Psyllid ID: psy4057

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240------
Protein Sequence
MNIILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK
Secondary Structure (PSIPRED)
ccccccccccccEEEEccccHHHHHHHHHHHHcccccEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccccccccEEEcccccccHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEcccccEEEEEEccHHHHHHHHHHHcccEEcccccEEEEEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccccEEEEEcccHHHHHHHHHHHHHccccEEEEEccccccccccEEEEEccHHHHHHHHHHccccEEccEEcEEEEcccccHHHHHHHcccccccHHccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHccccEEEEEEcccccEEEEEEccHHHHHHHHHHHccccccccccEEEEEEcc
Coil and Loop (DISEMBL)
MNIILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALrsmqgfpfydkpmriqysktdSDVISKIKGtfmerpkkvrkqpapvedpaeAKKSKKKAAKEQARLMQAQQQQMQALsvqqppvsqpappapmatagvpeqppnqilfltnlpeETSEMMLSMLFnqfpgfkevrlvpnrhdiaFVEFENEMQSAAAKLALhgfkitpthamKISFAKK
Flexible Loop (DISEMBL)
MNIILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKIkgtfmerpkkvrkqpapvedpaeakKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFkitpthamkisfakk
Low Complexity Region (SEG)
MNIILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPaeakkskkkaakeqarlmqaqqqqmqalsvqqppvsqpappapMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK
Disordered region (IsUnstruct)
**IILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS***************************************************************************************ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHA********
Disordered Region (DISOPRED)
*******ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD******IKGTFMERPKKVRK*******************************QMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK
Disordered Region (DISEMBL)
MNIILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFME**************************************************************GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK
Disordered Region (DISPRO)
*****AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFM****************************************************************VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNIILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK
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	246	2.2.26 [Sep-21-2011]
P45429	282	U1 small nuclear ribonucl	N/A	N/A	0.959	0.836	0.554	7e-72
Q2KIR1	282	U1 small nuclear ribonucl	yes	N/A	0.926	0.808	0.550	1e-71
Q06AA4	282	U1 small nuclear ribonucl	yes	N/A	0.926	0.808	0.550	1e-71
P09012	282	U1 small nuclear ribonucl	yes	N/A	0.926	0.808	0.547	3e-71
Q62189	287	U1 small nuclear ribonucl	yes	N/A	0.926	0.794	0.549	2e-70
Q9CQI7	225	U2 small nuclear ribonucl	no	N/A	0.865	0.946	0.599	3e-70
P43332	216	U1 small nuclear ribonucl	yes	N/A	0.776	0.884	0.668	5e-70
P08579	225	U2 small nuclear ribonucl	no	N/A	0.865	0.946	0.586	2e-69
Q8H1S6	229	U2 small nuclear ribonucl	yes	N/A	0.914	0.982	0.455	9e-53
O22922	232	U2 small nuclear ribonucl	no	N/A	0.926	0.982	0.443	2e-52

>sp|P45429|SNRPA_XENLA U1 small nuclear ribonucleoprotein A OS=Xenopus laevis GN=snrpa PE=2 SV=1

 Score =  270 bits (690), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 152/274 (55%), Positives = 184/274 (67%), Gaps = 38/274 (13%)

Query: 11  TNFVYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNA 66
            N +Y+ +    I   +LKKSLYAIFSQFGQI+DI+  + LKMRGQAFVIFKE +SATNA
Sbjct: 9   NNTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRNLKMRGQAFVIFKETSSATNA 68

Query: 67  LRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVR-KQPAPVEDPAEAKKSKKK 125
           LRSMQGFPFYDKPMRIQYSKTDSD+I+K+KGTF+ER +K + K+   V +    K +   
Sbjct: 69  LRSMQGFPFYDKPMRIQYSKTDSDIIAKMKGTFVERDRKRQEKRKVKVPEVQGVKNAMPG 128

Query: 126 AA-----KEQARLMQ-----AQQQQMQALSVQQPPVSQPA--PPAPMATAGVP------- 166
           AA       Q   MQ      Q  +M  ++ Q P +  P   PP  MA   +P       
Sbjct: 129 AALLPGVPGQMAAMQDMPGMTQAPRMMHMAGQAPYMHHPGMMPPPGMAPGQMPPGGMPHG 188

Query: 167 --------------EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAF 212
                         E PPN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDIAF
Sbjct: 189 QLMPGQMAPMQPISENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAF 248

Query: 213 VEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           VEF+NE+Q+ AA+ +L GFKIT +++MKISFAKK
Sbjct: 249 VEFDNEVQAGAARESLQGFKITQSNSMKISFAKK 282

Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP.
Xenopus laevis (taxid: 8355)

>sp|Q2KIR1|SNRPA_BOVIN U1 small nuclear ribonucleoprotein A OS=Bos taurus GN=SNRPA PE=2 SV=1

 Score =  269 bits (688), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 152/276 (55%), Positives = 183/276 (66%), Gaps = 48/276 (17%)

Query: 14  VYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
           +Y+ +    I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRS
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71

Query: 70  MQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQ-PAPVEDPAEAKKSKKKAAK 128
           MQGFPFYDKPMRIQY+KTDSD+I+K+KGTF+ER +K  K+ P   E PA  K  +  AA 
Sbjct: 72  MQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPAAKKAVQGGAAA 131

Query: 129 EQARLMQAQQQQMQALS-----------------------------VQQPPVSQPA---- 155
                +Q     M  ++                              Q PP + P     
Sbjct: 132 PVVGTVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQLPPGAMPPQQLM 191

Query: 156 ----PPA-PMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI 210
               PPA P++     E PPN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDI
Sbjct: 192 PGQMPPAQPLS-----ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDI 246

Query: 211 AFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           AFVEF+NE+Q+ AA+ AL GFKIT  +AMKISFAKK
Sbjct: 247 AFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282

Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.

Bos taurus (taxid: 9913)

>sp|Q06AA4|SNRPA_PIG U1 small nuclear ribonucleoprotein A OS=Sus scrofa GN=SNRPA PE=2 SV=1

 Score =  269 bits (687), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 152/276 (55%), Positives = 183/276 (66%), Gaps = 48/276 (17%)

Query: 14  VYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
           +Y+ +    I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRS
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71

Query: 70  MQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQ-PAPVEDPAEAKKSKKKAAK 128
           MQGFPFYDKPMRIQY+KTDSD+I+K+KGTF+ER +K  K+ P   E PA  K  +  AA 
Sbjct: 72  MQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPASKKAVQGGAAA 131

Query: 129 EQARLMQAQQQQMQALS-----------------------------VQQPPVSQPA---- 155
                +Q     M  ++                              Q PP + P     
Sbjct: 132 PVVGAVQGPVPGMPPMTQTPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLM 191

Query: 156 ----PPA-PMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI 210
               PPA P++     E PPN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDI
Sbjct: 192 PGQMPPAQPLS-----ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDI 246

Query: 211 AFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           AFVEF+NE+Q+ AA+ AL GFKIT  +AMKISFAKK
Sbjct: 247 AFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282

Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.

Sus scrofa (taxid: 9823)

>sp|P09012|SNRPA_HUMAN U1 small nuclear ribonucleoprotein A OS=Homo sapiens GN=SNRPA PE=1 SV=3

 Score =  268 bits (684), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 151/276 (54%), Positives = 182/276 (65%), Gaps = 48/276 (17%)

Query: 14  VYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
           +Y+ +    I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRS
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71

Query: 70  MQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQ-PAPVEDPAEAKKSKKKAAK 128
           MQGFPFYDKPMRIQY+KTDSD+I+K+KGTF+ER +K  K+ P   E PA  K  +   A 
Sbjct: 72  MQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGAT 131

Query: 129 EQARLMQAQQQQMQALS-----------------------------VQQPPVSQPA---- 155
                +Q     M  ++                              Q PP + P     
Sbjct: 132 PVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLM 191

Query: 156 ----PPA-PMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI 210
               PPA P++     E PPN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDI
Sbjct: 192 PGQMPPAQPLS-----ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDI 246

Query: 211 AFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           AFVEF+NE+Q+ AA+ AL GFKIT  +AMKISFAKK
Sbjct: 247 AFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282

Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.

Homo sapiens (taxid: 9606)

>sp|Q62189|SNRPA_MOUSE U1 small nuclear ribonucleoprotein A OS=Mus musculus GN=Snrpa PE=2 SV=3

 Score =  265 bits (677), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 151/275 (54%), Positives = 182/275 (66%), Gaps = 47/275 (17%)

Query: 14  VYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
           +Y+ +    I   +LKKSLYAIFSQFGQI+DI+  + +KMRGQAFVIFKE+ SATNALRS
Sbjct: 18  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRS 77

Query: 70  MQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQ-PAPVEDPAEAKKSKKKAAK 128
           MQGFPFYDKPMRIQY+KTDSD+I+K+KGT++ER +K  K+ P   E PA  K  +  AA 
Sbjct: 78  MQGFPFYDKPMRIQYAKTDSDIIAKMKGTYVERDRKREKRKPKSQETPAAKKAVQGGAAA 137

Query: 129 ----------------EQARLMQAQQQQMQALSV------------QQPPVSQPA----- 155
                           +  R+M     Q   +              Q PP + P      
Sbjct: 138 PVVGAVQPVPGMPPMPQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMP 197

Query: 156 ---PPA-PMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIA 211
              PPA P++     E PPN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDIA
Sbjct: 198 GQMPPAQPLS-----ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIA 252

Query: 212 FVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           FVEF+NE+Q+ AA+ AL GFKIT  +AMKISFAKK
Sbjct: 253 FVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 287

Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.

Mus musculus (taxid: 10090)

>sp|Q9CQI7|RU2B_MOUSE U2 small nuclear ribonucleoprotein B'' OS=Mus musculus GN=Snrpb2 PE=2 SV=1

 Score =  265 bits (677), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 142/237 (59%), Positives = 172/237 (72%), Gaps = 24/237 (10%)

Query: 14  VYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
           +Y+ +    I   +LK+SLYA+FSQFG ++DIVALKT+KMRGQAFVIFKE+ S+TNALR 
Sbjct: 9   IYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNALRQ 68

Query: 70  MQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKE 129
           +QGFPFY KPMRIQY+KTDSD+ISK++GTF ++ KK  K+ A   + A A  +KK     
Sbjct: 69  LQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTMEQAAAAANKKPG--- 125

Query: 130 QARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLS 189
                   Q    A + Q       A P P     VP+ PPN ILFL NLPEET+EMMLS
Sbjct: 126 --------QGTPNAANTQ-----GTAAPNPQ----VPDYPPNYILFLNNLPEETNEMMLS 168

Query: 190 MLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           MLFNQFPGFKEVRLVP RHDIAFVEFEN+ Q+ AA+ AL GFKITP+HAMKI++AKK
Sbjct: 169 MLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK 225

Involved in pre-mRNA splicing. This protein is associated with snRNP U2. It binds stem loop IV of U2 snRNA only in presence of the U2A' protein.

Mus musculus (taxid: 10090)

>sp|P43332|SNRPA_DROME U1 small nuclear ribonucleoprotein A OS=Drosophila melanogaster GN=snf PE=1 SV=1

 Score =  264 bits (674), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 147/220 (66%), Positives = 164/220 (74%), Gaps = 29/220 (13%)

Query: 27  SLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK 86
           SLYAIFSQFGQI+DIVALKTLKMRGQAFVIFKEI SA+NALR+MQGFPFYDKPM+I YSK
Sbjct: 26  SLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSK 85

Query: 87  TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSV 146
           +DSD+++KIKGTF ERPKKV+          +  K KK ++ E +               
Sbjct: 86  SDSDIVAKIKGTFKERPKKVKPPKPAPGTDEKKDKKKKPSSAENSN-------------- 131

Query: 147 QQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN 206
              P +Q             EQPPNQILFLTNLPEET+EMMLSMLFNQFPGFKEVRLVPN
Sbjct: 132 ---PNAQ------------TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN 176

Query: 207 RHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           RHDIAFVEF  E+QS AAK AL GFKITPTHAMKI+FAKK
Sbjct: 177 RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAKK 216

Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP (By similarity). Plays a role in regulating sex-lethal splicing.

Drosophila melanogaster (taxid: 7227)

>sp|P08579|RU2B_HUMAN U2 small nuclear ribonucleoprotein B'' OS=Homo sapiens GN=SNRPB2 PE=1 SV=1

 Score =  262 bits (669), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 139/237 (58%), Positives = 168/237 (70%), Gaps = 24/237 (10%)

Query: 14  VYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
           +Y+ +    I   +LK+SLYA+FSQFG ++DIVALKT+KMRGQAFVIFKE+ S+TNALR 
Sbjct: 9   IYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNALRQ 68

Query: 70  MQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKE 129
           +QGFPFY KPMRIQY+KTDSD+ISK++GTF ++ KK  K+ A   +      +KK     
Sbjct: 69  LQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTATTTNKKPG--- 125

Query: 130 QARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLS 189
                     Q    S      S P P        VP+ PPN ILFL NLPEET+EMMLS
Sbjct: 126 ----------QGTPNSANTQGNSTPNPQ-------VPDYPPNYILFLNNLPEETNEMMLS 168

Query: 190 MLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           MLFNQFPGFKEVRLVP RHDIAFVEFEN+ Q+ AA+ AL GFKITP+HAMKI++AKK
Sbjct: 169 MLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK 225

Involved in pre-mRNA splicing. This protein is associated with snRNP U2. It binds stem loop IV of U2 snRNA only in presence of the U2A' protein.

Homo sapiens (taxid: 9606)

>sp|Q8H1S6|RU2B2_ARATH U2 small nuclear ribonucleoprotein B'' 2 OS=Arabidopsis thaliana GN=At1g06960 PE=1 SV=1

 Score =  206 bits (525), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 113/248 (45%), Positives = 160/248 (64%), Gaps = 23/248 (9%)

Query: 3   IILAHICVTNFVYVTHISS----TDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFK 58
           ++ A I     +Y+ HI+      +LK+SLY +FSQFG+++D+VALKT K+RGQA+V+F 
Sbjct: 1   MLTADIPPNQSIYIKHINEKIKKEELKRSLYCLFSQFGRLLDVVALKTPKLRGQAWVVFT 60

Query: 59  EIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAE 118
           E+ +A+NA+R MQ FPFYDKPMRIQY+K+ SD ++K +G+F+         P   +   E
Sbjct: 61  EVTAASNAVRQMQNFPFYDKPMRIQYAKSKSDYVTKAEGSFV---------PKEKKMKQE 111

Query: 119 AKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTN 178
            K  +K+ A+E       QQ  M   +  Q     P P  P   +G    PPN ILF+ N
Sbjct: 112 EKVERKRHAEE------TQQPSMPNGATTQ--NGMPVP--PFQPSGQDTMPPNNILFIHN 161

Query: 179 LPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHA 238
           LP ET+ MML +LF Q+PGFKE+R++  +  IAFVE+E+++QS+ A  AL GFKITP + 
Sbjct: 162 LPIETNSMMLQLLFEQYPGFKEIRMIEAKPGIAFVEYEDDVQSSMAMQALQGFKITPQNP 221

Query: 239 MKISFAKK 246
           M +SFAKK
Sbjct: 222 MVVSFAKK 229

Involved in nuclear pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

>sp|O22922|RU2B1_ARATH U2 small nuclear ribonucleoprotein B'' OS=Arabidopsis thaliana GN=U2B'' PE=1 SV=1

 Score =  205 bits (522), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 110/248 (44%), Positives = 152/248 (61%), Gaps = 20/248 (8%)

Query: 3   IILAHICVTNFVYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFK 58
           ++ A I     +Y+ +    I   +LK+SLY +FSQFG+I+D+VALKT K+RGQA+V F 
Sbjct: 1   MLTADIPPNQSIYIQNLNERIKKEELKRSLYCLFSQFGRILDVVALKTPKLRGQAWVTFS 60

Query: 59  EIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAE 118
           E+ +A +A+R MQ FPFYDKPMR+QY+K  SD ++K +GTF+ + KK RKQ   VE   E
Sbjct: 61  EVTAAGHAVRQMQNFPFYDKPMRLQYAKAKSDCLAKAEGTFVPKDKK-RKQEEKVERKRE 119

Query: 119 AKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTN 178
             +    A                  S   P  +   P      +G    PPN ILF+ N
Sbjct: 120 DSQRPNTA---------------NGPSANGPSANNGVPAPSFQPSGQETMPPNNILFIQN 164

Query: 179 LPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHA 238
           LP ET+ MML +LF Q+PGFKE+R++  +  IAFVE+E+++Q++ A   L GFKITP + 
Sbjct: 165 LPHETTSMMLQLLFEQYPGFKEIRMIDAKPGIAFVEYEDDVQASIAMQPLQGFKITPQNP 224

Query: 239 MKISFAKK 246
           M ISFAKK
Sbjct: 225 MVISFAKK 232

Involved in nuclear pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

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	246
383847977	231	PREDICTED: U2 small nuclear ribonucleopr	0.902	0.961	0.720	8e-87
270047496	231	U1 small nuclear ribonucleoprotein A [Ap	0.902	0.961	0.720	1e-86
380024353	231	PREDICTED: U2 small nuclear ribonucleopr	0.902	0.961	0.720	1e-86
340726396	233	PREDICTED: u2 small nuclear ribonucleopr	0.902	0.952	0.716	3e-86
307195443	231	U2 small nuclear ribonucleoprotein B'' [	0.902	0.961	0.716	8e-86
156548050	230	PREDICTED: U2 small nuclear ribonucleopr	0.898	0.960	0.708	5e-83
58394659	216	AGAP011637-PA [Anopheles gambiae str. PE	0.829	0.944	0.649	2e-79
242247219	224	U1 small nuclear ribonucleoprotein A-lik	0.857	0.941	0.645	6e-79
312372120	216	hypothetical protein AND_20571 [Anophele	0.772	0.879	0.714	2e-78
255710361	202	U1 small nuclear ribonucleoprotein A [Oc	0.776	0.945	0.695	7e-78

>gi|383847977|ref|XP_003699629.1| PREDICTED: U2 small nuclear ribonucleoprotein B''-like [Megachile rotundata]

 Score =  325 bits (834), Expect = 8e-87,   Method: Compositional matrix adjust.
 Identities = 173/240 (72%), Positives = 193/240 (80%), Gaps = 18/240 (7%)

Query: 11  TNFVYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNA 66
            N +Y+ +    I   +LKKSLYAIFSQFGQI+DIVALKTLKMRGQAFVIFKEIASATNA
Sbjct: 6   NNTIYINNLNEKIKKDELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIASATNA 65

Query: 67  LRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKA 126
           LRSMQGFPFYDKPMRIQY+KTDSD+I+K+KGT+ ERPKK  K+  P  D  EAK++KK+ 
Sbjct: 66  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTYAERPKKP-KRVVPAAD-EEAKRAKKR- 122

Query: 127 AKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEM 186
           AKEQA+   +QQ    A   Q P          +  A VPEQPPNQILFLTNLP+ETSEM
Sbjct: 123 AKEQAK--HSQQISYHAGVPQHP---------GLVNAAVPEQPPNQILFLTNLPDETSEM 171

Query: 187 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENE+QS AAK AL GFKITP+HAMKISFAKK
Sbjct: 172 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEVQSGAAKDALQGFKITPSHAMKISFAKK 231

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270047496|ref|NP_001161808.1| U1 small nuclear ribonucleoprotein A [Apis mellifera]

 Score =  325 bits (833), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 173/240 (72%), Positives = 192/240 (80%), Gaps = 18/240 (7%)

Query: 11  TNFVYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNA 66
            N +Y+ +    I   +LKKSLYAIFSQFGQI+DIVALKTLKMRGQAFVIFKEIASATNA
Sbjct: 6   NNTIYINNLNVKIKKDELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIASATNA 65

Query: 67  LRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKA 126
           LRSMQGFPFYDKPMRIQY+KTDSD+I+K+KGT+ ERPKK  K+  P  D  EAK++KK+ 
Sbjct: 66  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTYAERPKKP-KRVVPAAD-EEAKRAKKR- 122

Query: 127 AKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEM 186
           AKEQA+     QQ      VQQ P         +    VPEQPPNQILFLTNLP+ETSEM
Sbjct: 123 AKEQAK---HSQQIGYHTGVQQHP--------GLVNTAVPEQPPNQILFLTNLPDETSEM 171

Query: 187 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENE+QS AAK AL GFKITP+HAMKISFAKK
Sbjct: 172 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEVQSGAAKDALQGFKITPSHAMKISFAKK 231

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380024353|ref|XP_003695965.1| PREDICTED: U2 small nuclear ribonucleoprotein B''-like [Apis florea]

 Score =  325 bits (832), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 173/240 (72%), Positives = 192/240 (80%), Gaps = 18/240 (7%)

Query: 11  TNFVYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNA 66
            N +Y+ +    I   +LKKSLYAIFSQFGQI+DIVALKTLKMRGQAFVIFKEIASATNA
Sbjct: 6   NNTIYINNLNEKIKKDELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIASATNA 65

Query: 67  LRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKA 126
           LRSMQGFPFYDKPMRIQY+KTDSD+I+K+KGT+ ERPKK  K+  P  D  EAK++KK+ 
Sbjct: 66  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTYAERPKKP-KRVVPAAD-EEAKRAKKR- 122

Query: 127 AKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEM 186
           AKEQA+     QQ      VQQ P         +    VPEQPPNQILFLTNLP+ETSEM
Sbjct: 123 AKEQAK---HSQQIGYHTGVQQHP--------GLVNTAVPEQPPNQILFLTNLPDETSEM 171

Query: 187 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENE+QS AAK AL GFKITP+HAMKISFAKK
Sbjct: 172 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEVQSGAAKDALQGFKITPSHAMKISFAKK 231

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340726396|ref|XP_003401545.1| PREDICTED: u2 small nuclear ribonucleoprotein B''-like [Bombus terrestris] gi|350423999|ref|XP_003493658.1| PREDICTED: U2 small nuclear ribonucleoprotein B''-like [Bombus impatiens]

 Score =  323 bits (829), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 172/240 (71%), Positives = 192/240 (80%), Gaps = 18/240 (7%)

Query: 11  TNFVYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNA 66
            N +Y+ +    I   +LKKSLYAIFSQFGQI+DIVALKTLKMRGQAFVIFKEIASATNA
Sbjct: 8   NNTIYINNLNEKIKKDELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIASATNA 67

Query: 67  LRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKA 126
           LRSMQGFPFYDKPMRIQY+KTDSD+I+K+KGT+ ERPKK  K+  P  D  EAK++KK+ 
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTYAERPKKP-KRVVPAAD-EEAKRAKKR- 124

Query: 127 AKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEM 186
           AKEQA+   +QQ    A   Q P          +    VPEQPPNQILFLTNLP+ETSEM
Sbjct: 125 AKEQAK--HSQQIGYHAGVPQHP---------GLVNTAVPEQPPNQILFLTNLPDETSEM 173

Query: 187 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENE+QS AAK AL GFKITP+HAMKISFAKK
Sbjct: 174 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEVQSGAAKDALQGFKITPSHAMKISFAKK 233

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307195443|gb|EFN77329.1| U2 small nuclear ribonucleoprotein B'' [Harpegnathos saltator]

 Score =  322 bits (826), Expect = 8e-86,   Method: Compositional matrix adjust.
 Identities = 172/240 (71%), Positives = 191/240 (79%), Gaps = 18/240 (7%)

Query: 11  TNFVYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNA 66
            N +Y+ +    I   +LKKSLYAIFSQFGQI+DIVALKTLKMRGQAFVIFKEI SATNA
Sbjct: 6   NNTIYINNLNEKIKKDELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSATNA 65

Query: 67  LRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKA 126
           LRSMQGFPFYDKPMRIQY+KTDSD+I+K+KGTF ERPKK  K+  P  D  EAK++KK+ 
Sbjct: 66  LRSMQGFPFYDKPMRIQYAKTDSDLIAKMKGTFAERPKKP-KRVVPAAD-EEAKRAKKR- 122

Query: 127 AKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEM 186
           AKEQA+   +QQ    A   Q P          +    VPEQPPNQILFLTNLP+ETSEM
Sbjct: 123 AKEQAK--HSQQIGYHAGVPQHP---------GLVNTAVPEQPPNQILFLTNLPDETSEM 171

Query: 187 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENE+QS AAK AL GFKITP+HAMKISFAKK
Sbjct: 172 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEVQSGAAKDALQGFKITPSHAMKISFAKK 231

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156548050|ref|XP_001606482.1| PREDICTED: U2 small nuclear ribonucleoprotein B''-like isoform 1 [Nasonia vitripennis] gi|345485456|ref|XP_003425274.1| PREDICTED: U2 small nuclear ribonucleoprotein B''-like isoform 2 [Nasonia vitripennis]

 Score =  313 bits (801), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 170/240 (70%), Positives = 188/240 (78%), Gaps = 19/240 (7%)

Query: 11  TNFVYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNA 66
            N +Y+ +    I   +LKKSLYAIFSQFGQI+DIVALKTLKMRGQAFVIFKEIASATNA
Sbjct: 6   NNTIYINNLNEKIKKDELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIASATNA 65

Query: 67  LRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKA 126
           LRSMQGFPFYDKPMRI YSKTDSD+I+K+KGTF ERPKK  K+  P  D       ++  
Sbjct: 66  LRSMQGFPFYDKPMRINYSKTDSDIIAKMKGTFTERPKK-PKRVIPAAD-------EEAK 117

Query: 127 AKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEM 186
             ++    QA+QQQM       P  +Q    A MA A VPEQPPNQILFLTNLP+ETSEM
Sbjct: 118 KAKKRAKEQAKQQQMG----YTPGAAQ---HAGMANAAVPEQPPNQILFLTNLPDETSEM 170

Query: 187 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENE+QS AAK AL GFKITP+HAMKISFAKK
Sbjct: 171 MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEVQSGAAKDALQGFKITPSHAMKISFAKK 230

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|58394659|ref|XP_320869.2| AGAP011637-PA [Anopheles gambiae str. PEST] gi|55235062|gb|EAA00418.2| AGAP011637-PA [Anopheles gambiae str. PEST]

 Score =  301 bits (770), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 154/237 (64%), Positives = 177/237 (74%), Gaps = 33/237 (13%)

Query: 14  VYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
           +Y+ +    I+  +LKKSLYAIFSQFGQI+DIVA KTLKMRGQAF+IFKEI+SATNA+R+
Sbjct: 9   IYINNLNEKINKVELKKSLYAIFSQFGQILDIVAYKTLKMRGQAFIIFKEISSATNAMRT 68

Query: 70  MQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKE 129
           MQGFPFYDKPMRI+YSKTDSD+I+K+KGTF ERPK+V KQP P++   E KK+KK     
Sbjct: 69  MQGFPFYDKPMRIKYSKTDSDMIAKLKGTFQERPKRV-KQPKPIQ--TEDKKAKK----- 120

Query: 130 QARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLS 189
                                +           +   EQPPNQILFLTNLPEET+EMMLS
Sbjct: 121 ---------------------LKNAGEVGATNNSATAEQPPNQILFLTNLPEETNEMMLS 159

Query: 190 MLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           MLFNQFPGFKEVRLVPNRHDIAFVEF  E+QS AA+ AL GFKITPTHAMKISFAKK
Sbjct: 160 MLFNQFPGFKEVRLVPNRHDIAFVEFATELQSGAAREALQGFKITPTHAMKISFAKK 216

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242247219|ref|NP_001156146.1| U1 small nuclear ribonucleoprotein A-like [Acyrthosiphon pisum] gi|239790514|dbj|BAH71814.1| ACYPI003668 [Acyrthosiphon pisum]

 Score =  299 bits (766), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 153/237 (64%), Positives = 182/237 (76%), Gaps = 26/237 (10%)

Query: 14  VYVTH----ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
           +Y+ +    I   DLKKSLYAIFSQFGQI+DIVA+K +KM GQAFVIFK+I S+TNALR+
Sbjct: 10  IYINNLNEKIKKDDLKKSLYAIFSQFGQILDIVAMKGIKMNGQAFVIFKDITSSTNALRA 69

Query: 70  MQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKE 129
           MQGFPFYDKPMRIQ++K++SD+I+K+KGTF+ER     ++        E  K ++KAAKE
Sbjct: 70  MQGFPFYDKPMRIQFAKSESDIIAKMKGTFVER-----QKKPKKPKDDEEAKKRRKAAKE 124

Query: 130 QARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLS 189
           QAR + AQQ                  P  ++   VPEQPPNQILFLTNLP+ET+EMMLS
Sbjct: 125 QARAL-AQQNN----------------PGGVSGGNVPEQPPNQILFLTNLPDETTEMMLS 167

Query: 190 MLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           MLFNQFPGFKEVRLVPNRHDIAFVEFENE QS  AKL+L+GFKITPTHAMKI+FAKK
Sbjct: 168 MLFNQFPGFKEVRLVPNRHDIAFVEFENEHQSNTAKLSLNGFKITPTHAMKITFAKK 224

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312372120|gb|EFR20150.1| hypothetical protein AND_20571 [Anopheles darlingi]

 Score =  297 bits (761), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 158/221 (71%), Positives = 172/221 (77%), Gaps = 31/221 (14%)

Query: 27  SLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK 86
           SLYAIFSQFGQI+DIVA KTL+MRGQAF+IFKEI SATNA+R+MQGFPFYDKPMRI YSK
Sbjct: 26  SLYAIFSQFGQILDIVAYKTLRMRGQAFIIFKEIGSATNAMRTMQGFPFYDKPMRINYSK 85

Query: 87  TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKK-KAAKEQARLMQAQQQQMQALS 145
           TDSD+I+K+KGTF ERPK+VR QP PV  P E KKSKK KAA E      +         
Sbjct: 86  TDSDMIAKLKGTFQERPKRVR-QPKPV--PTEEKKSKKQKAAGEVGATNNS--------- 133

Query: 146 VQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP 205
                          ATA   EQPPNQILFLTNLPEET+EMMLSMLFNQFPGFKEVRLVP
Sbjct: 134 ---------------ATA---EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVP 175

Query: 206 NRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           NRHDIAFVEF +E+QS AA+ AL GFKITPTHAMKISFAKK
Sbjct: 176 NRHDIAFVEFASEVQSGAAREALQGFKITPTHAMKISFAKK 216

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|255710361|gb|ACU31000.1| U1 small nuclear ribonucleoprotein A [Ochlerotatus triseriatus]

 Score =  296 bits (757), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 153/220 (69%), Positives = 167/220 (75%), Gaps = 29/220 (13%)

Query: 27  SLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK 86
           SLYAIFSQFGQI+DIVALKTLKMRGQAF+IFKEI SATNA+R+MQGFPFYDKPMRI YSK
Sbjct: 12  SLYAIFSQFGQILDIVALKTLKMRGQAFIIFKEIGSATNAMRTMQGFPFYDKPMRINYSK 71

Query: 87  TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSV 146
           TDSDVI+K+KGTF ERPKK  K P P++   E KKSKK+   E                 
Sbjct: 72  TDSDVIAKMKGTFKERPKKA-KAPKPIQQ--EDKKSKKQKNAEAG--------------- 113

Query: 147 QQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN 206
                      A   ++   EQPPNQILFLTNLPEET+EMMLSMLFNQFPGFKEVRLVPN
Sbjct: 114 -----------AAANSSATAEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN 162

Query: 207 RHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           RHDIAFVEF  E+QS AA+ AL GFKITPTHAMKISFAKK
Sbjct: 163 RHDIAFVEFATELQSGAAREALQGFKITPTHAMKISFAKK 202

Source: Ochlerotatus triseriatus

Species: Ochlerotatus triseriatus

Genus: Ochlerotatus

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	246
FB|FBgn0003449	216	snf "sans fille" [Drosophila m	0.394	0.449	0.785	1.6e-73
UNIPROTKB|Q2KIR1	282	SNRPA "U1 small nuclear ribonu	0.398	0.347	0.727	9.8e-68
UNIPROTKB|P09012	282	SNRPA "U1 small nuclear ribonu	0.398	0.347	0.727	9.8e-68
UNIPROTKB|Q06AA4	282	SNRPA "U1 small nuclear ribonu	0.398	0.347	0.727	9.8e-68
RGD|1307416	281	Snrpa "small nuclear ribonucle	0.398	0.348	0.727	9.8e-68
UNIPROTKB|F1M6Z8	285	Snrpa "Protein Snrpa" [Rattus	0.398	0.343	0.727	9.8e-68
ZFIN|ZDB-GENE-030131-2841	281	snrpa "small nuclear ribonucle	0.373	0.327	0.763	2.6e-67
UNIPROTKB|E1C0I4	226	SNRPB2 "Uncharacterized protei	0.333	0.362	0.817	4.2e-67
MGI|MGI:1855690	287	Snrpa "small nuclear ribonucle	0.398	0.341	0.707	6.8e-67
UNIPROTKB|G5E5Y0	218	SNRPB2 "Uncharacterized protei	0.378	0.426	0.698	8.7e-67

FB|FBgn0003449 snf "sans fille" [Drosophila melanogaster (taxid:7227)]

 Score = 392 (143.0 bits), Expect = 1.6e-73, Sum P(2) = 1.6e-73
 Identities = 77/98 (78%), Positives = 88/98 (89%)

Query:    19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
             I   +LKKSLYAIFSQFGQI+DIVALKTLKMRGQAFVIFKEI SA+NALR+MQGFPFYDK
Sbjct:    18 IKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDK 77

Query:    79 PMRIQYSKTDSDVISKIKGTFMERPKKVRK-QPAPVED 115
             PM+I YSK+DSD+++KIKGTF ERPKKV+  +PAP  D
Sbjct:    78 PMQIAYSKSDSDIVAKIKGTFKERPKKVKPPKPAPGTD 115

GO:0048477 "oogenesis" evidence=IMP;TAS

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISS;NAS;IDA

GO:0005681 "spliceosomal complex" evidence=ISS

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

GO:0019099 "female germ-line sex determination" evidence=NAS

GO:0005692 "U11 snRNP" evidence=ISS

GO:0030619 "U1 snRNA binding" evidence=IDA;NAS

GO:0003729 "mRNA binding" evidence=ISS;NAS

GO:0005634 "nucleus" evidence=IC;NAS;TAS

GO:0007539 "primary sex determination, soma" evidence=NAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0005685 "U1 snRNP" evidence=ISS

GO:0005686 "U2 snRNP" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0043234 "protein complex" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

GO:0035614 "snRNA stem-loop binding" evidence=IDA

GO:0030620 "U2 snRNA binding" evidence=IDA

UNIPROTKB|Q2KIR1 SNRPA "U1 small nuclear ribonucleoprotein A" [Bos taurus (taxid:9913)]

 Score = 370 (135.3 bits), Expect = 9.8e-68, Sum P(2) = 9.8e-68
 Identities = 72/99 (72%), Positives = 86/99 (86%)

Query:    19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
             I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct:    21 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80

Query:    79 PMRIQYSKTDSDVISKIKGTFMERPKKVRKQ-PAPVEDP 116
             PMRIQY+KTDSD+I+K+KGTF+ER +K  K+ P   E P
Sbjct:    81 PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETP 119

GO:0003723 "RNA binding" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0017069 "snRNA binding" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|P09012 SNRPA "U1 small nuclear ribonucleoprotein A" [Homo sapiens (taxid:9606)]

 Score = 370 (135.3 bits), Expect = 9.8e-68, Sum P(2) = 9.8e-68
 Identities = 72/99 (72%), Positives = 86/99 (86%)

Query:    19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
             I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct:    21 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80

Query:    79 PMRIQYSKTDSDVISKIKGTFMERPKKVRKQ-PAPVEDP 116
             PMRIQY+KTDSD+I+K+KGTF+ER +K  K+ P   E P
Sbjct:    81 PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETP 119

GO:0000166 "nucleotide binding" evidence=IEA

GO:0017069 "snRNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IDA

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

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

UNIPROTKB|Q06AA4 SNRPA "U1 small nuclear ribonucleoprotein A" [Sus scrofa (taxid:9823)]

 Score = 370 (135.3 bits), Expect = 9.8e-68, Sum P(2) = 9.8e-68
 Identities = 72/99 (72%), Positives = 86/99 (86%)

Query:    19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
             I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct:    21 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80

Query:    79 PMRIQYSKTDSDVISKIKGTFMERPKKVRKQ-PAPVEDP 116
             PMRIQY+KTDSD+I+K+KGTF+ER +K  K+ P   E P
Sbjct:    81 PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETP 119

GO:0003723 "RNA binding" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0017069 "snRNA binding" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

RGD|1307416 Snrpa "small nuclear ribonucleoprotein polypeptide A" [Rattus norvegicus (taxid:10116)]

 Score = 370 (135.3 bits), Expect = 9.8e-68, Sum P(2) = 9.8e-68
 Identities = 72/99 (72%), Positives = 86/99 (86%)

Query:    19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
             I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct:    21 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80

Query:    79 PMRIQYSKTDSDVISKIKGTFMERPKKVRKQ-PAPVEDP 116
             PMRIQY+KTDSD+I+K+KGTF+ER +K  K+ P   E P
Sbjct:    81 PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETP 119

GO:0003723 "RNA binding" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=ISO

UNIPROTKB|F1M6Z8 Snrpa "Protein Snrpa" [Rattus norvegicus (taxid:10116)]

 Score = 370 (135.3 bits), Expect = 9.8e-68, Sum P(2) = 9.8e-68
 Identities = 72/99 (72%), Positives = 86/99 (86%)

Query:    19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
             I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct:    25 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 84

Query:    79 PMRIQYSKTDSDVISKIKGTFMERPKKVRKQ-PAPVEDP 116
             PMRIQY+KTDSD+I+K+KGTF+ER +K  K+ P   E P
Sbjct:    85 PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETP 123

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0017069 "snRNA binding" evidence=IEA

ZFIN|ZDB-GENE-030131-2841 snrpa "small nuclear ribonucleoprotein polypeptide A" [Danio rerio (taxid:7955)]

 Score = 361 (132.1 bits), Expect = 2.6e-67, Sum P(2) = 2.6e-67
 Identities = 71/93 (76%), Positives = 83/93 (89%)

Query:    19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
             I   +LKKSLYAIFSQFGQI+DI+  +TLKM+GQAFVIFKEI SA+NALRSMQGFPFYDK
Sbjct:    21 IKKDELKKSLYAIFSQFGQILDILVSRTLKMKGQAFVIFKEINSASNALRSMQGFPFYDK 80

Query:    79 PMRIQYSKTDSDVISKIKGTFMERP-KKVRKQP 110
             PMRIQYSK DSD+I+K+KGTF+ER  KK +K+P
Sbjct:    81 PMRIQYSKQDSDIIAKMKGTFVERDRKKEKKKP 113

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0017069 "snRNA binding" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|E1C0I4 SNRPB2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 352 (129.0 bits), Expect = 4.2e-67, Sum P(2) = 4.2e-67
 Identities = 67/82 (81%), Positives = 74/82 (90%)

Query:   165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAA 224
             VP+ PPN ILFL NLPEET+EMMLSMLFNQFPGFKEVRLVP RHDIAFVEFENE Q+ AA
Sbjct:   145 VPDNPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENECQAGAA 204

Query:   225 KLALHGFKITPTHAMKISFAKK 246
             + AL GFKITP+HAMKI++AKK
Sbjct:   205 RDALQGFKITPSHAMKITYAKK 226

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IEA

GO:0017069 "snRNA binding" evidence=IEA

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

MGI|MGI:1855690 Snrpa "small nuclear ribonucleoprotein polypeptide A" [Mus musculus (taxid:10090)]

 Score = 362 (132.5 bits), Expect = 6.8e-67, Sum P(2) = 6.8e-67
 Identities = 70/99 (70%), Positives = 84/99 (84%)

Query:    19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
             I   +LKKSLYAIFSQFGQI+DI+  + +KMRGQAFVIFKE+ SATNALRSMQGFPFYDK
Sbjct:    27 IKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDK 86

Query:    79 PMRIQYSKTDSDVISKIKGTFMERPKKVRKQ-PAPVEDP 116
             PMRIQY+KTDSD+I+K+KGT++ER +K  K+ P   E P
Sbjct:    87 PMRIQYAKTDSDIIAKMKGTYVERDRKREKRKPKSQETP 125

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0017069 "snRNA binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|G5E5Y0 SNRPB2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 351 (128.6 bits), Expect = 8.7e-67, Sum P(2) = 8.7e-67
 Identities = 65/93 (69%), Positives = 81/93 (87%)

Query:    19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
             I   +LK+SLYA+FSQFG ++DIVALKT+KMRGQAFVIFKE+ S+TNALR +QGFPFY K
Sbjct:    18 IKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNALRQLQGFPFYGK 77

Query:    79 PMRIQYSKTDSDVISKIKGTFMERPKKVRKQPA 111
             PMRIQY+KTDSD+ISK++GTF ++ KK  K+ A
Sbjct:    78 PMRIQYAKTDSDIISKMRGTFADKEKKKEKKKA 110

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

GO:0017069 "snRNA binding" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8H1S6	RU2B2_ARATH	No assigned EC number	0.4556	0.9146	0.9825	yes	N/A
P08579	RU2B_HUMAN	No assigned EC number	0.5864	0.8658	0.9466	no	N/A
O74968	RU1A_SCHPO	No assigned EC number	0.3293	0.8170	0.8072	yes	N/A
Q0DKM4	RU1A_ORYSJ	No assigned EC number	0.4713	0.8861	0.8616	yes	N/A
P43332	SNRPA_DROME	No assigned EC number	0.6681	0.7764	0.8842	yes	N/A
Q62189	SNRPA_MOUSE	No assigned EC number	0.5490	0.9268	0.7944	yes	N/A
P09012	SNRPA_HUMAN	No assigned EC number	0.5471	0.9268	0.8085	yes	N/A
Q9CQI7	RU2B_MOUSE	No assigned EC number	0.5991	0.8658	0.9466	no	N/A
Q06AA4	SNRPA_PIG	No assigned EC number	0.5507	0.9268	0.8085	yes	N/A
P45429	SNRPA_XENLA	No assigned EC number	0.5547	0.9593	0.8368	N/A	N/A
Q2KIR1	SNRPA_BOVIN	No assigned EC number	0.5507	0.9268	0.8085	yes	N/A
Q54J05	RU2B_DICDI	No assigned EC number	0.4297	0.9024	0.9211	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	246
cd12479	80	cd12479, RRM2_SNF, RNA recognition motif 2 found i	9e-44
cd12481	80	cd12481, RRM2_U2B, RNA recognition motif 2 found i	4e-41
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	2e-40
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	6e-40
cd12480	80	cd12480, RRM2_U1A, RNA recognition motif 2 found i	2e-38
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	5e-38
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	1e-37
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	3e-37
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-14
smart00360	73	smart00360, RRM, RNA recognition motif	3e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-12
smart00360	73	smart00360, RRM, RNA recognition motif	3e-11
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	1e-10
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	4e-10
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	7e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-09
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	3e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-09
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	9e-09
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	1e-08
cd12425	76	cd12425, RRM4_PTBP1_like, RNA recognition motif 4	3e-08
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-08
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-07
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	3e-07
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	5e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-07
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	3e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-06
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	5e-06
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	1e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-05
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	2e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-05
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-05
cd12308	79	cd12308, RRM1_Spen, RNA recognition motif 1 in the	5e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	5e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	6e-05
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	8e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	9e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-04
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-04
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	1e-04
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	1e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-04
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	1e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-04
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	2e-04
cd12702	80	cd12702, RRM4_PTBP2, RNA recognition motif 4 in ve	2e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	2e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-04
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-04
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	3e-04
cd12433	86	cd12433, RRM_Yme2p_like, RNA recognition motif in	3e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	3e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	4e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-04
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	6e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	6e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	8e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	8e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.001
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	0.001
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.001
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	0.002
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.002
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	0.002
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.002
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.002
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	0.002
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	0.002
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	0.002
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.002
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	0.002
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	0.002
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	0.002
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	0.002
cd12693	96	cd12693, RRM2_PTBP1_like, RNA recognition motif 2	0.002
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	0.002
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.003
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	0.003
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.003
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	0.003
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	0.003
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.004
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.004
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	0.004
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	0.004
cd12682	76	cd12682, RRM_RBPMS, RNA recognition motif in verte	0.004
cd12694	86	cd12694, RRM2_hnRNPL_like, RNA recognition motif 2	0.004
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	0.004

