CCCCceEEEcCCCccccHHHHHHHhccCCCeEEEEEcccCCCCCcceEEEEEEcCHHHHHHHHHHhc
Q psy3016          31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN   97 (305)
Q Consensus        31 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~i~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~   97 (305)
                      ...-..||.-..|..+...||.++|+.||.|. |..+.+       .-|||...+.++|..++..+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd-------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC-------ceEEEEecCHHHHHHHHHHhc
Confidence            33445799999999999999999999999865 334444       359999999999999887543

>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=85.91  E-value=0.71  Score=31.70  Aligned_cols=57  Identities=23%  Similarity=0.316  Sum_probs=45.7

Q ss_pred             ccccccccCCCchhcHHHHHHHHhhcCcccchhhhhhhhhhcCcceeeecCccccccCCCcceeEeccCCCCcccCCCCC
Q psy3016         120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG  199 (305)
Q Consensus       120 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~d~~~~  199 (305)
                      ...-+|.-..|..+...+|.++|++||-|...                                        .+-|    
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~Vs----------------------------------------wIdd----   49 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQIS----------------------------------------WIDD----   49 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCE----------------------------------------EEET----
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEE----------------------------------------EecC----
Confidence            34568888999999999999999999988642                                        2222    


Q ss_pred             CccceEEEEeCChHHHHHHHHHhc
Q psy3016         200 NSKGFAFINYASFEASDASIDAMH  223 (305)
Q Consensus       200 ~~~g~afV~f~~~~~A~~Al~~l~  223 (305)
                         -.|||...+.++|..++..++
T Consensus        50 ---TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          50 ---TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             ---TEEEEECSCHHHHHHHHHHHH
T ss_pred             ---ceEEEEecCHHHHHHHHHHhc
Confidence               269999999999999888655