>gnl|CDD|240923 cd12479, RRM2_SNF, RNA recognition motif 2 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score =  142 bits (358), Expect = 9e-44
 Identities = 74/80 (92%), Positives = 77/80 (96%)

Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
           EQPPNQILFLTNLPEET+EMMLSMLFNQFPGFKEVRLVP RHDIAFVEFENE+QSAAAK 
Sbjct: 1   EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENEVQSAAAKE 60

Query: 227 ALHGFKITPTHAMKISFAKK 246
           AL GFKITPTHAMKI+FAKK
Sbjct: 61  ALQGFKITPTHAMKITFAKK 80

This subgroup corresponds to the RRM2 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila 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). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 80

>gnl|CDD|240925 cd12481, RRM2_U2B, RNA recognition motif 2 found in vertebrate U2 small nuclear ribonucleoprotein B" (U2B")

 Score =  135 bits (341), Expect = 4e-41
 Identities = 65/80 (81%), Positives = 72/80 (90%)

Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
           + PPN ILFL NLPEET+EMMLSMLFNQFPGFKEVRLVP RHDIAFVEFENE Q+ AA+ 
Sbjct: 1   DNPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENEAQAGAARD 60

Query: 227 ALHGFKITPTHAMKISFAKK 246
           AL GFKITP+HAMKI++AKK
Sbjct: 61  ALQGFKITPSHAMKITYAKK 80

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 to bind 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 and its nuclear transport 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 = 80

>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score =  133 bits (336), Expect = 2e-40
 Identities = 59/79 (74%), Positives = 73/79 (92%)

Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LK+SLYA+FSQFG ++DIVALKT+KMRGQAFVIFKE++SATNALR +QGFPFY K
Sbjct: 13 IKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNALRQLQGFPFYGK 72

Query: 79 PMRIQYSKTDSDVISKIKG 97
          PMRIQY+KTDSD++SK++G
Sbjct: 73 PMRIQYAKTDSDIVSKMRG 91

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

 Score =  132 bits (334), Expect = 6e-40
 Identities = 51/68 (75%), Positives = 62/68 (91%)

Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LK+SLYA+FSQFG ++DIVA KTLKMRGQAFV+FK++ SATNALR++QGFPFYDK
Sbjct: 11 IKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALRALQGFPFYDK 70

Query: 79 PMRIQYSK 86
          PMRIQY+K
Sbjct: 71 PMRIQYAK 78

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

>gnl|CDD|240924 cd12480, RRM2_U1A, RNA recognition motif 2 found in vertebrate U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A)

 Score =  128 bits (322), Expect = 2e-38
 Identities = 65/80 (81%), Positives = 73/80 (91%)

Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
           E PPN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDIAFVEF+NE+Q+ AA+ 
Sbjct: 1   ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARE 60

Query: 227 ALHGFKITPTHAMKISFAKK 246
           AL GFKIT ++AMKISFAKK
Sbjct: 61  ALQGFKITQSNAMKISFAKK 80

This subgroup corresponds to the RRM2 of U1A (also termed U1 snRNP A or U1-A), 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. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). U1A also binds to a flavivirus NS5 protein and plays an important role in virus replication. It contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and it may be free for binding other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 80

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

 Score =  127 bits (321), Expect = 5e-38
 Identities = 55/73 (75%), Positives = 59/73 (80%), Gaps = 1/73 (1%)

Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH 229
           PN+ILFL NLPEET++ ML MLFNQFPGFKEVRLVP R  IAFVEFE E Q+  A  AL 
Sbjct: 1   PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVP-RRGIAFVEFETEEQATVALQALQ 59

Query: 230 GFKITPTHAMKIS 242
           GFKITP HAMKIS
Sbjct: 60  GFKITPGHAMKIS 72

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

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score =  126 bits (318), Expect = 1e-37
 Identities = 58/68 (85%), Positives = 64/68 (94%)

Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          +   +LKKSLYAIFSQFGQI+DIVALKTLKMRGQAFV+FK+I+SATNALRSMQGFPFYDK
Sbjct: 11 VKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALRSMQGFPFYDK 70

Query: 79 PMRIQYSK 86
          PMRI YSK
Sbjct: 71 PMRIAYSK 78

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila 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). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score =  125 bits (315), Expect = 3e-37
 Identities = 58/75 (77%), Positives = 70/75 (93%)

Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 15 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 74

Query: 79 PMRIQYSKTDSDVIS 93
          PMRIQY+KTDSD+I+
Sbjct: 75 PMRIQYAKTDSDIIA 89

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), 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 and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

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

 Score = 64.5 bits (158), Expect = 5e-14
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 4/64 (6%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSAAAKLALH 229
           LF+ NLP +T+E  L  LF++F   + +R+V +        AFVEFE+E  +  A  AL+
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 230 GFKI 233
           G ++
Sbjct: 61  GKEL 64

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

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

 Score = 62.6 bits (153), Expect = 3e-13
 Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          ++V ++     ++ L  +FS+FG++  +  ++   T K +G AFV F+    A  AL ++
Sbjct: 2  LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61

Query: 71 QGFPFYDKPMRI 82
           G     +P+++
Sbjct: 62 NGKELDGRPLKV 73

Length = 73

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

 Score = 59.6 bits (145), Expect = 5e-12
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQ 71
          ++V ++     ++ L  +FS+FG+I  +  ++    K +G AFV F+    A  AL ++ 
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 72 GFPFYDKPMRIQ 83
          G     + +++ 
Sbjct: 61 GKELDGRKLKVS 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|214636 smart00360, RRM, RNA recognition motif

 Score = 57.6 bits (140), Expect = 3e-11
 Identities = 26/65 (40%), Positives = 39/65 (60%), Gaps = 5/65 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           LF+ NLP +T+E  L  LF++F   + VRLV ++        AFVEFE+E  +  A  AL
Sbjct: 2   LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61

Query: 229 HGFKI 233
           +G ++
Sbjct: 62  NGKEL 66

Length = 73

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

 Score = 55.6 bits (135), Expect = 1e-10
 Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQF-------GQIMDIVALKTLKMRGQAFVIFKEIASA 63
          +  +YV ++S    ++ L  IF +F         + DI  +   +M+GQAFV F     A
Sbjct: 1  SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIA 60

Query: 64 TNALRSMQGFPFYDKPMRIQYS 85
          T AL  + G+    KPM IQ+ 
Sbjct: 61 TKALNLVNGYVLKGKPMVIQFG 82

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 54.5 bits (132), Expect = 4e-10
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLV-PNRHDIAFVEFENEMQSAAAKLALHGFK 232
           LF+ NL   T+E  L  LF++ PGF+ +++       + FVEFE+   +  A  +L G  
Sbjct: 5   LFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGPVCFVEFEDVSFATQALNSLQGAV 64

Query: 233 ITPTH--AMKISFAK 245
           ++ +    ++I +AK
Sbjct: 65  LSSSDRGGIRIEYAK 79

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

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

 Score = 53.5 bits (129), Expect = 7e-10
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 4/64 (6%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSAAAKLALH 229
           LF+ NLP +T+E  L  LF++F   + VR+V ++       AFVEFE+   +  A  AL+
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 230 GFKI 233
           G ++
Sbjct: 61  GKEL 64

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 52.9 bits (128), Expect = 7e-10
 Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
          LY +FS FG +  I  LK  K  G AFV F    +A  A++ + G  F  +P+R+ YS
Sbjct: 1  LYKLFSPFGNVEKIKLLK--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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 53.0 bits (128), Expect = 1e-09
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI--VALKTLKMRGQAFVIFKEIASATNALRSMQ 71
          ++V ++     ++ L  +FS+FG I  I  V  +T + +G AFV F++   A  AL ++ 
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 72 GFPFYDKPMR 81
          G     + +R
Sbjct: 61 GKELGGRELR 70

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

>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 52.3 bits (126), Expect = 3e-09
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 6/68 (8%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENEMQSAAAKLA 227
           LF++ LP +  E  L+ LF  FPG++  RLV           + FV+F +   +AAA  A
Sbjct: 3   LFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAMDA 62

Query: 228 LHGFKITP 235
           L G++  P
Sbjct: 63  LQGYRFDP 70

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

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

 Score = 55.0 bits (131), Expect = 6e-09
 Identities = 26/126 (20%), Positives = 57/126 (45%), Gaps = 7/126 (5%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
           ++V ++     ++ L  +F +FG +  +  +   +T K RG AFV F+   SA  A+  +
Sbjct: 118 LFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEEL 177

Query: 71  QGFPFYDKPMRIQYSKTD----SDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKA 126
            G     +P+R+Q ++      S++ + +  +F ++  + +       D         K 
Sbjct: 178 NGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKT 237

Query: 127 AKEQAR 132
           A+E+  
Sbjct: 238 AEEELA 243

Length = 306

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 50.9 bits (122), Expect = 9e-09
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          VY+ +I  +  ++ L   FSQ+G+I  +     L+ +  AFV F  I++A  A+  ++  
Sbjct: 6  VYIGNIDDSLTEEKLRNDFSQYGEIESV---NYLREKNCAFVNFTNISNAIKAIDGVKSH 62

Query: 74 PFYDKPMRIQYSK 86
          P + K  +I Y K
Sbjct: 63 PLFKK-FKISYGK 74

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 50.2 bits (121), Expect = 1e-08
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 11/86 (12%)

Query: 7  HICVTNFVY-VTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATN 65
           + ++N +Y VT     D+   L+ +FS +G +  I+  +      QA V F  + SA N
Sbjct: 3  LVTISNLLYPVTV----DV---LHQVFSPYGAVEKILIFEKNT-GVQALVQFDSVESAEN 54

Query: 66 ALRSMQGFPFYDK--PMRIQYSKTDS 89
          A +++ G   YD    + IQ+S+   
Sbjct: 55 AKKALNGRNIYDGCCTLDIQFSRLKE 80

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 49.2 bits (118), Expect = 3e-08
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGF-KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK 232
           L L+N+P   +E  L  LF Q  G  K  +  P    +A ++  +  ++  A +ALH ++
Sbjct: 2   LHLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPKDRKMALIQMGSVEEAIEALIALHNYQ 61

Query: 233 ITPTHAMKISFAK 245
           ++ +  +++SF+K
Sbjct: 62  LSESSHLRVSFSK 74

This subfamily corresponds to the RRM4 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>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 = 48.9 bits (117), Expect = 4e-08
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 4/64 (6%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH----DIAFVEFENEMQSAAAKLALH 229
           LF++ LP   ++  L  LF +    K VRLV NR      +A+VE+ENE  ++ A L + 
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64

Query: 230 GFKI 233
           G +I
Sbjct: 65  GTEI 68

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 15 YVTHISSTDLKKSLYAIFSQFGQIMDIVALKT-LKMRGQAFVIFKEIASATNALRSMQGF 73
          +V +I+S    + L A+F QFG   DI  L T  K RG   V + +I +A  A R++QG 
Sbjct: 5  FVRNINSNVEDEELRALFEQFG---DIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGT 61

Query: 74 PFYDKPMRIQYS 85
              + + I +S
Sbjct: 62 ELGGRKLDIHFS 73

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|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 = 46.5 bits (111), Expect = 3e-07
 Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
          V+V +I     ++ L  IFS+ G ++    +    T K +G  F  F++I +A +A+R++
Sbjct: 1  VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 71 QGFPFYDKPMRIQYS 85
           G+ F  + +R+ ++
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|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 = 46.5 bits (111), Expect = 3e-07
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          VYV ++     ++ L   FS FG I ++   +  K +G AFV F    +A  A+ ++ G 
Sbjct: 3  VYVGNLPHGLTEEELQRTFSPFGAIEEV---RVFKDKGYAFVRFDTHEAAATAIVAVNGT 59

Query: 74 PFYDKPMRIQYSK 86
              + ++  + K
Sbjct: 60 SINGQTVKCSWGK 72

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

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

 Score = 46.5 bits (111), Expect = 3e-07
 Identities = 22/75 (29%), Positives = 39/75 (52%)

Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
          V   +YV ++      + LY +F ++G I  I    T + RG AFV++++I  A NA   
Sbjct: 1  VNRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDH 60

Query: 70 MQGFPFYDKPMRIQY 84
          + GF   ++ + + Y
Sbjct: 61 LSGFNVANRYLVVLY 75

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

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 46.0 bits (110), Expect = 5e-07
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 14/85 (16%)

Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ-----AFVIFKEIASAT 64
            N ++V ++     ++ L  +FS+          + LKM  +      FV F++++ AT
Sbjct: 1  PCNTLFVANLGPNTTEEELRQLFSRQ------PGFRRLKMHNKGGGPVCFVEFEDVSFAT 54

Query: 65 NALRSMQGFPFYDK---PMRIQYSK 86
           AL S+QG          +RI+Y+K
Sbjct: 55 QALNSLQGAVLSSSDRGGIRIEYAK 79

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

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

 Score = 49.2 bits (117), Expect = 5e-07
 Identities = 58/245 (23%), Positives = 100/245 (40%), Gaps = 25/245 (10%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           +YV+ +  T  +  L +IFS FGQI+    L    T   +G  F+ F +   A  A++++
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151

Query: 71  QGF--PFYDKPMRIQYSKTDSDVISKIKGTFME---RPKKVRKQPAPVEDPAEAKKSKKK 125
            G       +P+ ++++   S   SK   + +E    P+  R   + +   A        
Sbjct: 152 NGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHA 211

Query: 126 AAKEQ-------ARLMQAQQQQMQALSVQQPPVSQPAPPAPMAT----AGVPEQP-PNQI 173
           AA+ +       A L   QQQ   A        S PA     A     A +         
Sbjct: 212 AARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYC 271

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           +F+ NL  +T E +L  LF  F   + V+++ +          FV   N  ++A A L+L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 229 HGFKI 233
           +G+ +
Sbjct: 332 NGYTL 336

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

 Score = 48.0 bits (113), Expect = 1e-06
 Identities = 32/161 (19%), Positives = 63/161 (39%), Gaps = 10/161 (6%)

Query: 78  KPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQ 137
             + ++      +  +  +       +K+  + +P          +K+  + +       
Sbjct: 27  TELLLKEEYGGLEEANSKELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDG 86

Query: 138 QQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPG 197
           ++       ++   S  +P +         +  N  LF+ NLP + +E  L  LF +F  
Sbjct: 87  ERGYTKEFEEELFRSSESPKSRQ-----KSKEENNTLFVGNLPYDVTEEDLRELFKKFGP 141

Query: 198 FKEVRLVPNRH-----DIAFVEFENEMQSAAAKLALHGFKI 233
            K VRLV +R        AFVEFE+E  +  A   L+G ++
Sbjct: 142 VKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKEL 182

Length = 306

>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 = 44.9 bits (107), Expect = 1e-06
 Identities = 22/79 (27%), Positives = 47/79 (59%), Gaps = 3/79 (3%)

Query: 12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALR 68
          N ++V+ +S+   +K L A+FS+FG++ +++ +K   T + RG  FV F+ +  A  A+R
Sbjct: 2  NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 69 SMQGFPFYDKPMRIQYSKT 87
           + G     + ++++ +K 
Sbjct: 62 DLNGKELEGRVIKVEKAKR 80

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

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

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK-TLKMRGQAFVIFKEIASATNALRSMQG 72
          ++V  +S    K+ L   FS+ G+I+++  +K        AF+ F+   +A  A+ S   
Sbjct: 6  IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESENH 65

Query: 73 FPFYDKPMRIQY 84
              +K M +QY
Sbjct: 66 SMLKNKTMHVQY 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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRSM 70
          +YV  ++    +K L+A F  FG I DI   +  +T K RG AFV F+E   A  A+ +M
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 71 QGFPFYDKPMRI 82
               + + +R+
Sbjct: 61 NESELFGRTIRV 72

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

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

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMR------GQAFVIFKEIASATNAL 67
          +YV ++     +  L  IFS+FG++  I   K    +      G AFV FK+ +SA NAL
Sbjct: 3  IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 68 RSMQGFPFYDKPMRIQ 83
            + G     + + + 
Sbjct: 63 -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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 43.3 bits (103), Expect = 3e-06
 Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 5/57 (8%)

Query: 32 FSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF--YDKPMRIQYSK 86
          F +FG I  I        R  A++ ++ I +A  A  +++GFP     + +R+ ++ 
Sbjct: 19 FDRFGAIRRI---DYDPGRNYAYIEYESIEAAQAAKEALRGFPLGGPGRRLRVDFAD 72

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

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

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK 232
           +L++ NLP  T+E  L  LF+++   + V+ +    D AFV FE    +  A   ++G +
Sbjct: 3   VLYVRNLPLSTTEEQLRELFSEYGEVERVKKIK---DYAFVHFEERDDAVKAMEEMNGKE 59

Query: 233 ITPTHAMKISFAK 245
           +  +  +++S AK
Sbjct: 60  LEGS-PIEVSLAK 71

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

>gnl|CDD|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 = 43.3 bits (102), Expect = 5e-06
 Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 26 KSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
          +SL  +FS++GQI ++V +K   T + RG  FV F+    A +A+ +M G     + +R+
Sbjct: 15 QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRV 74

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

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 22/57 (38%), Positives = 30/57 (52%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
           L + NL    S+  L  LF+QF   K++R  P R    FVEF +   + AA  AL+G
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNG 60

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose 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. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

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

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           L +  LP++ ++  L  LF      +  ++V +R         FV++ +E  +  A   L
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 229 HGFKITPTHAMKISFA 244
           +GF+I     +K+S+A
Sbjct: 63  NGFEIRNKR-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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 3/46 (6%)

Query: 26 KSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALR 68
           SL   FSQFG+I + V +   +T K RG  FV FK+  SA  A +
Sbjct: 15 DSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

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|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          + V ++ S    + L ++FSQFG++ DI   +T     Q FV F +I +A  AL ++ G 
Sbjct: 4  LLVFNLDSPISDQELRSLFSQFGEVKDIR--ETPLRPSQKFVEFYDIRAAEAALDALNGR 61

Query: 74 PFYDKPMRIQ 83
          PF    ++++
Sbjct: 62 PFLGGRLKVK 71

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose 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. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>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 = 41.5 bits (98), Expect = 2e-05
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRS 69
          F+Y  H+ +    + LY +F+ FG ++     V   T + +   FV +    SA  A+++
Sbjct: 2  FIY--HLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKA 59

Query: 70 MQGFPFYDKPMRIQ 83
          M GF    K +++Q
Sbjct: 60 MNGFQVGGKRLKVQ 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|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 41.3 bits (97), Expect = 2e-05
 Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 3/58 (5%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF 231
           L++   P +TSE  +  +F+ +   KEV+++ N    AFVEFE+   +  AK ++HG 
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMISN---FAFVEFESLESAIRAKDSVHGK 56

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 9/67 (13%)

Query: 28 LYAIFSQFGQIM------DIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
          LY IFS  G ++      D++   T +  G A+V F+  A A  AL ++       KP+R
Sbjct: 16 LYEIFSPAGPVLSIRVCRDLI---TRRSLGYAYVNFQNPADAERALDTLNFDVIKGKPIR 72

Query: 82 IQYSKTD 88
          I +S+ D
Sbjct: 73 IMWSQRD 79

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

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIV-AL--KTLKMRGQAFVIFKEIASATNALRSM 70
          +YV ++S    ++ +Y +FS+ G I  I+  L   T    G  FV +     A NA++ +
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 71 QGFPFYDKPMRI 82
           G    D+ +R+
Sbjct: 61 NGTKLDDRIIRV 72

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|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split end) protein family

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 8  ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNAL 67
          +CV+N    + +S  D++  LY  F +FG +   V       R  A+V F+    A  A 
Sbjct: 4  LCVSNLP--SKLSDEDIEDVLYHEFKKFGDVSVRVLHDGEDER-VAYVNFRHPEDAREAK 60

Query: 68 RSMQGFPFYDKPMRIQYSK 86
           +      +D+P+ ++   
Sbjct: 61 HAKGRLVLFDRPLNVEPVY 79

This subfamily corresponds to the RRM1 domain in the Spen (split end) 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 possesses 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 known as 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 39.8 bits (94), Expect = 5e-05
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 3/63 (4%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH---DIAFVEFENEMQSAAAKLALHG 230
           L++ NLP   +E  L   F+ +   + VRLV N+      AFVEF +   + AA   L+G
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 231 FKI 233
             +
Sbjct: 61  LVL 63

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

>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 = 6e-05
 Identities = 16/63 (25%), Positives = 36/63 (57%), Gaps = 3/63 (4%)

Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
           VYV+++  +     L+ IFS++G+++ +  +K   T K +G AF++F +   A   +++
Sbjct: 3  TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 70 MQG 72
          +  
Sbjct: 63 LNN 65

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|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 = 39.9 bits (94), Expect = 7e-05
 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 6/66 (9%)

Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAA 224
            N+ LF++ L   T+E  L  LF++F   +EV L+ +          FV FE+   + AA
Sbjct: 1   GNK-LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAA 59

Query: 225 KLALHG 230
              L+G
Sbjct: 60  IRDLNG 65

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

 Score = 39.6 bits (93), Expect = 8e-05
 Identities = 18/72 (25%), Positives = 35/72 (48%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          +YV ++  T  +  L  +FSQ G I     ++       AFV + +  SA  AL++M G 
Sbjct: 1  LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 74 PFYDKPMRIQYS 85
              + +++ ++
Sbjct: 61 LILGQEIKVNWA 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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 39.7 bits (93), Expect = 9e-05
 Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 7/57 (12%)

Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQG 72
          I +  L+ +    F+ FG+I D   +K   T K +G  FV F +   A NA++SM G
Sbjct: 11 IDTETLRAA----FAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNG 63

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

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

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 5/58 (8%)

Query: 25 KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
          K+ L  IFS++G+I+ I   K     G  FV F     A  A+    G     + + I
Sbjct: 15 KEDLEEIFSKYGKILGISLHK-----GYGFVQFDNEEDARAAVAGENGREIAGQKLDI 67

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 28 LYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
          L  +FS++G I  +  +   KT + RG  FV F+ +  A  A   + G     + +R+ Y
Sbjct: 16 LREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRVDY 75

Query: 85 SKT 87
          S T
Sbjct: 76 SIT 78

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|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 30 AIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK 86
          A+F+ FG   D+V +K L   +  A +   +   A  AL  + G   + K +R+  SK
Sbjct: 16 ALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIRLHGKKLRVTLSK 73

This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)

Query: 25 KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
          +K L     ++G+I  I   + L+ +  AF+ F  I +A  AL+++ G   YD  +RI Y
Sbjct: 21 EKELRKECEKYGEIESI---RILREKACAFINFMNIPNAIAALQTLNGKKPYDTIVRINY 77

Query: 85 SK 86
           K
Sbjct: 78 GK 79

This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 82

>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 = 17/46 (36%), Positives = 24/46 (52%), Gaps = 3/46 (6%)

Query: 27 SLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
          SL   FSQ+G+I D V +K   T + RG  FV F   +    A+ +
Sbjct: 15 SLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

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

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

 Score = 42.3 bits (99), Expect = 1e-04
 Identities = 58/257 (22%), Positives = 101/257 (39%), Gaps = 37/257 (14%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQ 71
           V+V  I     +  L  +F + G I ++  +     + RG AFV F     A  A++ + 
Sbjct: 61  VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLN 120

Query: 72  GFPFYDKPMRIQYSKTDSDVI-------SKIKGTFMERPKKVRKQPAPV---EDPAEAKK 121
            +      +       D+  +       +K +   +E   KV +    V      A+ KK
Sbjct: 121 NYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKK 180

Query: 122 ----------SKKKAAKEQARLMQAQQQQM-QALSVQ-QPPVSQPAPPAPMATAGVPEQP 169
                     S + AA  + +LM  + Q     ++V    P  +      MA        
Sbjct: 181 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDV-MAKV------ 233

Query: 170 PNQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
             +IL++ NL   T+E ++   F++F PG  +V  V    D AFV FE+   +  A   L
Sbjct: 234 --KILYVRNLMTTTTEEIIEKSFSEFKPG--KVERVKKIRDYAFVHFEDREDAVKAMDEL 289

Query: 229 HGFKITPTHAMKISFAK 245
           +G K      ++++ AK
Sbjct: 290 NG-KELEGSEIEVTLAK 305

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 19/60 (31%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 177 TNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGF 231
           TNL E+  E  L  LF  F     V L  ++        AFV F     +  A   L+GF
Sbjct: 5   TNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGF 64

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 4/59 (6%)

Query: 25 KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
          +  L  IFS++G + D+V     K +G A V F    +A  A+ +  G P    P+ + 
Sbjct: 18 EDELRKIFSKYGDVSDVVVSS--KKKGSAIVEFASKKAAEAAVENECGLP--SNPLLVS 72

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

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNA 66
          V N  Y T  +  DL++    +F ++G++ D+   +   T + RG AFV F +   A +A
Sbjct: 3  VDNLTYRT--TPDDLRR----VFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDA 56

Query: 67 LRSMQGFPFYDKPMRIQ 83
          + +M G     + +R+Q
Sbjct: 57 MDAMDGKELDGRELRVQ 73

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|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 = 19/85 (22%), Positives = 36/85 (42%), Gaps = 13/85 (15%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ---------AFVIFKEIA 61
          TN +YV +++    ++ L   F +FG    + ++K +  R +          FV F   A
Sbjct: 2  TN-LYVGNLNPKVTEEVLCQEFGRFG---PLASVKIMWPRTEEERRRNRNCGFVAFMNRA 57

Query: 62 SATNALRSMQGFPFYDKPMRIQYSK 86
           A  AL  + G       +++ + K
Sbjct: 58 DAERALDELDGKDVMGYELKLGWGK 82

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|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 176 LTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
           L N+ +  +E  +   F +  P  +++ L P+ H+ A VEFE+   +  A L+L+G
Sbjct: 5   LFNVSDTVNEEQIKAFFEKIGPDVRKIELFPD-HEGALVEFESPSDAGKASLSLNG 59

This subfamily corresponds to the RRM4 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 = 71

>gnl|CDD|241146 cd12702, RRM4_PTBP2, RNA recognition motif 4 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 20/77 (25%), Positives = 38/77 (49%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
           PP+  L L+N+P+  +E  L  LF    G  +       H +A ++     ++  A + L
Sbjct: 1   PPSATLHLSNIPQSVTEEDLRTLFANTGGTVKAFKFFQDHKMALLQMSTVEEAIQALIDL 60

Query: 229 HGFKITPTHAMKISFAK 245
           H + +   H +++SF+K
Sbjct: 61  HNYNLGENHHLRVSFSK 77

This subgroup corresponds to the RRM4 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 80

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 6/60 (10%)

Query: 22 TDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKP 79
           DLKK    +FS FG + ++   +    K +G AFV F   A A  A++ + G     +P
Sbjct: 14 ADLKK----LFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRP 69

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

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 3/57 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
          +++ H+S    ++ L  +F ++G+I  I     +  RG A+V  +    A  AL+ +
Sbjct: 5  LWIGHLSKKVTEEDLKNLFEEYGEIQSI---DMIPPRGCAYVCMETRQDAHRALQKL 58

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

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 7/67 (10%)

Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPF 75
          I+  DL+     IF  FG+I  +   +   T + +G  F+ F +   A  AL  + GF  
Sbjct: 10 ITEDDLR----GIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFEL 65

Query: 76 YDKPMRI 82
            +P+++
Sbjct: 66 AGRPIKV 72

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|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 = 38.0 bits (89), Expect = 3e-04
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           +++ NLP   +E  L   F+ F   +EVR+  ++   AFV F+    +A A +A++G  I
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKG-YAFVRFDTHEAAATAIVAVNGTSI 61

Query: 234 TPTHAMKISFAKK 246
                +K S+ K+
Sbjct: 62  N-GQTVKCSWGKE 73

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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLV-PNRHDIA---FVEFENEMQSA 222
           +Q  N+ LFL NL    +E  L   F++F    EV +  P R   +   F++FEN   + 
Sbjct: 3   DQRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAH 62

Query: 223 AAKLALHGFKITPTHAMKISFAK 245
            AKLA+ G K+   + +KI + K
Sbjct: 63  RAKLAMSG-KVLRRNPIKIGYGK 84

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

>gnl|CDD|240879 cd12433, RRM_Yme2p_like, RNA recognition motif in yeast mitochondrial escape protein 2 (Yme2p) and similar proteins

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKP--MRIQYS 85
          LY++F  +G+I DI       +   A V F+ I  A +A   + GF   +    + IQY 
Sbjct: 21 LYSLFRPYGKIKDITPPPPDSLPRYATVTFRRIRGAISAKNCLHGFELNEGKTRLHIQYE 80

Query: 86 K 86
           
Sbjct: 81 P 81

This subfamily corresponds to the RRM of Yme2p, also termed protein RNA12, an inner mitochondrial membrane protein that plays a critical role in mitochondrial DNA transactions. It may serve as a mediator of nucleoid structure and number in mitochondria of the yeast Saccharomyces cerevisiae. Yme2p contains an exonuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal domain. . Length = 86

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 3/78 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRSM 70
          +YV +++       L  +F ++G I+D+   +   T + RG A+V F+++  A +AL  +
Sbjct: 3  LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 71 QGFPFYDKPMRIQYSKTD 88
              F  + + IQ+++ D
Sbjct: 63 DRTRFLGREIEIQFAQGD 80

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRL--VPNRHDIAFVEFENEMQSAAAKLAL 228
           N+IL++ NLP + S   L  LF ++   +++R+         AFV +E+   +  A   L
Sbjct: 2   NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 229 HGF 231
            GF
Sbjct: 62  SGF 64

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

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

 Score = 40.9 bits (96), Expect = 4e-04
 Identities = 28/159 (17%), Positives = 53/159 (33%), Gaps = 11/159 (6%)

Query: 19  ISSTDLKKSLYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASATNALRSMQGFPFY 76
           ++   L++    +FS+ G+I     +  +    RG  FV F     A  A+  M G    
Sbjct: 297 VTDEKLRE----LFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLG 352

Query: 77  DKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQA 136
            KP+ +  ++      + ++  FM+   ++R+ P     P      +     +  +    
Sbjct: 353 GKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMG--SPMGGAMGQPPYYGQGPQQQFN 410

Query: 137 QQQQMQALSVQQPPVSQP-APPAPMATAGVPEQ--PPNQ 172
            Q          P    P  P  P   A +     P   
Sbjct: 411 GQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRN 449

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

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 7/56 (12%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENE--MQSA 222
           LF+  L  +T+E  L   F ++   K +RLV ++        AF+EFE+E  M++A
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59

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|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 37.1 bits (86), Expect = 6e-04
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          VYV +I     +  L  +F  FG I++    +    RG AFV       A  A+  +QGF
Sbjct: 3  VYVGNIPPYTTQADLIPLFQNFGYILEF---RHQPDRGFAFVKLDTHEQAAMAIVQLQGF 59

Query: 74 PFYDKPMRIQYSK 86
          P + +P+R  + K
Sbjct: 60 PVHGRPLRCGWGK 72

This subfamily corresponds to the RRM3 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. 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 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 25 KKSLYAIFSQFGQI--MDIVALK-TLKMRGQAFVIFKEIASATNALRS 69
          ++ L  +FSQFG++    IV  K T   +G AFV FK   SA   L +
Sbjct: 14 EEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

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

 Score = 38.5 bits (89), Expect = 8e-04
 Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 4/64 (6%)

Query: 22  TDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
           TD   SL   F+ FG ++D   IV  +T + RG  FV F +  +AT A+  M G     +
Sbjct: 46  TD-DASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGR 104

Query: 79  PMRI 82
            +R+
Sbjct: 105 HIRV 108

Length = 144

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

 Score = 37.1 bits (87), Expect = 8e-04
 Identities = 21/74 (28%), Positives = 29/74 (39%), Gaps = 10/74 (13%)

Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGF--KEVRLVPNR-----HDIAFVEF---ENEM 219
           P   L L  L   T+E  +    +       K+VRL+ ++        AFVEF   E+  
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 220 QSAAAKLALHGFKI 233
           Q   A   L  F I
Sbjct: 61  QWMDALNNLDPFVI 74

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

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
          ++V  +S      +L+A FS F    D   +   K+ + RG  FV F+    A NA+  M
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 71 QGFPFYDKPMRIQY 84
           G     +P+R  +
Sbjct: 62 NGKWLGSRPIRCNW 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|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 = 36.6 bits (85), Expect = 0.001
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
          VYV+ I     ++ L A+FS  GQ++D  +       +R  AF+ F +   A  AL S+ 
Sbjct: 5  VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRF-AFIEFTDEEGARAAL-SLS 62

Query: 72 GFPFYDKPMRIQYSKT 87
          G      P+R+  SKT
Sbjct: 63 GTMLGFYPVRVLPSKT 78

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

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 5/75 (6%)

Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRS 69
          FVY  ++     +  L+ +FS FG + +   I  L T K +G  FV       A +A+ S
Sbjct: 5  FVY--NLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 70 MQGFPFYDKPMRIQY 84
          + G+    + +++ +
Sbjct: 63 LNGYRLGGRVLQVSF 77

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

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 16 VTHISSTDLKKSLYAIFSQFGQIMDI-VAL--KTLKMRGQAFVIFKEIASATNALRSMQG 72
          VT++S    +  L  +F  FG I  + +A   +T + RG AFV F     A  A+  + G
Sbjct: 4  VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 73 FPFYDKPMRIQYSK 86
          F + +  + ++++K
Sbjct: 64 FGYDNLILSVEWAK 77

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

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 9/79 (11%)

Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIA----FVEFEN----EMQS 221
           PN+I F+  +P +T+E  L   F++F   K+V+++ +R  ++    FV FE     E   
Sbjct: 2   PNRI-FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKIL 60

Query: 222 AAAKLALHGFKITPTHAMK 240
           A   L   G K+    A++
Sbjct: 61  AMGNLNFRGKKLNIGPAIR 79

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 17/56 (30%), Positives = 33/56 (58%), Gaps = 3/56 (5%)

Query: 30 AIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
           +FSQ+G+I+DI  +   KT K +G AF+ +++  S   A+ ++ G     + +R+
Sbjct: 28 CVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRV 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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKM----RGQAFVIFKEIASATNALRS 69
          ++V  ++    K  L  IFS +G + D V L   +     RG A+V F+    A  A++ 
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKD-VDLPIDREVNLPRGYAYVEFESPEDAEKAIKH 59

Query: 70 MQG 72
          M G
Sbjct: 60 MDG 62

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

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 14/80 (17%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ-------AFVIFKEIASATNA 66
          +YV ++  T     L   FSQ G++      K ++M G        AFV F E  S  NA
Sbjct: 7  IYVGNLDPTTTADQLLEFFSQAGEV------KYVRMAGDETQPTRYAFVEFAEQTSVINA 60

Query: 67 LRSMQGFPFYDKPMRIQYSK 86
          L+ + G  F  +P+++ +S 
Sbjct: 61 LK-LNGAMFGGRPLKVNHSN 79

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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 19/62 (30%), Positives = 31/62 (50%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
          T  +++ ++  T     L   F +FG+I+DI   K       AF+ + +IAS   A+R M
Sbjct: 2  TRTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKM 61

Query: 71 QG 72
           G
Sbjct: 62 DG 63

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>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 = 35.7 bits (83), Expect = 0.002
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          V+V  +     +  L ++F  FG   +IV +K    +G  FV F   A+A  A++ +QG 
Sbjct: 4  VFVGGLDPAVTEDELRSLFGPFG---EIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGT 60

Query: 74 PFYDKPMRIQY 84
                +R+ +
Sbjct: 61 IIGGSRIRLSW 71

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|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 = 35.6 bits (83), Expect = 0.002
 Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 28 LYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQG 72
          + A+F ++G I ++  ++   T + +G AFV F     A  A+ ++ G
Sbjct: 16 VRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 63

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 9/76 (11%)

Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDI-VAL--KTLKMRGQAFVIFKEIASATNA 66
          V N  Y       DL+K    +FS+FG++ ++ VA+  K+ K +G A+V+F +   A  A
Sbjct: 7  VRNLPYSC--KEDDLEK----LFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60

Query: 67 LRSMQGFPFYDKPMRI 82
           + + G  F  + + I
Sbjct: 61 YKELDGKVFQGRLIHI 76

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 6/48 (12%)

Query: 31 IFSQFGQI--MDIVALKTLKMRGQ----AFVIFKEIASATNALRSMQG 72
          +FS++G+I   D +  K+  ++GQ     FV F+    A  AL+S+ G
Sbjct: 19 LFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNG 66

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 4/64 (6%)

Query: 26 KSLYAIFSQFGQIMDIVAL----KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
          K LY  FS FG I+    +     T   +G AF+ +    ++  A+ +M G    ++P+ 
Sbjct: 16 KLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPIT 75

Query: 82 IQYS 85
          + Y+
Sbjct: 76 VSYA 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|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 5/61 (8%)

Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY--DKPMRIQYS 85
          L A+ S FG++     +  L+ + QA V    + SA + +      P     + + IQYS
Sbjct: 16 LIALVSPFGKV---TNVLLLRGKNQALVEMDSVESAKSMVDYYLTVPALIRGRRVYIQYS 72

Query: 86 K 86
           
Sbjct: 73 N 73

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

>gnl|CDD|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 = 0.002
 Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 9  CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATN 65
          C+  F    + +  DL++    +FS++G +  +  +   +T + RG AFV F+ I  +  
Sbjct: 1  CLGVFGLSLYTTERDLRE----VFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKE 56

Query: 66 ALRSMQGFPFYDKPMRIQYSKT 87
          A+    G     + +R+ YS T
Sbjct: 57 AMEHANGMELDGRRIRVDYSIT 78

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|241137 cd12693, RRM2_PTBP1_like, RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 10/87 (11%)

Query: 2  NIILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIA 61
          N +L  + V N  Y     + D+   L+ IFS+FG ++ I+   T   + QA + F +  
Sbjct: 1  NTVL-RVIVENMTYPV---TLDV---LHQIFSKFGTVLKIITF-TKNNQFQALIQFADAV 52

Query: 62 SATNALRSMQGFPFYDK--PMRIQYSK 86
          SA  A  S+ G   Y+    +RI YSK
Sbjct: 53 SAQAAKLSLDGQNIYNGCCTLRIDYSK 79

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 96

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
          TN V++  +  +  ++ L   FS++G ++ +V     + RGQA V F ++ +A  A+  M
Sbjct: 7  TNCVWLDGLDESVTEQYLTRHFSRYGPVVHVV---IDRQRGQALVFFDKVEAAQAAVNEM 63

Query: 71 QGFPFYDKPMRIQY 84
          +G     + +++ +
Sbjct: 64 KGRKLGGRKLQVDF 77

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

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

 Score = 35.1 bits (81), Expect = 0.003
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 5/71 (7%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          +YV        + ++  IFS +G + ++  +        AFV F+ + SA  A  S+ G 
Sbjct: 2  LYVRPFPPDTSESAIREIFSPYGAVKEVKMISNF-----AFVEFESLESAIRAKDSVHGK 56

Query: 74 PFYDKPMRIQY 84
             + P+ + Y
Sbjct: 57 VLNNNPLYVTY 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|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 35.1 bits (81), Expect = 0.003
 Identities = 21/61 (34%), Positives = 27/61 (44%), Gaps = 4/61 (6%)

Query: 174 LFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK 232
           LF+    P  T E  +  LF  F       +   R   AFVEFE+   +  A  ALHG +
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI---RKTFAFVEFEDSEDATKALEALHGSR 58

Query: 233 I 233
           I
Sbjct: 59  I 59

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

 Score = 35.2 bits (82), Expect = 0.003
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVR---LVPNRHD-IAFVEFENEMQSAAAKLAL 228
            L++TN P    +  +  LF Q+     +R   L  N+     +V+F +  +SAAA +AL
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSP-ESAAAAVAL 60

Query: 229 HGFKITPTHAM--KIS 242
              K+   + +  KIS
Sbjct: 61  LNGKLGEGYKLVVKIS 76

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
          T +V+   ++   LKK+    FS FG I++I      K +   FV F+++ SA  A+  +
Sbjct: 6  TLYVHGYGLTEEILKKA----FSPFGNIINI---SMEKEKNCGFVTFEKMESADRAIAEL 58

Query: 71 QGFPFYDKPMRIQYSK 86
           G       +++  ++
Sbjct: 59 NGTTVQGVQLKVSLAR 74

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 3/48 (6%)

Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
          ++SL   FS++G+++D V +K   T + RG  FV F + +S    L +
Sbjct: 12 EESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 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|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
           LF+ NLP + +E     LF+++    EV L        F+  +    +  AK  L G
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFL-NKEKGFGFIRLDTRTNAEKAKAELDG 59

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

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 15/72 (20%)

Query: 22 TDLKKSLYAIFSQFGQIMDIVALKTL---------KMRGQAFVIFKEIASATNALRSMQG 72
          TD  + L    ++ G    +V +K++         K +G A+V F   A+A      ++G
Sbjct: 11 TD--EDLEGALAEAG----VVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEG 64

Query: 73 FPFYDKPMRIQY 84
            F  K   + Y
Sbjct: 65 REFNGKKCVVTY 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|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 11/68 (16%)

Query: 7  HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ--AFVIFKEIASAT 64
          H+ V N      +S    ++ L  +F ++G + D+V        G+   FV +  I  A 
Sbjct: 3  HLVVANGGLGNGVS----REELLRVFEKYGTVEDLVMP-----PGKPYCFVSYSSIEDAA 53

Query: 65 NALRSMQG 72
           A  ++ G
Sbjct: 54 AAYDALNG 61

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

>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 13/87 (14%)

Query: 12 NFVYVTHISSTD-----LKKSLYAIFSQFGQIMDIVALKTLKMRGQ------AFVIFKEI 60
          N VYV  +         LKK  Y  F Q+G+I  IV  +     G       A+V +   
Sbjct: 6  NLVYVVGLPPRLADEEVLKKPEY--FGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRK 63

Query: 61 ASATNALRSMQGFPFYDKPMRIQYSKT 87
            A   ++++ GF    + ++  +  T
Sbjct: 64 EDALRCIQAVDGFYLDGRLLKASFGTT 90

This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T. Length = 98

>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding protein with multiple splicing (RBP-MS)

 Score = 35.0 bits (80), Expect = 0.004
 Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRL-VPNRHDIAFVEFENEMQSAAAKLALHG 230
           + LF++ LP +     L +LF  F G++   + + ++  + FV F++  ++ AAK AL+G
Sbjct: 2   RTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNG 61

Query: 231 FKITP 235
            +  P
Sbjct: 62  IRFDP 66

This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. . Length = 76

>gnl|CDD|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 4/64 (6%)

Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK--PMRIQYS 85
          +Y I +  G+++ IV  +  K   QA V F  + SA  A  ++ G   Y     ++I+Y+
Sbjct: 20 IYTICNPHGKVLRIVIFR--KNGVQAMVEFDSVDSAQRAKAALNGADIYAGCCTLKIEYA 77

Query: 86 KTDS 89
          K D 
Sbjct: 78 KPDR 81

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both nuclear and cytoplasmic roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 86

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

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 5/63 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           L++ NLP   +E  L  LF QF      R++ +R         FVE E   ++ AA   L
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 229 HGF 231
           +G 
Sbjct: 62  NGT 64

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	246
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
KOG0148|consensus	321		100.0
KOG0117|consensus	506		100.0
KOG4206|consensus	221		99.98
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.97
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.97
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.97
KOG0131|consensus	203		99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
KOG0144|consensus	510		99.96
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.96
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.96
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
KOG0145|consensus	360		99.95
KOG0127|consensus	678		99.95
KOG0127|consensus	678		99.94
KOG0109|consensus	346		99.94
KOG0145|consensus	360		99.93
KOG0110|consensus	725		99.92
KOG0123|consensus	369		99.92
KOG0124|consensus	544		99.91
KOG0147|consensus	549		99.91
KOG0144|consensus	510		99.9
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.89
KOG0146|consensus	371		99.89
KOG0123|consensus	369		99.87
KOG0105|consensus	241		99.86
KOG1457|consensus	284		99.86
KOG1190|consensus	492		99.84
KOG0148|consensus	321		99.84
KOG0147|consensus	549		99.83
KOG0110|consensus	725		99.81
KOG1190|consensus	492		99.8
KOG0124|consensus	544		99.78
KOG1548|consensus	382		99.78
KOG4205|consensus	311		99.77
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.77
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.75
KOG0106|consensus	216		99.74
KOG4212|consensus	608		99.71
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.7
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.7
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.67
PLN03120	260	nucleic acid binding protein; Provisional	99.66
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.66
KOG1456|consensus	494		99.66
KOG1456|consensus	494		99.65
KOG0107|consensus	195		99.65
KOG0114|consensus	124		99.64
KOG0114|consensus	124		99.64
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.64
KOG0121|consensus	153		99.63
KOG0120|consensus	500		99.63
PLN03121	243	nucleic acid binding protein; Provisional	99.62
PLN03120	260	nucleic acid binding protein; Provisional	99.6
KOG0125|consensus	376		99.6
KOG0121|consensus	153		99.59
KOG0107|consensus	195		99.59
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.59
KOG4211|consensus	510		99.59
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.57
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.57
KOG0122|consensus	270		99.57
KOG0111|consensus	298		99.57
KOG0122|consensus	270		99.57
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.55
PLN03213	759	repressor of silencing 3; Provisional	99.54
KOG4207|consensus	256		99.53
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.53
KOG0149|consensus	247		99.52
KOG0125|consensus	376		99.52
KOG0126|consensus	219		99.52
KOG4207|consensus	256		99.51
smart00362	72	RRM_2 RNA recognition motif.	99.51
KOG0113|consensus	335		99.5
KOG4212|consensus	608		99.5
smart00362	72	RRM_2 RNA recognition motif.	99.5
KOG4206|consensus	221		99.49
PLN03121	243	nucleic acid binding protein; Provisional	99.49
KOG0130|consensus	170		99.48
PLN03213	759	repressor of silencing 3; Provisional	99.48
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.45
KOG0113|consensus	335		99.45
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.42
KOG0130|consensus	170		99.42
KOG0105|consensus	241		99.41
KOG0111|consensus	298		99.41
smart00360	71	RRM RNA recognition motif.	99.41
smart00360	71	RRM RNA recognition motif.	99.41
KOG0117|consensus	506		99.39
KOG0108|consensus	435		99.38
KOG0131|consensus	203		99.37
KOG0108|consensus	435		99.33
KOG0126|consensus	219		99.32
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.32
smart00361	70	RRM_1 RNA recognition motif.	99.3
KOG0112|consensus	975		99.29
KOG0149|consensus	247		99.28
KOG0109|consensus	346		99.24
KOG1365|consensus	508		99.24
KOG0129|consensus	520		99.24
smart00361	70	RRM_1 RNA recognition motif.	99.21
KOG0132|consensus	894		99.2
KOG0120|consensus	500		99.2
KOG0132|consensus	894		99.16
KOG4454|consensus	267		99.12
KOG0415|consensus	479		99.12
KOG0153|consensus	377		99.09
KOG0146|consensus	371		99.09
KOG0153|consensus	377		99.09
KOG1457|consensus	284		99.07
KOG0415|consensus	479		99.06
KOG4208|consensus	214		99.04
KOG4660|consensus	549		98.98
KOG4676|consensus	479		98.97
KOG4660|consensus	549		98.94
KOG4661|consensus	940		98.92
KOG4661|consensus	940		98.89
KOG4210|consensus	285		98.87
KOG0226|consensus	290		98.87
KOG4208|consensus	214		98.87
KOG0151|consensus	877		98.85
KOG2193|consensus	584		98.83
KOG0533|consensus	243		98.83
KOG4211|consensus	510		98.78
KOG0128|consensus	881		98.76
KOG0533|consensus	243		98.74
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.71
KOG4205|consensus	311		98.71
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.66
KOG4454|consensus	267		98.62
KOG0151|consensus	877		98.6
KOG1548|consensus	382		98.58
KOG0116|consensus	419		98.57
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.5
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.48
KOG0106|consensus	216		98.46
KOG0226|consensus	290		98.41
KOG4209|consensus	231		98.41
KOG4209|consensus	231		98.37
KOG0116|consensus	419		98.35
KOG4307|consensus	944		98.3
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.3
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.07
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.98
KOG1365|consensus	508		97.91
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.88
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.8
KOG2314|consensus	698		97.79
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.79
KOG2314|consensus	698		97.78
KOG1995|consensus	351		97.77
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.76
KOG0115|consensus	275		97.74
KOG1995|consensus	351		97.73
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.69
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.66
KOG4307|consensus	944		97.65
KOG0128|consensus	881		97.6
KOG2202|consensus	260		97.58
KOG3152|consensus	278		97.58
KOG2202|consensus	260		97.57
KOG4210|consensus	285		97.55
KOG1855|consensus	484		97.55
KOG1855|consensus	484		97.53
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.42
KOG1996|consensus	378		97.41
KOG4676|consensus	479		97.38
KOG1996|consensus	378		97.35
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.23
KOG3152|consensus	278		97.21
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	97.21
KOG2416|consensus	718		97.18
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.11
KOG2416|consensus	718		97.04
KOG4574|consensus	1007		96.8
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.8
KOG0112|consensus	975		96.73
KOG0115|consensus	275		96.73
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.61
KOG0129|consensus	520		96.58
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.46
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.42
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.17
KOG0804|consensus	493		96.06
KOG2193|consensus	584		96.01
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.98
KOG4849|consensus	498		95.88
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.51
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.37
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.36
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	95.27
KOG2068|consensus	327		94.98
KOG4849|consensus	498		94.89
KOG0804|consensus	493		94.86
KOG2591|consensus	684		94.77
KOG2068|consensus	327		94.75
KOG4285|consensus	350		94.74
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.48
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.42
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.4
KOG2253|consensus	668		94.2
KOG2253|consensus	668		93.67
KOG2135|consensus	526		93.66
KOG4574|consensus	1007		93.16
KOG4285|consensus	350		92.72
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	92.3
KOG2135|consensus	526		92.24
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	92.21
KOG2591|consensus	684		90.88
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	87.65
KOG2318|consensus	650		84.95
KOG4483|consensus	528		84.63
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	83.22
KOG2318|consensus	650		82.7
KOG4019|consensus	193		82.07

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=1.1e-34  Score=242.56  Aligned_cols=163  Identities=20%  Similarity=0.382  Sum_probs=145.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.++++++|+++|+.||+|++|+|+++.   +++|||||+|.++++|.+|++.||+..+.+++|+|.
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            45578999999999999999999999999999999998764   788999999999999999999999999999999999


Q ss_pred             EccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCC
Q psy4057          84 YSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATA  163 (246)
Q Consensus        84 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (246)
                      ++....                                                                          
T Consensus       183 ~a~p~~--------------------------------------------------------------------------  188 (346)
T TIGR01659       183 YARPGG--------------------------------------------------------------------------  188 (346)
T ss_pred             cccccc--------------------------------------------------------------------------
Confidence            974321                                                                          


Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCC-CC
Q psy4057         164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITP-TH  237 (246)
Q Consensus       164 ~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~-g~  237 (246)
                         .....++|||+|||.++|+++|+++|++||.|+.++++.++     ++||||+|.+.++|.+|++.||+..+.+ ++
T Consensus       189 ---~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~  265 (346)
T TIGR01659       189 ---ESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQ  265 (346)
T ss_pred             ---cccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCce
Confidence               11135679999999999999999999999999999999875     4899999999999999999999999873 37


Q ss_pred             ceEEEeecC
Q psy4057         238 AMKISFAKK  246 (246)
Q Consensus       238 ~l~v~~ak~  246 (246)
                      +|+|.||+.
T Consensus       266 ~l~V~~a~~  274 (346)
T TIGR01659       266 PLTVRLAEE  274 (346)
T ss_pred             eEEEEECCc
Confidence            899999863

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).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=1.7e-34  Score=245.54  Aligned_cols=234  Identities=18%  Similarity=0.301  Sum_probs=155.0

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      +..+|||+|||.++++++|+++|++||+|.+|+++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.++.
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            57899999999999999999999999999999998764   789999999999999999999999999999999999986


Q ss_pred             CCccccccccCcccccccccc----------------C-CCCCCC-ChhHHhhhhh--hhHHHHHHHHHHHHHHHhcc--
Q psy4057          87 TDSDVISKIKGTFMERPKKVR----------------K-QPAPVE-DPAEAKKSKK--KAAKEQARLMQAQQQQMQAL--  144 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~----------------~-~~~~~~-~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~--  144 (246)
                      +...... ....++.+....-                . ....+. .....+....  ...+.+..++..........  
T Consensus        82 ~~~~~~~-~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~  160 (352)
T TIGR01661        82 PSSDSIK-GANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCT  160 (352)
T ss_pred             ccccccc-cceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCc
Confidence            5432111 1111111111000                0 000000 0111111111  12233333332111000000  


Q ss_pred             -----ccc-CCC------------------------------------C-----------------------------CC
Q psy4057         145 -----SVQ-QPP------------------------------------V-----------------------------SQ  153 (246)
Q Consensus       145 -----~~~-~~~------------------------------------~-----------------------------~~  153 (246)
                           .+. .+.                                    .                             ..
T Consensus       161 ~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (352)
T TIGR01661       161 EPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHA  240 (352)
T ss_pred             eeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccc
Confidence                 000 000                                    0                             00


Q ss_pred             CCCCCCCC-----------CCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCC
Q psy4057         154 PAPPAPMA-----------TAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFEN  217 (246)
Q Consensus       154 ~~~~~~~~-----------~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~  217 (246)
                      +....+..           .........+.+|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+
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            00000000           0000012234579999999999999999999999999999999976     6999999999


Q ss_pred             HHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         218 EMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       218 ~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .++|..|+..|||+.|+ |+.|+|+|+.
T Consensus       321 ~~~A~~Ai~~lnG~~~~-gr~i~V~~~~  347 (352)
T TIGR01661       321 YDEAAMAILSLNGYTLG-NRVLQVSFKT  347 (352)
T ss_pred             HHHHHHHHHHhCCCEEC-CeEEEEEEcc
Confidence            99999999999999999 9999999963

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=100.00  E-value=1.1e-32  Score=242.02  Aligned_cols=170  Identities=18%  Similarity=0.247  Sum_probs=144.5

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ...++|||+||++++++++|+++|++||.|.+|.++.+.   +++|||||+|.+.++|++|++.|||..+.|++|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            456899999999999999999999999999999998764   78999999999999999999999999999999999864


Q ss_pred             cCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCC
Q psy4057          86 KTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV  165 (246)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (246)
                      .......                                               ....                   ...
T Consensus       185 ~~~p~a~-----------------------------------------------~~~~-------------------~~~  198 (612)
T TIGR01645       185 SNMPQAQ-----------------------------------------------PIID-------------------MVQ  198 (612)
T ss_pred             ccccccc-----------------------------------------------cccc-------------------ccc
Confidence            2211000                                               0000                   000


Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ......++|||+|||.++++++|+++|+.||.|.++++.++.     +|||||+|.+.++|..|+..|||+.++ |+.|+
T Consensus       199 ~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elg-Gr~Lr  277 (612)
T TIGR01645       199 EEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLG-GQYLR  277 (612)
T ss_pred             ccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeC-CeEEE
Confidence            112246789999999999999999999999999999999864     689999999999999999999999999 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.+|.
T Consensus       278 V~kAi  282 (612)
T TIGR01645       278 VGKCV  282 (612)
T ss_pred             EEecC
Confidence            99863

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148|consensus

Probab=100.00  E-value=1e-32  Score=213.32  Aligned_cols=173  Identities=23%  Similarity=0.392  Sum_probs=150.6

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      +--+||+.|..+++-++|++-|.+||+|.+++++||.   ++||||||.|-+.++|++||..|||.=|.+|.|+-.||.+
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            4457889999999999999999999999999999976   8999999999999999999999999999999999999977


Q ss_pred             CccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCC
Q psy4057          88 DSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE  167 (246)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (246)
                      +........-+|.                                       ...                      ...
T Consensus       142 Kp~e~n~~~ltfd---------------------------------------eV~----------------------NQs  160 (321)
T KOG0148|consen  142 KPSEMNGKPLTFD---------------------------------------EVY----------------------NQS  160 (321)
T ss_pred             CccccCCCCccHH---------------------------------------HHh----------------------ccC
Confidence            7521111000000                                       000                      013


Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      .+.++++||+|++..+|+++|++.|++||.|.+||+.++. ||+||.|.+.|.|.+||..|||++|+ |..++++|+|+
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q-GYaFVrF~tkEaAahAIv~mNntei~-G~~VkCsWGKe  237 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ-GYAFVRFETKEAAAHAIVQMNNTEIG-GQLVRCSWGKE  237 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc-ceEEEEecchhhHHHHHHHhcCceeC-ceEEEEecccc
Confidence            5579999999999999999999999999999999999998 89999999999999999999999999 99999999985

>KOG0117|consensus

Probab=100.00  E-value=1.7e-32  Score=225.26  Aligned_cols=228  Identities=21%  Similarity=0.268  Sum_probs=161.7

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCcc-CCeeEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPF-YDKPMRIQ   83 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~-~g~~l~v~   83 (246)
                      .+.++.|||++||.|+.|++|..+|++.|+|.+++++.+   +.+||||||+|++.+.|++|++.||+..| .|+.|.|+
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            467899999999999999999999999999999999987   38999999999999999999999999998 79999999


Q ss_pred             EccCCccccccccCcccccccccc---------C-----CCCCCCChhH--HhhhhhhhHHHHHHHHHHHH--HHHhccc
Q psy4057          84 YSKTDSDVISKIKGTFMERPKKVR---------K-----QPAPVEDPAE--AKKSKKKAAKEQARLMQAQQ--QQMQALS  145 (246)
Q Consensus        84 ~a~~~~~~~~~~~~~~~~~~~~~~---------~-----~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~--~~~~~~~  145 (246)
                      .+..+.....   |...++.++.+         .     ....+.....  .+.-.+.-.+++..++....  +....+-
T Consensus       160 ~Svan~RLFi---G~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klw  236 (506)
T KOG0117|consen  160 VSVANCRLFI---GNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLW  236 (506)
T ss_pred             EeeecceeEe---ccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeec
Confidence            9866543222   11111111110         0     0011111111  11112222222222222111  1111122


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHH
Q psy4057         146 VQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK  225 (246)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al  225 (246)
                      ..++.+.+.++-..+..+   ....-..|||+||+.++|+|.|+.+|++||.|.+|+.++|   ||||.|.++++|.+||
T Consensus       237 gn~~tVdWAep~~e~ded---~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD---YaFVHf~eR~davkAm  310 (506)
T KOG0117|consen  237 GNAITVDWAEPEEEPDED---TMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD---YAFVHFAEREDAVKAM  310 (506)
T ss_pred             CCcceeeccCcccCCChh---hhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc---eeEEeecchHHHHHHH
Confidence            233334444432222112   2234789999999999999999999999999999999866   9999999999999999


Q ss_pred             HHhCCCccCCCCceEEEeec
Q psy4057         226 LALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       226 ~~l~g~~i~~g~~l~v~~ak  245 (246)
                      +.|||++|+ |..|.|.+||
T Consensus       311 ~~~ngkeld-G~~iEvtLAK  329 (506)
T KOG0117|consen  311 KETNGKELD-GSPIEVTLAK  329 (506)
T ss_pred             HHhcCceec-CceEEEEecC
Confidence            999999999 9999999998

>KOG4206|consensus

Probab=99.98  E-value=3.8e-31  Score=200.86  Aligned_cols=214  Identities=50%  Similarity=0.794  Sum_probs=174.4

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHH----HhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeE
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYA----IFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPM   80 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~----~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (246)
                      +....|+.||||.||++....++|+.    +|++||.|.+|...++.+.+|.|||.|.+.+.|..|+..|+|..+.|++|
T Consensus         3 ~~~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~m   82 (221)
T KOG4206|consen    3 PMSVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPM   82 (221)
T ss_pred             ccccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchh
Confidence            45678888999998888777777666    99999999999999999999999999999999999999999999999999


Q ss_pred             EEEEccCCccccccccCccccccccccC-CCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCC
Q psy4057          81 RIQYSKTDSDVISKIKGTFMERPKKVRK-QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAP  159 (246)
Q Consensus        81 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (246)
                      +|+||+.+++++.+..++++++.++... +........                      ..++.....+.  ...++  
T Consensus        83 riqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~----------------------~~ng~~~~~~~--~~~p~--  136 (221)
T KOG4206|consen   83 RIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPL----------------------DTNGHFYNMNR--MNLPP--  136 (221)
T ss_pred             heecccCccchhhccCceeccccCccccccccccCCcc----------------------ccccccccccc--ccCCC--
Confidence            9999999999999988888877766544 222111000                      00000000000  00000  


Q ss_pred             CCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         160 MATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       160 ~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                       +. .....+++.+||+.|||.+++.+.|..+|++|+..+.++++...++.|||+|.+...|..|.+.|+|..|-....|
T Consensus       137 -p~-~~~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m  214 (221)
T KOG4206|consen  137 -PF-LAQMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTM  214 (221)
T ss_pred             -Cc-cccCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceE
Confidence             00 1345778999999999999999999999999999999999999999999999999999999999999999878999


Q ss_pred             EEEeecC
Q psy4057         240 KISFAKK  246 (246)
Q Consensus       240 ~v~~ak~  246 (246)
                      +|.||+|
T Consensus       215 ~i~~a~K  221 (221)
T KOG4206|consen  215 QITFAKK  221 (221)
T ss_pred             EecccCC
Confidence            9999986

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.97  E-value=1.7e-30  Score=228.37  Aligned_cols=195  Identities=20%  Similarity=0.311  Sum_probs=147.8

Q ss_pred             CCCCcEEEecCCCh-hhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           8 ICVTNFVYVTHISS-TDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         8 ~~~~~~l~V~nl~~-~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      .+++.+|||+||+. .+++++|+++|+.||.|.+|+++++  .+|+|||+|.+.++|..|++.|||..+.|++|+|.+++
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~--~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~  349 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN--KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSK  349 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            45789999999997 6999999999999999999999886  47999999999999999999999999999999999986


Q ss_pred             CCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                      ......... +...+..     ....+....                      ....+          ..+  .......
T Consensus       350 ~~~~~~~~~-~~~~~~~-----~~~~d~~~~----------------------~~~r~----------~~~--~~~~~~~  389 (481)
T TIGR01649       350 QQNVQPPRE-GQLDDGL-----TSYKDYSSS----------------------RNHRF----------KKP--GSANKNN  389 (481)
T ss_pred             cccccCCCC-CcCcCCC-----cccccccCC----------------------ccccC----------CCc--ccccccc
Confidence            553211100 0000000     000000000                      00000          000  0000112


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCC--ceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCC----
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPG--FKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTH----  237 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~--i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~----  237 (246)
                      ..+++.+|||+|||.++++++|+++|+.||.  |..+++.++.   +++|||+|.+.++|..|+..|||+.|. ++    
T Consensus       390 ~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~-~~~~~~  468 (481)
T TIGR01649       390 IQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLN-EPNGSA  468 (481)
T ss_pred             cCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHHHhcCCccC-CCCCCc
Confidence            3568999999999999999999999999998  8889887754   689999999999999999999999999 65    


Q ss_pred             --ceEEEeec
Q psy4057         238 --AMKISFAK  245 (246)
Q Consensus       238 --~l~v~~ak  245 (246)
                        .|+|+|||
T Consensus       469 ~~~lkv~fs~  478 (481)
T TIGR01649       469 PYHLKVSFST  478 (481)
T ss_pred             cceEEEEecc
Confidence              59999997

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).

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.97  E-value=8.3e-31  Score=230.12  Aligned_cols=171  Identities=22%  Similarity=0.428  Sum_probs=145.5

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..+.++|||+|||..+++++|+++|++||.|.+|.++.+.   +++|||||+|.+.++|.+|+. |+|..+.|++|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            3467899999999999999999999999999999998764   789999999999999999997 999999999999998


Q ss_pred             ccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCC
Q psy4057          85 SKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAG  164 (246)
Q Consensus        85 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (246)
                      +........                                              ....                   ..
T Consensus       165 ~~~~~~~~~----------------------------------------------~~~~-------------------~~  179 (457)
T TIGR01622       165 SQAEKNRAA----------------------------------------------KAAT-------------------HQ  179 (457)
T ss_pred             cchhhhhhh----------------------------------------------hccc-------------------cc
Confidence            643321000                                              0000                   00


Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       165 ~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                      ....+..++|||+|||..+|+++|+++|+.||.|..|.++.+.     +|||||+|.+.++|..|+..|||..|. |++|
T Consensus       180 ~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~-g~~i  258 (457)
T TIGR01622       180 PGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELA-GRPI  258 (457)
T ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEEC-CEEE
Confidence            0112347899999999999999999999999999999999754     489999999999999999999999999 9999


Q ss_pred             EEEeec
Q psy4057         240 KISFAK  245 (246)
Q Consensus       240 ~v~~ak  245 (246)
                      +|.||+
T Consensus       259 ~v~~a~  264 (457)
T TIGR01622       259 KVGYAQ  264 (457)
T ss_pred             EEEEcc
Confidence            999975

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.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.97  E-value=2.2e-30  Score=227.70  Aligned_cols=168  Identities=20%  Similarity=0.212  Sum_probs=140.6

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHh--cCCccCCeeEEEEEccC
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM--QGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l--ng~~~~g~~l~v~~a~~   87 (246)
                      |+++|||+|||.++++++|+++|++||.|.+|.+++   +++||||+|.+.++|++|+..+  ++..+.|++|+|.|+..
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~---~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~   77 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP---GKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTS   77 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC---CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCC
Confidence            789999999999999999999999999999998876   5799999999999999999974  78999999999999854


Q ss_pred             CccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCC
Q psy4057          88 DSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE  167 (246)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (246)
                      +....  ...                                            ...                   ....
T Consensus        78 ~~~~~--~~~--------------------------------------------~~~-------------------~~~~   92 (481)
T TIGR01649        78 QEIKR--DGN--------------------------------------------SDF-------------------DSAG   92 (481)
T ss_pred             ccccc--CCC--------------------------------------------Ccc-------------------cCCC
Confidence            42100  000                                            000                   0001


Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCc-cEEEEEeCCHHHHHHHHHHhCCCccCCC-CceEEEeec
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-DIAFVEFENEMQSAAAKLALHGFKITPT-HAMKISFAK  245 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~-g~afV~f~~~~~A~~Al~~l~g~~i~~g-~~l~v~~ak  245 (246)
                      .....+|+|+||+..+|+++|+++|+.||.|.+|.+.+++. ++|||+|.+.++|.+|++.|||..|.+| ++|+|.|||
T Consensus        93 ~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk  172 (481)
T TIGR01649        93 PNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAK  172 (481)
T ss_pred             CCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEec
Confidence            11245789999999999999999999999999999988763 6999999999999999999999999743 689999987

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.97  E-value=2.9e-30  Score=226.53  Aligned_cols=221  Identities=18%  Similarity=0.253  Sum_probs=150.5

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccC-CeeEEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFY-DKPMRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~-g~~l~v~~a~~   87 (246)
                      .++|||+|||.+++|++|+++|++||.|.++++++|.  +++|||||+|.+.++|++|++.||+..+. |+.|.|..+..
T Consensus        58 ~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~  137 (578)
T TIGR01648        58 GCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVD  137 (578)
T ss_pred             CCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccccc
Confidence            5899999999999999999999999999999998764  78999999999999999999999999884 78888877654


Q ss_pred             CccccccccCccccccccccC-------------CCCCCCChhHHhhhhh--hhHHHHHHHHHHHHHHHh---c----cc
Q psy4057          88 DSDVISKIKGTFMERPKKVRK-------------QPAPVEDPAEAKKSKK--KAAKEQARLMQAQQQQMQ---A----LS  145 (246)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~---~----~~  145 (246)
                      .................-.+.             ...............+  ....++..+.........   +    ..
T Consensus       138 ~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~Vd  217 (578)
T TIGR01648       138 NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVD  217 (578)
T ss_pred             CceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEE
Confidence            332222111100000000000             0000000111111111  122333333321110000   0    01


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccC--CCceEEEEeeCCccEEEEEeCCHHHHHH
Q psy4057         146 VQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF--PGFKEVRLVPNRHDIAFVEFENEMQSAA  223 (246)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~--G~i~~v~~~~~~~g~afV~f~~~~~A~~  223 (246)
                      |..|...          .........++|||+|||.++++++|+++|+.|  |.|++|.+++   +||||+|.+.++|.+
T Consensus       218 wA~p~~~----------~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r---gfAFVeF~s~e~A~k  284 (578)
T TIGR01648       218 WAEPEEE----------VDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR---DYAFVHFEDREDAVK  284 (578)
T ss_pred             eeccccc----------ccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec---CeEEEEeCCHHHHHH
Confidence            1111100          011122346899999999999999999999999  9999998874   599999999999999


Q ss_pred             HHHHhCCCccCCCCceEEEeec
Q psy4057         224 AKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       224 Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      |++.|||+.|+ |+.|+|+||+
T Consensus       285 Ai~~lnG~~i~-Gr~I~V~~Ak  305 (578)
T TIGR01648       285 AMDELNGKELE-GSEIEVTLAK  305 (578)
T ss_pred             HHHHhCCCEEC-CEEEEEEEcc
Confidence            99999999999 9999999996

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.

>KOG0131|consensus

Probab=99.97  E-value=3e-30  Score=188.93  Aligned_cols=163  Identities=21%  Similarity=0.347  Sum_probs=143.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      +.....+|||+||+..++++.|+++|-+.|+|.++.+.++.   ..+||||++|.++++|+.|+.-||...+.|++|+|.
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            34557899999999999999999999999999999999987   578999999999999999999999999999999999


Q ss_pred             EccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCC
Q psy4057          84 YSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATA  163 (246)
Q Consensus        84 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (246)
                      .+....                                                                          
T Consensus        85 kas~~~--------------------------------------------------------------------------   90 (203)
T KOG0131|consen   85 KASAHQ--------------------------------------------------------------------------   90 (203)
T ss_pred             eccccc--------------------------------------------------------------------------
Confidence            874211                                                                          


Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceE-EEEeeC-----CccEEEEEeCCHHHHHHHHHHhCCCccCCCC
Q psy4057         164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE-VRLVPN-----RHDIAFVEFENEMQSAAAKLALHGFKITPTH  237 (246)
Q Consensus       164 ~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~-v~~~~~-----~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~  237 (246)
                        .....+..|||+||.+++++..|.+.|+.||.+.. -.++++     .+|||||.|.+.+.+.+|+.+|||..++ ++
T Consensus        91 --~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~-nr  167 (203)
T KOG0131|consen   91 --KNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLC-NR  167 (203)
T ss_pred             --ccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhc-CC
Confidence              12334688999999999999999999999999944 334443     2579999999999999999999999999 99


Q ss_pred             ceEEEeecC
Q psy4057         238 AMKISFAKK  246 (246)
Q Consensus       238 ~l~v~~ak~  246 (246)
                      ++.|+||+|
T Consensus       168 ~itv~ya~k  176 (203)
T KOG0131|consen  168 PITVSYAFK  176 (203)
T ss_pred             ceEEEEEEe
Confidence            999999986

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

Probab=99.97  E-value=1.1e-29  Score=227.97  Aligned_cols=157  Identities=22%  Similarity=0.384  Sum_probs=140.3

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      .+|||+|||.+++|++|+++|++||.|.+|+++++.   +++|||||+|.+.++|.+|++.+|+..+.|++|+|.|+..+
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~   80 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            379999999999999999999999999999999875   67899999999999999999999999999999999997533


Q ss_pred             ccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCC
Q psy4057          89 SDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQ  168 (246)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (246)
                      ...                                                                           ..
T Consensus        81 ~~~---------------------------------------------------------------------------~~   85 (562)
T TIGR01628        81 PSL---------------------------------------------------------------------------RR   85 (562)
T ss_pred             ccc---------------------------------------------------------------------------cc
Confidence            210                                                                           01


Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ....+|||+|||.++++++|+++|+.||.|..++++.+.    +|||||+|.+.++|..|++.|||..+. |+.|.|...
T Consensus        86 ~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~-~~~i~v~~~  164 (562)
T TIGR01628        86 SGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLN-DKEVYVGRF  164 (562)
T ss_pred             cCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEec-CceEEEecc
Confidence            124579999999999999999999999999999998864    589999999999999999999999999 899988654

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

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

Probab=99.96  E-value=5.7e-29  Score=223.43  Aligned_cols=178  Identities=20%  Similarity=0.353  Sum_probs=146.6

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccC----CeeEEE
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFY----DKPMRI   82 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~----g~~l~v   82 (246)
                      ...++|||+||+.++++++|+++|+.||.|.++.++++.  +++|||||.|.+.++|.+|++.|||..+.    |+.+.|
T Consensus       176 ~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v  255 (562)
T TIGR01628       176 KKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYV  255 (562)
T ss_pred             cCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEe
Confidence            445789999999999999999999999999999998765  67899999999999999999999999999    999999


Q ss_pred             EEccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCC
Q psy4057          83 QYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMAT  162 (246)
Q Consensus        83 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (246)
                      .++..+........                                   .       ......                 
T Consensus       256 ~~a~~k~er~~~~~-----------------------------------~-------~~~~~~-----------------  276 (562)
T TIGR01628       256 GRAQKRAEREAELR-----------------------------------R-------KFEELQ-----------------  276 (562)
T ss_pred             ecccChhhhHHHHH-----------------------------------h-------hHHhhh-----------------
Confidence            88754421100000                                   0       000000                 


Q ss_pred             CCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCc
Q psy4057         163 AGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHA  238 (246)
Q Consensus       163 ~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~  238 (246)
                      ..........+|||+||+..+|+++|+++|+.||.|.+++++.+.    +|||||+|.+.++|.+|+..|||+.++ |++
T Consensus       277 ~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~-gk~  355 (562)
T TIGR01628       277 QERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLG-GKP  355 (562)
T ss_pred             hhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeC-Cce
Confidence            000012347789999999999999999999999999999999875    589999999999999999999999999 999


Q ss_pred             eEEEeecC
Q psy4057         239 MKISFAKK  246 (246)
Q Consensus       239 l~v~~ak~  246 (246)
                      |.|.||++
T Consensus       356 l~V~~a~~  363 (562)
T TIGR01628       356 LYVALAQR  363 (562)
T ss_pred             eEEEeccC
Confidence            99999864

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0144|consensus

Probab=99.96  E-value=7.6e-29  Score=203.00  Aligned_cols=158  Identities=21%  Similarity=0.413  Sum_probs=139.2

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcC-CccC--CeeEEEEE
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQG-FPFY--DKPMRIQY   84 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng-~~~~--g~~l~v~~   84 (246)
                      .-++||+-||..++|.||+++|++||.|.+|.+++|+   .++|||||.|.+.++|.+|+..|++ .++.  .++|.|.|
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~  113 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKY  113 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecc
Confidence            4579999999999999999999999999999999987   7889999999999999999999987 4454  47788999


Q ss_pred             ccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCC
Q psy4057          85 SKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAG  164 (246)
Q Consensus        85 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (246)
                      ++....                                                                          
T Consensus       114 Ad~E~e--------------------------------------------------------------------------  119 (510)
T KOG0144|consen  114 ADGERE--------------------------------------------------------------------------  119 (510)
T ss_pred             cchhhh--------------------------------------------------------------------------
Confidence            854421                                                                          


Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCc-cC-CCCc
Q psy4057         165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFK-IT-PTHA  238 (246)
Q Consensus       165 ~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~-i~-~g~~  238 (246)
                        .-+..+.|||+-|+..+|+.+++++|++||.|+++++++|.    +|||||.|.+.+.|..|++.|||.. +. ...+
T Consensus       120 --r~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~P  197 (510)
T KOG0144|consen  120 --RIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQP  197 (510)
T ss_pred             --ccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCc
Confidence              11357889999999999999999999999999999999976    7999999999999999999999964 44 2478


Q ss_pred             eEEEee
Q psy4057         239 MKISFA  244 (246)
Q Consensus       239 l~v~~a  244 (246)
                      |.|.||
T Consensus       198 LVVkFA  203 (510)
T KOG0144|consen  198 LVVKFA  203 (510)
T ss_pred             eEEEec
Confidence            999997

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.96  E-value=1.4e-27  Score=212.47  Aligned_cols=186  Identities=14%  Similarity=0.177  Sum_probs=141.2

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .+.++|||+|||..+++++|+++|+.||.|..+.++++   +.++|||||+|.+.++|..|++.|||..+.|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            34689999999999999999999999999999998875   478999999999999999999999999999999999998


Q ss_pred             cCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCC
Q psy4057          86 KTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV  165 (246)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (246)
                      ............           .  .        ...                 ....    +       +..+.....
T Consensus       373 ~~~~~~~~~~~~-----------~--~--------~~~-----------------~~~~----~-------~~~~~~~~~  403 (509)
T TIGR01642       373 CVGANQATIDTS-----------N--G--------MAP-----------------VTLL----A-------KALSQSILQ  403 (509)
T ss_pred             ccCCCCCCcccc-----------c--c--------ccc-----------------cccc----c-------ccchhhhcc
Confidence            543210000000           0  0        000                 0000    0       000000001


Q ss_pred             CCCCCCcEEEEcCCCCC--C--------CHHHHHHHHccCCCceEEEEeeCC--------ccEEEEEeCCHHHHHHHHHH
Q psy4057         166 PEQPPNQILFLTNLPEE--T--------SEMMLSMLFNQFPGFKEVRLVPNR--------HDIAFVEFENEMQSAAAKLA  227 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~--~--------t~e~l~~~f~~~G~i~~v~~~~~~--------~g~afV~f~~~~~A~~Al~~  227 (246)
                      ....++.+|+|.||...  +        ..++|+++|+.||.|++|.|+...        .|+|||+|.+.++|+.|+..
T Consensus       404 ~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~  483 (509)
T TIGR01642       404 IGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEG  483 (509)
T ss_pred             ccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHH
Confidence            13457899999999642  1        236899999999999999998742        37899999999999999999


Q ss_pred             hCCCccCCCCceEEEee
Q psy4057         228 LHGFKITPTHAMKISFA  244 (246)
Q Consensus       228 l~g~~i~~g~~l~v~~a  244 (246)
                      |||..|. |+.|.|.|.
T Consensus       484 lnGr~~~-gr~v~~~~~  499 (509)
T TIGR01642       484 MNGRKFN-DRVVVAAFY  499 (509)
T ss_pred             cCCCEEC-CeEEEEEEe
Confidence            9999999 999999985

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.96  E-value=6.1e-27  Score=205.68  Aligned_cols=230  Identities=18%  Similarity=0.248  Sum_probs=145.9

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      +.+++|||+|||..+++++|+++|++||.|..|.++++.   +++|||||+|.+.++|..|++.|||..+.|++|.|.++
T Consensus       184 p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a  263 (457)
T TIGR01622       184 PNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYA  263 (457)
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEc
Confidence            447899999999999999999999999999999998764   67899999999999999999999999999999999997


Q ss_pred             cCCccccccccCccccccccccC--CCCCCCChhHHhh---------hhhhhHHHHHHHHHHHHHHHhcc---cccCCCC
Q psy4057          86 KTDSDVISKIKGTFMERPKKVRK--QPAPVEDPAEAKK---------SKKKAAKEQARLMQAQQQQMQAL---SVQQPPV  151 (246)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~  151 (246)
                      ......... ...+.........  .............         ............+.    .....   ....|..
T Consensus       264 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~  338 (457)
T TIGR01622       264 QDSTYLLDA-ANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQ----KLQRDGIIDPNIPSR  338 (457)
T ss_pred             cCCCccccc-hhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhc----ccccccccccccccc
Confidence            632211110 0000000000000  0000000000000         00000000000000    00000   0000000


Q ss_pred             CCCC-CCCCC---CCCCCCCCCCCcEEEEcCCCCCCC----------HHHHHHHHccCCCceEEEEee-CCccEEEEEeC
Q psy4057         152 SQPA-PPAPM---ATAGVPEQPPNQILFLTNLPEETS----------EMMLSMLFNQFPGFKEVRLVP-NRHDIAFVEFE  216 (246)
Q Consensus       152 ~~~~-~~~~~---~~~~~~~~~~~~~l~v~nL~~~~t----------~e~l~~~f~~~G~i~~v~~~~-~~~g~afV~f~  216 (246)
                      .... .+...   .........++.+|+|.||....+          .++|++.|++||.|+.|.+.. ...|++||+|.
T Consensus       339 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~~~G~~fV~F~  418 (457)
T TIGR01622       339 YATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFS  418 (457)
T ss_pred             ccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCCCceeEEEEEC
Confidence            0000 00000   001111345789999999955444          368999999999999999984 44699999999


Q ss_pred             CHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         217 NEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       217 ~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      +.++|.+|++.|||+.|+ |+.|.+.|.
T Consensus       419 ~~e~A~~A~~~lnGr~f~-gr~i~~~~~  445 (457)
T TIGR01622       419 SVDAALAAFQALNGRYFG-GKMITAAFV  445 (457)
T ss_pred             CHHHHHHHHHHhcCcccC-CeEEEEEEE
Confidence            999999999999999999 999999986

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.95  E-value=3.1e-27  Score=210.16  Aligned_cols=184  Identities=17%  Similarity=0.244  Sum_probs=135.8

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhcc------------CCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQF------------GQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY   76 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~f------------G~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~   76 (246)
                      ...++|||+|||.++++++|.++|..+            +.|..+.+   .+.+|||||+|.+.++|..|+. |||..|.
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~---~~~kg~afVeF~~~e~A~~Al~-l~g~~~~  248 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI---NKEKNFAFLEFRTVEEATFAMA-LDSIIYS  248 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE---CCCCCEEEEEeCCHHHHhhhhc-CCCeEee
Confidence            457899999999999999999999975            33444443   3578999999999999999995 9999999


Q ss_pred             CeeEEEEEccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCC
Q psy4057          77 DKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAP  156 (246)
Q Consensus        77 g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (246)
                      |++|+|.........   ....                                           .......+.......
T Consensus       249 g~~l~v~r~~~~~~~---~~~~-------------------------------------------~~~~~~~~~~~~~~~  282 (509)
T TIGR01642       249 NVFLKIRRPHDYIPV---PQIT-------------------------------------------PEVSQKNPDDNAKNV  282 (509)
T ss_pred             CceeEecCccccCCc---cccC-------------------------------------------CCCCCCCCccccccc
Confidence            999999764321100   0000                                           000000000000000


Q ss_pred             CCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCC
Q psy4057         157 PAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGF  231 (246)
Q Consensus       157 ~~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~  231 (246)
                        .............++|||+|||..+|+++|+++|+.||.|..+.++.+.     +|||||+|.+.++|..|+..|||.
T Consensus       283 --~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~  360 (509)
T TIGR01642       283 --EKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGK  360 (509)
T ss_pred             --ccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCC
Confidence              0000001112356899999999999999999999999999999998863     689999999999999999999999


Q ss_pred             ccCCCCceEEEeec
Q psy4057         232 KITPTHAMKISFAK  245 (246)
Q Consensus       232 ~i~~g~~l~v~~ak  245 (246)
                      .|+ |+.|.|.+|.
T Consensus       361 ~~~-~~~l~v~~a~  373 (509)
T TIGR01642       361 DTG-DNKLHVQRAC  373 (509)
T ss_pred             EEC-CeEEEEEECc
Confidence            999 9999999974

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0145|consensus

Probab=99.95  E-value=2.3e-27  Score=182.88  Aligned_cols=159  Identities=19%  Similarity=0.417  Sum_probs=143.3

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      +...|.|--||..+++++|+.+|+..|+|++|+++||+   ++-||+||-|.++++|.+|+..|||..+..++|+|.|++
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyAR  119 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYAR  119 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEecc
Confidence            34567888999999999999999999999999999987   777999999999999999999999999999999999986


Q ss_pred             CCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                      +-++                                                                            
T Consensus       120 PSs~----------------------------------------------------------------------------  123 (360)
T KOG0145|consen  120 PSSD----------------------------------------------------------------------------  123 (360)
T ss_pred             CChh----------------------------------------------------------------------------
Confidence            5542                                                                            


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCC-CCceE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITP-THAMK  240 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~-g~~l~  240 (246)
                       ......|||.+||..+|+.+|.++|++||.|..-+++.|.     +|.|||.|+.+++|..|+..|||.+-.+ ..+|.
T Consensus       124 -~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepIt  202 (360)
T KOG0145|consen  124 -SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPIT  202 (360)
T ss_pred             -hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeE
Confidence             2247789999999999999999999999999888888776     6899999999999999999999987752 47899


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.||.
T Consensus       203 VKFan  207 (360)
T KOG0145|consen  203 VKFAN  207 (360)
T ss_pred             EEecC
Confidence            99985

>KOG0127|consensus

Probab=99.95  E-value=3.5e-27  Score=198.29  Aligned_cols=181  Identities=21%  Similarity=0.303  Sum_probs=146.7

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      .||||++||++.+-++|.++|+.+|+|..+.+..++   .++|||||+|+-.++++.|+...++..|.|+.|+|.++..+
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            899999999999999999999999999999998865   67899999999999999999999999999999999998655


Q ss_pred             ccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCC
Q psy4057          89 SDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQ  168 (246)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (246)
                      ........+                .....                      ...+.+.             ......-.
T Consensus        86 ~r~e~~~~~----------------e~~~v----------------------eK~~~q~-------------~~~k~~v~  114 (678)
T KOG0127|consen   86 ARSEEVEKG----------------ENKAV----------------------EKPIEQK-------------RPTKAKVD  114 (678)
T ss_pred             ccchhcccc----------------cchhh----------------------hcccccC-------------Ccchhhcc
Confidence            321100000                00000                      0000000             00011123


Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .+...|+|+|||+.|...+|+.+|+.||.|..|.|++..    .|||||.|.+..+|..|++.|||..|+ |++|.|.||
T Consensus       115 ~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~-gR~VAVDWA  193 (678)
T KOG0127|consen  115 LPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKID-GRPVAVDWA  193 (678)
T ss_pred             CccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceec-CceeEEeee
Confidence            347899999999999999999999999999999999855    589999999999999999999999999 999999997

>KOG0127|consensus

Probab=99.94  E-value=3.8e-26  Score=192.08  Aligned_cols=227  Identities=21%  Similarity=0.292  Sum_probs=146.5

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      .-+|.|.|||..+.+.+|..+|+.||.|.+|.|++.+  +..|||||+|.+..+|.+|++.+||..|.||+|.|.||-.+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            5689999999999999999999999999999999644  77799999999999999999999999999999999998655


Q ss_pred             ccccccccCccccccccccC----CC-CCCCC-------hhHHh------hhhhhhHHHHHHHHHHHHHHHhcc-cccCC
Q psy4057          89 SDVISKIKGTFMERPKKVRK----QP-APVED-------PAEAK------KSKKKAAKEQARLMQAQQQQMQAL-SVQQP  149 (246)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~----~~-~~~~~-------~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~  149 (246)
                      ......... ..+..+....    ++ ..+..       .....      .+.............    ..... ....+
T Consensus       197 d~ye~ta~~-~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Ee----e~~~vDd~e~S  271 (678)
T KOG0127|consen  197 DTYEDTAHE-EKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEE----EEDDVDDEESS  271 (678)
T ss_pred             ccccccchh-hhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccc----ccccccccccc
Confidence            321110000 0000000000    00 00000       00000      000000000000000    00000 00000


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHH
Q psy4057         150 PVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAA  224 (246)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A  224 (246)
                      ..+.+.+.... ...........+|||+|||+++|+++|..+|++||+|..+.++.++     .|+|||.|.+...|+.|
T Consensus       272 ~~~~~~k~~q~-k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~c  350 (678)
T KOG0127|consen  272 GKKESDKKAQN-KTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNC  350 (678)
T ss_pred             ccCcccchhcc-ccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHH
Confidence            00011100000 0012233456999999999999999999999999999999999976     58999999999999999


Q ss_pred             HHHh-----CC-CccCCCCceEEEee
Q psy4057         225 KLAL-----HG-FKITPTHAMKISFA  244 (246)
Q Consensus       225 l~~l-----~g-~~i~~g~~l~v~~a  244 (246)
                      |..-     .| ..++ |+-|+|..|
T Consensus       351 i~~Aspa~e~g~~ll~-GR~Lkv~~A  375 (678)
T KOG0127|consen  351 IEAASPASEDGSVLLD-GRLLKVTLA  375 (678)
T ss_pred             HHhcCccCCCceEEEe-ccEEeeeec
Confidence            9987     33 4566 899998765

>KOG0109|consensus

Probab=99.94  E-value=1.1e-26  Score=181.61  Aligned_cols=145  Identities=19%  Similarity=0.388  Sum_probs=136.5

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCccc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDV   91 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~~   91 (246)
                      -+|||+|||..+++.+|+.+|++||+|.+|.|++     +||||..++...|..||+.|+|.+|+|.-|.|+-++.++  
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK-----NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs--   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK-----NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS--   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec-----ccceEEeecccccHHHHhhcccceecceEEEEEeccccC--
Confidence            3699999999999999999999999999999965     899999999999999999999999999999999986553  


Q ss_pred             cccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCCCC
Q psy4057          92 ISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPN  171 (246)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (246)
                                                                                                   .++
T Consensus        76 -----------------------------------------------------------------------------k~s   78 (346)
T KOG0109|consen   76 -----------------------------------------------------------------------------KAS   78 (346)
T ss_pred             -----------------------------------------------------------------------------CCc
Confidence                                                                                         268


Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ++|+|+|+.+.|+.++|+..|++||.|..+.+++|   |+||.|+..++|..|+..|||++|+ |++|+|+.+
T Consensus        79 tkl~vgNis~tctn~ElRa~fe~ygpviecdivkd---y~fvh~d~~eda~~air~l~~~~~~-gk~m~vq~s  147 (346)
T KOG0109|consen   79 TKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD---YAFVHFDRAEDAVEAIRGLDNTEFQ-GKRMHVQLS  147 (346)
T ss_pred             cccccCCCCccccCHHHhhhhcccCCceeeeeecc---eeEEEEeeccchHHHHhcccccccc-cceeeeeee
Confidence            88999999999999999999999999999999976   8999999999999999999999999 999999875

>KOG0145|consensus

Probab=99.93  E-value=5e-25  Score=170.08  Aligned_cols=207  Identities=22%  Similarity=0.360  Sum_probs=145.6

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCC--eeEEEEEc
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYD--KPMRIQYS   85 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g--~~l~v~~a   85 (246)
                      +..|||.+||..++..+|..+|++||.|..-+|+-|   +.+||.|||.|....+|+.||..|||..-.|  .+|.|.|+
T Consensus       127 ~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFa  206 (360)
T KOG0145|consen  127 DANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFA  206 (360)
T ss_pred             ccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEec
Confidence            567999999999999999999999999988877765   3799999999999999999999999988765  56999998


Q ss_pred             cCCccccc--cccCccccccccccC-CCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCC
Q psy4057          86 KTDSDVIS--KIKGTFMERPKKVRK-QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMAT  162 (246)
Q Consensus        86 ~~~~~~~~--~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (246)
                      ...+....  .....+... .++-. .-.++..                         ........+......+.+++..
T Consensus       207 nnPsq~t~~a~ls~ly~sp-~rr~~Gp~hh~~~-------------------------r~r~~~~~~~~~~~~rfsP~~~  260 (360)
T KOG0145|consen  207 NNPSQKTNQALLSQLYQSP-ARRYGGPMHHQAQ-------------------------RFRLDNLLNPHAAQARFSPMTI  260 (360)
T ss_pred             CCcccccchhhhHHhhcCc-cccCCCcccchhh-------------------------hhccccccchhhhhccCCCccc
Confidence            54422100  000000000 00000 0000000                         0000000000000011111111


Q ss_pred             CC--------CC-CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHh
Q psy4057         163 AG--------VP-EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL  228 (246)
Q Consensus       163 ~~--------~~-~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l  228 (246)
                      +.        .+ ......+|||-||.++..+.-|.++|++||-|..|++++|-     +|||||.+.+-++|..|+..|
T Consensus       261 d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sL  340 (360)
T KOG0145|consen  261 DGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL  340 (360)
T ss_pred             cccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHh
Confidence            11        11 22248899999999999999999999999999999999975     699999999999999999999


Q ss_pred             CCCccCCCCceEEEee
Q psy4057         229 HGFKITPTHAMKISFA  244 (246)
Q Consensus       229 ~g~~i~~g~~l~v~~a  244 (246)
                      ||+.++ ++.|.|+|-
T Consensus       341 NGy~lg-~rvLQVsFK  355 (360)
T KOG0145|consen  341 NGYRLG-DRVLQVSFK  355 (360)
T ss_pred             cCcccc-ceEEEEEEe
Confidence            999999 999999984

>KOG0110|consensus

Probab=99.92  E-value=1.5e-24  Score=187.57  Aligned_cols=164  Identities=22%  Similarity=0.318  Sum_probs=141.8

Q ss_pred             EEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC------CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL------KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        13 ~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      +|||.||+++++.++|..+|...|.|.++.|....      .|.|||||+|.+.++|+.|++.|+|+.+.|+.|.|.++.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            39999999999999999999999999999776533      356999999999999999999999999999999999986


Q ss_pred             CCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                      .......                                                 +                   ...+
T Consensus       597 ~k~~~~~-------------------------------------------------g-------------------K~~~  608 (725)
T KOG0110|consen  597 NKPASTV-------------------------------------------------G-------------------KKKS  608 (725)
T ss_pred             Ccccccc-------------------------------------------------c-------------------cccc
Confidence            2211000                                                 0                   0111


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC-C----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN-R----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~-~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .....+.|+|+|||+..+..+++.+|+.||.+.+|+|+.. .    +|||||+|-+..+|.+|+.+|.++.++ |++|.+
T Consensus       609 ~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHly-GRrLVL  687 (725)
T KOG0110|consen  609 KKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLY-GRRLVL  687 (725)
T ss_pred             cccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhccccee-chhhhe
Confidence            2334789999999999999999999999999999999986 2    589999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      +||+
T Consensus       688 EwA~  691 (725)
T KOG0110|consen  688 EWAK  691 (725)
T ss_pred             ehhc
Confidence            9997

>KOG0123|consensus

Probab=99.92  E-value=8.3e-24  Score=178.16  Aligned_cols=146  Identities=25%  Similarity=0.397  Sum_probs=133.9

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCccc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDV   91 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~~   91 (246)
                      .+||||   +++++..|++.|+++|+|.+|++++|-.+-|||||.|.++++|.+|+++||...+.|++|+|.|+..+.  
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~--   76 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP--   76 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC--
Confidence            478999   999999999999999999999999976566999999999999999999999999999999999985442  


Q ss_pred             cccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCCCC
Q psy4057          92 ISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPN  171 (246)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (246)
                                                                                                      
T Consensus        77 --------------------------------------------------------------------------------   76 (369)
T KOG0123|consen   77 --------------------------------------------------------------------------------   76 (369)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..+||+||+++++..+|.++|+.||+|.+|++..+.   +|| ||+|.+.++|.+|+..|||..+. ++.|.|...
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~-~kki~vg~~  150 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLN-GKKIYVGLF  150 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccC-CCeeEEeec
Confidence            119999999999999999999999999999999977   578 99999999999999999999999 888888543

>KOG0124|consensus

Probab=99.91  E-value=2.7e-24  Score=173.24  Aligned_cols=164  Identities=20%  Similarity=0.284  Sum_probs=139.1

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      ++||||.|+++..|+-|+.-|.+||+|.+|.+.-|.   ++||||||+|+-+|.|+-|+++|||..+.||.|+|.+...-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            689999999999999999999999999999887665   89999999999999999999999999999999999863211


Q ss_pred             ccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCC
Q psy4057          89 SDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQ  168 (246)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (246)
                      ..                                       +..-+...+                           ++.
T Consensus       194 pQ---------------------------------------AQpiID~vq---------------------------eeA  207 (544)
T KOG0124|consen  194 PQ---------------------------------------AQPIIDMVQ---------------------------EEA  207 (544)
T ss_pred             cc---------------------------------------cchHHHHHH---------------------------HHH
Confidence            10                                       000000000                           011


Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ....++||..+.++++++||++.|+.||+|+.|.+.++.     +|||||+|.+..+...|+..||=+.++ |..|+|.
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLG-GQyLRVG  285 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLG-GQYLRVG  285 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcc-cceEecc
Confidence            236679999999999999999999999999999999966     689999999999999999999999999 9999885

>KOG0147|consensus

Probab=99.91  E-value=4.7e-24  Score=180.04  Aligned_cols=229  Identities=15%  Similarity=0.166  Sum_probs=148.1

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..|-.+|||+||..+.+++.|+.+|++||.|+.|.+..+   ++++|||||+|.+.++|++|+++|||+.+.|+.|+|..
T Consensus       275 ~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~  354 (549)
T KOG0147|consen  275 TGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSV  354 (549)
T ss_pred             ccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEE
Confidence            345555999999999999999999999999999999876   48999999999999999999999999999999999988


Q ss_pred             ccCCccccccccCccccccccccCCCCCCCChhHHhhhhhh--------hHHHHHHHHHHHHHHH-hcccccCCCCCCCC
Q psy4057          85 SKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKK--------AAKEQARLMQAQQQQM-QALSVQQPPVSQPA  155 (246)
Q Consensus        85 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  155 (246)
                      .....+....-. ...+....  .....+.......+.+..        ..+.+..+.....+.. ......+.......
T Consensus       355 v~~r~~~~~a~~-~~~d~D~~--d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~  431 (549)
T KOG0147|consen  355 VTERVDTKEAAV-TQFDFDED--DRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVD  431 (549)
T ss_pred             eeeecccccccc-cccccchh--hccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccC
Confidence            654433221100 00000000  000000000000000000        0011111111000000 00000000011111


Q ss_pred             CCCCCCCCCCCCCCCCcEEEEcCCCC--CCC--------HHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHH
Q psy4057         156 PPAPMATAGVPEQPPNQILFLTNLPE--ETS--------EMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK  225 (246)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~l~v~nL~~--~~t--------~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al  225 (246)
                      ++.-    ...-.+++.|+.++|+-.  ..|        .|++.+.|+.||+|.+|.|.++..|+.||.|.+.+.|..|.
T Consensus       432 p~~~----~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~  507 (549)
T KOG0147|consen  432 PADA----SPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAV  507 (549)
T ss_pred             cccc----ccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHH
Confidence            1100    111237899999999733  222        36888999999999999999998899999999999999999


Q ss_pred             HHhCCCccCCCCceEEEee
Q psy4057         226 LALHGFKITPTHAMKISFA  244 (246)
Q Consensus       226 ~~l~g~~i~~g~~l~v~~a  244 (246)
                      .+|||++|. |+.|...|-
T Consensus       508 ~alhgrWF~-gr~Ita~~~  525 (549)
T KOG0147|consen  508 KALHGRWFA-GRMITAKYL  525 (549)
T ss_pred             HHHhhhhhc-cceeEEEEe
Confidence            999999999 999999883

>KOG0144|consensus

Probab=99.90  E-value=4.5e-23  Score=169.32  Aligned_cols=85  Identities=27%  Similarity=0.454  Sum_probs=75.8

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCc-c--CCeeEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFP-F--YDKPMR   81 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~-~--~g~~l~   81 (246)
                      ++...++|||+-|+..++|.+++++|++||.|++|.|+|+.  .+||||||+|.+.+.|..||+.|||.. +  ...+|.
T Consensus       120 r~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLV  199 (510)
T KOG0144|consen  120 RIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLV  199 (510)
T ss_pred             ccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceE
Confidence            34567899999999999999999999999999999999965  899999999999999999999999943 4  458899


Q ss_pred             EEEccCCccc
Q psy4057          82 IQYSKTDSDV   91 (246)
Q Consensus        82 v~~a~~~~~~   91 (246)
                      |.|++.+.+.
T Consensus       200 VkFADtqkdk  209 (510)
T KOG0144|consen  200 VKFADTQKDK  209 (510)
T ss_pred             EEecccCCCc
Confidence            9999876553

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.89  E-value=3.8e-21  Score=169.64  Aligned_cols=81  Identities=20%  Similarity=0.339  Sum_probs=75.1

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ...++|||+||+.++++++|+++|+.||.|.++++.++.   +++|||||+|.+.++|.+|++.||+..+.|+.|+|.++
T Consensus       202 ~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kA  281 (612)
T TIGR01645       202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  281 (612)
T ss_pred             cccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEec
Confidence            345799999999999999999999999999999999864   68999999999999999999999999999999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ...+
T Consensus       282 i~pP  285 (612)
T TIGR01645       282 VTPP  285 (612)
T ss_pred             CCCc
Confidence            7644

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.

>KOG0146|consensus

Probab=99.89  E-value=1.1e-22  Score=157.80  Aligned_cols=235  Identities=22%  Similarity=0.337  Sum_probs=149.0

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEcc--CCCCccEEEEEEcCHHHHHHHHHHhcCCc-cCC--eeEEEEE
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQGFP-FYD--KPMRIQY   84 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~--~~~~kg~aFV~f~~~~~A~~Ai~~lng~~-~~g--~~l~v~~   84 (246)
                      .+++||||-|...-.|+|++.+|..||.|++|.+++  |+.+||+|||.|.+..+|+.||..|+|.. +.|  .-|-|.|
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            478999999999999999999999999999999997  45899999999999999999999999943 444  5588899


Q ss_pred             ccCCcccccccc-------Ccccccccc-------------cc-------------------------------------
Q psy4057          85 SKTDSDVISKIK-------GTFMERPKK-------------VR-------------------------------------  107 (246)
Q Consensus        85 a~~~~~~~~~~~-------~~~~~~~~~-------------~~-------------------------------------  107 (246)
                      ++.+.+...++-       |.+......             ..                                     
T Consensus        98 ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A~  177 (371)
T KOG0146|consen   98 ADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAAA  177 (371)
T ss_pred             ccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhcccccC
Confidence            876543222111       111000000             00                                     


Q ss_pred             C-CCCC-CCChh---------------HHhhhhh-hhHHHHHHHH------------------HHHHHHHhcccccC---
Q psy4057         108 K-QPAP-VEDPA---------------EAKKSKK-KAAKEQARLM------------------QAQQQQMQALSVQQ---  148 (246)
Q Consensus       108 ~-~~~~-~~~~~---------------~~~~~~~-~~~~~~~~~~------------------~~~~~~~~~~~~~~---  148 (246)
                      . .... .....               -.+.... ..+...+...                  .-.+....+.+...   
T Consensus       178 Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aay  257 (371)
T KOG0146|consen  178 PVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAAY  257 (371)
T ss_pred             CcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhhc
Confidence            0 0000 00000               0000000 0000000000                  00000000000000   


Q ss_pred             CCC---CCCCCCCCCC--CCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCH
Q psy4057         149 PPV---SQPAPPAPMA--TAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENE  218 (246)
Q Consensus       149 ~~~---~~~~~~~~~~--~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~  218 (246)
                      |..   ..+..|.++.  ....-..|..|.|||--||.+..+.+|...|-.||.|++.++.-|+     +.||||.|++.
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp  337 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNP  337 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCc
Confidence            000   0000011111  1112367789999999999999999999999999999999988877     57999999999


Q ss_pred             HHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         219 MQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       219 ~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .+|++||+.|||+.|+ =++|+|..-|
T Consensus       338 ~SaQaAIqAMNGFQIG-MKRLKVQLKR  363 (371)
T KOG0146|consen  338 ASAQAAIQAMNGFQIG-MKRLKVQLKR  363 (371)
T ss_pred             hhHHHHHHHhcchhhh-hhhhhhhhcC
Confidence            9999999999999999 7999987643

>KOG0123|consensus

Probab=99.87  E-value=1.9e-21  Score=163.92  Aligned_cols=170  Identities=21%  Similarity=0.333  Sum_probs=144.2

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      |-..+-...|||.||+++++-.+|++.|+.||.|.+|++..+. .++|| ||+|.++++|++|++.+||..+.|+.|.|.
T Consensus        70 m~s~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg  148 (369)
T KOG0123|consen   70 MWSQRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVG  148 (369)
T ss_pred             ehhccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEe
Confidence            3344444559999999999999999999999999999999876 68999 999999999999999999999999999999


Q ss_pred             EccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCC
Q psy4057          84 YSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATA  163 (246)
Q Consensus        84 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (246)
                      ....+........                                                                   
T Consensus       149 ~~~~~~er~~~~~-------------------------------------------------------------------  161 (369)
T KOG0123|consen  149 LFERKEEREAPLG-------------------------------------------------------------------  161 (369)
T ss_pred             eccchhhhccccc-------------------------------------------------------------------
Confidence            8755532111000                                                                   


Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       164 ~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                       . ....-+.+++.|++.+.+++.|...|+.||.|..+.++.+.    ++||||.|.+.+.|..|+..|||..++ +..+
T Consensus       162 -~-~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~-~~~~  238 (369)
T KOG0123|consen  162 -E-YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFG-DKEL  238 (369)
T ss_pred             -c-hhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCC-ccce
Confidence             0 22246678899999999999999999999999999999965    589999999999999999999999998 8888


Q ss_pred             EEEeec
Q psy4057         240 KISFAK  245 (246)
Q Consensus       240 ~v~~ak  245 (246)
                      .|.-+.
T Consensus       239 ~V~~aq  244 (369)
T KOG0123|consen  239 YVGRAQ  244 (369)
T ss_pred             eecccc
Confidence            876543

>KOG0105|consensus

Probab=99.86  E-value=1.6e-20  Score=138.31  Aligned_cols=173  Identities=16%  Similarity=0.217  Sum_probs=133.1

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      ..+++|||+|||.++.+.+|.++|.+||.|..|.+......-+||||+|++..+|+.||..-+|..+.|..|+|+++..-
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            45789999999999999999999999999999988665566799999999999999999999999999999999997543


Q ss_pred             ccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCC
Q psy4057          89 SDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQ  168 (246)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (246)
                      ...... .+.+.                                         .+.....+......+         +.-
T Consensus        84 r~s~~~-~G~y~-----------------------------------------gggrgGgg~gg~rgp---------psr  112 (241)
T KOG0105|consen   84 RSSSDR-RGSYS-----------------------------------------GGGRGGGGGGGRRGP---------PSR  112 (241)
T ss_pred             Cccccc-ccccC-----------------------------------------CCCCCCCCCCcccCC---------ccc
Confidence            211100 00000                                         000000000000000         011


Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKIT  234 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~  234 (246)
                      -..-.+.|++||.+-+|++|++....-|.|....+.++  |+++|+|...|+.+-|+..|+...+.
T Consensus       113 rSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD--g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  113 RSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD--GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             ccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc--cceeeeeeehhhHHHHHHhhcccccc
Confidence            12457889999999999999999999999999999988  58999999999999999999987764

>KOG1457|consensus

Probab=99.86  E-value=1.7e-21  Score=147.42  Aligned_cols=221  Identities=18%  Similarity=0.271  Sum_probs=137.4

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC----CCccEEEEEEcCHHHHHHHHHHhcCCcc---CCeeEEEE
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL----KMRGQAFVIFKEIASATNALRSMQGFPF---YDKPMRIQ   83 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~----~~kg~aFV~f~~~~~A~~Ai~~lng~~~---~g~~l~v~   83 (246)
                      =+||||.+||.|+...+|+.+|..|--.+...+.-+.    ..+.+||++|.+..+|..|+..|||..|   .+.+|+|+
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            4899999999999999999999999778887665443    3458999999999999999999999988   58899999


Q ss_pred             EccCCccccccccCc------ccccc---cccc-C-CCCCCCChhHHhhh-hhhhHHHHHHHHHHHHHHHhcccccCCCC
Q psy4057          84 YSKTDSDVISKIKGT------FMERP---KKVR-K-QPAPVEDPAEAKKS-KKKAAKEQARLMQAQQQQMQALSVQQPPV  151 (246)
Q Consensus        84 ~a~~~~~~~~~~~~~------~~~~~---~~~~-~-~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (246)
                      +++..........+.      .....   +... . ..+++......... .+++..+-.....-.+.......+..|..
T Consensus       114 lAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~a  193 (284)
T KOG1457|consen  114 LAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPSA  193 (284)
T ss_pred             ehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCcc
Confidence            998765433322221      00000   0000 0 11111111000000 00000000000000000000000111110


Q ss_pred             CCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-ccEEEEEeCCHHHHHHHHHHhCC
Q psy4057         152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFENEMQSAAAKLALHG  230 (246)
Q Consensus       152 ~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~~~A~~Al~~l~g  230 (246)
                      ..+.-   -............+|||.||..+||+++|+.+|++|.....+++.... ...||++|.+.+.|..||..|+|
T Consensus       194 ~a~l~---ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg  270 (284)
T KOG1457|consen  194 NAHLE---KSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQG  270 (284)
T ss_pred             cchhh---hhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhc
Confidence            00000   000111234458899999999999999999999999998887776643 45899999999999999999999


Q ss_pred             CccC
Q psy4057         231 FKIT  234 (246)
Q Consensus       231 ~~i~  234 (246)
                      ..+.
T Consensus       271 ~~~s  274 (284)
T KOG1457|consen  271 NLLS  274 (284)
T ss_pred             ceec
Confidence            8774

>KOG1190|consensus

Probab=99.84  E-value=1.1e-19  Score=148.51  Aligned_cols=191  Identities=20%  Similarity=0.353  Sum_probs=143.3

Q ss_pred             CcEEEecCC-ChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCc
Q psy4057          11 TNFVYVTHI-SSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDS   89 (246)
Q Consensus        11 ~~~l~V~nl-~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~   89 (246)
                      +..|.|.|| .+.+|.+-|+-+|+-||+|.+|+|+..++  ..|.|+|.+...|+-|++.|+|..++|++|+|.+++...
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk--d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK--DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC--cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcc
Confidence            577888888 55788888999999999999999988643  779999999999999999999999999999999997654


Q ss_pred             cccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCC
Q psy4057          90 DVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQP  169 (246)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (246)
                      -...+. |       ..+..-..++..+                      +...+            ..+...--....|
T Consensus       375 vqlp~e-g-------q~d~glT~dy~~s----------------------pLhrf------------kkpgsKN~~ni~P  412 (492)
T KOG1190|consen  375 VQLPRE-G-------QEDQGLTKDYGNS----------------------PLHRF------------KKPGSKNYQNIFP  412 (492)
T ss_pred             ccCCCC-C-------CccccccccCCCC----------------------chhhc------------cCcccccccccCC
Confidence            211110 0       0000000000000                      00000            0000001123678


Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCc-eEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGF-KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i-~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      |+.+|.+.|+|.++++|+|+.+|..-|.. +-.++..+.+.+|++.+.+.|+|..|+-.|+.+.++++..|+|+|+|
T Consensus       413 psatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSk  489 (492)
T KOG1190|consen  413 PSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSK  489 (492)
T ss_pred             chhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceeecccCChhHhhhhccccccccCCCCceEEEEeec
Confidence            99999999999999999999999998877 44555555557999999999999999999999999988899999997

>KOG0148|consensus

Probab=99.84  E-value=3.2e-20  Score=144.31  Aligned_cols=130  Identities=16%  Similarity=0.349  Sum_probs=110.6

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCccc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDV   91 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~~   91 (246)
                      ++|||+||+.+++|+-|-.||++.|.|.+++++.+                                .|.|.++..... 
T Consensus         7 rtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~--------------------------------e~~v~wa~~p~n-   53 (321)
T KOG0148|consen    7 RTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD--------------------------------ELKVNWATAPGN-   53 (321)
T ss_pred             ceEEeeccChhhHHHHHHHHHHhccccccceeehh--------------------------------hhccccccCccc-
Confidence            89999999999999999999999999999999875                                356666533310 


Q ss_pred             cccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCCCC
Q psy4057          92 ISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPN  171 (246)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (246)
                                                                                             .+-+.....
T Consensus        54 -----------------------------------------------------------------------Qsk~t~~~h   62 (321)
T KOG0148|consen   54 -----------------------------------------------------------------------QSKPTSNQH   62 (321)
T ss_pred             -----------------------------------------------------------------------CCCCccccc
Confidence                                                                                   000111235


Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      -.+||+.|...++-|+|++.|.+||+|.++++++|.     +|||||.|.+.++|..||+.|||.+|+ +|.|+--||-|
T Consensus        63 fhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG-~R~IRTNWATR  141 (321)
T KOG0148|consen   63 FHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLG-RRTIRTNWATR  141 (321)
T ss_pred             eeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeec-cceeecccccc
Confidence            678999999999999999999999999999999976     699999999999999999999999999 99999998743

>KOG0147|consensus

Probab=99.83  E-value=4.7e-21  Score=162.04  Aligned_cols=169  Identities=22%  Similarity=0.366  Sum_probs=136.6

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      --+++|+--|+...+..+|.++|+.+|.|.+|+++.|.   +++|.|+|+|.+.++...|+. |.|..++|.+|.|+.+.
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccH
Confidence            34667776677777889999999999999999999876   788999999999999999996 99999999999999863


Q ss_pred             CCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                      .....                                           .  ++..+..       .          ....
T Consensus       257 aeknr-------------------------------------------~--a~~s~a~-------~----------~k~~  274 (549)
T KOG0147|consen  257 AEKNR-------------------------------------------A--ANASPAL-------Q----------GKGF  274 (549)
T ss_pred             HHHHH-------------------------------------------H--Hhccccc-------c----------cccc
Confidence            22110                                           0  0000000       0          0000


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .. |-..|||+||.+++++++|+.+|+.||.|..|.+..+.     +|||||+|.+.++|..|+..|||+++- |+.|+|
T Consensus       275 ~~-p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelA-Gr~ikV  352 (549)
T KOG0147|consen  275 TG-PMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELA-GRLIKV  352 (549)
T ss_pred             cc-chhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceec-CceEEE
Confidence            11 22229999999999999999999999999999999974     689999999999999999999999999 999998


Q ss_pred             Ee
Q psy4057         242 SF  243 (246)
Q Consensus       242 ~~  243 (246)
                      +.
T Consensus       353 ~~  354 (549)
T KOG0147|consen  353 SV  354 (549)
T ss_pred             EE
Confidence            74

>KOG0110|consensus

Probab=99.81  E-value=3e-19  Score=155.02  Aligned_cols=207  Identities=19%  Similarity=0.254  Sum_probs=140.3

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      .....+.++|+|||..+..++|...|..||+|..|.+.+   .--.|.|.|.++.+|+.|.+.|....+...++.+.++.
T Consensus       381 ~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~---~G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP  457 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPP---GGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAP  457 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccccceeecCc---ccceeeeeecCccchHHHHHHhchhhhccCccccccCh
Confidence            345678899999999999999999999999999996653   22349999999999999999999999999999999875


Q ss_pred             CCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCC-C
Q psy4057          87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAG-V  165 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~  165 (246)
                      ...-... ...............+...+..                         +..  ..+.....++.-...... .
T Consensus       458 ~dvf~~~-pka~~~~~e~~~~~ee~~~Er~-------------------------s~~--d~~v~eD~d~te~ss~a~~a  509 (725)
T KOG0110|consen  458 EDVFTED-PKADDLSAESRSKMEENPSERV-------------------------SAE--DGQVEEDKDPTEESSLARVA  509 (725)
T ss_pred             hhhccCC-ccccccccccccccccCcceec-------------------------ccc--cccccccCCccccccchhhh
Confidence            4422111 1000000000000000000000                         000  000000000000000000 1


Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--------ccEEEEEeCCHHHHHHHHHHhCCCccCCCC
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--------HDIAFVEFENEMQSAAAKLALHGFKITPTH  237 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~  237 (246)
                      ......+.|||+||++++|.++|..+|...|.|.++.|...+        .|||||+|.+.++|++|++.|+|+.++ |+
T Consensus       510 ~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvld-GH  588 (725)
T KOG0110|consen  510 EDEETETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLD-GH  588 (725)
T ss_pred             hccccchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceec-Cc
Confidence            111122339999999999999999999999999999887744        289999999999999999999999999 99


Q ss_pred             ceEEEeec
Q psy4057         238 AMKISFAK  245 (246)
Q Consensus       238 ~l~v~~ak  245 (246)
                      .|.|+++.
T Consensus       589 ~l~lk~S~  596 (725)
T KOG0110|consen  589 KLELKISE  596 (725)
T ss_pred             eEEEEecc
Confidence            99999874

>KOG1190|consensus

Probab=99.80  E-value=1.7e-18  Score=141.69  Aligned_cols=213  Identities=20%  Similarity=0.287  Sum_probs=139.3

Q ss_pred             EEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCe--eEEEEEccCCccc
Q psy4057          14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK--PMRIQYSKTDSDV   91 (246)
Q Consensus        14 l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~--~l~v~~a~~~~~~   91 (246)
                      ++|.|+-+.++-+-|+.+|++||.|.+|.-.. +...-.|.|+|.+.++|+.|...|+|..+..-  +|+|.|++-....
T Consensus       153 ~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~-Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~Ln  231 (492)
T KOG1190|consen  153 TIIENMFYPVSLDVLHQVFSKFGFVLKIITFT-KNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLN  231 (492)
T ss_pred             EEeccceeeeEHHHHHHHHhhcceeEEEEEEe-cccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccce
Confidence            34599999999999999999999999985543 23445599999999999999999999888543  4788887653211


Q ss_pred             cccccCccccccccccC-CCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCC-
Q psy4057          92 ISKIKGTFMERPKKVRK-QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQP-  169 (246)
Q Consensus        92 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  169 (246)
                      ..-.      +.+.++- .......     ..++........+..    ..+... ..|...+.........+ -.... 
T Consensus       232 vKyn------ndkSRDyTnp~LP~g-----d~~p~l~~~~~aa~~----~~~~~~-g~p~aip~~~~~a~~a~-~~~~~~  294 (492)
T KOG1190|consen  232 VKYN------NDKSRDYTNPDLPVG-----DGQPSLDQLMAAAFG----SVPAVH-GAPLAIPSGAAGANAAD-GKIESP  294 (492)
T ss_pred             eecc------ccccccccCCCCCCC-----ccccccchhhhcccc----cccccc-CCcccCCccchhhcccc-cccccC
Confidence            1000      0011110 1111000     111111111111000    000000 01222111110000010 11111 


Q ss_pred             -CCcEEEEcCCCC-CCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 -PNQILFLTNLPE-ETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 -~~~~l~v~nL~~-~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                       .+.+|.|.||.. .+|.+.|..+|+.||.|.+|++..+++..|+|+|.+...|+.|++.|+|..++ |++|+|.|+|
T Consensus       295 ~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~-gk~lrvt~SK  371 (492)
T KOG1190|consen  295 SANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLY-GKKLRVTLSK  371 (492)
T ss_pred             CCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceec-CceEEEeecc
Confidence             278999998755 89999999999999999999999999889999999999999999999999999 9999999997

>KOG0124|consensus

Probab=99.78  E-value=1.6e-17  Score=134.44  Aligned_cols=84  Identities=20%  Similarity=0.344  Sum_probs=76.4

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      +....++|||..+.+|.+++||+..|+.||+|..|.+-+..   .+||||||+|.+..+-..|+..||-+.+.|+.|+|.
T Consensus       206 eAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVG  285 (544)
T KOG0124|consen  206 EAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVG  285 (544)
T ss_pred             HHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecc
Confidence            34567899999999999999999999999999999998865   789999999999999999999999999999999998


Q ss_pred             EccCCcc
Q psy4057          84 YSKTDSD   90 (246)
Q Consensus        84 ~a~~~~~   90 (246)
                      .+....+
T Consensus       286 k~vTPP~  292 (544)
T KOG0124|consen  286 KCVTPPD  292 (544)
T ss_pred             cccCCCc
Confidence            8765544

>KOG1548|consensus

Probab=99.78  E-value=1.5e-17  Score=133.52  Aligned_cols=193  Identities=18%  Similarity=0.242  Sum_probs=137.2

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeE--------EEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeE
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPM   80 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~--------v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (246)
                      +..|||.|||.++|.+++.++|+++|-|..        |++.++.  ..+|-|.+.|-..+++.-|+.-|++..+.|+.|
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~  213 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKL  213 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEE
Confidence            566999999999999999999999997744        5666654  778999999999999999999999999999999


Q ss_pred             EEEEccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCC
Q psy4057          81 RIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPM  160 (246)
Q Consensus        81 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (246)
                      +|+.|+.+.      +|.+....+...+  ..+    ..+....               ....+.|+.-.          
T Consensus       214 rVerAkfq~------Kge~~~~~k~k~k--~~~----~kk~~k~---------------q~k~~dw~pd~----------  256 (382)
T KOG1548|consen  214 RVERAKFQM------KGEYDASKKEKGK--CKD----KKKLKKQ---------------QQKLLDWRPDR----------  256 (382)
T ss_pred             EEehhhhhh------ccCcCcccccccc--ccc----HHHHHHH---------------HHhhcccCCCc----------
Confidence            999986552      2222111111000  000    0000000               11111121111          


Q ss_pred             CCCCCCCCCCCcEEEEcCCCC----CCC-------HHHHHHHHccCCCceEEEEee-CCccEEEEEeCCHHHHHHHHHHh
Q psy4057         161 ATAGVPEQPPNQILFLTNLPE----ETS-------EMMLSMLFNQFPGFKEVRLVP-NRHDIAFVEFENEMQSAAAKLAL  228 (246)
Q Consensus       161 ~~~~~~~~~~~~~l~v~nL~~----~~t-------~e~l~~~f~~~G~i~~v~~~~-~~~g~afV~f~~~~~A~~Al~~l  228 (246)
                        ...+.....++|+++|+-.    ..+       +++|++.++.||.|.+|.|.. .+.|.+-|.|.+.+.|..|++.|
T Consensus       257 --~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m  334 (382)
T KOG1548|consen  257 --DDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTM  334 (382)
T ss_pred             --cccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHh
Confidence              0111233588999999843    233       467888899999999887764 34689999999999999999999


Q ss_pred             CCCccCCCCceEEEe
Q psy4057         229 HGFKITPTHAMKISF  243 (246)
Q Consensus       229 ~g~~i~~g~~l~v~~  243 (246)
                      +|+.|+ |+.|.-+.
T Consensus       335 ~GR~fd-gRql~A~i  348 (382)
T KOG1548|consen  335 DGRWFD-GRQLTASI  348 (382)
T ss_pred             cCeeec-ceEEEEEE
Confidence            999999 89887654

>KOG4205|consensus

Probab=99.77  E-value=1.3e-18  Score=142.04  Aligned_cols=161  Identities=20%  Similarity=0.333  Sum_probs=134.5

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...+|||++|+-+++++.|+++|++||+|.++.++++.   +++||+||+|.+.+....++. ...+++.|+.|.+..+.
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            67899999999999999999999999999999999876   889999999999999999876 44578899999888875


Q ss_pred             CCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                      +..+..                                                                       ...
T Consensus        84 ~r~~~~-----------------------------------------------------------------------~~~   92 (311)
T KOG4205|consen   84 SREDQT-----------------------------------------------------------------------KVG   92 (311)
T ss_pred             Cccccc-----------------------------------------------------------------------ccc
Confidence            543210                                                                       000


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .......+||++||.+++++++++.|++||.|.++-++.|.     +||+||.|.+.++..+++. ...+.|. |+.+.|
T Consensus        93 ~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~-gk~vev  170 (311)
T KOG4205|consen   93 RHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFN-GKKVEV  170 (311)
T ss_pred             cccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeec-CceeeE
Confidence            11257899999999999999999999999999999988866     5899999999999888754 5666777 787777


Q ss_pred             Eee
Q psy4057         242 SFA  244 (246)
Q Consensus       242 ~~a  244 (246)
                      .-|
T Consensus       171 krA  173 (311)
T KOG4205|consen  171 KRA  173 (311)
T ss_pred             eec
Confidence            644

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.77  E-value=4.2e-18  Score=125.81  Aligned_cols=81  Identities=22%  Similarity=0.386  Sum_probs=74.9

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ..+++|||+|||.++++++|+++|++||.|.+|.++.+.   +++|||||+|.+.++|+.|++.||+..+.|++|+|.++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            357899999999999999999999999999999998764   78999999999999999999999999999999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ..+.
T Consensus       112 ~~~~  115 (144)
T PLN03134        112 NDRP  115 (144)
T ss_pred             CcCC
Confidence            6553

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.75  E-value=1.8e-17  Score=122.52  Aligned_cols=77  Identities=21%  Similarity=0.359  Sum_probs=72.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ...+++|||+|||..+|+++|+++|++||.|.++.++.++     +|||||+|.+.++|+.|++.|||..|+ |++|+|+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~-Gr~l~V~  109 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELN-GRHIRVN  109 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC-CEEEEEE
Confidence            3358899999999999999999999999999999999865     589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      |++
T Consensus       110 ~a~  112 (144)
T PLN03134        110 PAN  112 (144)
T ss_pred             eCC
Confidence            986

>KOG0106|consensus

Probab=99.74  E-value=7.1e-18  Score=129.88  Aligned_cols=166  Identities=19%  Similarity=0.241  Sum_probs=131.0

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCccc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDV   91 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~~   91 (246)
                      ..+||++|++.+.+.+|.++|..||.|.++.+..     ||+||.|.+..+|..|+..+|+..|.|-.+.|.++......
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~-----gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~   76 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN-----GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRG   76 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec-----ccceeccCchhhhhcccchhcCceecceeeeeecccccccc
Confidence            3689999999999999999999999999997743     89999999999999999999999999988888887643211


Q ss_pred             cccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCCCC
Q psy4057          92 ISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPN  171 (246)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (246)
                      ....                                             ..+.  ..+.          ...........
T Consensus        77 ~g~~---------------------------------------------~~g~--r~~~----------~~~~~~p~~s~   99 (216)
T KOG0106|consen   77 RGRP---------------------------------------------RGGD--RRSD----------SRRYRPPSRTH   99 (216)
T ss_pred             cCCC---------------------------------------------CCCC--ccch----------hhccCCccccc
Confidence            1000                                             0000  0000          00111123358


Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      +.++|.|+...+.+.+|.+.|+++|.+.....   +.+++||+|.+.++|..|+..|+|..+. +++|.+.+
T Consensus       100 ~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra~~~l~~~~~~-~~~l~~~~  167 (216)
T KOG0106|consen  100 FRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRALEKLDGKKLN-GRRISVEK  167 (216)
T ss_pred             ceeeeccchhhhhHHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhcchhccchhhc-Cceeeecc
Confidence            88999999999999999999999999944444   4468999999999999999999999999 99998854

>KOG4212|consensus

Probab=99.71  E-value=1.1e-15  Score=126.39  Aligned_cols=206  Identities=16%  Similarity=0.191  Sum_probs=139.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhh-ccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFS-QFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~-~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...-.+.+||.|||++....+|+++|. +.|+|+.|.++-|.  ++||+|.|+|+++|.+++|++.||...+.||+|.|.
T Consensus        40 ~~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vK  119 (608)
T KOG4212|consen   40 VAARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVK  119 (608)
T ss_pred             cccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEe
Confidence            344567799999999999999999996 77999999988765  899999999999999999999999999999999986


Q ss_pred             EccC-Cccccc---cc-cCccccc-------c--cc-------ccC-CCCCCCChhHH---------------hhhhhhh
Q psy4057          84 YSKT-DSDVIS---KI-KGTFMER-------P--KK-------VRK-QPAPVEDPAEA---------------KKSKKKA  126 (246)
Q Consensus        84 ~a~~-~~~~~~---~~-~~~~~~~-------~--~~-------~~~-~~~~~~~~~~~---------------~~~~~~~  126 (246)
                      -... +.+...   +. .+.+...       .  +.       ... ....|.+..+.               .+..-..
T Consensus       120 Ed~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl  199 (608)
T KOG4212|consen  120 EDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGL  199 (608)
T ss_pred             ccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccc
Confidence            5322 111000   00 0000000       0  00       000 00111111111               1111111


Q ss_pred             HHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC
Q psy4057         127 AKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN  206 (246)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~  206 (246)
                      ..+..+       +.                     +. -..|....+||.||.+.+....|++.|.--|.|..|.+-.+
T Consensus       200 ~~~Flr-------~~---------------------h~-f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~id  250 (608)
T KOG4212|consen  200 SASFLR-------SL---------------------HI-FSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSID  250 (608)
T ss_pred             hhhhhh-------hc---------------------cC-CCCCccceeeeeccccccchHHHHHHhccceeeeeeceeec
Confidence            111111       00                     00 13345778899999999999999999999999999988886


Q ss_pred             C----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         207 R----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       207 ~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      +    +|+|.++|.+.-.|-.|+..|++.-.. .+++.+.
T Consensus       251 KeG~s~G~~vi~y~hpveavqaIsml~~~g~~-~~~~~~R  289 (608)
T KOG4212|consen  251 KEGNSRGFAVIEYDHPVEAVQAISMLDRQGLF-DRRMTVR  289 (608)
T ss_pred             cccccCCeeEEEecchHHHHHHHHhhccCCCc-cccceee
Confidence            6    689999999999999999999975544 4555544

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.70  E-value=8e-17  Score=137.05  Aligned_cols=80  Identities=18%  Similarity=0.453  Sum_probs=74.1

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ..+++|||+|||.++++++|+++|++||.|.+++++++.   +++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~  346 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFK  346 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            345589999999999999999999999999999999764   78999999999999999999999999999999999997


Q ss_pred             cCC
Q psy4057          86 KTD   88 (246)
Q Consensus        86 ~~~   88 (246)
                      ..+
T Consensus       347 ~~~  349 (352)
T TIGR01661       347 TNK  349 (352)
T ss_pred             cCC
Confidence            654

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>PF00076 RRM_1: RNA recognition motif

Probab=99.70  E-value=6.6e-17  Score=104.93  Aligned_cols=68  Identities=31%  Similarity=0.503  Sum_probs=64.5

Q ss_pred             EEecCCChhhhHHHHHHHhhccCCeeEEEEccC--CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEE
Q psy4057          14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT--LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR   81 (246)
Q Consensus        14 l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~--~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (246)
                      |||+|||.++++++|+++|++||.|..+.+..+  ++.+++|||+|.+.++|..|++.|||..+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999885  47789999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>PF00076 RRM_1: RNA recognition motif

Probab=99.67  E-value=2.4e-16  Score=102.26  Aligned_cols=66  Identities=33%  Similarity=0.554  Sum_probs=62.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC----CccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       174 l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      |||+|||.++|+++|+++|++||.|..+.+..+    .+++|||+|.+.++|..|++.|||..+. |+.|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKIN-GRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEET-TEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEEC-ccCcC
Confidence            799999999999999999999999999999995    2589999999999999999999999999 88875

(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 ....

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.66  E-value=4e-16  Score=123.31  Aligned_cols=75  Identities=23%  Similarity=0.279  Sum_probs=71.8

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      .++|||+|||+.+++++|+++|+.||.|++|.|.+++.++|||||+|.++++|..|+. |||..|.|+.|+|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            5899999999999999999999999999999999988788999999999999999996 99999999999999974

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.66  E-value=7.9e-16  Score=135.94  Aligned_cols=137  Identities=15%  Similarity=0.157  Sum_probs=101.7

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhcc--CCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQF--GQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~f--G~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      .+.++|||+||+.++++++|+++|++|  |.|++|.++     ++||||+|.+.++|.+|++.|||..|.|+.|+|.+++
T Consensus       231 ~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-----rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Ak  305 (578)
T TIGR01648       231 AKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-----RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAK  305 (578)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-----cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            346889999999999999999999999  999999774     4799999999999999999999999999999999997


Q ss_pred             CCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                      +.........+.        ..                                  +.    +.   .............
T Consensus       306 p~~~~~~~~~~r--------g~----------------------------------gg----~~---~~~~~~~~~~g~~  336 (578)
T TIGR01648       306 PVDKKSYVRYTR--------GT----------------------------------GG----RG---KERQAARQSLGQV  336 (578)
T ss_pred             CCCccccccccc--------cc----------------------------------CC----Cc---ccccccccccCcc
Confidence            653210000000        00                                  00    00   0000000001122


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCce
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFK  199 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~  199 (246)
                      ..+.+.++++.|++++.+++.+..+|..+|.|.
T Consensus       337 ~sp~s~~~~~g~~~~~~~~~~~~~~f~~~g~~~  369 (578)
T TIGR01648       337 YDPASRSLAYEDYYYHPPYAPSLHFPRMPGPIR  369 (578)
T ss_pred             cCccccccccccccccccccchhhccccCcccc
Confidence            456799999999999999999999999999864

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.

>KOG1456|consensus

Probab=99.66  E-value=1.4e-14  Score=117.79  Aligned_cols=232  Identities=16%  Similarity=0.200  Sum_probs=148.9

Q ss_pred             CCCCCcEEEe--cCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccC-C-eeEEE
Q psy4057           7 HICVTNFVYV--THISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY-D-KPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V--~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~-g-~~l~v   82 (246)
                      ...|++.|.+  -|--+..+-+-|+.++.+.|+|..|.|++.  +--.|.|+|.+.+.|++|.+.|||..|. | =+|+|
T Consensus       116 s~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKI  193 (494)
T KOG1456|consen  116 SATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKI  193 (494)
T ss_pred             CCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cceeeEEeechhHHHHHHHhhcccccccccceeEEE
Confidence            4566777766  577778899999999999999999999874  5567999999999999999999998874 3 46899


Q ss_pred             EEccCCccccccccC-ccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccc---cCCCCCCCCCCC
Q psy4057          83 QYSKTDSDVISKIKG-TFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSV---QQPPVSQPAPPA  158 (246)
Q Consensus        83 ~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~  158 (246)
                      +||++.....-+... ++.-..... ........+...+..++......+..   |...-.+..+   -.|..-.+.+-.
T Consensus       194 eyAkP~rlnV~knd~DtwDyTlp~~-~~~~~~g~~~~~r~~~p~~~~~~pss---~~G~h~~y~sg~~~~p~~~~P~r~~  269 (494)
T KOG1456|consen  194 EYAKPTRLNVQKNDKDTWDYTLPDL-RGPYDPGRNHYDRQRQPAPLGYHPSS---RGGGHSGYYSGDRHGPPHPPPSRYR  269 (494)
T ss_pred             EecCcceeeeeecCCccccccCCCC-CCCCCCCCCCCccccCCCccCCChhh---cCCCCCCCcccccCCCCCCCCCCCc
Confidence            999876432222211 111110000 00000001111111111000000000   0000000000   000000000000


Q ss_pred             -----CCCCCCCCCCCCCcEEEEcCCCC-CCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCc
Q psy4057         159 -----PMATAGVPEQPPNQILFLTNLPE-ETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK  232 (246)
Q Consensus       159 -----~~~~~~~~~~~~~~~l~v~nL~~-~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~  232 (246)
                           +....+.....+++++.|-+|.. ..+-+.|.++|..||.|.+|++++...|.|.|++.+...-++|+..||+..
T Consensus       270 ~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~  349 (494)
T KOG1456|consen  270 DGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIP  349 (494)
T ss_pred             cccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCc
Confidence                 00011123455799999999988 667899999999999999999999998999999999999999999999999


Q ss_pred             cCCCCceEEEeec
Q psy4057         233 ITPTHAMKISFAK  245 (246)
Q Consensus       233 i~~g~~l~v~~ak  245 (246)
                      +. |.+|.|.++|
T Consensus       350 lf-G~kl~v~~Sk  361 (494)
T KOG1456|consen  350 LF-GGKLNVCVSK  361 (494)
T ss_pred             cc-cceEEEeecc
Confidence            98 9999999987

>KOG1456|consensus

Probab=99.65  E-value=3.4e-15  Score=121.26  Aligned_cols=168  Identities=23%  Similarity=0.277  Sum_probs=136.8

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHH--HhcCCccCCeeEEE
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALR--SMQGFPFYDKPMRI   82 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~--~lng~~~~g~~l~v   82 (246)
                      +-+..++-.|.|++|-..++|.+|-+-.+.||.|..+.++.   .+..|.|+|++++.|.+++.  .-|...+.|+.--+
T Consensus        25 phk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P---~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~  101 (494)
T KOG1456|consen   25 PHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMP---HKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALF  101 (494)
T ss_pred             CCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEecc---ccceeeeeeccccchhhheehhccCcccccCchhhc
Confidence            34677889999999999999999999999999999988766   56779999999999999986  23445667777666


Q ss_pred             EEccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCC
Q psy4057          83 QYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMAT  162 (246)
Q Consensus        83 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (246)
                      .|+..+..  .+.                                                                   
T Consensus       102 NyStsq~i--~R~-------------------------------------------------------------------  112 (494)
T KOG1456|consen  102 NYSTSQCI--ERP-------------------------------------------------------------------  112 (494)
T ss_pred             ccchhhhh--ccC-------------------------------------------------------------------
Confidence            67643321  000                                                                   


Q ss_pred             CCCCCCCCCcEEEEc--CCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCC-Cce
Q psy4057         163 AGVPEQPPNQILFLT--NLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPT-HAM  239 (246)
Q Consensus       163 ~~~~~~~~~~~l~v~--nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g-~~l  239 (246)
                       ......++.+|++.  |--+.+|-+.|..++...|.|.+|.|.+.+--.|.|+|++.+.|++|..+|||..|+.| ++|
T Consensus       113 -g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTL  191 (494)
T KOG1456|consen  113 -GDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTL  191 (494)
T ss_pred             -CCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeE
Confidence             01233468888886  54558899999999999999999999998744799999999999999999999999866 899


Q ss_pred             EEEeec
Q psy4057         240 KISFAK  245 (246)
Q Consensus       240 ~v~~ak  245 (246)
                      +|+|||
T Consensus       192 KIeyAk  197 (494)
T KOG1456|consen  192 KIEYAK  197 (494)
T ss_pred             EEEecC
Confidence            999998

>KOG0107|consensus

Probab=99.65  E-value=7.9e-16  Score=112.70  Aligned_cols=76  Identities=22%  Similarity=0.365  Sum_probs=72.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      +..+.|||+||+..+++.+|..+|..||.+..|+|..++.|||||+|++..+|..|+..|+|..|+ |..++|++++
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~c-G~r~rVE~S~   83 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDIC-GSRIRVELST   83 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCcccc-CceEEEEeec
Confidence            358999999999999999999999999999999999999999999999999999999999999999 9999999864

>KOG0114|consensus

Probab=99.64  E-value=2.5e-15  Score=100.61  Aligned_cols=75  Identities=21%  Similarity=0.431  Sum_probs=70.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..++.|||+|||+++|.|+..++|.+||.|.-|++-...  +|.|||.|++..+|.+|++.|+|+.++ ++.|.|-|.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~-~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVD-NRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccC-CceEEEEec
Confidence            359999999999999999999999999999999988755  699999999999999999999999999 999999773

>KOG0114|consensus

Probab=99.64  E-value=1.7e-15  Score=101.40  Aligned_cols=79  Identities=23%  Similarity=0.467  Sum_probs=74.7

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...++-|||.|||++++.++..++|.+||.|.-|++-.+...+|.|||.|++..+|++|++.|+|..+.++.+.|-|..
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            3457899999999999999999999999999999998888999999999999999999999999999999999999864

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.64  E-value=1.2e-15  Score=128.09  Aligned_cols=78  Identities=24%  Similarity=0.442  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .....++|||+|||.++|+++|+++|+.||.|++|+|+.+.     +|||||+|.+.++|..|+..|||..+. +++|+|
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~-gr~i~V  181 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVR-NKRLKV  181 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccC-Cceeee
Confidence            45568999999999999999999999999999999999875     489999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .|++
T Consensus       182 ~~a~  185 (346)
T TIGR01659       182 SYAR  185 (346)
T ss_pred             eccc
Confidence            9986

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).

>KOG0121|consensus

Probab=99.63  E-value=5.1e-16  Score=107.89  Aligned_cols=80  Identities=28%  Similarity=0.426  Sum_probs=73.7

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      .....++||||+||+.-++|++|+++|+++|+|..|.|--+.   ...|||||+|-+.++|..|+..++|+.+..++|+|
T Consensus        31 ~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~  110 (153)
T KOG0121|consen   31 EALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRI  110 (153)
T ss_pred             HHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceee
Confidence            345679999999999999999999999999999999887665   45699999999999999999999999999999999


Q ss_pred             EEc
Q psy4057          83 QYS   85 (246)
Q Consensus        83 ~~a   85 (246)
                      .+.
T Consensus       111 D~D  113 (153)
T KOG0121|consen  111 DWD  113 (153)
T ss_pred             ecc
Confidence            985

>KOG0120|consensus

Probab=99.63  E-value=1.1e-15  Score=131.11  Aligned_cols=181  Identities=19%  Similarity=0.234  Sum_probs=139.3

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ....++||++||...++.++.++...||.+....++.+.   .++||||.+|.++.....|+..|||..+.+++|.|+.+
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            445789999999999999999999999999887777654   78999999999999999999999999999999999998


Q ss_pred             cCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCC
Q psy4057          86 KTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV  165 (246)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (246)
                      ............                                              .       .....+.-+.....
T Consensus       367 ~~g~~~~~~~~~----------------------------------------------~-------~~~~~~~i~~~~~q  393 (500)
T KOG0120|consen  367 IVGASNANVNFN----------------------------------------------I-------SQSQVPGIPLLMTQ  393 (500)
T ss_pred             hccchhccccCC----------------------------------------------c-------cccccccchhhhcc
Confidence            655321111110                                              0       00000000011123


Q ss_pred             CCCCCCcEEEEcCCC--CCCC--------HHHHHHHHccCCCceEEEEeeC-C-------ccEEEEEeCCHHHHHHHHHH
Q psy4057         166 PEQPPNQILFLTNLP--EETS--------EMMLSMLFNQFPGFKEVRLVPN-R-------HDIAFVEFENEMQSAAAKLA  227 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~--~~~t--------~e~l~~~f~~~G~i~~v~~~~~-~-------~g~afV~f~~~~~A~~Al~~  227 (246)
                      ....+..+|++.|+-  .+..        -|+++..|+.||.|..|.+... .       .|..||+|.+.+++++|+..
T Consensus       394 ~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~  473 (500)
T KOG0120|consen  394 MAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEE  473 (500)
T ss_pred             cCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHH
Confidence            456678889988862  2222        1477788999999999999886 2       37899999999999999999


Q ss_pred             hCCCccCCCCceEEEe
Q psy4057         228 LHGFKITPTHAMKISF  243 (246)
Q Consensus       228 l~g~~i~~g~~l~v~~  243 (246)
                      |+|++|. |+++..+|
T Consensus       474 L~GrKF~-nRtVvtsY  488 (500)
T KOG0120|consen  474 LTGRKFA-NRTVVASY  488 (500)
T ss_pred             ccCceeC-CcEEEEEe
Confidence            9999999 99998887

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.62  E-value=2.7e-15  Score=116.82  Aligned_cols=77  Identities=22%  Similarity=0.295  Sum_probs=72.8

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      .+.+|||+||++.+++++|+++|+.||+|++|.|++++.++++|||+|.++++|..|+. |||..|.|++|.|..+..
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            45899999999999999999999999999999999999888999999999999999996 999999999999998653

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.60  E-value=4.7e-15  Score=117.28  Aligned_cols=73  Identities=21%  Similarity=0.307  Sum_probs=68.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .++|||+|||+++|+++|+++|+.||.|.+|+++.++  +|||||+|.+.++|..|+. |||..|. |+.|+|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~-gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIV-DQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeC-CceEEEEecc
Confidence            5799999999999999999999999999999999975  6899999999999999995 9999999 9999999874

>KOG0125|consensus

Probab=99.60  E-value=1.6e-15  Score=121.29  Aligned_cols=78  Identities=19%  Similarity=0.307  Sum_probs=73.0

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      -++|+|.|||+...+-||+..|.+||.|.+|.|+.+. .|||||||+|.++++|++|-++|||..+.||+|.|..+..+
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchh
Confidence            3799999999999999999999999999999888665 78999999999999999999999999999999999998554

>KOG0121|consensus

Probab=99.59  E-value=3.4e-15  Score=103.80  Aligned_cols=73  Identities=18%  Similarity=0.318  Sum_probs=69.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      .+++|||+||++.+++|+|.++|+++|.|.+|-+-.|+     -|||||+|.+.++|..|++.++|+.++ .++|+|.|
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLd-dr~ir~D~  112 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLD-DRPIRIDW  112 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCccc-ccceeeec
Confidence            59999999999999999999999999999999988877     489999999999999999999999999 89999987

>KOG0107|consensus

Probab=99.59  E-value=5.1e-15  Score=108.49  Aligned_cols=81  Identities=25%  Similarity=0.378  Sum_probs=74.5

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      .-+-.++|||+||+..+++.||...|..||.|.+|.|-+  ...|||||+|++..+|..|+..|+|..|.|..|+|+.+.
T Consensus         6 ~~~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvAr--nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    6 DRNGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVAR--NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             ccCCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEee--cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            335589999999999999999999999999999999977  477999999999999999999999999999999999987


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      ...
T Consensus        84 G~~   86 (195)
T KOG0107|consen   84 GRP   86 (195)
T ss_pred             CCc
Confidence            654

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.59  E-value=2.2e-14  Score=117.34  Aligned_cols=167  Identities=21%  Similarity=0.300  Sum_probs=119.8

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      .++|||+|||.++++++|+++|..||.|..+.+..+.   +++|+|||.|.+.++|..|++.++|..|.|++|.|.++..
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            5999999999999999999999999999999988774   8999999999999999999999999999999999999643


Q ss_pred             -CccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          88 -DSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        88 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                       ...... ...           .  ..                     ..   .....                ......
T Consensus       195 ~~~~~~~-~~~-----------~--~~---------------------~~---~~~~~----------------~~~~~~  220 (306)
T COG0724         195 ASQPRSE-LSN-----------N--LD---------------------AS---FAKKL----------------SRGKAL  220 (306)
T ss_pred             ccccccc-ccc-----------c--cc---------------------hh---hhccc----------------cccccc
Confidence             100000 000           0  00                     00   00000                001122


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCc-----cEEEEEeCCHHHHHHHHHHhCCC
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAAKLALHGF  231 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~-----g~afV~f~~~~~A~~Al~~l~g~  231 (246)
                      .......+++.|++..++...+...|..+|.+....+.....     ...++.+.....+..+.......
T Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  290 (306)
T COG0724         221 LLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKK  290 (306)
T ss_pred             cccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccchhHHHhhhhhhccccce
Confidence            445688999999999999999999999999997777776542     22334444444444444444443

>KOG4211|consensus

Probab=99.59  E-value=8.3e-14  Score=117.07  Aligned_cols=160  Identities=18%  Similarity=0.226  Sum_probs=120.9

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC-CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCcc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT-LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSD   90 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~-~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~   90 (246)
                      ..|-+.+||-.+|++||.++|+.++ |+++.+.+. ++..|-|||+|.+++++.+|++ .+-..+..|.|.|.-+.....
T Consensus        11 ~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~e~   88 (510)
T KOG4211|consen   11 FEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGAEA   88 (510)
T ss_pred             eEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCccc
Confidence            3444599999999999999999999 999888776 7999999999999999999998 666777778888887754421


Q ss_pred             ccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCCC
Q psy4057          91 VISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPP  170 (246)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (246)
                                                                                .+..++..+        .....
T Consensus        89 ----------------------------------------------------------d~~~~~~g~--------~s~~~  102 (510)
T KOG4211|consen   89 ----------------------------------------------------------DWVMRPGGP--------NSSAN  102 (510)
T ss_pred             ----------------------------------------------------------cccccCCCC--------CCCCC
Confidence                                                                      000011110        11246


Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceE-EEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKE-VRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~-v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ..+|-+++||++||++||.++|+.--.+.. |.++.+.    .|-|||.|++.+.|+.||.. |-..|. .+-|.|
T Consensus       103 d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iG-hRYIEv  176 (510)
T KOG4211|consen  103 DGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIG-HRYIEV  176 (510)
T ss_pred             CceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhc-cceEEe
Confidence            788999999999999999999998666655 4445444    47899999999999999874 444455 455554

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.57  E-value=1.1e-14  Score=94.47  Aligned_cols=68  Identities=28%  Similarity=0.502  Sum_probs=61.8

Q ss_pred             EEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEE
Q psy4057          14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR   81 (246)
Q Consensus        14 l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (246)
                      |||+|||..+++++|.++|+.||.|..+.+..+.  .++++|||+|.+.++|.+|++.++|..+.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            7999999999999999999999999999998764  5789999999999999999999999999999875

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 ....

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.57  E-value=1.4e-14  Score=94.03  Aligned_cols=66  Identities=33%  Similarity=0.570  Sum_probs=60.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       174 l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      |+|+|||.++++++|+++|+.||.|..+++..++    +++|||+|.+.++|..|++.++|..++ |+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~-g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEID-GRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEET-TEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEEC-CEEcC
Confidence            7899999999999999999999999999999985    589999999999999999999999999 88874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0122|consensus

Probab=99.57  E-value=2.2e-14  Score=110.50  Aligned_cols=75  Identities=28%  Similarity=0.434  Sum_probs=72.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ...+|-|.||+.++++++|.++|.+||.|.++.|.+|+     +|||||.|.++++|++||..|||+-++ +-.|+|+|+
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd-~LILrvEws  266 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYD-NLILRVEWS  266 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccc-eEEEEEEec
Confidence            57889999999999999999999999999999999987     699999999999999999999999999 899999999


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      |
T Consensus       267 k  267 (270)
T KOG0122|consen  267 K  267 (270)
T ss_pred             C
Confidence            7

>KOG0111|consensus

Probab=99.57  E-value=2.6e-15  Score=113.77  Aligned_cols=81  Identities=28%  Similarity=0.430  Sum_probs=75.9

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .-.++|||++|..+++|.-|...|-+||.|.+|.+.-|.   +.||||||+|.-.|+|..||..||+..+.||+|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            457999999999999999999999999999999998765   88999999999999999999999999999999999999


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ++..
T Consensus        88 kP~k   91 (298)
T KOG0111|consen   88 KPEK   91 (298)
T ss_pred             CCcc
Confidence            7654

>KOG0122|consensus

Probab=99.57  E-value=1e-14  Score=112.28  Aligned_cols=79  Identities=25%  Similarity=0.417  Sum_probs=74.0

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      -+++|-|.||+.+++|++|.+||.+||.|..|.+.++.   .+||||||.|.+.++|.+||..|||.=+..--|+|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            45679999999999999999999999999999998865   899999999999999999999999999999999999997


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      +.
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            64

>PF13893 RRM_5: RNA recognition motif

Probab=99.55  E-value=2.6e-14  Score=88.49  Aligned_cols=56  Identities=29%  Similarity=0.511  Sum_probs=52.4

Q ss_pred             HHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         188 LSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       188 l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      |+++|++||.|.++.+.++..++|||+|.+.++|..|++.|||..+. |++|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~-g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFN-GRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEET-TEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEC-CcEEEEEEC
Confidence            68899999999999999887789999999999999999999999999 999999997

(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 ....

>PLN03213 repressor of silencing 3; Provisional

Probab=99.54  E-value=2.4e-14  Score=120.29  Aligned_cols=80  Identities=19%  Similarity=0.207  Sum_probs=72.8

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCH--HHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEI--ASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~--~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .....+||||||++++++++|..+|..||.|.+|.|+|.. .||||||+|.+.  .++.+||..|||..+.|+.|+|..|
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRET-GRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTK-GRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeccc-CCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            3456899999999999999999999999999999999653 399999999988  7899999999999999999999998


Q ss_pred             cCC
Q psy4057          86 KTD   88 (246)
Q Consensus        86 ~~~   88 (246)
                      ++.
T Consensus        86 KP~   88 (759)
T PLN03213         86 KEH   88 (759)
T ss_pred             cHH
Confidence            653

>KOG4207|consensus

Probab=99.53  E-value=1.6e-14  Score=108.55  Aligned_cols=80  Identities=23%  Similarity=0.385  Sum_probs=74.0

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      +.--.+|-|.||++.++-++|+.+|++||.|-+|.|.+|.   .++|||||.|....+|+.|++.|+|.++.|+.|+|+.
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~   89 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQM   89 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehh
Confidence            3345678999999999999999999999999999999876   7889999999999999999999999999999999998


Q ss_pred             ccC
Q psy4057          85 SKT   87 (246)
Q Consensus        85 a~~   87 (246)
                      |+-
T Consensus        90 ary   92 (256)
T KOG4207|consen   90 ARY   92 (256)
T ss_pred             hhc
Confidence            764

>PF13893 RRM_5: RNA recognition motif

Probab=99.53  E-value=7.8e-14  Score=86.35  Aligned_cols=56  Identities=36%  Similarity=0.748  Sum_probs=51.5

Q ss_pred             HHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        28 l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      |+++|++||+|.++.+.+..  +++|||+|.+.++|+.|++.|||..+.|++|+|.||
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            67999999999999997754  799999999999999999999999999999999986

(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 ....

>KOG0149|consensus

Probab=99.52  E-value=1.9e-14  Score=110.34  Aligned_cols=75  Identities=21%  Similarity=0.357  Sum_probs=67.7

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      -.+||||+|+-++..+.|+++|++||+|++..++.|+   +|||||||+|++.++|.+|++.. .-.|.||+-.|.+|.
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNLAS   89 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccchhh
Confidence            4689999999999999999999999999999999876   99999999999999999999844 356799998888764

>KOG0125|consensus

Probab=99.52  E-value=4.6e-14  Score=113.00  Aligned_cols=76  Identities=22%  Similarity=0.393  Sum_probs=70.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ....++|+|+|+|+...+-||+..|++||.|.+|.|+-+.   +|||||+|++.++|.+|...|||..|. ||+|.|--|
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VE-GRkIEVn~A  171 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVE-GRKIEVNNA  171 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceee-ceEEEEecc
Confidence            3357899999999999999999999999999999999865   689999999999999999999999999 999999754

>KOG0126|consensus

Probab=99.52  E-value=1e-15  Score=112.74  Aligned_cols=77  Identities=21%  Similarity=0.473  Sum_probs=72.3

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      -+.-|||||||++++|.||.-.|++||+|.+|.++||.   +|+||||+.|++..+.--|+..|||..+.||+|+|....
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            35679999999999999999999999999999999875   899999999999999999999999999999999998753

>KOG4207|consensus

Probab=99.51  E-value=2.9e-14  Score=107.19  Aligned_cols=75  Identities=23%  Similarity=0.334  Sum_probs=71.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .-..|.|-||-+.++.++|+.+|++||.|-+|.|+.|+     +|||||.|.+..+|+.|+++|+|..++ |+.|+|++|
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ld-gRelrVq~a   90 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLD-GRELRVQMA   90 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeec-cceeeehhh
Confidence            46789999999999999999999999999999999987     599999999999999999999999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      |
T Consensus        91 r   91 (256)
T KOG4207|consen   91 R   91 (256)
T ss_pred             h
Confidence            6

>smart00362 RRM_2 RNA recognition motif

Probab=99.51  E-value=1.1e-13  Score=89.45  Aligned_cols=69  Identities=33%  Similarity=0.555  Sum_probs=64.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      +|+|+|||..+++++|+++|++||.+..+.+..+.   +++|||+|.+.++|..|+..|+|..+. |++|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~-~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLG-GRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEEC-CEEEeeC
Confidence            48999999999999999999999999999999875   689999999999999999999999999 8988873

>KOG0113|consensus

Probab=99.50  E-value=6.6e-14  Score=110.74  Aligned_cols=80  Identities=15%  Similarity=0.270  Sum_probs=75.2

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      .-|-+||||+-|+++++|..|+..|+.||+|+.|.|+++.   +++|||||+|..+.+...|.+..+|..|.|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            4688999999999999999999999999999999999874   8999999999999999999999999999999999988


Q ss_pred             ccC
Q psy4057          85 SKT   87 (246)
Q Consensus        85 a~~   87 (246)
                      -..
T Consensus       178 ERg  180 (335)
T KOG0113|consen  178 ERG  180 (335)
T ss_pred             ccc
Confidence            543

>KOG4212|consensus

Probab=99.50  E-value=2.3e-12  Score=106.99  Aligned_cols=74  Identities=16%  Similarity=0.228  Sum_probs=69.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..|+|||+|||+++||+.|++-|..||.|..+.++...+..++|.|.++++|.+|+..|||.+++ |+.|+|.|.
T Consensus       535 Ka~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~-Gr~I~V~y~  608 (608)
T KOG4212|consen  535 KACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLD-GRNIKVTYF  608 (608)
T ss_pred             cccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCccc-CceeeeeeC
Confidence            47889999999999999999999999999999997766566899999999999999999999999 999999984

>smart00362 RRM_2 RNA recognition motif

Probab=99.50  E-value=1.6e-13  Score=88.66  Aligned_cols=71  Identities=27%  Similarity=0.492  Sum_probs=65.6

Q ss_pred             EEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057          13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus        13 ~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      +|||+|||..++.++|+++|.+||.|..+.+.++. .++++|||+|.+.++|+.|+..+++..+.|++|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999888763 677999999999999999999999999999998863

>KOG4206|consensus

Probab=99.49  E-value=1.1e-13  Score=105.90  Aligned_cols=78  Identities=32%  Similarity=0.478  Sum_probs=72.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHH----HHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSM----LFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~----~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ..++.+|||.||...+..++|++    +|++||.|.+|...+..  +|.|||.|.+.+.|..|+..|+|+.|+ |++|+|
T Consensus         6 ~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFy-gK~mri   84 (221)
T KOG4206|consen    6 VNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFY-GKPMRI   84 (221)
T ss_pred             cCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCccc-Cchhhe
Confidence            44566999999999999999998    99999999999988766  699999999999999999999999999 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      +|||.
T Consensus        85 qyA~s   89 (221)
T KOG4206|consen   85 QYAKS   89 (221)
T ss_pred             ecccC
Confidence            99984

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.49  E-value=2.2e-13  Score=106.25  Aligned_cols=72  Identities=19%  Similarity=0.240  Sum_probs=66.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ...+|+|+||++.+|+++|+++|+.||.|.+|++++++  .++|||+|.+.++|..|+ .|||..|. +++|.|.-
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~-d~~I~It~   77 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIV-DQRVCITR   77 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeC-CceEEEEe
Confidence            46899999999999999999999999999999999976  479999999999999998 69999999 89998864

>KOG0130|consensus

Probab=99.48  E-value=9.2e-14  Score=97.58  Aligned_cols=74  Identities=26%  Similarity=0.401  Sum_probs=70.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ....|||.++....|+++|.+.|..||+|+.+.+-.++     +|||+|+|.+.++|+.|+..|||..+- |..|.|.|+
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll-~q~v~VDw~  149 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELL-GQNVSVDWC  149 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhh-CCceeEEEE
Confidence            48899999999999999999999999999999999988     589999999999999999999999999 999999985

>PLN03213 repressor of silencing 3; Provisional

Probab=99.48  E-value=2.1e-13  Score=114.69  Aligned_cols=77  Identities=16%  Similarity=0.191  Sum_probs=71.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-ccEEEEEeCCH--HHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFENE--MQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~--~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .....+|||+||++.+++++|+.+|+.||.|.+|.|++.. +|||||+|.+.  .++.+|+..|||..+. |+.|+|.-|
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWK-GR~LKVNKA   85 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWK-GGRLRLEKA   85 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeec-CceeEEeec
Confidence            3457899999999999999999999999999999999743 79999999987  7899999999999999 999999988


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      |
T Consensus        86 K   86 (759)
T PLN03213         86 K   86 (759)
T ss_pred             c
Confidence            7

>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=99.45  E-value=8.1e-13  Score=85.85  Aligned_cols=70  Identities=36%  Similarity=0.615  Sum_probs=65.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      +|+|+|||..+++++|+++|+.||.|..+.+..++    .++|||+|.+.++|..|++.++|..+. |+++.|.|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~-~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELG-GRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeEC-CeEEEEeC
Confidence            48899999999999999999999999999999876    689999999999999999999999999 99999875

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0113|consensus

Probab=99.45  E-value=5.8e-13  Score=105.46  Aligned_cols=78  Identities=29%  Similarity=0.456  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...|-+||||.-|++++++..|+..|+.||.|+.|+|+.+.     +|||||+|.+..+...|...-+|..|+ |+.|.|
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Id-grri~V  175 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKID-GRRILV  175 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceec-CcEEEE
Confidence            45689999999999999999999999999999999999975     699999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .|-+
T Consensus       176 DvER  179 (335)
T KOG0113|consen  176 DVER  179 (335)
T ss_pred             Eecc
Confidence            8743

>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=99.42  E-value=1.7e-12  Score=84.35  Aligned_cols=72  Identities=25%  Similarity=0.538  Sum_probs=66.7

Q ss_pred             EEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057          13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus        13 ~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      +|+|+|||..+++++|+++|..||.|..+.+..+.  ..+++|||+|.+.++|..|++.+++..+.|+++.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            58999999999999999999999999999998765  4689999999999999999999999999999998864

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=99.42  E-value=4.3e-13  Score=94.25  Aligned_cols=77  Identities=16%  Similarity=0.337  Sum_probs=70.5

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      +-.|||.++..+.+|+++++.|..||+|.+|.+-.|.   =.+|||+|+|.+.++|+.|++.+||..+.|.+|.|.|+..
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            4468999999999999999999999999999987665   4579999999999999999999999999999999998753

>KOG0105|consensus

Probab=99.41  E-value=3.6e-13  Score=99.68  Aligned_cols=75  Identities=23%  Similarity=0.462  Sum_probs=68.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .++.|||+|||.++.+.+|.++|.+||.|..|.+..-+  ..||||+|++..+|..|+..-+|+.++ |++|+|+|++
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdyd-g~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYD-GCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccC-cceEEEEecc
Confidence            57899999999999999999999999999887765533  579999999999999999999999999 9999999975

>KOG0111|consensus

Probab=99.41  E-value=1.3e-13  Score=104.59  Aligned_cols=75  Identities=24%  Similarity=0.433  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..++|||++|..++++..|...|-+||.|.+|.++.|-     +|||||+|.-.|+|.+||..||+.++. |++|+|-||
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~-GrtirVN~A   87 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELF-GRTIRVNLA   87 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhc-ceeEEEeec
Confidence            57899999999999999999999999999999999864     689999999999999999999999999 999999999


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      |
T Consensus        88 k   88 (298)
T KOG0111|consen   88 K   88 (298)
T ss_pred             C
Confidence            7

>smart00360 RRM RNA recognition motif

Probab=99.41  E-value=1.1e-12  Score=84.35  Aligned_cols=66  Identities=36%  Similarity=0.581  Sum_probs=61.1

Q ss_pred             EcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         176 LTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       176 v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      |+|||..+++++|+++|++||.|..+.+..++     +|+|||+|.+.++|..|+..|+|..+. |+.|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~-~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELD-GRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeC-CcEEEeC
Confidence            57999999999999999999999999998875     479999999999999999999999998 8998874

>smart00360 RRM RNA recognition motif

Probab=99.41  E-value=1.2e-12  Score=84.17  Aligned_cols=68  Identities=26%  Similarity=0.494  Sum_probs=62.3

Q ss_pred             ecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057          16 VTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus        16 V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      |+|||..+++++|+++|++||.|..+.+..+   +.++|+|||+|.+.++|..|+..+++..+.|+.|+|.
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            5799999999999999999999999988875   3678999999999999999999999999999998873

>KOG0117|consensus

Probab=99.39  E-value=2.6e-12  Score=106.90  Aligned_cols=76  Identities=24%  Similarity=0.406  Sum_probs=71.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      +..+-|||+.||.++.+++|.-+|++.|+|-++|++.++     +|||||.|.+.+.|+.|++.||+++|-.|+.|.|+.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            569999999999999999999999999999999999974     799999999999999999999999998899999976


Q ss_pred             e
Q psy4057         244 A  244 (246)
Q Consensus       244 a  244 (246)
                      +
T Consensus       161 S  161 (506)
T KOG0117|consen  161 S  161 (506)
T ss_pred             e
Confidence            4

>KOG0108|consensus

Probab=99.38  E-value=1.4e-12  Score=111.49  Aligned_cols=77  Identities=25%  Similarity=0.471  Sum_probs=73.3

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      ++|||||+|+++++++|.++|+..|.|.++++..|+   +.+||||++|.+.++|..|++.|||.++.||+|+|.|+...
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            999999999999999999999999999999998765   88999999999999999999999999999999999997544

>KOG0131|consensus

Probab=99.37  E-value=8.9e-13  Score=97.39  Aligned_cols=74  Identities=26%  Similarity=0.345  Sum_probs=70.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ...+|||+||+..++++.|.++|-+.|+|.++++++++     +||||++|.++|+|.-|++.||.-+++ |++|+|.-|
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLY-grpIrv~ka   86 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLY-GRPIRVNKA   86 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhc-CceeEEEec
Confidence            57899999999999999999999999999999999976     699999999999999999999999999 999999764

>KOG0108|consensus

Probab=99.33  E-value=3.3e-12  Score=109.18  Aligned_cols=73  Identities=27%  Similarity=0.440  Sum_probs=70.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      +.+||+|+|+++++++|.++|+..|.|.+++++.|+     +||||++|.+.++|..|++.|||.++. |++|+|.|+.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~-gr~l~v~~~~   96 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFN-GRKLRVNYAS   96 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccC-CceEEeeccc
Confidence            999999999999999999999999999999999987     689999999999999999999999999 9999999975

>KOG0126|consensus

Probab=99.32  E-value=1.5e-13  Score=101.43  Aligned_cols=76  Identities=21%  Similarity=0.423  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ....+.-|||+|||+.+|+.+|--+|++||+|++|.+++|.     +||||+-|++..+...|+..|||..|. |+.|+|
T Consensus        31 ~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~-gRtirV  109 (219)
T KOG0126|consen   31 EYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKIL-GRTIRV  109 (219)
T ss_pred             hcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceec-ceeEEe
Confidence            44568899999999999999999999999999999999987     689999999999999999999999999 999999


Q ss_pred             Ee
Q psy4057         242 SF  243 (246)
Q Consensus       242 ~~  243 (246)
                      .-
T Consensus       110 DH  111 (219)
T KOG0126|consen  110 DH  111 (219)
T ss_pred             ee
Confidence            63

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.32  E-value=8.4e-12  Score=101.98  Aligned_cols=74  Identities=38%  Similarity=0.570  Sum_probs=70.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..+|||+|||.++|+++|.++|..||.|..+.+..++     +|+|||+|.+.++|..|+..|+|..|. |++|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~-~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELE-GRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeEC-CceeEeeccc
Confidence            7999999999999999999999999999999999875     589999999999999999999999999 9999999853

>smart00361 RRM_1 RNA recognition motif

Probab=99.30  E-value=9.9e-12  Score=80.47  Aligned_cols=57  Identities=21%  Similarity=0.376  Sum_probs=48.4

Q ss_pred             HHHHHHhh----ccCCeeEEE-EccC-----CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057          26 KSLYAIFS----QFGQIMDIV-ALKT-----LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus        26 ~~l~~~F~----~fG~i~~v~-~~~~-----~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ++|+++|+    +||.|.+|. +..+     +.++|+|||+|.+.++|.+|+..|||..+.|+.|++
T Consensus         3 ~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        3 EDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             hhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            45666666    999999985 3322     568999999999999999999999999999999986

>KOG0112|consensus

Probab=99.29  E-value=2.6e-12  Score=114.97  Aligned_cols=158  Identities=15%  Similarity=0.201  Sum_probs=135.7

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ...+++||++||...+++.+|+..|..+|.|++|.|-+..  ..-.||||.|.+...+-.|...+.+..|....+++.+.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            3468999999999999999999999999999999886653  44478999999999999999989887776556666663


Q ss_pred             cCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCC
Q psy4057          86 KTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV  165 (246)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (246)
                      ..                                                                              
T Consensus       449 ~~------------------------------------------------------------------------------  450 (975)
T KOG0112|consen  449 QP------------------------------------------------------------------------------  450 (975)
T ss_pred             cc------------------------------------------------------------------------------
Confidence            11                                                                              


Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCC-CceEEEee
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPT-HAMKISFA  244 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g-~~l~v~~a  244 (246)
                       ...+++.+++++|+..+....|.+.|..||.|..|.+-.+. .||+|.|.+...|+.|+..|-|+.|+++ ++++|.||
T Consensus       451 -kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq-~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla  528 (975)
T KOG0112|consen  451 -KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQ-PYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLA  528 (975)
T ss_pred             -ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCC-cceeeecccCccchhhHHHHhcCcCCCCCcccccccc
Confidence             23368899999999999999999999999999987776665 6999999999999999999999999853 88999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus       529 ~  529 (975)
T KOG0112|consen  529 S  529 (975)
T ss_pred             c
Confidence            5

>KOG0149|consensus

Probab=99.28  E-value=9.3e-12  Score=95.74  Aligned_cols=72  Identities=19%  Similarity=0.249  Sum_probs=62.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      +..-+.|||+||+-.++.|+|++.|++||+|+++.|+-|+     +|||||+|.+.++|.+|++..|- .|+ ||+-.+
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~p-iId-GR~aNc   85 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNP-IID-GRKANC   85 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCC-ccc-cccccc
Confidence            4457899999999999999999999999999999999987     69999999999999999987655 466 665444

>KOG0109|consensus

Probab=99.24  E-value=8.3e-12  Score=98.68  Aligned_cols=70  Identities=31%  Similarity=0.511  Sum_probs=66.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..|||+|||..+++.+|+.+|++||+|..+.|+++   ||||..++...|.-|++.|||++++ |..|.|+=+|
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN---YgFVHiEdktaaedairNLhgYtLh-g~nInVeaSk   72 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN---YGFVHIEDKTAAEDAIRNLHGYTLH-GVNINVEASK   72 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc---cceEEeecccccHHHHhhcccceec-ceEEEEEecc
Confidence            36899999999999999999999999999999987   8999999999999999999999999 9999998766

>KOG1365|consensus

Probab=99.24  E-value=4.9e-11  Score=97.66  Aligned_cols=181  Identities=19%  Similarity=0.208  Sum_probs=117.1

Q ss_pred             CcEEEe--cCCChhhhHHHHHHHhhcc----CCeeEEEEcc--CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057          11 TNFVYV--THISSTDLKKSLYAIFSQF----GQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus        11 ~~~l~V--~nl~~~~~e~~l~~~F~~f----G~i~~v~~~~--~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      .+-+.|  ++||+++++.++.++|.+-    |..+.|..++  |++..|-|||.|.++++|+.|+.+ |...+.-|.|.+
T Consensus       159 ~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIEl  237 (508)
T KOG1365|consen  159 ENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIEL  237 (508)
T ss_pred             ccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHH
Confidence            344555  8999999999999999632    2355554443  668889999999999999999983 333444444444


Q ss_pred             EEccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCC--
Q psy4057          83 QYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPM--  160 (246)
Q Consensus        83 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  160 (246)
                      ..+...                                               +.++..+...+. |..-....|.-+  
T Consensus       238 FRSTaa-----------------------------------------------Evqqvlnr~~s~-pLi~~~~sp~~p~~  269 (508)
T KOG1365|consen  238 FRSTAA-----------------------------------------------EVQQVLNREVSE-PLIPGLTSPLLPGG  269 (508)
T ss_pred             HHHhHH-----------------------------------------------HHHHHHHhhccc-cccCCCCCCCCCCC
Confidence            443211                                               111111111000 000000111100  


Q ss_pred             CCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceE---EEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCcc
Q psy4057         161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE---VRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKI  233 (246)
Q Consensus       161 ~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~---v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i  233 (246)
                      +..-.+......+|-+++||+..+.|+|.++|..|-.-++   |.++.+.    .|-|||+|.+.+.|..|....+.+..
T Consensus       270 p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~m  349 (508)
T KOG1365|consen  270 PARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLM  349 (508)
T ss_pred             ccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhc
Confidence            1112223344789999999999999999999998865432   5666655    47899999999999999999888766


Q ss_pred             CCCCceEE
Q psy4057         234 TPTHAMKI  241 (246)
Q Consensus       234 ~~g~~l~v  241 (246)
                      . ++.|.|
T Consensus       350 k-~RYiEv  356 (508)
T KOG1365|consen  350 K-SRYIEV  356 (508)
T ss_pred             c-cceEEE
Confidence            5 677766

>KOG0129|consensus

Probab=99.24  E-value=3.3e-10  Score=96.31  Aligned_cols=174  Identities=19%  Similarity=0.190  Sum_probs=116.4

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-----CCcc---EEEEEEcCHHHHHHHHHHhcCCccCCee
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-----KMRG---QAFVIFKEIASATNALRSMQGFPFYDKP   79 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-----~~kg---~aFV~f~~~~~A~~Ai~~lng~~~~g~~   79 (246)
                      ..-++.||||+||.+++|+.|...|..||.+..=.-.+..     ..+|   |+|+.|+++.+++.-+..+.-   ....
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~~~~  332 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---GEGN  332 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---cccc
Confidence            3457899999999999999999999999976432211111     4556   999999999999887665432   2222


Q ss_pred             EEEEEccCCc-cccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCC
Q psy4057          80 MRIQYSKTDS-DVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPA  158 (246)
Q Consensus        80 l~v~~a~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (246)
                      +.+..+.+.. +.                                                ......|+.....--    
T Consensus       333 ~yf~vss~~~k~k------------------------------------------------~VQIrPW~laDs~fv----  360 (520)
T KOG0129|consen  333 YYFKVSSPTIKDK------------------------------------------------EVQIRPWVLADSDFV----  360 (520)
T ss_pred             eEEEEecCccccc------------------------------------------------ceeEEeeEeccchhh----
Confidence            2222221110 00                                                000000000000000    


Q ss_pred             CCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHc-cCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHH----h
Q psy4057         159 PMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFN-QFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLA----L  228 (246)
Q Consensus       159 ~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~-~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~----l  228 (246)
                         ........+.+|+||++||.-++-++|..+|+ -||.|..+-|-.|+     +|-|=|.|.+..+=.+||.+    |
T Consensus       361 ---~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql  437 (520)
T KOG0129|consen  361 ---LDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQL  437 (520)
T ss_pred             ---hccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEE
Confidence               00112344799999999999999999999999 89999999888884     68899999999999999886    5


Q ss_pred             CCCccCCCCceEE
Q psy4057         229 HGFKITPTHAMKI  241 (246)
Q Consensus       229 ~g~~i~~g~~l~v  241 (246)
                      +..+|+  +++.|
T Consensus       438 ~h~d~~--KRVEI  448 (520)
T KOG0129|consen  438 DHTDID--KRVEI  448 (520)
T ss_pred             eccccc--eeeee
Confidence            666666  45555

>smart00361 RRM_1 RNA recognition motif

Probab=99.21  E-value=4.7e-11  Score=77.27  Aligned_cols=57  Identities=16%  Similarity=0.273  Sum_probs=48.8

Q ss_pred             HHHHHHHHc----cCCCceEEE-EeeC-------CccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         185 EMMLSMLFN----QFPGFKEVR-LVPN-------RHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       185 ~e~l~~~f~----~~G~i~~v~-~~~~-------~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      +++|+++|+    .||.|.++. ++.+       .+|+|||+|.+.++|..|+..|||+.+. |+.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~-gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFD-GRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEEC-CEEEEeC
Confidence            577888888    999999885 4332       2689999999999999999999999999 9998863

>KOG0132|consensus

Probab=99.20  E-value=3.7e-11  Score=106.16  Aligned_cols=73  Identities=25%  Similarity=0.488  Sum_probs=70.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ++||||+.|+..+++.+|.++|+.||.|.+|.++..+ +||||.+.++.+|.+|++.|+...+. ++.|+|.||.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R-~cAfI~M~~RqdA~kalqkl~n~kv~-~k~Iki~Wa~  493 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR-GCAFIKMVRRQDAEKALQKLSNVKVA-DKTIKIAWAV  493 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC-ceeEEEEeehhHHHHHHHHHhccccc-ceeeEEeeec
Confidence            8999999999999999999999999999999999888 79999999999999999999999999 9999999983

>KOG0120|consensus

Probab=99.20  E-value=4.8e-11  Score=102.81  Aligned_cols=176  Identities=21%  Similarity=0.325  Sum_probs=130.8

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhcc-----------C-CeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCC
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQF-----------G-QIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD   77 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~f-----------G-~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (246)
                      ..+.+||++++....++..-.+|..-           | .+..+.+   ...+++||++|.+.+.|..|+. +++..+.|
T Consensus       174 q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~---n~~~nfa~ie~~s~~~at~~~~-~~~~~f~g  249 (500)
T KOG0120|consen  174 QARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQL---NLEKNFAFIEFRSISEATEAMA-LDGIIFEG  249 (500)
T ss_pred             hhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeee---cccccceeEEecCCCchhhhhc-ccchhhCC
Confidence            46789999999999999988888765           3 2445444   2478999999999999999998 88999999


Q ss_pred             eeEEEEEccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCC
Q psy4057          78 KPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPP  157 (246)
Q Consensus        78 ~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (246)
                      +++++..-..... ..  .                                           ......+        ...
T Consensus       250 ~~~~~~r~~d~~~-~p--~-------------------------------------------~~~~~~~--------~~~  275 (500)
T KOG0120|consen  250 RPLKIRRPHDYQP-VP--G-------------------------------------------ITLSPSQ--------LGK  275 (500)
T ss_pred             CCceecccccccC-Cc--c-------------------------------------------chhhhcc--------ccc
Confidence            9998865321110 00  0                                           0000000        000


Q ss_pred             CCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCc
Q psy4057         158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFK  232 (246)
Q Consensus       158 ~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~  232 (246)
                      ..+.............++|+|||..+++++++++...||.+...+++.+.     +||||.+|.+......|+..|||..
T Consensus       276 ~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~  355 (500)
T KOG0120|consen  276 VGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQ  355 (500)
T ss_pred             cCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhh
Confidence            00000011122346789999999999999999999999999999988865     6899999999999999999999999


Q ss_pred             cCCCCceEEEee
Q psy4057         233 ITPTHAMKISFA  244 (246)
Q Consensus       233 i~~g~~l~v~~a  244 (246)
                      ++ ++.|.|+.|
T Consensus       356 lg-d~~lvvq~A  366 (500)
T KOG0120|consen  356 LG-DKKLVVQRA  366 (500)
T ss_pred             hc-CceeEeehh
Confidence            99 899998765

>KOG0132|consensus

Probab=99.16  E-value=8.7e-11  Score=103.86  Aligned_cols=75  Identities=24%  Similarity=0.434  Sum_probs=70.8

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      ++|||||+|+..+++.||..+|+.||+|.+|.++.   ++++|||.+....+|.+|+.+|+...+.++.|+|.|+...
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~---~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP---PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc---CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            78999999999999999999999999999998865   8899999999999999999999999999999999998543

>KOG4454|consensus

Probab=99.12  E-value=2e-11  Score=92.85  Aligned_cols=140  Identities=18%  Similarity=0.184  Sum_probs=112.6

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .++..++|||+|+...++|+-|.++|.+-|+|.+|.|..+. ....||||.|.++-+...|++-+||..+.++++.|.+-
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            56678999999999999999999999999999999887654 22249999999999999999999999999999988873


Q ss_pred             cCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCC
Q psy4057          86 KTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV  165 (246)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (246)
                      ...+.                                                                           
T Consensus        85 ~G~sh---------------------------------------------------------------------------   89 (267)
T KOG4454|consen   85 CGNSH---------------------------------------------------------------------------   89 (267)
T ss_pred             cCCCc---------------------------------------------------------------------------
Confidence            21110                                                                           


Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCc
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFK  232 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~  232 (246)
                                 .-|...++.+.+...|+.-|.+..+++..++    +.++|+.|-..-+.-.|+....+..
T Consensus        90 -----------apld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~  149 (267)
T KOG4454|consen   90 -----------APLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLE  149 (267)
T ss_pred             -----------chhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccC
Confidence                       0144567888999999999999888888754    3578888877666667777666644

>KOG0415|consensus

Probab=99.12  E-value=8.4e-11  Score=95.42  Aligned_cols=84  Identities=21%  Similarity=0.342  Sum_probs=76.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..||.+.|||..|.+-++.++|.-+|+.||.|.+|.++++.   -+-.||||+|.+.++...|.=+|++..+.++.|.|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            46899999999999999999999999999999999999986   455899999999999999999999999999999999


Q ss_pred             EccCCcc
Q psy4057          84 YSKTDSD   90 (246)
Q Consensus        84 ~a~~~~~   90 (246)
                      |+.+-+.
T Consensus       315 FSQSVsk  321 (479)
T KOG0415|consen  315 FSQSVSK  321 (479)
T ss_pred             hhhhhhh
Confidence            9865443

>KOG0153|consensus

Probab=99.09  E-value=3e-10  Score=92.01  Aligned_cols=75  Identities=21%  Similarity=0.369  Sum_probs=67.2

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHh-cCCccCCeeEEEEEccC
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM-QGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l-ng~~~~g~~l~v~~a~~   87 (246)
                      ...+|||++|...++|.+|++.|.+||+|++|.+..   .+++|||+|.+.++|+.|.+++ |.+.+.|++|.|.|+.+
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~---~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP---RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeec---ccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            468999999999999999999999999999998865   5679999999999999988765 55677999999999876

>KOG0146|consensus

Probab=99.09  E-value=1.3e-10  Score=91.09  Aligned_cols=82  Identities=22%  Similarity=0.317  Sum_probs=75.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      +.|.++.|||-.||.+....+|...|-+||.|.+.++.-|+   .+|.|+||.|.|+.+|+.||..|||+.|.=++|+|+
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            56788999999999999999999999999999999888665   799999999999999999999999999999999998


Q ss_pred             EccCC
Q psy4057          84 YSKTD   88 (246)
Q Consensus        84 ~a~~~   88 (246)
                      +-+++
T Consensus       361 LKRPk  365 (371)
T KOG0146|consen  361 LKRPK  365 (371)
T ss_pred             hcCcc
Confidence            85443

>KOG0153|consensus

Probab=99.09  E-value=3.9e-10  Score=91.37  Aligned_cols=77  Identities=22%  Similarity=0.397  Sum_probs=68.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHh-CCCccCCCCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL-HGFKITPTHAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l-~g~~i~~g~~l~v~~ak  245 (246)
                      .....++|||+||-..+++.+|++.|.+||+|+.++++..+ ++|||+|.+.++|..|...+ |...|+ |.+|.|.|++
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~-~CAFv~ftTR~aAE~Aae~~~n~lvI~-G~Rl~i~Wg~  301 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK-GCAFVTFTTREAAEKAAEKSFNKLVIN-GFRLKIKWGR  301 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc-ccceeeehhhHHHHHHHHhhcceeeec-ceEEEEEeCC
Confidence            34458999999999899999999999999999999999988 69999999999999987775 555677 9999999985

>KOG1457|consensus

Probab=99.07  E-value=1.6e-09  Score=82.91  Aligned_cols=76  Identities=28%  Similarity=0.475  Sum_probs=67.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHhCCCccCC--CCceEE
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR------HDIAFVEFENEMQSAAAKLALHGFKITP--THAMKI  241 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l~g~~i~~--g~~l~v  241 (246)
                      .-++|||.+||.++..-+|..+|.+|...+...+....      +.+||+.|.+..+|..|+..|||.+|+.  +.+|+|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            48999999999999999999999999888766665533      2489999999999999999999999975  689999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      ++||
T Consensus       113 ElAK  116 (284)
T KOG1457|consen  113 ELAK  116 (284)
T ss_pred             eehh
Confidence            9997

>KOG0415|consensus

Probab=99.06  E-value=2.7e-10  Score=92.55  Aligned_cols=78  Identities=24%  Similarity=0.519  Sum_probs=73.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCc-----cEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~-----g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ...||..+|||+-|.+-+|+|+|.-+|++||.|..+.++++.+     .||||+|.+.++..+|.-.|++.-|+ .++|.
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLID-DrRIH  312 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLID-DRRIH  312 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeec-cceEE
Confidence            3567899999999999999999999999999999999999884     49999999999999999999999999 89999


Q ss_pred             EEee
Q psy4057         241 ISFA  244 (246)
Q Consensus       241 v~~a  244 (246)
                      |.|+
T Consensus       313 VDFS  316 (479)
T KOG0415|consen  313 VDFS  316 (479)
T ss_pred             eehh
Confidence            9986

>KOG4208|consensus

Probab=99.04  E-value=9.6e-10  Score=83.17  Aligned_cols=82  Identities=22%  Similarity=0.342  Sum_probs=72.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhcc-CCeeEEEEcc---CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQF-GQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~f-G~i~~v~~~~---~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ...+...+||..+|....+.++..+|.+| |.+..+++.|   +|.|+|||||+|.+++.|..|-+.||+.-+.|+-|.|
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            34456788999999999999999999999 7777777755   4589999999999999999999999999999999999


Q ss_pred             EEccCC
Q psy4057          83 QYSKTD   88 (246)
Q Consensus        83 ~~a~~~   88 (246)
                      .+-.+.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            997544

>KOG4660|consensus

Probab=98.98  E-value=5e-10  Score=96.00  Aligned_cols=176  Identities=21%  Similarity=0.234  Sum_probs=113.8

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      -.+.++|+|.|||..+++++|+.+|+.||+|..|+.  +...+|..||+|-+..+|+.|+.+|++..+.|+.|.......
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~--t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~  149 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE--TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGAR  149 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc--ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCccc
Confidence            456899999999999999999999999999999643  335779999999999999999999999999999988222111


Q ss_pred             CccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCC
Q psy4057          88 DSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE  167 (246)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (246)
                      ...    ..                                            ..+...      ......+.+......
T Consensus       150 ~~~----~~--------------------------------------------~~~~~~------~~~~~~p~a~s~pgg  175 (549)
T KOG4660|consen  150 RAM----GL--------------------------------------------QSGTSF------LNHFGSPLANSPPGG  175 (549)
T ss_pred             ccc----hh--------------------------------------------cccchh------hhhccchhhcCCCCC
Confidence            100    00                                            000000      000000000011111


Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .+....+.+  |++..+...+.-.++.+|.+.. +-..--+-.-|++|.+..++..+...+ |..+. +....+.++
T Consensus       176 ~~~~~~~g~--l~P~~s~~~~~~~~~~~~~~~~-~~~~~~~hq~~~~~~~~~s~a~~~~~~-G~~~s-~~~~v~t~S  247 (549)
T KOG4660|consen  176 WPRGQLFGM--LSPTRSSILLEHISSVDGSSPG-RETPLLNHQRFVEFADNRSYAFSEPRG-GFLIS-NSSGVITFS  247 (549)
T ss_pred             CcCCcceee--eccchhhhhhhcchhccCcccc-ccccchhhhhhhhhccccchhhcccCC-ceecC-CCCceEEec
Confidence            222333333  8888888888888888898865 433322225677787777776665544 66666 555555554

>KOG4676|consensus

Probab=98.97  E-value=5.8e-10  Score=91.65  Aligned_cols=197  Identities=14%  Similarity=0.120  Sum_probs=128.2

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC------CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL------KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      .....|.|.||.+..+.++++.+|.-.|.|..+.++.+.      -....|||-|.+..++..|.+ |-++.|-|+-|.|
T Consensus         5 ~~~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv   83 (479)
T KOG4676|consen    5 SSLGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIV   83 (479)
T ss_pred             CCCceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEE
Confidence            344589999999999999999999999999999988743      234789999999999999998 8889999999988


Q ss_pred             EEccCCc--ccccc---ccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCC
Q psy4057          83 QYSKTDS--DVISK---IKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPP  157 (246)
Q Consensus        83 ~~a~~~~--~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (246)
                      .......  +....   ..++.+......+..-..+          .               ++ ....-.|.+.-..|+
T Consensus        84 ~p~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~----------~---------------~l-t~~nh~p~ailktP~  137 (479)
T KOG4676|consen   84 RPYGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGD----------R---------------PL-TKINHSPNAILKTPE  137 (479)
T ss_pred             EecCCCCCccHHHHHhcCcccccccccCCCCccCCC----------C---------------cc-ccccCCccceecCCC
Confidence            7653221  11000   0001110000000000000          0               00 000000111111122


Q ss_pred             CCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-ccEEEEEeCCHHHHHHHHHHhCCCcc
Q psy4057         158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFENEMQSAAAKLALHGFKI  233 (246)
Q Consensus       158 ~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~~~A~~Al~~l~g~~i  233 (246)
                      .+++..........++++|++|+..+...++..+|..+|+|...++..+. ..+|.++|....+...|++ ++|+.+
T Consensus       138 Lp~~~~A~kleeirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gre~  213 (479)
T KOG4676|consen  138 LPPQAAAKKLEEIRRTREVQSLISAAILPESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGRER  213 (479)
T ss_pred             CChHhhhhhhHHHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcchhh
Confidence            22222222333346899999999999999999999999999888877754 4578899999888888876 566554

>KOG4660|consensus

Probab=98.94  E-value=1.2e-09  Score=93.80  Aligned_cols=72  Identities=29%  Similarity=0.419  Sum_probs=67.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ..+..+|+|-|||..+++++|+.+|+.||+|+.|+-.+...|..||+|.|..+|++|+++|++.+|. |+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~-~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIA-GKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhh-hhhhc
Confidence            4568999999999999999999999999999999999988899999999999999999999999999 77765

>KOG4661|consensus

Probab=98.92  E-value=2.8e-09  Score=91.65  Aligned_cols=79  Identities=19%  Similarity=0.330  Sum_probs=72.3

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .-++.|||.+|+..+.-.+|+.+|++||.|+-.+++.+-   ..+.|+||++.+.++|.+||+.|+.+.|+|+-|.|..+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            457889999999999999999999999999998888654   56789999999999999999999999999999999998


Q ss_pred             cC
Q psy4057          86 KT   87 (246)
Q Consensus        86 ~~   87 (246)
                      +.
T Consensus       483 KN  484 (940)
T KOG4661|consen  483 KN  484 (940)
T ss_pred             cc
Confidence            64

>KOG4661|consensus

Probab=98.89  E-value=3.4e-09  Score=91.12  Aligned_cols=75  Identities=19%  Similarity=0.279  Sum_probs=69.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      -++.|||.+|...+.--+|+++|++||.|+-.+|+.+.     +.||||++.+.++|.+||+.||-++++ |+.|.|.-|
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELH-GrmISVEka  482 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELH-GRMISVEKA  482 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhc-ceeeeeeec
Confidence            47899999999888888999999999999999999865     579999999999999999999999999 999999887


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      |
T Consensus       483 K  483 (940)
T KOG4661|consen  483 K  483 (940)
T ss_pred             c
Confidence            6

>KOG4210|consensus

Probab=98.87  E-value=2.8e-09  Score=87.22  Aligned_cols=168  Identities=15%  Similarity=0.124  Sum_probs=127.1

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEcc---CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~---~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...++|++++.....+.+...++...|......+..   ...++|++.+.|...+.+..|+.........+..+......
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            367889999999999988889999999776664443   33889999999999999999999443345555554444432


Q ss_pred             CCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                      .....   ..+                                          +                     .....
T Consensus       167 ~~~~~---~~n------------------------------------------~---------------------~~~~~  180 (285)
T KOG4210|consen  167 RRGLR---PKN------------------------------------------K---------------------LSRLS  180 (285)
T ss_pred             ccccc---ccc------------------------------------------h---------------------hcccc
Confidence            22100   000                                          0                     01122


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ..+..+.++|.||++++++++|+..|..+|.|..+++..++     .|+|+|.|.+...+..|+.. +...++ ++++.+
T Consensus       181 ~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~-~~~~~~  258 (285)
T KOG4210|consen  181 SGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIG-GRPLRL  258 (285)
T ss_pred             cCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCccc-Cccccc
Confidence            34456666699999999999999999999999999999976     57999999999999999887 778888 899998


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .+.+
T Consensus       259 ~~~~  262 (285)
T KOG4210|consen  259 EEDE  262 (285)
T ss_pred             ccCC
Confidence            8764

>KOG0226|consensus

Probab=98.87  E-value=3.1e-09  Score=82.84  Aligned_cols=141  Identities=18%  Similarity=0.334  Sum_probs=109.2

Q ss_pred             HHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCccccccccCccccccccc
Q psy4057          29 YAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKV  106 (246)
Q Consensus        29 ~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~  106 (246)
                      ...|+-+-.+....+.++.  ..++++|+.|.....-.++-..-++..+.-+++++.-...-                  
T Consensus       117 ~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtsw------------------  178 (290)
T KOG0226|consen  117 PVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSW------------------  178 (290)
T ss_pred             hhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeecccccc------------------
Confidence            5778888777777777776  56699999999888877777766666665555444332111                  


Q ss_pred             cCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHH
Q psy4057         107 RKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEM  186 (246)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~t~e  186 (246)
                                                              +-|.             -..-....-.||.+-|..+++++
T Consensus       179 ----------------------------------------edPs-------------l~ew~~~DfRIfcgdlgNevnd~  205 (290)
T KOG0226|consen  179 ----------------------------------------EDPS-------------LAEWDEDDFRIFCGDLGNEVNDD  205 (290)
T ss_pred             ----------------------------------------CCcc-------------cccCccccceeecccccccccHH
Confidence                                                    1111             11122347789999999999999


Q ss_pred             HHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         187 MLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       187 ~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .|.+.|.+|......+++++.     +||+||.|.+..++..|+..|||.-++ +++|++
T Consensus       206 vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVg-srpikl  264 (290)
T KOG0226|consen  206 VLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVG-SRPIKL  264 (290)
T ss_pred             HHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccc-cchhHh
Confidence            999999999999999999976     589999999999999999999999999 888765

>KOG4208|consensus

Probab=98.87  E-value=9.7e-09  Score=77.81  Aligned_cols=76  Identities=25%  Similarity=0.412  Sum_probs=68.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccC-CCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~-G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      .......+++..+|..+.+-.+...|.+| |.+.++++.+++     +|||||+|++.+.|.-|-+.||++-+. ++.|.
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~-e~lL~  123 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLM-EHLLE  123 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhh-hheee
Confidence            45568889999999999999999999999 777888887765     589999999999999999999999999 89998


Q ss_pred             EEe
Q psy4057         241 ISF  243 (246)
Q Consensus       241 v~~  243 (246)
                      +.|
T Consensus       124 c~v  126 (214)
T KOG4208|consen  124 CHV  126 (214)
T ss_pred             eEE
Confidence            876

>KOG0151|consensus

Probab=98.85  E-value=7.9e-09  Score=90.93  Aligned_cols=78  Identities=26%  Similarity=0.417  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCc
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--------HDIAFVEFENEMQSAAAKLALHGFKITPTHA  238 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~  238 (246)
                      ..|..+.|||+||+++++++.|...|++||+|..++++--+        +.||||-|-+..+|.+|+..|+|..+. +..
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~-~~e  248 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVM-EYE  248 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeee-eee
Confidence            36779999999999999999999999999999888887643        469999999999999999999999999 999


Q ss_pred             eEEEeec
Q psy4057         239 MKISFAK  245 (246)
Q Consensus       239 l~v~~ak  245 (246)
                      |++.|+|
T Consensus       249 ~K~gWgk  255 (877)
T KOG0151|consen  249 MKLGWGK  255 (877)
T ss_pred             eeecccc
Confidence            9999987

>KOG2193|consensus

Probab=98.83  E-value=4.1e-10  Score=93.45  Aligned_cols=146  Identities=18%  Similarity=0.266  Sum_probs=119.0

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcC-CccCCeeEEEEEccC
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQG-FPFYDKPMRIQYSKT   87 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng-~~~~g~~l~v~~a~~   87 (246)
                      +.+|++||.+.++..+|..+|..--      +.-.+   --.|||||.+.+...|.+|++.++| ..+.|+++.+.++-.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak------~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAK------IPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhcccc------CCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            5689999999999999999997652      11111   1239999999999999999999999 668999999988644


Q ss_pred             CccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCC
Q psy4057          88 DSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE  167 (246)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (246)
                      +..                                                                             
T Consensus        76 kkq-----------------------------------------------------------------------------   78 (584)
T KOG2193|consen   76 KKQ-----------------------------------------------------------------------------   78 (584)
T ss_pred             HHH-----------------------------------------------------------------------------
Confidence            421                                                                             


Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccE--EEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI--AFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~--afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                        .++.+-++|+|+...++.|..+..+||.+..+-.+.-....  .=|+|.+.+.+..|+..|||..+. +..++|.|
T Consensus        79 --rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~e-n~~~k~~Y  153 (584)
T KOG2193|consen   79 --RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLE-NQHLKVGY  153 (584)
T ss_pred             --HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhh-hhhhhccc
Confidence              24457799999999999999999999999887776544222  335689999999999999999999 88888887

>KOG0533|consensus

Probab=98.83  E-value=2e-08  Score=79.60  Aligned_cols=80  Identities=21%  Similarity=0.354  Sum_probs=72.1

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      -..+|+|.||++.++.+||.++|..||.+..+.+..+.  ++.|.|-|.|...++|..|++.+||..+.|++|.+..+..
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            34789999999999999999999999999988887654  7889999999999999999999999999999999988755


Q ss_pred             Cc
Q psy4057          88 DS   89 (246)
Q Consensus        88 ~~   89 (246)
                      .+
T Consensus       162 ~~  163 (243)
T KOG0533|consen  162 PS  163 (243)
T ss_pred             cc
Confidence            43

>KOG4211|consensus

Probab=98.78  E-value=1.6e-07  Score=79.80  Aligned_cols=208  Identities=15%  Similarity=0.132  Sum_probs=113.5

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeE-EEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMD-IVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~-v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      +...|-+.+||+.|+++||.++|+..-.+.. |.+.-+.  ++.|-|||+|++.+.|++|+. -|...+.-|-|.|..+.
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRSS  180 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehhH
Confidence            3457888999999999999999998876655 3333333  677999999999999999998 45567777888887763


Q ss_pred             CCccccccccC--cccccccccc--C--CCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcc---cccC------CCC
Q psy4057          87 TDSDVISKIKG--TFMERPKKVR--K--QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQAL---SVQQ------PPV  151 (246)
Q Consensus        87 ~~~~~~~~~~~--~~~~~~~~~~--~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~------~~~  151 (246)
                      ... .......  ....++...+  .  +...+...... ....   ..+..   +.....-++   ....      ...
T Consensus       181 ~~e-~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~-~~~~---~~r~g---~~~~g~~g~~~~~~~~d~~~~gs~~  252 (510)
T KOG4211|consen  181 RAE-VKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRD-PGRN---ATRYG---AGGEGYYGFSRYPSLQDYGNFGSYG  252 (510)
T ss_pred             HHH-HHhhccccccccCCCCccccccCCccccccccccC-CCcc---ccccc---cccCCccccccCccccccccccccc
Confidence            221 1110000  0000000000  0  11001000000 0000   00000   000000000   0000      000


Q ss_pred             CCC--CCCCC-------CCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCc-eEEEEeeCC--ccEEEEEeCCHH
Q psy4057         152 SQP--APPAP-------MATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGF-KEVRLVPNR--HDIAFVEFENEM  219 (246)
Q Consensus       152 ~~~--~~~~~-------~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i-~~v~~~~~~--~g~afV~f~~~~  219 (246)
                      ...  ..+..       .+.......+....+..++||++.+..++.+.|+..-.+ ..|.+-++.  .|-|+|+|.+.+
T Consensus       253 ~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~~v~i~ig~dGr~TGEAdveF~t~e  332 (510)
T KOG4211|consen  253 GGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPYRVHIEIGPDGRATGEADVEFATGE  332 (510)
T ss_pred             cccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCceeEEEEeCCCCccCCcceeecccch
Confidence            000  00000       001111122234788889999999999999999987666 444444443  478999999999


Q ss_pred             HHHHHHH
Q psy4057         220 QSAAAKL  226 (246)
Q Consensus       220 ~A~~Al~  226 (246)
                      +|..|+.
T Consensus       333 dav~Ams  339 (510)
T KOG4211|consen  333 DAVGAMG  339 (510)
T ss_pred             hhHhhhc
Confidence            9999975

>KOG0128|consensus

Probab=98.76  E-value=8.2e-10  Score=98.84  Aligned_cols=130  Identities=19%  Similarity=0.225  Sum_probs=109.5

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEc---cCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~---~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      ..++||.||+..+.+.+|...|.++|.++.+.+.   ..++.+|+|++.|..+++|.+|+.-. ...+.|          
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~-d~~~~g----------  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFR-DSCFFG----------  735 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhh-hhhhhh----------
Confidence            3578999999999999999999999998887665   23378899999999999999999833 222222          


Q ss_pred             CccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCC
Q psy4057          88 DSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE  167 (246)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (246)
                                                                                                      
T Consensus       736 --------------------------------------------------------------------------------  735 (881)
T KOG0128|consen  736 --------------------------------------------------------------------------------  735 (881)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKIT  234 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~  234 (246)
                         ...|+|+|+|+..|.++|+.+|+.+|.+.+++++..+    +|.|+|.|.+..+|..+...+++..+-
T Consensus       736 ---K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~r  803 (881)
T KOG0128|consen  736 ---KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKR  803 (881)
T ss_pred             ---hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhh
Confidence               2337899999999999999999999999999887755    578999999999999998888776654

>KOG0533|consensus

Probab=98.74  E-value=5.6e-08  Score=77.05  Aligned_cols=76  Identities=24%  Similarity=0.313  Sum_probs=68.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCc----cEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH----DIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~----g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .......|+|.|||+.|++++|+++|..||.+..+-+..++.    |.|=|.|...++|..|++.+||..++ |++|++.
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ld-G~~mk~~  157 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALD-GRPMKIE  157 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccC-CceeeeE
Confidence            344568899999999999999999999999999999999873    69999999999999999999998888 8998886


Q ss_pred             e
Q psy4057         243 F  243 (246)
Q Consensus       243 ~  243 (246)
                      .
T Consensus       158 ~  158 (243)
T KOG0533|consen  158 I  158 (243)
T ss_pred             E
Confidence            5

>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=98.71  E-value=1.1e-07  Score=61.74  Aligned_cols=69  Identities=22%  Similarity=0.382  Sum_probs=46.9

Q ss_pred             cEEEEcCCCCCCCHHH----HHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         172 QILFLTNLPEETSEMM----LSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~----l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..|+|.|||.+.+...    |++++..+|. +-+.+.   .+.|+|.|.+.+.|.+|...|+|-.+. |..|.|+|.+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGG-kVl~v~---~~tAilrF~~~~~A~RA~KRmegEdVf-G~kI~v~~~~   75 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGG-KVLSVS---GGTAILRFPNQEFAERAQKRMEGEDVF-GNKISVSFSP   75 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT---EEE-----TT-EEEEESSHHHHHHHHHHHTT--SS-SS--EEESS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCC-EEEEEe---CCEEEEEeCCHHHHHHHHHhhcccccc-cceEEEEEcC
Confidence            4689999999888764    5567777766 223332   267999999999999999999999999 9999999974

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4205|consensus

Probab=98.71  E-value=1.9e-08  Score=82.78  Aligned_cols=80  Identities=20%  Similarity=0.323  Sum_probs=71.7

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ....++||++||.++++++|+++|.+||.|..+.++.|.   +.+||+||+|.+++++.+++. ..-+.|.|+.+.|..|
T Consensus        95 ~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA  173 (311)
T KOG4205|consen   95 LRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRA  173 (311)
T ss_pred             cceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeec
Confidence            356799999999999999999999999999999888765   788999999999999999988 6678899999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      .++.
T Consensus       174 ~pk~  177 (311)
T KOG4205|consen  174 IPKE  177 (311)
T ss_pred             cchh
Confidence            7654

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.66  E-value=2.3e-07  Score=63.15  Aligned_cols=74  Identities=20%  Similarity=0.316  Sum_probs=62.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccC--CCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccC---CCCceEE
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQF--PGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKIT---PTHAMKI  241 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~--G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~---~g~~l~v  241 (246)
                      ++|-|+|+|...|+++|.+++...  |...-+.++-|-     .|||||.|.+.+.|..-.+.++|+...   ..+.+.|
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            689999999999999999887543  666666666653     489999999999999999999998764   2588999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      +||+
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            9986

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4454|consensus

Probab=98.62  E-value=1.7e-08  Score=77.12  Aligned_cols=75  Identities=23%  Similarity=0.242  Sum_probs=68.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      .+..++|||.|+...+++|-|.++|-+-|+|.+|.|..++   ..||||.|.++.+..-|++.|||-.+. +..++|.+
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~-~~e~q~~~   83 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLE-EDEEQRTL   83 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhc-cchhhccc
Confidence            3468999999999999999999999999999999999876   249999999999999999999999999 88888865

>KOG0151|consensus

Probab=98.60  E-value=8.5e-08  Score=84.62  Aligned_cols=79  Identities=25%  Similarity=0.396  Sum_probs=71.4

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEcc--CC----CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TL----KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~--~~----~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      |-+..|||+||++.++++.|-..|..||+|-.|+++-  +.    +.+.+|||.|-+..+|++|+..|+|..+.+..|++
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            4467899999999999999999999999999998873  22    56789999999999999999999999999999999


Q ss_pred             EEccC
Q psy4057          83 QYSKT   87 (246)
Q Consensus        83 ~~a~~   87 (246)
                      .|++.
T Consensus       252 gWgk~  256 (877)
T KOG0151|consen  252 GWGKA  256 (877)
T ss_pred             ccccc
Confidence            99854

>KOG1548|consensus

Probab=98.58  E-value=2.2e-07  Score=75.64  Aligned_cols=75  Identities=13%  Similarity=0.166  Sum_probs=67.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCc--------eEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCC
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGF--------KEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTH  237 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i--------~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~  237 (246)
                      .++.|||.|||.++|.+++..+|+.+|.|        -.|+|.++.    +|-|.+.|-..++...|+..|++..+. |+
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r-g~  211 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELR-GK  211 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccccc-Cc
Confidence            47889999999999999999999999999        356777765    578999999999999999999999999 99


Q ss_pred             ceEEEeec
Q psy4057         238 AMKISFAK  245 (246)
Q Consensus       238 ~l~v~~ak  245 (246)
                      .|+|+-||
T Consensus       212 ~~rVerAk  219 (382)
T KOG1548|consen  212 KLRVERAK  219 (382)
T ss_pred             EEEEehhh
Confidence            99998775

>KOG0116|consensus

Probab=98.57  E-value=1.1e-07  Score=81.19  Aligned_cols=76  Identities=18%  Similarity=0.226  Sum_probs=64.5

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEcc-C--CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK-T--LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~-~--~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ....+|||+|||.+++.++|.+.|..||.|+...|.. .  .++..||||+|.+.++++.|++. +...+.|+++.|+--
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEK  364 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEec
Confidence            3445599999999999999999999999999976654 2  24449999999999999999994 488889999999763

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.50  E-value=4.5e-07  Score=63.12  Aligned_cols=68  Identities=24%  Similarity=0.247  Sum_probs=44.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCC-----ccCCCCceEE
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF-----KITPTHAMKI  241 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~-----~i~~g~~l~v  241 (246)
                      ++|.|.+++..++.++|++.|+.||.|..|.+.++. ..|+|.|.+.+.|+.|+..+.-.     .|. +..+.+
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~-~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~-~~~~~~   74 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD-TEGYVRFKTPEAAQKALEKLKEANDGKLKIK-GKEVTL   74 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT--SEEEEEESS---HHHHHHHHHHTTTS-B-TT-SSSEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC-CEEEEEECCcchHHHHHHHHHhccCCceEEc-CceEEE
Confidence            578999999999999999999999999999999988 47999999999999999987544     444 455444

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.48  E-value=6.9e-07  Score=58.12  Aligned_cols=69  Identities=19%  Similarity=0.404  Sum_probs=47.7

Q ss_pred             cEEEecCCChhhhHHH----HHHHhhccC-CeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          12 NFVYVTHISSTDLKKS----LYAIFSQFG-QIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~----l~~~F~~fG-~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ..|||.|||.+.....    |+.++.-+| .|.+|       +.+.|.|.|.+.+.|.+|...|+|-.++|+.|.|.|..
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            4689999998665544    666777775 67776       45889999999999999999999999999999999974


Q ss_pred             C
Q psy4057          87 T   87 (246)
Q Consensus        87 ~   87 (246)
                      .
T Consensus        76 ~   76 (90)
T PF11608_consen   76 K   76 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0106|consensus

Probab=98.46  E-value=1.5e-07  Score=73.06  Aligned_cols=70  Identities=19%  Similarity=0.358  Sum_probs=64.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..+||++||..+.+.+|..+|..||.+.++.+..   ||+||+|.+..+|.-|+..|||..+. |..+.|.|++
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~---gf~fv~fed~rda~Dav~~l~~~~l~-~e~~vve~~r   71 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN---GFGFVEFEDPRDADDAVHDLDGKELC-GERLVVEHAR   71 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec---ccceeccCchhhhhcccchhcCceec-ceeeeeeccc
Confidence            3589999999999999999999999998887764   58999999999999999999999999 7669999986

>KOG0226|consensus

Probab=98.41  E-value=2.7e-07  Score=72.20  Aligned_cols=76  Identities=20%  Similarity=0.314  Sum_probs=67.1

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      -+.+||.+.|..+++.+.|-..|.+|-.-...+++++   ++++||+||.|.++.++..|+.+|||..+..++|...-+
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            4678999999999999999999999987666666655   489999999999999999999999999999999887654

>KOG4209|consensus

Probab=98.41  E-value=5.7e-07  Score=71.41  Aligned_cols=77  Identities=17%  Similarity=0.289  Sum_probs=69.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .....+.+||+|+.+.+|.+++...|+.||.|..+-++.++     +||+||+|.+.+.+..|+. |||..|. |+.+.|
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~-~~~i~v  174 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIP-GPAIEV  174 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccc-ccccee
Confidence            44568899999999999999999999999999988888865     5799999999999999999 9999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      ++.+
T Consensus       175 t~~r  178 (231)
T KOG4209|consen  175 TLKR  178 (231)
T ss_pred             eeee
Confidence            8754

>KOG4209|consensus

Probab=98.37  E-value=5.7e-07  Score=71.42  Aligned_cols=79  Identities=16%  Similarity=0.203  Sum_probs=70.8

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      .....++||+|+.+.++-+++...|+.||.|..|.+..+.   .++|||||+|.+.+.+.+|+. |||..+.|+.+.|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            3456899999999999999999999999999877777654   679999999999999999999 999999999999988


Q ss_pred             ccC
Q psy4057          85 SKT   87 (246)
Q Consensus        85 a~~   87 (246)
                      ...
T Consensus       177 ~r~  179 (231)
T KOG4209|consen  177 KRT  179 (231)
T ss_pred             eee
Confidence            643

>KOG0116|consensus

Probab=98.35  E-value=8.4e-07  Score=75.93  Aligned_cols=71  Identities=27%  Similarity=0.333  Sum_probs=59.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC---C--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN---R--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~---~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ...|||+|||.++++.+|+++|..||.|+...|...   .  ..||||+|.+.+.++.|+++= -..++ +++|.|+-
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig-~~kl~Vee  363 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIG-GRKLNVEE  363 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccC-CeeEEEEe
Confidence            555999999999999999999999999977766552   2  269999999999999998865 55566 88888864

>KOG4307|consensus

Probab=98.30  E-value=2.4e-06  Score=75.59  Aligned_cols=184  Identities=15%  Similarity=0.072  Sum_probs=122.7

Q ss_pred             CcEEEe--cCCChhhhHHHHHHHhhccCCeeEEEEccCC--CC-ccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          11 TNFVYV--THISSTDLKKSLYAIFSQFGQIMDIVALKTL--KM-RGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        11 ~~~l~V--~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~-kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ..++||  .++.+...+.+++++|..-- |..+.+..+.  .+ .|.++|.|....++++|+. -|...+-.|.+.+..+
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~~-~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~~~R~~q~~P~  386 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGRN-AQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDDVNRPFQTGPP  386 (944)
T ss_pred             chhheeeecccccccccchhhhhcCccc-ccccchhhhhcCCCcCCceEEEecCcchHHHHHh-cCchhhhhcceeecCC
Confidence            566777  89999999999999987554 5555444443  44 6999999999999999988 5667777888888776


Q ss_pred             cCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCC----CCCCCCCC
Q psy4057          86 KTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQ----PAPPAPMA  161 (246)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~  161 (246)
                      ....-.   ..+.                                          ....+...+-...    ...++.+.
T Consensus       387 g~~~~~---~a~~------------------------------------------~~~~~~~~~~~~~hg~p~~~pr~~~  421 (944)
T KOG4307|consen  387 GNLGRN---GAPP------------------------------------------FQAGVPPPVIQNNHGRPIAPPRAMV  421 (944)
T ss_pred             Cccccc---cCcc------------------------------------------ccccCCCCcccccCCCCCCCccccc
Confidence            433210   0000                                          0000000000000    00111111


Q ss_pred             CC---CCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceE-EEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCcc
Q psy4057         162 TA---GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE-VRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKI  233 (246)
Q Consensus       162 ~~---~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~-v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i  233 (246)
                      ..   .-...+..-+|||..||..+++.++-+.|..--.|++ |.|.+..    .+.|||.|.+.+++..|...-+.+.+
T Consensus       422 ~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~  501 (944)
T KOG4307|consen  422 RPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYP  501 (944)
T ss_pred             CCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhccccccc
Confidence            11   1123446889999999999999999999998777766 6666644    46899999999999999877666666


Q ss_pred             CCCCceEEE
Q psy4057         234 TPTHAMKIS  242 (246)
Q Consensus       234 ~~g~~l~v~  242 (246)
                      + .+.|+|.
T Consensus       502 G-~r~irv~  509 (944)
T KOG4307|consen  502 G-HRIIRVD  509 (944)
T ss_pred             C-ceEEEee
Confidence            6 6888874

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.30  E-value=5.1e-06  Score=56.61  Aligned_cols=76  Identities=20%  Similarity=0.241  Sum_probs=61.6

Q ss_pred             cEEEecCCChhhhHHHHHHHhhcc--CCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccC----CeeEEE
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQF--GQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFY----DKPMRI   82 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~f--G~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~----g~~l~v   82 (246)
                      .||.|+|||...+.++|.+++...  |...-+.++-|.   .+.|||||-|.+++.|....+..+|..+.    .+...|
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            589999999999999999888643  666666666554   56799999999999999999999997774    455677


Q ss_pred             EEccC
Q psy4057          83 QYSKT   87 (246)
Q Consensus        83 ~~a~~   87 (246)
                      .||+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88753

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.07  E-value=1.4e-05  Score=55.71  Aligned_cols=70  Identities=17%  Similarity=0.304  Sum_probs=44.3

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcC-----CccCCeeEEEEE
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG-----FPFYDKPMRIQY   84 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng-----~~~~g~~l~v~~   84 (246)
                      ..|.|.+++.+++.++|++.|+.||.|..|.+.+   ....|+|.|.++++|+.|++.+..     ..+.+..+.+..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~---G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR---GDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--T---T-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecC---CCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            4678888999999999999999999999887644   445799999999999999987743     456666666655

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=97.98  E-value=1.8e-05  Score=47.78  Aligned_cols=52  Identities=10%  Similarity=0.270  Sum_probs=42.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHH
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK  225 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al  225 (246)
                      +.|-|.+.+.+..++ +...|..||+|.++.+.... .+.+|.|.+..+|.+|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~~-~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPEST-NWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCCC-cEEEEEECCHHHHHhhC
Confidence            567888998876655 55588899999999988544 58999999999999985

>KOG1365|consensus

Probab=97.91  E-value=0.00029  Score=58.66  Aligned_cols=149  Identities=15%  Similarity=0.130  Sum_probs=95.8

Q ss_pred             EecCCChhhhHHHHHHHhhccCCeeE-EEEcc--CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCccc
Q psy4057          15 YVTHISSTDLKKSLYAIFSQFGQIMD-IVALK--TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDV   91 (246)
Q Consensus        15 ~V~nl~~~~~e~~l~~~F~~fG~i~~-v~~~~--~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~~   91 (246)
                      -.++||..-+..++-.+|...-...- +.++.  -++.-|.|.|.|.+.+.-+-|++ -+...+.++.|.|-.+....-.
T Consensus        64 RaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~Rdlalk-Rhkhh~g~ryievYka~ge~f~  142 (508)
T KOG1365|consen   64 RARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALK-RHKHHMGTRYIEVYKATGEEFL  142 (508)
T ss_pred             EecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhH-hhhhhccCCceeeeccCchhhe
Confidence            34899999999888888875531111 11122  22445899999999999999987 4566677888888766433211


Q ss_pred             cccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcc--cccCCCCCCCCCCCCCCCCCCCCCC
Q psy4057          92 ISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQAL--SVQQPPVSQPAPPAPMATAGVPEQP  169 (246)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~  169 (246)
                      -                                                ..+.  ...+++.+               -.
T Consensus       143 ~------------------------------------------------iagg~s~e~~~fls---------------k~  159 (508)
T KOG1365|consen  143 K------------------------------------------------IAGGTSNEAAPFLS---------------KE  159 (508)
T ss_pred             E------------------------------------------------ecCCccccCCCCCC---------------cc
Confidence            0                                                0010  00001100               00


Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccC----CCceEEEEeeC--C--ccEEEEEeCCHHHHHHHHHH
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQF----PGFKEVRLVPN--R--HDIAFVEFENEMQSAAAKLA  227 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~----G~i~~v~~~~~--~--~g~afV~f~~~~~A~~Al~~  227 (246)
                      .--.|-+++||+++++.++..+|...    |..+.|.++..  .  .|-|||.|..+++|+.|+..
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH
Confidence            12344568999999999999999632    24456666553  2  57899999999999999875

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.88  E-value=3.1e-05  Score=63.17  Aligned_cols=74  Identities=9%  Similarity=0.326  Sum_probs=61.1

Q ss_pred             CCcEEEEcCCCCCCCHHHH------HHHHccCCCceEEEEeeCC------ccE--EEEEeCCHHHHHHHHHHhCCCccCC
Q psy4057         170 PNQILFLTNLPEETSEMML------SMLFNQFPGFKEVRLVPNR------HDI--AFVEFENEMQSAAAKLALHGFKITP  235 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l------~~~f~~~G~i~~v~~~~~~------~g~--afV~f~~~~~A~~Al~~l~g~~i~~  235 (246)
                      ....+||-+||+.+..|++      .+.|++||.|..|.+-+.-      .+.  .+|.|.+.++|.+||...+|...+ 
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D-  191 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD-  191 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccccc-
Confidence            3566788889988877652      3679999999988877643      122  499999999999999999999999 


Q ss_pred             CCceEEEee
Q psy4057         236 THAMKISFA  244 (246)
Q Consensus       236 g~~l~v~~a  244 (246)
                      |+.|+..|+
T Consensus       192 Gr~lkatYG  200 (480)
T COG5175         192 GRVLKATYG  200 (480)
T ss_pred             CceEeeecC
Confidence            999999986

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.80  E-value=4.8e-05  Score=62.11  Aligned_cols=77  Identities=22%  Similarity=0.386  Sum_probs=60.3

Q ss_pred             CcEEEecCCChhhhHHH------HHHHhhccCCeeEEEEccCC---CC-ccEE--EEEEcCHHHHHHHHHHhcCCccCCe
Q psy4057          11 TNFVYVTHISSTDLKKS------LYAIFSQFGQIMDIVALKTL---KM-RGQA--FVIFKEIASATNALRSMQGFPFYDK   78 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~------l~~~F~~fG~i~~v~~~~~~---~~-kg~a--FV~f~~~~~A~~Ai~~lng~~~~g~   78 (246)
                      .+-+||-+|++.+-.++      =.++|.+||.|..|.+-+.-   .+ -+.+  +|+|.+.++|.+||.+.+|..+.||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            35678877776554444      25899999999999886532   12 1334  9999999999999999999999999


Q ss_pred             eEEEEEccC
Q psy4057          79 PMRIQYSKT   87 (246)
Q Consensus        79 ~l~v~~a~~   87 (246)
                      .|+..|...
T Consensus       194 ~lkatYGTT  202 (480)
T COG5175         194 VLKATYGTT  202 (480)
T ss_pred             eEeeecCch
Confidence            999999643

>KOG2314|consensus

Probab=97.79  E-value=7.7e-05  Score=64.86  Aligned_cols=74  Identities=14%  Similarity=0.244  Sum_probs=62.0

Q ss_pred             CCCcEEEEcCCCCCCC------HHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCc
Q psy4057         169 PPNQILFLTNLPEETS------EMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHA  238 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t------~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~  238 (246)
                      ....+++|.|.|.--.      ...|..+|+++|++..+.++.+.    +||.|++|.+..+|+.|++.|||+.++.+++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            4588999999986221      23567889999999999998755    6899999999999999999999999997788


Q ss_pred             eEEE
Q psy4057         239 MKIS  242 (246)
Q Consensus       239 l~v~  242 (246)
                      +.|.
T Consensus       136 f~v~  139 (698)
T KOG2314|consen  136 FFVR  139 (698)
T ss_pred             EEee
Confidence            7764

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.79  E-value=0.00019  Score=52.29  Aligned_cols=73  Identities=21%  Similarity=0.314  Sum_probs=55.3

Q ss_pred             CCCCCcEEEecC---------CChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCC
Q psy4057           7 HICVTNFVYVTH---------ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD   77 (246)
Q Consensus         7 ~~~~~~~l~V~n---------l~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (246)
                      -.||..||.|.=         .=.+....+|.+.|..||++.-|+...     +.-.|+|.+-++|.+|+. ++|..+.|
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~-----~~mwVTF~dg~sALaals-~dg~~v~g   96 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG-----DTMWVTFRDGQSALAALS-LDGIQVNG   96 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET-----TCEEEEESSCHHHHHHHH-GCCSEETT
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC-----CeEEEEECccHHHHHHHc-cCCcEECC
Confidence            468899999821         223445668999999999888776643     578999999999999999 99999999


Q ss_pred             eeEEEEEc
Q psy4057          78 KPMRIQYS   85 (246)
Q Consensus        78 ~~l~v~~a   85 (246)
                      +.|+|..-
T Consensus        97 ~~l~i~LK  104 (146)
T PF08952_consen   97 RTLKIRLK  104 (146)
T ss_dssp             EEEEEEE-
T ss_pred             EEEEEEeC
Confidence            99999984

; PDB: 1UFW_A 2DNR_A.

>KOG2314|consensus

Probab=97.78  E-value=0.00011  Score=64.05  Aligned_cols=74  Identities=23%  Similarity=0.355  Sum_probs=61.5

Q ss_pred             CcEEEecCCCh------hhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCcc-CCeeEE
Q psy4057          11 TNFVYVTHISS------TDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPF-YDKPMR   81 (246)
Q Consensus        11 ~~~l~V~nl~~------~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~-~g~~l~   81 (246)
                      ..+|+|.|+|-      +..+.-|..+|+++|+|....+.-+.  .++||.|++|.+..+|+.|+.+|||..+ ..++..
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            56788877763      44556688999999999999887554  7889999999999999999999999888 577777


Q ss_pred             EEE
Q psy4057          82 IQY   84 (246)
Q Consensus        82 v~~   84 (246)
                      |..
T Consensus       138 v~~  140 (698)
T KOG2314|consen  138 VRL  140 (698)
T ss_pred             eeh
Confidence            765

>KOG1995|consensus

Probab=97.77  E-value=3.3e-05  Score=63.61  Aligned_cols=79  Identities=20%  Similarity=0.306  Sum_probs=67.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceE--------EEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCcc
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE--------VRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKI  233 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~--------v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i  233 (246)
                      ......++||-+||..++..+|...|.++|.|..        |++..++     ++-|.|.|.+...|+.|+.-++++.|
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            4556889999999999999999999999999932        2333333     57899999999999999999999999


Q ss_pred             CCCCceEEEeecC
Q psy4057         234 TPTHAMKISFAKK  246 (246)
Q Consensus       234 ~~g~~l~v~~ak~  246 (246)
                      . |.+|+|.+|.+
T Consensus       142 ~-gn~ikvs~a~~  153 (351)
T KOG1995|consen  142 C-GNTIKVSLAER  153 (351)
T ss_pred             c-CCCchhhhhhh
Confidence            9 89999998764

>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=97.76  E-value=0.00016  Score=49.64  Aligned_cols=72  Identities=11%  Similarity=0.169  Sum_probs=50.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEE------------EeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCc
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVR------------LVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHA  238 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~------------~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~  238 (246)
                      .+-|.|-+.|.. .-..+-+.|++||.|.+..            -.....++--|.|.+..+|.+||+ -||..|.++--
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            556788888887 4456788899999997765            233334799999999999999987 79999983344


Q ss_pred             eEEEee
Q psy4057         239 MKISFA  244 (246)
Q Consensus       239 l~v~~a  244 (246)
                      +-|.|.
T Consensus        84 vGV~~~   89 (100)
T PF05172_consen   84 VGVKPC   89 (100)
T ss_dssp             EEEEE-
T ss_pred             EEEEEc
Confidence            446664

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=97.74  E-value=0.00012  Score=57.71  Aligned_cols=59  Identities=19%  Similarity=0.230  Sum_probs=50.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCC
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHG  230 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g  230 (246)
                      ..|+|.||...++.|.|.+.|++||.|.+..+.-|.    .+-++|.|...-.|.+|+..+.-
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhcc
Confidence            569999999999999999999999999665555543    35799999999999999998843

>KOG1995|consensus

Probab=97.73  E-value=3.8e-05  Score=63.28  Aligned_cols=83  Identities=16%  Similarity=0.225  Sum_probs=71.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeE--------EEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPF   75 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~--------v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~   75 (246)
                      .-.-..+|||-.|+..+++++|.++|.++|.|..        |.+.++.   +.|+-|.|+|.+...|+.|++-.++..+
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            3445679999999999999999999999997743        3444443   7889999999999999999999999999


Q ss_pred             CCeeEEEEEccCCc
Q psy4057          76 YDKPMRIQYSKTDS   89 (246)
Q Consensus        76 ~g~~l~v~~a~~~~   89 (246)
                      .|.+|+|..+....
T Consensus       142 ~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  142 CGNTIKVSLAERRT  155 (351)
T ss_pred             cCCCchhhhhhhcc
Confidence            99999999886554

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.69  E-value=0.00027  Score=51.48  Aligned_cols=72  Identities=22%  Similarity=0.370  Sum_probs=54.1

Q ss_pred             CCCCCcEEEEcCCC-----CCCCHH----HHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCC
Q psy4057         167 EQPPNQILFLTNLP-----EETSEM----MLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTH  237 (246)
Q Consensus       167 ~~~~~~~l~v~nL~-----~~~t~e----~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~  237 (246)
                      .+||..++.|.=+.     ....++    +|.+.|..||.+.-+|++.+   .-.|+|.+-++|.+|+. |+|.++. |+
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~---~mwVTF~dg~sALaals-~dg~~v~-g~   97 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD---TMWVTFRDGQSALAALS-LDGIQVN-GR   97 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT---CEEEEESSCHHHHHHHH-GCCSEET-TE
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC---eEEEEECccHHHHHHHc-cCCcEEC-CE
Confidence            57788888886444     123333    77788999999999999886   48999999999999966 9999999 99


Q ss_pred             ceEEEe
Q psy4057         238 AMKISF  243 (246)
Q Consensus       238 ~l~v~~  243 (246)
                      .|+|..
T Consensus        98 ~l~i~L  103 (146)
T PF08952_consen   98 TLKIRL  103 (146)
T ss_dssp             EEEEEE
T ss_pred             EEEEEe
Confidence            999975

; PDB: 1UFW_A 2DNR_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.66  E-value=0.00021  Score=43.15  Aligned_cols=52  Identities=21%  Similarity=0.374  Sum_probs=42.4

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHH
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNAL   67 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai   67 (246)
                      +.|-|.+.+.+..+ ++...|..||+|.++.+.   ....+.+|.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~---~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVP---ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcC---CCCcEEEEEECCHHHHHhhC
Confidence            45677888877765 566689999999998764   35789999999999999985

>KOG4307|consensus

Probab=97.65  E-value=0.0002  Score=63.84  Aligned_cols=72  Identities=21%  Similarity=0.355  Sum_probs=62.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCc-eEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGF-KEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i-~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      .++|-+.|+|++++-+||-++|..|-.+ -+|++-.+.    .|-|.|-|++.++|.+|...|+++.|. ++.+.+..
T Consensus       867 p~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  867 PRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIR-NRVVSLRI  943 (944)
T ss_pred             CeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCccc-ceeEEEEe
Confidence            4488899999999999999999999887 556665544    478999999999999999999999999 89988754

>KOG0128|consensus

Probab=97.60  E-value=2.8e-06  Score=76.76  Aligned_cols=155  Identities=19%  Similarity=0.118  Sum_probs=113.3

Q ss_pred             cEEEecCCChhhhHH-HHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          12 NFVYVTHISSTDLKK-SLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~-~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      +..++.++.+...+. .....|..+|.|+.|.+...+   ....++++.+....++..|.. ..+..+.++...+..+..
T Consensus       572 ~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~~ad~  650 (881)
T KOG0128|consen  572 REKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVGLADA  650 (881)
T ss_pred             hhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccCCCCCc
Confidence            344556776655555 578899999999999887633   344589999999999999987 677778888887777654


Q ss_pred             CccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCC
Q psy4057          88 DSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE  167 (246)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (246)
                      ......                                                ...                   ....
T Consensus       651 ~~~~~~------------------------------------------------~kv-------------------s~n~  663 (881)
T KOG0128|consen  651 EEKEEN------------------------------------------------FKV-------------------SPNE  663 (881)
T ss_pred             hhhhhc------------------------------------------------cCc-------------------CchH
Confidence            421000                                                000                   0001


Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEee----CC-ccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP----NR-HDIAFVEFENEMQSAAAKLALHGFKIT  234 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~----~~-~g~afV~f~~~~~A~~Al~~l~g~~i~  234 (246)
                      .....++|++||+..+.+++|...|..+|.+..+++..    ++ +|+|+++|...++|.+|+....++.++
T Consensus       664 ~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  664 IRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            12356789999999999999999999999997777652    22 689999999999999998877666554

>KOG2202|consensus

Probab=97.58  E-value=4.4e-05  Score=60.14  Aligned_cols=61  Identities=18%  Similarity=0.439  Sum_probs=53.5

Q ss_pred             HHHHHHhh-ccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          26 KSLYAIFS-QFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        26 ~~l~~~F~-~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ++++.-|. +||+|+++.+....  ...|-++|.|..+++|++|++.||+.-|.|++|...++.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            55666666 99999999887655  678999999999999999999999999999999999863

>KOG3152|consensus

Probab=97.58  E-value=5e-05  Score=59.76  Aligned_cols=66  Identities=20%  Similarity=0.309  Sum_probs=59.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCc-----------------cEEEEEeCCHHHHHHHHHHhCCCc
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----------------DIAFVEFENEMQSAAAKLALHGFK  232 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~-----------------g~afV~f~~~~~A~~Al~~l~g~~  232 (246)
                      ..-+||++++|+.+...-|++++++||.|-+|.|-+...                 .-|-|+|.+...|......|||..
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            467899999999999999999999999999999888430                 138999999999999999999999


Q ss_pred             cCC
Q psy4057         233 ITP  235 (246)
Q Consensus       233 i~~  235 (246)
                      |+|
T Consensus       153 Igg  155 (278)
T KOG3152|consen  153 IGG  155 (278)
T ss_pred             cCC
Confidence            994

>KOG2202|consensus

Probab=97.57  E-value=4.5e-05  Score=60.13  Aligned_cols=58  Identities=14%  Similarity=0.169  Sum_probs=49.2

Q ss_pred             HHHHHHHc-cCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         186 MMLSMLFN-QFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       186 e~l~~~f~-~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      |++...++ +||+|+.+.+-.+.    .|.++|.|...++|++|++.|||.+|. |++|...+.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~-G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYN-GRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCcccc-CCcceeeec
Confidence            45555666 99999988776654    478999999999999999999999999 999988764

>KOG4210|consensus

Probab=97.55  E-value=6.3e-05  Score=61.87  Aligned_cols=80  Identities=19%  Similarity=0.229  Sum_probs=69.4

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ++..-.+|++++..+++++|+..|..+|.|..+++..+.   ..+|+|+|.|.+..++..++.. +...+.|+++.+.+.
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            333444499999999999999999999999999888654   7889999999999999999987 788899999999997


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ....
T Consensus       262 ~~~~  265 (285)
T KOG4210|consen  262 EPRP  265 (285)
T ss_pred             CCCc
Confidence            6654

>KOG1855|consensus

Probab=97.55  E-value=9e-05  Score=62.42  Aligned_cols=65  Identities=18%  Similarity=0.211  Sum_probs=57.2

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC----------------CCccEEEEEEcCHHHHHHHHHHhc
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL----------------KMRGQAFVIFKEIASATNALRSMQ   71 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~----------------~~kg~aFV~f~~~~~A~~Ai~~ln   71 (246)
                      .-++++|.+.|||.+-.-+.|.++|+.+|.|..|+|+.-+                ..+-+|+|+|...+.|.+|.+.||
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            3478999999999999999999999999999999999751                135679999999999999999775


Q ss_pred             C
Q psy4057          72 G   72 (246)
Q Consensus        72 g   72 (246)
                      .
T Consensus       308 ~  308 (484)
T KOG1855|consen  308 P  308 (484)
T ss_pred             h
Confidence            4

>KOG1855|consensus

Probab=97.53  E-value=6.8e-05  Score=63.12  Aligned_cols=65  Identities=26%  Similarity=0.359  Sum_probs=56.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC------C------------ccEEEEEeCCHHHHHHHHHHh
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN------R------------HDIAFVEFENEMQSAAAKLAL  228 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~------~------------~g~afV~f~~~~~A~~Al~~l  228 (246)
                      .+.++++|.+.|||.+-.-+.|.++|+.+|.|+.|++..-      .            +-+|+|+|.+.+.|.+|.+.|
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            3458999999999999888999999999999999998763      1            237999999999999999988


Q ss_pred             CCC
Q psy4057         229 HGF  231 (246)
Q Consensus       229 ~g~  231 (246)
                      +..
T Consensus       307 ~~e  309 (484)
T KOG1855|consen  307 NPE  309 (484)
T ss_pred             chh
Confidence            654

>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=97.42  E-value=0.0011  Score=45.50  Aligned_cols=74  Identities=19%  Similarity=0.267  Sum_probs=53.4

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEc-cC---------CCCccEEEEEEcCHHHHHHHHHHhcCCccCCee
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL-KT---------LKMRGQAFVIFKEIASATNALRSMQGFPFYDKP   79 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~-~~---------~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~   79 (246)
                      ..+.|-|-+.|+. .-..+.+.|++||.|.+..-. ++         ....++--|+|.++.+|.+|+. -||..+.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            3566888888888 445788999999999887411 11         2456899999999999999999 7999999887


Q ss_pred             EE-EEEc
Q psy4057          80 MR-IQYS   85 (246)
Q Consensus        80 l~-v~~a   85 (246)
                      |- |.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            65 5564

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.

>KOG1996|consensus

Probab=97.41  E-value=0.00042  Score=55.70  Aligned_cols=74  Identities=22%  Similarity=0.249  Sum_probs=59.2

Q ss_pred             CCcEEEEcCCC--CCCC---HHHHHHHHccCCCceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCc
Q psy4057         170 PNQILFLTNLP--EETS---EMMLSMLFNQFPGFKEVRLVPNR------HDIAFVEFENEMQSAAAKLALHGFKITPTHA  238 (246)
Q Consensus       170 ~~~~l~v~nL~--~~~t---~e~l~~~f~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~  238 (246)
                      ++++|.++|+-  ..+.   +++++..+++||.|.+|.|....      .--.||+|.+.++|.+|+-.|||+.|+ |+.
T Consensus       280 ptkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFG-Gr~  358 (378)
T KOG1996|consen  280 PTKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFG-GRV  358 (378)
T ss_pred             chHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceec-cee
Confidence            56677777753  2444   34788999999999888777654      124899999999999999999999999 999


Q ss_pred             eEEEee
Q psy4057         239 MKISFA  244 (246)
Q Consensus       239 l~v~~a  244 (246)
                      ++-.|-
T Consensus       359 v~A~Fy  364 (378)
T KOG1996|consen  359 VSACFY  364 (378)
T ss_pred             eeheec
Confidence            887763

>KOG4676|consensus

Probab=97.38  E-value=0.00019  Score=59.86  Aligned_cols=68  Identities=19%  Similarity=0.344  Sum_probs=59.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--------HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .+|.|.||.++.|.++++.+|...|.|..++|.++-        ...|||.|.|...+..| +.|.++.|- ++.|.|
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~va-QhLtntvfv-draliv   83 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVA-QHLTNTVFV-DRALIV   83 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHH-hhhccceee-eeeEEE
Confidence            389999999999999999999999999999998843        24799999999988887 889998887 666655

>KOG1996|consensus

Probab=97.35  E-value=0.00062  Score=54.79  Aligned_cols=65  Identities=15%  Similarity=0.288  Sum_probs=55.5

Q ss_pred             hhhhHHHHHHHhhccCCeeEEEEccCC----CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          21 STDLKKSLYAIFSQFGQIMDIVALKTL----KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        21 ~~~~e~~l~~~F~~fG~i~~v~~~~~~----~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .+..++++.+-+++||.|.+|.|....    .-.---||+|...++|.+|+-.|||..|.||.++.+|-
T Consensus       296 d~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  296 DEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             cHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            466788899999999999999888664    12245899999999999999999999999999987763

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.23  E-value=0.0018  Score=42.36  Aligned_cols=57  Identities=25%  Similarity=0.352  Sum_probs=44.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCC
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG  230 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g  230 (246)
                      ...+.+|+ +|..+...||.++|+.||.|. |..+.+-  .|||...+.+.|..|+..+.-
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT--SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT--SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT--EEEEEECCCHHHHHHHHHHTT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC--cEEEEeecHHHHHHHHHHhcc
Confidence            46677777 999999999999999999964 5555553  599999999999999998864

; 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.

>KOG3152|consensus

Probab=97.21  E-value=0.00023  Score=56.10  Aligned_cols=70  Identities=20%  Similarity=0.179  Sum_probs=59.9

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-----------CCc--c--EEEEEEcCHHHHHHHHHHhcCCc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-----------KMR--G--QAFVIFKEIASATNALRSMQGFP   74 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-----------~~k--g--~aFV~f~~~~~A~~Ai~~lng~~   74 (246)
                      ....||+++||+.+....|+++|+.||.|-.|.+-...           .++  .  -|.|+|.+...|..+.+.||+..
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            45789999999999999999999999999999886522           111  1  28899999999999999999999


Q ss_pred             cCCee
Q psy4057          75 FYDKP   79 (246)
Q Consensus        75 ~~g~~   79 (246)
                      +.|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            98876

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=97.21  E-value=0.0036  Score=45.21  Aligned_cols=74  Identities=24%  Similarity=0.287  Sum_probs=61.4

Q ss_pred             CCCCCcEEEe----cCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           7 HICVTNFVYV----THISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V----~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ..+|=.+|.|    .|+....+-..+....+.||+|.+|.++    .+..|.|.|.+..+|-+|+...+. ...|..+.|
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c----GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qC  156 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC----GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQC  156 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec----CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEe
Confidence            3577788888    7888877778899999999999999774    346799999999999999997765 667888888


Q ss_pred             EEc
Q psy4057          83 QYS   85 (246)
Q Consensus        83 ~~a   85 (246)
                      .|-
T Consensus       157 sWq  159 (166)
T PF15023_consen  157 SWQ  159 (166)
T ss_pred             ecc
Confidence            773

>KOG2416|consensus

Probab=97.18  E-value=0.0004  Score=60.94  Aligned_cols=80  Identities=10%  Similarity=0.221  Sum_probs=66.1

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhh-ccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCcc---CCeeEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFS-QFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF---YDKPMR   81 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~-~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~---~g~~l~   81 (246)
                      ...++++.|||.||.--.|.-+|+.++. ..|.|++..|-   +-|..|||.|.+.++|..-.+.|||..+   .++.|.
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmD---kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMD---KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHHHHH---HhhcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            3557899999999999999999999999 55666665332   2456799999999999999999999887   678899


Q ss_pred             EEEccCC
Q psy4057          82 IQYSKTD   88 (246)
Q Consensus        82 v~~a~~~   88 (246)
                      +.|+...
T Consensus       516 adf~~~d  522 (718)
T KOG2416|consen  516 ADFVRAD  522 (718)
T ss_pred             eeecchh
Confidence            9997543

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.11  E-value=0.004  Score=40.75  Aligned_cols=55  Identities=22%  Similarity=0.313  Sum_probs=42.2

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhc
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ   71 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~ln   71 (246)
                      +...||. .|..+...||.++|++||.|.--.|     +...|||...+.+.|..|+..+.
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi-----~dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWI-----NDTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEEEEE-----CTTEEEEEECCCHHHHHHHHHHT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEEEEE-----cCCcEEEEeecHHHHHHHHHHhc
Confidence            4455566 9999999999999999998766555     44679999999999999988775

; 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.

>KOG2416|consensus

Probab=97.04  E-value=0.00085  Score=58.93  Aligned_cols=78  Identities=18%  Similarity=0.273  Sum_probs=62.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHcc-CCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCcc--CCCCceEEEe
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQ-FPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI--TPTHAMKISF  243 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~-~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i--~~g~~l~v~~  243 (246)
                      ..+++.+|+|.||-.-.|.-+|+.++.+ .|.|...++-+- +..|||.|.+.++|.....+|||-.-  .+++.|.+.|
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkI-KShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf  518 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKI-KSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADF  518 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHh-hcceeEecccHHHHHHHHHHHhccccCCCCCceeEeee
Confidence            4557999999999998999999999994 555566644333 35799999999999999999999543  3358899999


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      +.
T Consensus       519 ~~  520 (718)
T KOG2416|consen  519 VR  520 (718)
T ss_pred             cc
Confidence            75

>KOG4574|consensus

Probab=96.80  E-value=0.00091  Score=61.02  Aligned_cols=74  Identities=20%  Similarity=0.236  Sum_probs=63.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCC-CCceEEEeec
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITP-THAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~-g~~l~v~~ak  245 (246)
                      -....+.|.+-..+---|..+|+.||.|.+++.+++- ..|.|+|.+.+.|..|+++|+|+++.. |-+.+|+|||
T Consensus       298 qp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~-N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak  372 (1007)
T KOG4574|consen  298 QPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL-NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAK  372 (1007)
T ss_pred             cchhhhhcccccchHHHHHHHHHhhcchhhheecccc-cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecc
Confidence            3444556666677778899999999999999998877 479999999999999999999998633 7899999997

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.80  E-value=0.011  Score=36.68  Aligned_cols=55  Identities=18%  Similarity=0.255  Sum_probs=46.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccC----CCceEEEEeeCCccEEEEEeCCHHHHHHHHHHh
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQF----PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL  228 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~----G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l  228 (246)
                      ....|+|+|+. +++.++++..|..|    +. .+|..+.|.  .|=|.|.+.+.|.+||.+|
T Consensus         4 rpeavhirGvd-~lsT~dI~~y~~~y~~~~~~-~~IEWIdDt--ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVD-ELSTDDIKAYFSEYFDEEGP-FRIEWIDDT--SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eeceEEEEcCC-CCCHHHHHHHHHHhcccCCC-ceEEEecCC--cEEEEECCHHHHHHHHHcC
Confidence            35679999997 48889999999999    43 678888886  4999999999999999865

>KOG0112|consensus

Probab=96.73  E-value=0.0024  Score=58.76  Aligned_cols=78  Identities=18%  Similarity=0.217  Sum_probs=69.3

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCC--eeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD--KPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g--~~l~v~~   84 (246)
                      ...+++.+|+++|..-+....|...|..||.|..|.+   .....||+|+|.+...|+.|++.|-|..+.|  ++++|.|
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy---~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdl  527 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY---RHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDL  527 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeec---ccCCcceeeecccCccchhhHHHHhcCcCCCCCccccccc
Confidence            5678999999999999999999999999999999755   2467899999999999999999999999954  7799999


Q ss_pred             ccC
Q psy4057          85 SKT   87 (246)
Q Consensus        85 a~~   87 (246)
                      +..
T Consensus       528 a~~  530 (975)
T KOG0112|consen  528 ASP  530 (975)
T ss_pred             ccC
Confidence            865

>KOG0115|consensus

Probab=96.73  E-value=0.0022  Score=50.78  Aligned_cols=75  Identities=21%  Similarity=0.210  Sum_probs=62.6

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcC----CccCCeeEEEEE
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQG----FPFYDKPMRIQY   84 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng----~~~~g~~l~v~~   84 (246)
                      +..|||.||+.-++-+.|..-|+.||+|+.-.++-|.  +..+-++|.|.+.-.|.+|.+.++-    .+..+++..|..
T Consensus        31 ~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   31 HAELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             cceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            4889999999999999999999999999998777665  5668899999999999999998843    444566666665


Q ss_pred             c
Q psy4057          85 S   85 (246)
Q Consensus        85 a   85 (246)
                      .
T Consensus       111 ~  111 (275)
T KOG0115|consen  111 M  111 (275)
T ss_pred             h
Confidence            4

>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=96.61  E-value=0.022  Score=39.89  Aligned_cols=68  Identities=16%  Similarity=0.167  Sum_probs=52.3

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccC-CeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFG-QIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFY   76 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG-~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~   76 (246)
                      ..+..+.+.-.|+-...++|..+.+.+- .|..+++++++ .++-.+.+.|.+.++|.......||..|.
T Consensus        11 ~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   11 RRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             CCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            3344444466666677767766666664 57889999998 57778999999999999999999998873

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0129|consensus

Probab=96.58  E-value=0.0079  Score=52.23  Aligned_cols=63  Identities=17%  Similarity=0.180  Sum_probs=57.0

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhh-ccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHH
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFS-QFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRS   69 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~-~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~   69 (246)
                      .+-|.+|||||+||--++-++|-.+|. -||-|.-+-|-.|.   =.+|-|=|+|.+..+--+||..
T Consensus       366 ~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  366 PIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            467899999999999999999999999 89999999888775   3569999999999999999983

>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=96.46  E-value=0.0079  Score=46.19  Aligned_cols=60  Identities=18%  Similarity=0.241  Sum_probs=46.3

Q ss_pred             CHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhC--CCccCCCCceEEEeec
Q psy4057         184 SEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH--GFKITPTHAMKISFAK  245 (246)
Q Consensus       184 t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~--g~~i~~g~~l~v~~ak  245 (246)
                      ....|+++|..|+.+..+.+++.=+ -..|.|.+.+.|..|+..|+  +..+. |..+++.|+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFr-Ri~v~f~~~~~A~~~r~~l~~~~~~~~-g~~l~~yf~~   69 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFR-RIRVVFESPESAQRARQLLHWDGTSFN-GKRLRVYFGQ   69 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTT-EEEEE-SSTTHHHHHHHTST--TSEET-TEE-EEE---
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCC-EEEEEeCCHHHHHHHHHHhcccccccC-CCceEEEEcc
Confidence            4578999999999998887777542 39999999999999999999  99999 8999999974

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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.42  E-value=0.023  Score=41.13  Aligned_cols=74  Identities=16%  Similarity=0.203  Sum_probs=54.4

Q ss_pred             CCCCCcEEEEcCCCCCC----CHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEET----SEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~----t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .+||-.+|.|+=|..++    +...+...++.||+|.+|-+--.  ..|+|.|.+..+|=.|+.+++.. .. |..++.+
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr--qsavVvF~d~~SAC~Av~Af~s~-~p-gtm~qCs  157 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR--QSAVVVFKDITSACKAVSAFQSR-AP-GTMFQCS  157 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC--ceEEEEehhhHHHHHHHHhhcCC-CC-CceEEee
Confidence            56777888886554433    33345556789999998776543  36999999999999999999883 44 6777777


Q ss_pred             ee
Q psy4057         243 FA  244 (246)
Q Consensus       243 ~a  244 (246)
                      |-
T Consensus       158 Wq  159 (166)
T PF15023_consen  158 WQ  159 (166)
T ss_pred             cc
Confidence            63

>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=96.17  E-value=0.13  Score=35.96  Aligned_cols=76  Identities=12%  Similarity=0.248  Sum_probs=57.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccC-CCceEEEEeeCCcc---EEEEEeCCHHHHHHHHHHhCCCccCC--CCceEEE
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHD---IAFVEFENEMQSAAAKLALHGFKITP--THAMKIS  242 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~-G~i~~v~~~~~~~g---~afV~f~~~~~A~~Al~~l~g~~i~~--g~~l~v~  242 (246)
                      .....+++...|..++-++|..+.+.+ ..|..++++++...   .++++|.+.++|..=...+||+.|..  ..+++|-
T Consensus        11 ~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~Chvv   90 (110)
T PF07576_consen   11 RRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVV   90 (110)
T ss_pred             CCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEE
Confidence            345566666677777778888777766 44589999998742   58999999999999999999998852  3556665


Q ss_pred             ee
Q psy4057         243 FA  244 (246)
Q Consensus       243 ~a  244 (246)
                      |-
T Consensus        91 fV   92 (110)
T PF07576_consen   91 FV   92 (110)
T ss_pred             EE
Confidence            54

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0804|consensus

Probab=96.06  E-value=0.018  Score=49.26  Aligned_cols=71  Identities=17%  Similarity=0.247  Sum_probs=62.9

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhcc-CCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccC
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQF-GQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFY   76 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~f-G~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~   76 (246)
                      .+..++..|+|--+|..++..||..++..| ..|.+|+++||+ .++-...|.|.+.++|....+.+||..|.
T Consensus        69 ~~~~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   69 KNASSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             ccCCCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            345568999999999999999999998876 469999999998 77788999999999999999999998874

>KOG2193|consensus

Probab=96.01  E-value=0.0091  Score=50.65  Aligned_cols=69  Identities=19%  Similarity=0.202  Sum_probs=54.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCc-eEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCc-cCCCCceEEEee
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGF-KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK-ITPTHAMKISFA  244 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i-~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~-i~~g~~l~v~~a  244 (246)
                      .||++||.+.++..+|.++|...-.- ..-.+++  +||+||.+.+..-|.+|++.++|.. +. |+++.|.++
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~k--~gyafvd~pdq~wa~kaie~~sgk~elq-Gkr~e~~~s   73 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK--SGYAFVDCPDQQWANKAIETLSGKVELQ-GKRQEVEHS   73 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceeee--cceeeccCCchhhhhhhHHhhchhhhhc-Cceeeccch
Confidence            58999999999999999999864111 1111222  3899999999999999999999975 55 899888663

>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=95.98  E-value=0.024  Score=43.61  Aligned_cols=62  Identities=24%  Similarity=0.375  Sum_probs=46.2

Q ss_pred             hhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhc--CCccCCeeEEEEEcc
Q psy4057          22 TDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ--GFPFYDKPMRIQYSK   86 (246)
Q Consensus        22 ~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~ln--g~~~~g~~l~v~~a~   86 (246)
                      ....+.|.++|..|+.+.....++.   =+-..|.|.+.+.|..|...|+  +..+.|..++|.|+.
T Consensus         6 ~~~~~~l~~l~~~~~~~~~~~~L~s---FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen    6 PDNLAELEELFSTYDPPVQFSPLKS---FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             ---HHHHHHHHHTT-SS-EEEEETT---TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             hhhHHHHHHHHHhcCCceEEEEcCC---CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            3455789999999999988877664   3449999999999999999999  899999999999984

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.

>KOG4849|consensus

Probab=95.88  E-value=0.0088  Score=49.47  Aligned_cols=73  Identities=12%  Similarity=0.183  Sum_probs=59.9

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccC--CeeEEEEcc---CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFG--QIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG--~i~~v~~~~---~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      .-++||+||.--+|.+||.+....-|  .+.+++...   ++++||||+|...+..+.++-++-|...+++|+.-.|.
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            45789999999999999999888877  234444443   34899999999999999999999999999999876554

>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=95.51  E-value=0.017  Score=44.11  Aligned_cols=65  Identities=12%  Similarity=0.136  Sum_probs=45.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHcc-CCCc---eEEEEeeCC-------ccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQ-FPGF---KEVRLVPNR-------HDIAFVEFENEMQSAAAKLALHGFKIT  234 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~-~G~i---~~v~~~~~~-------~g~afV~f~~~~~A~~Al~~l~g~~i~  234 (246)
                      ....|.|++||+.+|++++.+.++. ++.-   ..+.-..+.       ..-|+|.|.+.++...=...++|+.|.
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~   81 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFV   81 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEE
Confidence            4668999999999999999997776 5555   333322322       235999999999999999999998774

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.

>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=95.37  E-value=0.015  Score=44.48  Aligned_cols=81  Identities=11%  Similarity=0.126  Sum_probs=51.0

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhc-cCCe---eEEEEccCC-----CCccEEEEEEcCHHHHHHHHHHhcCCccCC
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQ-FGQI---MDIVALKTL-----KMRGQAFVIFKEIASATNALRSMQGFPFYD   77 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~-fG~i---~~v~~~~~~-----~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (246)
                      .......|.|++||+.++++++++.++. ++.-   ..+.-....     ..-..|+|.|.+.+++......++|..|.+
T Consensus         3 ~~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D   82 (176)
T PF03467_consen    3 KEKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVD   82 (176)
T ss_dssp             ------EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-
T ss_pred             CcccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEEC
Confidence            4455678999999999999999998887 7765   233211111     122569999999999999999999988743


Q ss_pred             -----eeEEEEEccC
Q psy4057          78 -----KPMRIQYSKT   87 (246)
Q Consensus        78 -----~~l~v~~a~~   87 (246)
                           .+-.|.+|..
T Consensus        83 ~kg~~~~~~VE~Apy   97 (176)
T PF03467_consen   83 SKGNEYPAVVEFAPY   97 (176)
T ss_dssp             TTS-EEEEEEEE-SS
T ss_pred             CCCCCcceeEEEcch
Confidence                 2345677654

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.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.36  E-value=0.084  Score=32.74  Aligned_cols=53  Identities=23%  Similarity=0.326  Sum_probs=40.8

Q ss_pred             cEEEecCCChhhhHHHHHHHhhcc----CCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHh
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQF----GQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM   70 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~f----G~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l   70 (246)
                      ..|+|.++. +++-++++.+|..|    + ...|..+.|    ..|-|.|.+.+.|.+|+..|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~-~~~IEWIdD----tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEG-PFRIEWIDD----TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCC-CceEEEecC----CcEEEEECCHHHHHHHHHcC
Confidence            578898774 46667888999888    5 455655554    55999999999999998754

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=95.27  E-value=0.97  Score=36.96  Aligned_cols=76  Identities=14%  Similarity=0.224  Sum_probs=58.1

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC----------CCccEEEEEEcCHHHHHHH----HHHhcC--Cc
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL----------KMRGQAFVIFKEIASATNA----LRSMQG--FP   74 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~----------~~kg~aFV~f~~~~~A~~A----i~~lng--~~   74 (246)
                      +|.|...|+..+++--.+...|.+||+|++|.++.+.          .......+.|-+.+.+-..    ++.|+.  ..
T Consensus        15 TRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~~   94 (309)
T PF10567_consen   15 TRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKTK   94 (309)
T ss_pred             eHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHHh
Confidence            5677778999999889999999999999999998754          3446789999999888654    344443  44


Q ss_pred             cCCeeEEEEEcc
Q psy4057          75 FYDKPMRIQYSK   86 (246)
Q Consensus        75 ~~g~~l~v~~a~   86 (246)
                      +.-..|.+.++.
T Consensus        95 L~S~~L~lsFV~  106 (309)
T PF10567_consen   95 LKSESLTLSFVS  106 (309)
T ss_pred             cCCcceeEEEEE
Confidence            566667777753

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG2068|consensus

Probab=94.98  E-value=0.011  Score=48.76  Aligned_cols=76  Identities=22%  Similarity=0.364  Sum_probs=58.4

Q ss_pred             cEEEecCCChhhhHHHH---HHHhhccCCeeEEEEccCCC------CccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057          12 NFVYVTHISSTDLKKSL---YAIFSQFGQIMDIVALKTLK------MRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l---~~~F~~fG~i~~v~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      +-+||-+|+.++-.+++   .++|.+||.|.+|.+.++..      .-..++|+|...++|..||...+|..+.|+.++.
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            45667677755544443   36899999999998877541      1134999999999999999999999999999888


Q ss_pred             EEccC
Q psy4057          83 QYSKT   87 (246)
Q Consensus        83 ~~a~~   87 (246)
                      .+...
T Consensus       158 ~~gtt  162 (327)
T KOG2068|consen  158 SLGTT  162 (327)
T ss_pred             hhCCC
Confidence            77644

>KOG4849|consensus

Probab=94.89  E-value=0.034  Score=46.10  Aligned_cols=78  Identities=15%  Similarity=0.156  Sum_probs=61.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCC--ceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPG--FKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~--i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ....-++||+||--.+|++||.+....-|-  +.++++..++     +|||+|...+..+.++.++.|--++|++-.+..
T Consensus        77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   77 EGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             cCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            335678999999888899999888776553  3666676665     689999999999999999999999999445555


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      ++|-|
T Consensus       157 ~~~NK  161 (498)
T KOG4849|consen  157 LSYNK  161 (498)
T ss_pred             eccch
Confidence            56543

>KOG0804|consensus

Probab=94.86  E-value=0.22  Score=42.93  Aligned_cols=78  Identities=10%  Similarity=0.276  Sum_probs=62.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccC-CCceEEEEeeCCc---cEEEEEeCCHHHHHHHHHHhCCCccCC--CCceE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRH---DIAFVEFENEMQSAAAKLALHGFKITP--THAMK  240 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~-G~i~~v~~~~~~~---g~afV~f~~~~~A~~Al~~l~g~~i~~--g~~l~  240 (246)
                      ...++..|+|-.+|..+|--||-.++..| ..|.+++++++..   =..+|+|.+.++|..=.+.+||..|..  ....+
T Consensus        70 ~~~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e~Ch  149 (493)
T KOG0804|consen   70 NASSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPEVCH  149 (493)
T ss_pred             cCCCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCcccee
Confidence            34448999999999999999999998765 5569999999763   259999999999999999999988752  34455


Q ss_pred             EEee
Q psy4057         241 ISFA  244 (246)
Q Consensus       241 v~~a  244 (246)
                      |-|.
T Consensus       150 ll~V  153 (493)
T KOG0804|consen  150 LLYV  153 (493)
T ss_pred             EEEE
Confidence            5444

>KOG2591|consensus

Probab=94.77  E-value=0.078  Score=46.72  Aligned_cols=67  Identities=19%  Similarity=0.301  Sum_probs=54.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHcc--CCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCC--CccCCCCce
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQ--FPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG--FKITPTHAM  239 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~--~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g--~~i~~g~~l  239 (246)
                      ..|+++++-+|..+..|+++-+|..  +..+.++.+--+.  -=||+|++..+|+.|...|.-  .+|. |++|
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~--nWyITfesd~DAQqAykylreevk~fq-gKpI  244 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND--NWYITFESDTDAQQAYKYLREEVKTFQ-GKPI  244 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC--ceEEEeecchhHHHHHHHHHHHHHhhc-Ccch
Confidence            4677888999999999999999974  6788888888776  379999999999999988754  3455 5554

>KOG2068|consensus

Probab=94.75  E-value=0.011  Score=48.78  Aligned_cols=73  Identities=15%  Similarity=0.304  Sum_probs=57.1

Q ss_pred             CcEEEEcCCCCCCCHHHHH---HHHccCCCceEEEEeeCCc--------cEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         171 NQILFLTNLPEETSEMMLS---MLFNQFPGFKEVRLVPNRH--------DIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~---~~f~~~G~i~~v~~~~~~~--------g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                      ..-+||-+|+..+..+.+.   +.|.+||.|..|..-.+..        .-++|+|...++|..||...+|...+ |+.+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~d-g~~l  155 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDD-GRAL  155 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhh-hhhh
Confidence            3556777788777655443   4588999999888877551        24999999999999999999999999 8887


Q ss_pred             EEEee
Q psy4057         240 KISFA  244 (246)
Q Consensus       240 ~v~~a  244 (246)
                      +.+|+
T Consensus       156 ka~~g  160 (327)
T KOG2068|consen  156 KASLG  160 (327)
T ss_pred             HHhhC
Confidence            77664

>KOG4285|consensus

Probab=94.74  E-value=0.059  Score=43.91  Aligned_cols=64  Identities=11%  Similarity=0.135  Sum_probs=48.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCc
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHA  238 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~  238 (246)
                      ..-+-|-++|+.-. ..|..+|++||.|++.....+. .|-.|.|.++-+|++||. -||+.|+ |..
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ng-NwMhirYssr~~A~KALs-kng~ii~-g~v  260 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNG-NWMHIRYSSRTHAQKALS-KNGTIID-GDV  260 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecCCCC-ceEEEEecchhHHHHhhh-hcCeeec-cce
Confidence            44555667776433 4578899999999876666333 699999999999999987 6898888 544

>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=94.48  E-value=0.19  Score=31.60  Aligned_cols=55  Identities=13%  Similarity=0.169  Sum_probs=45.4

Q ss_pred             CCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         182 ETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       182 ~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .++-++++..+..|+- .  ++..++.| =||.|.+..+|.++....+|+.+. +.+|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~--~I~~d~tG-fYIvF~~~~Ea~rC~~~~~~~~~f-~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-D--RIRDDRTG-FYIVFNDSKEAERCFRAEDGTLFF-TYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-c--eEEecCCE-EEEEECChHHHHHHHHhcCCCEEE-EEEEEe
Confidence            5688899999999876 3  44566667 689999999999999999999988 776654

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=94.42  E-value=0.068  Score=34.57  Aligned_cols=67  Identities=15%  Similarity=0.168  Sum_probs=38.0

Q ss_pred             EEEe-cCCChhhhHHHHHHHhhccCCe-----eEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          13 FVYV-THISSTDLKKSLYAIFSQFGQI-----MDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        13 ~l~V-~nl~~~~~e~~l~~~F~~fG~i-----~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ++|| .+=-..++..+|..++..-+.|     -.|.+     ...|+||+-... .|..++..|++..+.|++++|+.|
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I-----~~~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDI-----FDNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE------SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEE-----eeeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            4566 2333455667777777766444     45555     457899998765 889999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=94.40  E-value=0.36  Score=31.16  Aligned_cols=59  Identities=17%  Similarity=0.214  Sum_probs=36.0

Q ss_pred             CCCCHHHHHHHHccCCCc-----eEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         181 EETSEMMLSMLFNQFPGF-----KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       181 ~~~t~e~l~~~f~~~G~i-----~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..++..+|-.++...+.|     -+|.+..   .|+||+-.. +.|..+++.|++..+. |++++|+.|
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-EVAEKVLEALNGKKIK-GKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S---S-EEEEE-T-T-HHHHHHHHTT--SS-S----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee---eEEEEEECH-HHHHHHHHHhcCCCCC-CeeEEEEEC
Confidence            377888899998888777     2344433   379999874 5888999999999999 999999865

; PDB: 2G0C_A 3MOJ_B.

>KOG2253|consensus

Probab=94.20  E-value=0.072  Score=47.87  Aligned_cols=72  Identities=15%  Similarity=0.193  Sum_probs=61.1

Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       164 ~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      .....++..++||+|+...+.++-++.+...+|.|.......    |||..|....-+..|+..|+-..++ |..+.
T Consensus        33 ~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~----fgf~~f~~~~~~~ra~r~~t~~~~~-~~kl~  104 (668)
T KOG2253|consen   33 VFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK----FGFCEFLKHIGDLRASRLLTELNID-DQKLI  104 (668)
T ss_pred             cccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh----hcccchhhHHHHHHHHHHhcccCCC-cchhh
Confidence            344567899999999999999999999999999997655443    9999999999999999999998887 55443

>KOG2253|consensus

Probab=93.67  E-value=0.07  Score=47.94  Aligned_cols=75  Identities=16%  Similarity=0.123  Sum_probs=65.5

Q ss_pred             cccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           4 ILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         4 ~~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..+..+|..++||+|+.+.+..+-+..+...+|-|-++....      |||..|....-+..|+..++...+.|..+.+.
T Consensus        33 ~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   33 VFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK------FGFCEFLKHIGDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             cccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh------hcccchhhHHHHHHHHHHhcccCCCcchhhcc
Confidence            456788999999999999999999999999999887764333      89999999999999999999999988887765


Q ss_pred             E
Q psy4057          84 Y   84 (246)
Q Consensus        84 ~   84 (246)
                      .
T Consensus       107 ~  107 (668)
T KOG2253|consen  107 V  107 (668)
T ss_pred             c
Confidence            5

>KOG2135|consensus

Probab=93.66  E-value=0.046  Score=47.16  Aligned_cols=60  Identities=25%  Similarity=0.313  Sum_probs=50.9

Q ss_pred             hHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          24 LKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        24 ~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      +.++|-..|.+||.|+.|.+-..   --.|.|+|.+..+|-.|.. ..+..|.|+.|+|.|...
T Consensus       386 t~a~ln~hfA~fG~i~n~qv~~~---~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  386 TIADLNPHFAQFGEIENIQVDYS---SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             hHhhhhhhhhhcCccccccccCc---hhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            56788999999999999977432   3459999999999988876 788999999999999754

>KOG4574|consensus

Probab=93.16  E-value=0.068  Score=49.40  Aligned_cols=70  Identities=27%  Similarity=0.394  Sum_probs=59.6

Q ss_pred             EecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCcc--CCeeEEEEEccC
Q psy4057          15 YVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF--YDKPMRIQYSKT   87 (246)
Q Consensus        15 ~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~--~g~~l~v~~a~~   87 (246)
                      ++.|.+-..+-.-|..+|++||.|.+.+.+++.   ..|.|.|...++|-.|.+.++|..+  -|-+.+|.+|+.
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            345666777888899999999999998777654   5599999999999999999999776  788999999865

>KOG4285|consensus

Probab=92.72  E-value=0.28  Score=40.11  Aligned_cols=64  Identities=16%  Similarity=0.197  Sum_probs=49.0

Q ss_pred             ecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEE-EEE
Q psy4057          16 VTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR-IQY   84 (246)
Q Consensus        16 V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~-v~~   84 (246)
                      |.+.+.... .-+..+|++||.|.+....   +.-++-.|.|.+.-+|++|+. .||..|.|..|. |..
T Consensus       202 VfGFppg~~-s~vL~~F~~cG~Vvkhv~~---~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  202 VFGFPPGQV-SIVLNLFSRCGEVVKHVTP---SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKP  266 (350)
T ss_pred             EeccCccch-hHHHHHHHhhCeeeeeecC---CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeee
Confidence            356655443 3567899999999987553   466899999999999999998 788888877644 444

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=92.30  E-value=0.76  Score=28.94  Aligned_cols=55  Identities=15%  Similarity=0.291  Sum_probs=43.9

Q ss_pred             hhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057          22 TDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus        22 ~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      .++-++++..+..|+ -..|..-+    .| =||.|.+..+|+++....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I~~d~----tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRIRDDR----TG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCC-cceEEecC----CE-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            346688999999999 56654433    24 589999999999999999999998887754

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2135|consensus

Probab=92.24  E-value=0.083  Score=45.68  Aligned_cols=73  Identities=21%  Similarity=0.239  Sum_probs=58.5

Q ss_pred             CCcEEEEcCCCCCC-CHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEET-SEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~-t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..+.|-+.-.|+.. +..+|...|.+||.|..|.+-... --|+|+|.+..+|-.| ...++..|. |+.|+|-|-+
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~-~~a~vTF~t~aeag~a-~~s~~avln-nr~iKl~whn  444 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS-LHAVVTFKTRAEAGEA-YASHGAVLN-NRFIKLFWHN  444 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCch-hhheeeeeccccccch-hccccceec-CceeEEEEec
Confidence            45666666666644 678999999999999999988773 4599999999999776 447888999 9999998843

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=92.21  E-value=0.24  Score=33.06  Aligned_cols=26  Identities=12%  Similarity=0.238  Sum_probs=22.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHc
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFN  193 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~  193 (246)
                      ....+++.|.|||....+|+|++..+
T Consensus        49 ~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen   49 GVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             cccCCEEEEeCCCCCCChhhheeeEE
Confidence            44688999999999999999988754

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2591|consensus

Probab=90.88  E-value=0.51  Score=41.88  Aligned_cols=68  Identities=15%  Similarity=0.234  Sum_probs=50.6

Q ss_pred             CCcEEEe-cCCChhhhHHHHHHHhhc--cCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcC--CccCCeeEE
Q psy4057          10 VTNFVYV-THISSTDLKKSLYAIFSQ--FGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG--FPFYDKPMR   81 (246)
Q Consensus        10 ~~~~l~V-~nl~~~~~e~~l~~~F~~--fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng--~~~~g~~l~   81 (246)
                      .+|||.| +.||...-+++++.||+.  +-++.+|..-   .+.+ =||+|.+..+|+.|...|..  .+|.|++|.
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa---~N~n-WyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFA---HNDN-WYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeee---ecCc-eEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            3556655 999999999999999986  4556665332   1222 69999999999999887754  567777753

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=87.65  E-value=0.87  Score=33.61  Aligned_cols=64  Identities=16%  Similarity=0.096  Sum_probs=48.2

Q ss_pred             CCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          18 HISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        18 nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      +++.......+.......|.+.-..+     ..++..++|.+.+++.+++. .....+.|..+.+....+
T Consensus        28 ~~~~~~l~~~l~~~W~~~~~~~i~~l-----~~~~fl~~F~~~~d~~~vl~-~~p~~~~~~~~~l~~W~~   91 (153)
T PF14111_consen   28 PISLSALEQELAKIWKLKGGVKIRDL-----GDNLFLFQFESEEDRQRVLK-GGPWNFNGHFLILQRWSP   91 (153)
T ss_pred             CCCHHHHHHHHHHHhCCCCcEEEEEe-----CCCeEEEEEEeccceeEEEe-cccccccccchhhhhhcc
Confidence            35567777778887777775554444     56899999999999999988 556777888888876543

>KOG2318|consensus

Probab=84.95  E-value=5.7  Score=35.74  Aligned_cols=79  Identities=18%  Similarity=0.275  Sum_probs=61.3

Q ss_pred             CCCCcEEEecCCCh-hhhHHHHHHHhhcc----CCeeEEEEccCC-------------C---------------------
Q psy4057           8 ICVTNFVYVTHISS-TDLKKSLYAIFSQF----GQIMDIVALKTL-------------K---------------------   48 (246)
Q Consensus         8 ~~~~~~l~V~nl~~-~~~e~~l~~~F~~f----G~i~~v~~~~~~-------------~---------------------   48 (246)
                      ..++++|-|.||.- .+...+|.-+|+.|    |.|.+|.|+.+.             .                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            45688999999865 35566788888877    699999988531             1                     


Q ss_pred             ---------------Cc-cEEEEEEcCHHHHHHHHHHhcCCcc--CCeeEEEEEcc
Q psy4057          49 ---------------MR-GQAFVIFKEIASATNALRSMQGFPF--YDKPMRIQYSK   86 (246)
Q Consensus        49 ---------------~k-g~aFV~f~~~~~A~~Ai~~lng~~~--~g~~l~v~~a~   86 (246)
                                     -+ -||.|+|.++++|.+..+.++|+.|  -|..|.++|..
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIP  306 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIP  306 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeecC
Confidence                           01 3799999999999999999999998  46667777753

>KOG4483|consensus

Probab=84.63  E-value=2.1  Score=36.55  Aligned_cols=56  Identities=18%  Similarity=0.231  Sum_probs=49.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCc-eEEEEeeCCccEEEEEeCCHHHHHHHHHH
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGF-KEVRLVPNRHDIAFVEFENEMQSAAAKLA  227 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i-~~v~~~~~~~g~afV~f~~~~~A~~Al~~  227 (246)
                      -.++|-|.++|...-.+||...|+.|++- -+|.++.+.  .||-.|.+...|..||..
T Consensus       390 lpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt--halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  390 LPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT--HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             ccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc--eeEEeecchHHHHHHhhc
Confidence            57899999999999999999999999775 788888886  599999999999999875

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=83.22  E-value=1.7  Score=35.60  Aligned_cols=74  Identities=14%  Similarity=0.229  Sum_probs=56.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC------------ccEEEEEeCCHHHHHH----HHHHhCC--C
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR------------HDIAFVEFENEMQSAA----AKLALHG--F  231 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~------------~g~afV~f~~~~~A~~----Al~~l~g--~  231 (246)
                      .++.|.+.|+..+++-..+-..|.+||.|++|.++.+.            .....+.|-+.+.+..    .++.|.-  +
T Consensus        14 rTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~   93 (309)
T PF10567_consen   14 RTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKT   93 (309)
T ss_pred             eeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHH
Confidence            48889999999999999999999999999999999976            2468888998877653    3333332  2


Q ss_pred             ccCCCCceEEEee
Q psy4057         232 KITPTHAMKISFA  244 (246)
Q Consensus       232 ~i~~g~~l~v~~a  244 (246)
                      .+. ...|.++|.
T Consensus        94 ~L~-S~~L~lsFV  105 (309)
T PF10567_consen   94 KLK-SESLTLSFV  105 (309)
T ss_pred             hcC-CcceeEEEE
Confidence            345 677777764

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG2318|consensus

Probab=82.70  E-value=7.2  Score=35.11  Aligned_cols=67  Identities=21%  Similarity=0.249  Sum_probs=54.2

Q ss_pred             CCCCcEEEEcCCCC-CCCHHHHHHHHccC----CCceEEEEeeCC-----------------------------------
Q psy4057         168 QPPNQILFLTNLPE-ETSEMMLSMLFNQF----PGFKEVRLVPNR-----------------------------------  207 (246)
Q Consensus       168 ~~~~~~l~v~nL~~-~~t~e~l~~~f~~~----G~i~~v~~~~~~-----------------------------------  207 (246)
                      ...+++|=|.||.- .+.-++|.-+|+.|    |.|.+|.|.+..                                   
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            44688999999964 67788888888755    588888876621                                   


Q ss_pred             --------c---------cEEEEEeCCHHHHHHHHHHhCCCccC
Q psy4057         208 --------H---------DIAFVEFENEMQSAAAKLALHGFKIT  234 (246)
Q Consensus       208 --------~---------g~afV~f~~~~~A~~Al~~l~g~~i~  234 (246)
                              +         =||+|+|.+++.|......++|..|.
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfE  294 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFE  294 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceec
Confidence                    0         17999999999999999999999997

>KOG4019|consensus

Probab=82.07  E-value=1.3  Score=33.67  Aligned_cols=73  Identities=21%  Similarity=0.296  Sum_probs=54.5

Q ss_pred             CcEEEEcCCCCCCCH-----HHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         171 NQILFLTNLPEETSE-----MMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~-----e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ...+++++++..+-.     ....++|.+|.+....++.+.- +..-|.|.+.+.|..|.-.++++.|.++..++..||
T Consensus        10 p~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrsf-rrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~yfa   87 (193)
T KOG4019|consen   10 PTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRSF-RRVRINFSNPEAAADARIKLHSTSFNGKNELKLYFA   87 (193)
T ss_pred             cceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHhh-ceeEEeccChhHHHHHHHHhhhcccCCCceEEEEEc
Confidence            455777777765432     2445777887777766666655 357889999999999999999999994448888776

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	246
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		5e-37
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		7e-37
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		3e-33
2b0g_A	83	Solution Structure Of Drosophila Melanogaster Snf R		8e-37
2k3k_A	104	Solution Structure Of Drosophila Melanogaster Snf R		4e-36
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		2e-33
2u1a_A	88	Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20		8e-33
1m5k_C	100	Crystal Structure Of A Hairpin Ribozyme In The Cata		9e-33
1a9n_B	96	Crystal Structure Of The Spliceosomal U2b''-U2a' Pr		1e-31
2nz4_A	94	Structural Investigation Of The Glms Ribozyme Bound		2e-31
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		2e-31
1urn_A	97	U1a MutantRNA COMPLEX + GLYCEROL Length = 97		2e-31
1u6b_A	98	Crystal Structure Of A Self-Splicing Group I Intron		2e-31
3bo2_A	95	A Relaxed Active Site Following Exon Ligation By A		2e-31
3k0j_A	96	Crystal Structure Of The E. Coli Thim Riboswitch In		7e-31
3iwn_C	91	Co-Crystal Structure Of A Bacterial C-Di-Gmp Ribosw		8e-31
3l3c_A	90	Crystal Structure Of The Bacillus Anthracis Glms Ri		9e-31
1drz_A	97	U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOM		5e-29
3cul_A	98	Aminoacyl-Trna Synthetase Ribozyme Length = 98		5e-29
1cx0_A	95	Hepatitis Delta Virus Ribozyme Length = 95		1e-28
2a3j_A	127	Structure Of Urndesign, A Complete Computational Re		6e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		4e-05
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		1e-04
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-04
3lqv_A	115	Branch Recognition By Sf3b14 Length = 115		2e-04
2f9d_A	125	2.5 Angstrom Resolution Structure Of The Spliceosom		2e-04
2fho_B	87	Nmr Solution Structure Of The Human Spliceosomal Pr		2e-04

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score =  150 bits (380), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 69/91 (75%), Positives = 83/91 (91%)
Query: 19  ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
           I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 20  IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 79  PMRIQYSKTDSDVISKIKGTFMERPKKVRKQ 109
           PMRIQY+KTDSD+I+K+KGTF+ER +K  K+
Sbjct: 80  PMRIQYAKTDSDIIAKMKGTFVERDRKREKR 110

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score =  150 bits (378), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 69/91 (75%), Positives = 83/91 (91%)
Query: 19  ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
           I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 21  IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 79  PMRIQYSKTDSDVISKIKGTFMERPKKVRKQ 109
           PMRIQY+KTDSD+I+K+KGTF+ER +K  K+
Sbjct: 81  PMRIQYAKTDSDIIAKMKGTFVERDRKREKR 111

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score =  138 bits (347), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 65/80 (81%), Positives = 72/80 (90%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
           E PPN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDIAFVEF+NE+Q+ AA+ 
Sbjct: 203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARD 262
Query: 227 ALHGFKITPTHAMKISFAKK 246
           AL GFKIT  +AMKISFAKK
Sbjct: 263 ALQGFKITQNNAMKISFAKK 282

>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2 Length = 83

Iteration: 1
 Score =  150 bits (378), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 72/80 (90%), Positives = 75/80 (93%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
           EQPPNQILFLTNLPEET+EMMLSMLFNQFPGFKEVRLVPNRHDIAFVEF  E+QS AAK 
Sbjct: 4   EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKE 63
Query: 227 ALHGFKITPTHAMKISFAKK 246
           AL GFKITPTHAMKI+FAKK
Sbjct: 64  ALQGFKITPTHAMKITFAKK 83

>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1 Length = 104

Iteration: 1
 Score =  147 bits (372), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 68/79 (86%), Positives = 76/79 (96%)
Query: 27  SLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK 86
           SLYAIFSQFGQI+DIVALKTLKMRGQAFVIFKEI SA+NALR+MQGFPFYDKPM+I YSK
Sbjct: 26  SLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSK 85
Query: 87  TDSDVISKIKGTFMERPKK 105
           +DSD+++KIKGTF ERPKK
Sbjct: 86  SDSDIVAKIKGTFKERPKK 104

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score =  139 bits (350), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 63/82 (76%), Positives = 77/82 (93%)
Query: 19  ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
           I   +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 20  IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 79  PMRIQYSKTDSDVISKIKGTFM 100
           PMRIQY+KTDSD+I+K+KGTF+
Sbjct: 80  PMRIQYAKTDSDIIAKMKGTFV 101

>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20 Structures Length = 88

Iteration: 1
 Score =  137 bits (344), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 65/80 (81%), Positives = 72/80 (90%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
           E PPN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDIAFVEF+NE+Q+ AA+ 
Sbjct: 9   ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARD 68
Query: 227 ALHGFKITPTHAMKISFAKK 246
           AL GFKIT  +AMKISFAKK
Sbjct: 69  ALQGFKITQNNAMKISFAKK 88

>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The Catalytically-Active Conformation Length = 100

Iteration: 1
 Score =  136 bits (343), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 62/80 (77%), Positives = 75/80 (93%)
Query: 19  ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
           I   +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 21  IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 79  PMRIQYSKTDSDVISKIKGT 98
           PMRIQY+KTDSD+I+K+KGT
Sbjct: 81  PMRIQYAKTDSDIIAKMKGT 100

>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein Complex Bound To A Fragment Of U2 Small Nuclear Rna Length = 96

Iteration: 1
 Score =  133 bits (334), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 59/79 (74%), Positives = 72/79 (91%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LK+SLYA+FSQFG ++DIVALKT+KMRGQAFVIFKE+ S+TNALR +QGFPFY K
Sbjct: 18 IKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNALRQLQGFPFYGK 77
Query: 79 PMRIQYSKTDSDVISKIKG 97
          PMRIQY+KTDSD+ISK++G
Sbjct: 78 PMRIQYAKTDSDIISKMRG 96

>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its Catalytic Cofactor Length = 94

Iteration: 1
 Score =  132 bits (332), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 60/78 (76%), Positives = 73/78 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 17 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 76
Query: 79 PMRIQYSKTDSDVISKIK 96
          PMRIQY+KTDSD+I+K+K
Sbjct: 77 PMRIQYAKTDSDIIAKMK 94

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score =  132 bits (332), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 60/75 (80%), Positives = 70/75 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 21 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 79 PMRIQYSKTDSDVIS 93
          PMRIQY+KTDSD+I+
Sbjct: 81 PMRIQYAKTDSDIIA 95

>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL Length = 97

Iteration: 1
 Score =  132 bits (331), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 60/78 (76%), Positives = 73/78 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 79 PMRIQYSKTDSDVISKIK 96
          PMRIQY+KTDSD+I+K+K
Sbjct: 80 PMRIQYAKTDSDIIAKMK 97

>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With Both Exons Length = 98

Iteration: 1
 Score =  132 bits (331), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 60/78 (76%), Positives = 73/78 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 21 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 79 PMRIQYSKTDSDVISKIK 96
          PMRIQY+KTDSD+I+K+K
Sbjct: 81 PMRIQYAKTDSDIIAKMK 98

>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I Intron Length = 95

Iteration: 1
 Score =  132 bits (331), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 60/78 (76%), Positives = 73/78 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 18 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 77
Query: 79 PMRIQYSKTDSDVISKIK 96
          PMRIQY+KTDSD+I+K+K
Sbjct: 78 PMRIQYAKTDSDIIAKMK 95

>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In Complex With Thiamine Pyrophosphate And The U1a Crystallization Module Length = 96

Iteration: 1
 Score =  130 bits (327), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 59/77 (76%), Positives = 72/77 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 79 PMRIQYSKTDSDVISKI 95
          PMRIQY+KTDSD+I+K+
Sbjct: 80 PMRIQYAKTDSDIIAKM 96

>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch Length = 91

Iteration: 1
 Score =  130 bits (326), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 59/76 (77%), Positives = 71/76 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 16 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 75
Query: 79 PMRIQYSKTDSDVISK 94
          PMRIQY+KTDSD+I+K
Sbjct: 76 PMRIQYAKTDSDIIAK 91

>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme Bound To Glc6p Length = 90

Iteration: 1
 Score =  130 bits (326), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 59/76 (77%), Positives = 71/76 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 15 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 74
Query: 79 PMRIQYSKTDSDVISK 94
          PMRIQY+KTDSD+I+K
Sbjct: 75 PMRIQYAKTDSDIIAK 90

>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC Ribozyme Complex Length = 97

Iteration: 1
 Score =  124 bits (311), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 57/78 (73%), Positives = 69/78 (88%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LK RGQAFVIFKE++SATNALRS QGFPFYDK
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDK 79
Query: 79 PMRIQYSKTDSDVISKIK 96
          P RIQY+KTDSD+I+K K
Sbjct: 80 PXRIQYAKTDSDIIAKXK 97

>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme Length = 98

Iteration: 1
 Score =  124 bits (311), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 57/78 (73%), Positives = 69/78 (88%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LK RGQAFVIFKE++SATNALRS QGFPFYDK
Sbjct: 21 IKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDK 80
Query: 79 PMRIQYSKTDSDVISKIK 96
          P RIQY+KTDSD+I+K K
Sbjct: 81 PXRIQYAKTDSDIIAKXK 98

>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme Length = 95

Iteration: 1
 Score =  123 bits (308), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 56/76 (73%), Positives = 68/76 (89%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LK RGQAFVIFKE++SATNALRS QGFPFYDK
Sbjct: 18 IKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDK 77
Query: 79 PMRIQYSKTDSDVISK 94
          P RIQY+KTDSD+I+K
Sbjct: 78 PXRIQYAKTDSDIIAK 93

>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign Of Human U1a Protein Length = 127

Iteration: 1
 Score = 47.8 bits (112), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 4/85 (4%)
Query: 7   HICVTNFVYVTHIS----STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIAS 62
           H   +  V +T+I+       L+  LYA+ S  G I+DIV   +    G+A+++F    S
Sbjct: 25  HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQES 84
Query: 63  ATNALRSMQGFPFYDKPMRIQYSKT 87
           A   + + QG+PF   P+ I +S+T
Sbjct: 85  AQAFVEAFQGYPFQGNPLVITFSET 109

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 3/80 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          ++V  +S    ++SL  +FS++GQI ++V +K   T + RG  FV F+ I  A +A+ +M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 71 QGFPFYDKPMRIQYSKTDSD 90
           G     + +R+  +   SD
Sbjct: 75 NGKSVDGRQIRVDQAGKSSD 94

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQ 71
          +++  ++    +K L A+F + G I +++ +K  T K RG AF+ F+  A A NA + M 
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 72 GFPFYDKPMRIQYSKTDS 89
          G   + K ++++ +K  S
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          +YV  +     +  L  IF  FG+I +IV +K   T + +G  F+ F +   A  AL  +
Sbjct: 8  LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 71 QGFPFYDKPMRIQY 84
           GF    +PMR+ +
Sbjct: 68 NGFELAGRPMRVGH 81

>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14 Length = 115

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/64 (29%), Positives = 35/64 (54%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
          V   +Y+ ++      + +Y IF ++G I  I    T + RG A+V++++I  A NA+  
Sbjct: 7  VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH 66
Query: 70 MQGF 73
          + GF
Sbjct: 67 LSGF 70

>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal Protein P14 Bound To Region Of Sf3b155 Length = 125

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 39/75 (52%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
          V   +Y+ ++      + +Y IF ++G I  I    T + RG A+V++++I  A NA   
Sbjct: 17 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 76
Query: 70 MQGFPFYDKPMRIQY 84
          + GF   ++ + + Y
Sbjct: 77 LSGFNVCNRYLVVLY 91

>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein Complex P14-Sf3b155 Length = 87

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 39/75 (52%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
          V   +Y+ ++      + +Y IF ++G I  I    T + RG A+V++++I  A NA   
Sbjct: 11 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 70
Query: 70 MQGFPFYDKPMRIQY 84
          + GF   ++ + + Y
Sbjct: 71 LSGFNVCNRYLVVLY 85

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	246
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-59
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-41
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	9e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-37
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	8e-37
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-31
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-10
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-26
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-25
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-25
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	9e-07
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-21
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-07
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	8e-14
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-09
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-13
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	6e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-11
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-13
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-05
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-12
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-12
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-09
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	6e-12
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-11
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	7e-10
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-11
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	9e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	9e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-07
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-10
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-10
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	9e-07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-06
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-10
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-10
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	8e-10
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-09
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-05
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-09
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-09
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-04
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-09
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-06
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-09
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-05
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-04
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	7e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-05
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-09
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-07
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-04
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-08
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-08
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-08
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-08
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-08
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-07
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-08
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-07
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-05
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-04
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-08
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	8e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-08
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-08
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-04
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-08
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-05
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-08
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-08
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-06
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-08
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-05
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-08
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-05
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-04
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-08
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-08
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-08
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-08
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-08
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-06
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-08
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-05
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-08
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-08
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-07
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-04
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-04
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-08
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-07
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	5e-08
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-05
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-08
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-05
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-08
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-05
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-08
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	8e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	6e-06
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	9e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	7e-04
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	9e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-06
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-07
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-06
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-07
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-04
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-05
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-04
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-06
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-07
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-04
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-07
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-06
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-07
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-07
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-06
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-05
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-07
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-06
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-07
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-06
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-05
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-07
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-07
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-05
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-07
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-07
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-07
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-07
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-07
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-06
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-07
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-06
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-07
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-05
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	6e-07
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-05
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-06
1x4e_A	85	RNA binding motif, single-stranded interacting pro	7e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	7e-05
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	8e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	9e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-06
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-06
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-06
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-06
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-05
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-06
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-06
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-06
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-06
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-04
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	4e-06
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-06
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	6e-04
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-06
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-04
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	8e-06
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-05
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-05
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-04
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-05
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	2e-05
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-05
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	7e-04
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-05
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-05
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-05
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	8e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-05
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	9e-05
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-04
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	9e-05
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-04
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-04
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-04
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-04
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-04
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	7e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-04
2div_A	99	TRNA selenocysteine associated protein; structural	3e-04
2div_A	99	TRNA selenocysteine associated protein; structural	7e-04
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-04
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-04
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	9e-04

>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 =  186 bits (473), Expect = 9e-59
 Identities = 139/262 (53%), Positives = 165/262 (62%), Gaps = 34/262 (12%)

Query: 19  ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
           I   +LKKSLYAIFSQFGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 21  IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80

Query: 79  PMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQ 138
           PMRIQY+KTDSD+I+K+KGTF+ER +K  K+    ++    KK+ +              
Sbjct: 81  PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGP 140

Query: 139 QQMQALSVQQPPVSQPAPPAPMATAGVPEQP----------------------------- 169
                   Q P +    P  P         P                             
Sbjct: 141 VPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQP 200

Query: 170 -----PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAA 224
                PN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDIAFVEF+NE+Q+ AA
Sbjct: 201 LSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAA 260

Query: 225 KLALHGFKITPTHAMKISFAKK 246
           + AL GFKIT  +AMKISFAKK
Sbjct: 261 RDALQGFKITQNNAMKISFAKK 282

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 51.8 bits (123), Expect = 4e-08
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 7/88 (7%)

Query: 165 VPEQPPNQILFLTNLPEETSE----MMLSMLFNQFPGFKEVRLVPNRH--DIAFVEFENE 218
           VPE  PN  +++ NL E+  +      L  +F+QF    ++ +  +      AFV F+  
Sbjct: 3   VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEV 62

Query: 219 MQSAAAKLALHGFKITPTHAMKISFAKK 246
             +  A  ++ GF       M+I +AK 
Sbjct: 63  SSATNALRSMQGFPFY-DKPMRIQYAKT 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 = 51.0 bits (121), Expect = 7e-08
 Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 7   HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNA 66
                + +++T++     +  L  +F+QF    ++  +        AFV F     A  A
Sbjct: 203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP--GRHDIAFVEFDNEVQAGAA 260

Query: 67  LRSMQGFPFY-DKPMRIQYSK 86
             ++QGF    +  M+I ++K
Sbjct: 261 RDALQGFKITQNNAMKISFAK 281

>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 =  138 bits (348), Expect = 8e-41
 Identities = 43/235 (18%), Positives = 83/235 (35%), Gaps = 46/235 (19%)

Query: 14  VYVTHISSTDLK-KSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
           + V++++   +  +SL+ +F  +G +  +  L     +  A V   +   A  A+  + G
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF--NKKENALVQMADGNQAQLAMSHLNG 63

Query: 73  FPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQAR 132
              + KP+RI  SK  +                      P E   +   +K        R
Sbjct: 64  HKLHGKPIRITLSKHQNV-------------------QLPREGQEDQGLTKDYGNSPLHR 104

Query: 133 LMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLF 192
                                     P +       PP+  L L+N+P   SE  L +LF
Sbjct: 105 F-----------------------KKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLF 141

Query: 193 NQFPGF-KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           +   G  K  +       +A ++  +  ++  A + LH   +   H +++SF+K 
Sbjct: 142 SSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 196

>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 = 50.3 bits (120), Expect = 6e-08
 Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 11  TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
           +  +++++I  +  ++ L  +FS  G ++        K R  A +    +  A  AL  +
Sbjct: 120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ-KDRKMALIQMGSVEEAVQALIDL 178

Query: 71  QGFPFYD-KPMRIQYSKT 87
                 +   +R+ +SK+
Sbjct: 179 HNHDLGENHHLRVSFSKS 196

>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 = 47.2 bits (112), Expect = 9e-07
 Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 171 NQILFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH 229
           N +L ++NL PE  +   L +LF  +   + V+++ N+ + A V+  +  Q+  A   L+
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62

Query: 230 GFKITPTHAMKISFAKK 246
           G K+     ++I+ +K 
Sbjct: 63  GHKL-HGKPIRITLSKH 78

>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 =  129 bits (326), Expect = 3e-37
 Identities = 42/235 (17%), Positives = 86/235 (36%), Gaps = 46/235 (19%)

Query: 14  VYVTHISSTDLK-KSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
           + V++++   +  +SL+ +F  +G +  +  L     +  A V   +   A  A+  + G
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF--NKKENALVQMADGNQAQLAMSHLNG 94

Query: 73  FPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQAR 132
              + KP+RI  SK  +  + +                                      
Sbjct: 95  HKLHGKPIRITLSKHQNVQLPR-------------------------------------- 116

Query: 133 LMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLF 192
             + Q+ Q         P+ +   P       +   PP+  L L+N+P   SE  L +LF
Sbjct: 117 --EGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI--FPPSATLHLSNIPPSVSEEDLKVLF 172

Query: 193 NQFPGF-KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           +   G  K  +       +A ++  +  ++  A + LH   +   H +++SF+K 
Sbjct: 173 SSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 227

>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 = 51.2 bits (122), Expect = 4e-08
 Identities = 22/105 (20%), Positives = 44/105 (41%), Gaps = 6/105 (5%)

Query: 147 QQPPVSQPAPPAPMATAGV----PEQPPNQILFLTNL-PEETSEMMLSMLFNQFPGFKEV 201
                S    P       +         N +L ++NL PE  +   L +LF  +   + V
Sbjct: 6   HHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV 65

Query: 202 RLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           +++ N+ + A V+  +  Q+  A   L+G K+     ++I+ +K 
Sbjct: 66  KILFNKKENALVQMADGNQAQLAMSHLNGHKL-HGKPIRITLSKH 109

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 49.6 bits (118), Expect = 1e-07
 Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 11  TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
           +  +++++I  +  ++ L  +FS  G ++        K R  A +    +  A  AL  +
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF-KFFQKDRKMALIQMGSVEEAVQALIDL 209

Query: 71  QGFPFYD-KPMRIQYSKT 87
                 +   +R+ +SK+
Sbjct: 210 HNHDLGENHHLRVSFSKS 227

>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 =  124 bits (313), Expect = 8e-37
 Identities = 60/78 (76%), Positives = 73/78 (93%)

Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
          I   +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79

Query: 79 PMRIQYSKTDSDVISKIK 96
          PMRIQY+KTDSD+I+K+K
Sbjct: 80 PMRIQYAKTDSDIIAKMK 97

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 51.8 bits (125), Expect = 3e-09
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 165 VPEQPPNQILFLTNLPEETSE----MMLSMLFNQFPGFKEVRLV--PNRHDIAFVEFENE 218
           VPE  PN  +++ NL E+  +      L  +F++F    ++ +         AFV F+  
Sbjct: 2   VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61

Query: 219 MQSAAAKLALHGFKITPTHAMKISFAKK 246
             +  A  ++ GF       M+I +AK 
Sbjct: 62  SSATNALRSMQGFPFY-DKPMRIQYAKT 88

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score =  111 bits (278), Expect = 3e-31
 Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 18  HISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD 77
            +    L+  LYA+ S  G I+DIV   +    G+A+++F    SA   + + QG+PF  
Sbjct: 40  EVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQG 99

Query: 78  KPMRIQYSKTDSDVISKIKGTFMERPKK 105
            P+ I +S+T    +++  G+       
Sbjct: 100 NPLVITFSETPQSQVAE-DGSLEHHHHH 126

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 54.5 bits (131), Expect = 6e-10
 Identities = 16/106 (15%), Positives = 41/106 (38%), Gaps = 7/106 (6%)

Query: 147 QQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSE----MMLSMLFNQFPGFKEVR 202
                 +    +P   +  P   P+Q++ +TN+  E  +     +L  L +      ++ 
Sbjct: 5   AAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIV 64

Query: 203 L--VPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           +    +    A++ F  +  + A   A  G+     + + I+F++ 
Sbjct: 65  VDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQ-GNPLVITFSET 109

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 97.0 bits (242), Expect = 6e-26
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 3/80 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQI---MDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
           +Y+ ++S    ++ L ++F++F +         + T +MRGQAF+ F     A  AL  +
Sbjct: 28  LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87

Query: 71  QGFPFYDKPMRIQYSKTDSD 90
            G+  Y K + I++ K    
Sbjct: 88  NGYKLYGKILVIEFGKNKKQ 107

>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 = 54.2 bits (131), Expect = 7e-10
 Identities = 23/99 (23%), Positives = 38/99 (38%), Gaps = 6/99 (6%)

Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI- 210
           S          +      PN++L+L NL    +E  L  LF +F   K   +        
Sbjct: 6   SGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGR 65

Query: 211 ----AFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK 245
               AF+ F N+  +  A   ++G+K+     + I F K
Sbjct: 66  MRGQAFITFPNKEIAWQALHLVNGYKLY-GKILVIEFGK 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 = 99.0 bits (246), Expect = 1e-25
 Identities = 26/241 (10%), Positives = 70/241 (29%), Gaps = 53/241 (21%)

Query: 14  VYVTHISSTDL-KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
           + V  +  + +    ++ +F  +G +  +  +K     G A V   +  +   A+  +  
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMK--SKPGAAMVEMADGYAVDRAITHLNN 64

Query: 73  FPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQAR 132
              + + M +  SK  + +  +  G             +     +               
Sbjct: 65  NFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFST-------------- 110

Query: 133 LMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLF 192
                                     P   A    Q P+ +L   N P E +E     + 
Sbjct: 111 --------------------------PEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEIC 144

Query: 193 NQFPGFKEVRLV-----PNRHDIAFVEFENEMQSAAAKLALHGFKITPT-----HAMKIS 242
           ++    +   +        R     +E++++  +      L+ +++        + +K+ 
Sbjct: 145 DELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC 204

Query: 243 F 243
           F
Sbjct: 205 F 205

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 47.8 bits (113), Expect = 5e-07
 Identities = 11/79 (13%), Positives = 31/79 (39%), Gaps = 2/79 (2%)

Query: 169 PPNQILFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLA 227
             + +L +  L   + +   +  +F  +   ++V+ + ++   A VE  +      A   
Sbjct: 2   ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITH 61

Query: 228 LHGFKITPTHAMKISFAKK 246
           L+   +     M +  +K+
Sbjct: 62  LNNNFM-FGQKMNVCVSKQ 79

>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 = 42.0 bits (98), Expect = 5e-05
 Identities = 7/79 (8%), Positives = 23/79 (29%), Gaps = 3/79 (3%)

Query: 9   CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATN 65
             +N ++  +      +++ + I  + G        V     +      + +   + A  
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180

Query: 66  ALRSMQGFPFYDKPMRIQY 84
            L  +  +   +      Y
Sbjct: 181 TLGFLNHYQMKNPNGPYPY 199

>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 = 95.3 bits (237), Expect = 7e-25
 Identities = 23/94 (24%), Positives = 44/94 (46%), Gaps = 8/94 (8%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQI--------MDIVALKTLKMRGQAFVIFKEIASATN 65
           +YV +++    +K L  IF ++            DI  +K  +M+GQAF+      +A  
Sbjct: 48  IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107

Query: 66  ALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTF 99
           AL+   G+  + KPM +Q++++        +G  
Sbjct: 108 ALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR 141

>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 = 46.4 bits (110), Expect = 9e-07
 Identities = 21/137 (15%), Positives = 44/137 (32%), Gaps = 21/137 (15%)

Query: 119 AKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTN 178
                 +   E     + ++ ++    ++   V +   P            PN  +++ N
Sbjct: 3   LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGE----------PNCRIYVKN 52

Query: 179 LPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----------AFVEFENEMQSAAAKLAL 228
           L +   E  L  +F ++  F                      AF+   NE  +A A    
Sbjct: 53  LAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEA 112

Query: 229 HGFKITPTHAMKISFAK 245
           +G+ +     M + FA+
Sbjct: 113 NGYVLF-GKPMVVQFAR 128

>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 = 85.9 bits (213), Expect = 1e-21
 Identities = 21/96 (21%), Positives = 47/96 (48%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
           +Y+ ++      + +Y IF ++G I  I    T + RG A+V++++I  A NA+  + GF
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGF 70

Query: 74  PFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQ 109
              ++ + + Y   +            E+ K ++++
Sbjct: 71  NVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEK 106

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 15/66 (22%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH--DIAFVEFENEMQSAAAKLA 227
            N+IL++ NLP + +   +  +F ++   +++R+         A+V +E+   +  A   
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH 66

Query: 228 LHGFKI 233
           L GF +
Sbjct: 67  LSGFNV 72

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 70.4 bits (173), Expect = 5e-15
 Identities = 35/233 (15%), Positives = 75/233 (32%), Gaps = 71/233 (30%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKTLKMRGQAFVIFKEIASATN 65
           +YV +I     ++++   F+   ++          ++A++  + +  AF+ F+ +   T 
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 66  ALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKK 125
           A+ +  G  F  + ++I+                  RP   +  P   E+P         
Sbjct: 67  AM-AFDGIIFQGQSLKIR------------------RPHDYQPLPGMSENP--------- 98

Query: 126 AAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSE 185
                                             + +  VP+      LF+  LP   ++
Sbjct: 99  ----------------------------SVYVPGVVSTVVPDSAHK--LFIGGLPNYLND 128

Query: 186 MMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKI 233
             +  L   F   K   LV +         AF E+ +   +  A   L+G ++
Sbjct: 129 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181

>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 = 50.4 bits (121), Expect = 6e-08
 Identities = 13/75 (17%), Positives = 31/75 (41%), Gaps = 3/75 (4%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           +++  + +      +  + + FG +     +K   T   +G AF  + +I     A+  +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176

Query: 71  QGFPFYDKPMRIQYS 85
            G    DK + +Q +
Sbjct: 177 NGMQLGDKKLLVQRA 191

>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 = 68.5 bits (168), Expect = 6e-14
 Identities = 34/262 (12%), Positives = 80/262 (30%), Gaps = 52/262 (19%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
           + +  +      + ++ + S +     +      K +G AFV       A  A+ +    
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDYE----LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQS 80

Query: 74  PFYDKPMRIQYSKTDSDVI----------SKIKGTF-----MERPKKVRKQPAPVEDPAE 118
              ++ + +Q   TD+ +            + +        +ER   V  +         
Sbjct: 81  RLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSE--------R 132

Query: 119 AKKSK--------KKAAKEQA-RLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQP 169
             +SK        KK +  +A   +  +    + L V     +             P   
Sbjct: 133 TGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVH---WTDAGQLT-------PALL 182

Query: 170 PNQILFLTNLPEETSEM-MLSMLFNQFPGFKEVRLVPNRH----DIAFVEFENEMQSAAA 224
            ++ L +  LP   +++  L    +        +L   +       A +E+E    +  A
Sbjct: 183 HSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEA 242

Query: 225 KLALHGFKITPTHAMKISFAKK 246
           +    G  +     +++SF   
Sbjct: 243 QQQADGLSLG-GSHLRVSFCAP 263

>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 = 50.7 bits (122), Expect = 8e-08
 Identities = 10/92 (10%), Positives = 28/92 (30%), Gaps = 3/92 (3%)

Query: 14  VYVTHIS-STDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSM 70
           + V  +    +   +L    S         +   +  +++G A + ++    A  A +  
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 246

Query: 71  QGFPFYDKPMRIQYSKTDSDVISKIKGTFMER 102
            G       +R+ +        S +      +
Sbjct: 247 DGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQ 278

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 65.4 bits (159), Expect = 8e-14
 Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 13  FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
            + V ++        L+ IFS+FG ++ I+       + QA + + +  SA +A  S+ G
Sbjct: 30  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-NNQFQALLQYADPVSAQHAKLSLDG 88

Query: 73  FPFYDKP--MRIQYSKTDSDVISK 94
              Y+    +RI +SK  S  +  
Sbjct: 89  QNIYNACCTLRIDFSKLTSLNVKY 112

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 53.5 bits (128), Expect = 2e-09
 Identities = 24/105 (22%), Positives = 47/105 (44%), Gaps = 5/105 (4%)

Query: 145 SVQQPPVSQPAPPAPMATAGVPEQPPNQILFLT--NLPEETSEMMLSMLFNQF-PGFKEV 201
           SVQ   ++  A  A +   G+     + +L +   NL    +  +L  +F++F    K +
Sbjct: 1   SVQSGNLALAASAAAVDA-GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKII 59

Query: 202 RLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPT-HAMKISFAK 245
               N    A +++ + + +  AKL+L G  I      ++I F+K
Sbjct: 60  TFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 104

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 63.9 bits (155), Expect = 2e-13
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 4/84 (4%)

Query: 13  FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
            + + +         LY + +  G++  IV  K  +   QA V F+ +  A  A  ++ G
Sbjct: 27  LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK--RNGIQAMVEFESVLCAQKAKAALNG 84

Query: 73  FPFYDK--PMRIQYSKTDSDVISK 94
              Y     ++I+Y++     + +
Sbjct: 85  ADIYAGCCTLKIEYARPTRLNVIR 108

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 48.9 bits (116), Expect = 6e-08
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 168 QPPNQILFLT--NLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
              N++L L+  N     +  +L  + N     + + +       A VEFE+ + +  AK
Sbjct: 20  SGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAK 79

Query: 226 LALHGFKITP-THAMKISFAK 245
            AL+G  I      +KI +A+
Sbjct: 80  AALNGADIYAGCCTLKIEYAR 100

>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 = 63.0 bits (154), Expect = 3e-13
 Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
          T  ++V  +       +L   F +FG I  I     +K    A++ ++ + +A  A   M
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTI---DHVKGDSFAYIQYESLDAAQAACAKM 73

Query: 71 QGFPF--YDKPMRIQYSKTD 88
          +GFP    D+ +R+ ++K+ 
Sbjct: 74 RGFPLGGPDRRLRVDFAKSG 93

>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 = 57.6 bits (140), Expect = 3e-11
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
            P   L++  L   TS   L+  F++F   + +  V      A++++E+   + AA   +
Sbjct: 15  NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD-SFAYIQYESLDAAQAACAKM 73

Query: 229 HGFKIT-PTHAMKISFAK 245
            GF +  P   +++ FAK
Sbjct: 74  RGFPLGGPDRRLRVDFAK 91

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 61.9 bits (151), Expect = 6e-13
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 5/73 (6%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          +YV     T     L   FS FG I+D+        R  AFV ++++ SA  A+  + G 
Sbjct: 18 LYVYGEDMTP--TLLRGAFSPFGNIIDL---SMDPPRNCAFVTYEKMESADQAVAELNGT 72

Query: 74 PFYDKPMRIQYSK 86
                +++  ++
Sbjct: 73 QVESVQLKVNIAR 85

>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 = 41.5 bits (98), Expect = 2e-05
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 4/81 (4%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
                   L++     + +  +L   F+ F    ++ + P R+  AFV +E    +  A 
Sbjct: 10  RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRN-CAFVTYEKMESADQAV 66

Query: 226 LALHGFKITPTHAMKISFAKK 246
             L+G ++  +  +K++ A+K
Sbjct: 67  AELNGTQVE-SVQLKVNIARK 86

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 61.2 bits (149), Expect = 1e-12
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
           Y+ +I     +  L  +F  FG I+D    K    +G  F+ +     A   + ++  F
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDF---KHYPEKGCCFIKYDTHEQAAVCIVALANF 86

Query: 74 PFYDKPMRIQYSK 86
          PF  + +R  + K
Sbjct: 87 PFQGRNLRTGWGK 99

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 57.7 bits (140), Expect = 3e-11
 Identities = 20/103 (19%), Positives = 41/103 (39%), Gaps = 7/103 (6%)

Query: 145 SVQQPPVSQPAPPAPMATAGVPEQPPNQI-LFLTNLPEETSEMMLSMLFNQFPGFKEVRL 203
           ++  PP   P     +    +   PP     ++ N+P   +E  L  LF  F    + + 
Sbjct: 4   TIGLPPQVNPQAVDHI----IRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKH 59

Query: 204 VPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
            P +    F++++   Q+A   +AL  F       ++  + K+
Sbjct: 60  YPEKG-CCFIKYDTHEQAAVCIVALANFPFQ-GRNLRTGWGKE 100

>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 = 62.0 bits (150), Expect = 3e-12
 Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 13  FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
            + V ++        L+ IFS+FG ++ I+       + QA + + +  SA +A  S+ G
Sbjct: 48  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-NNQFQALLQYADPVSAQHAKLSLDG 106

Query: 73  FPFYDKP--MRIQYSKTDSDVISK 94
              Y+    +RI +SK  S  +  
Sbjct: 107 QNIYNACCTLRIDFSKLTSLNVKY 130

>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 = 56.6 bits (136), Expect = 3e-10
 Identities = 26/115 (22%), Positives = 50/115 (43%), Gaps = 4/115 (3%)

Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLT--NLPEETSEMMLSMLF 192
            + Q  +QA++  Q      A  A    AG+     + +L +   NL    +  +L  +F
Sbjct: 8   GSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIF 67

Query: 193 NQFPGF-KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPT-HAMKISFAK 245
           ++F    K +    N    A +++ + + +  AKL+L G  I      ++I F+K
Sbjct: 68  SKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 122

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 59.8 bits (145), Expect = 5e-12
 Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          V++  +    ++  L     +FG I  +     +  + QA V F+++  A NA+      
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYV---VVMPKKRQALVEFEDVLGACNAVNYAADN 80

Query: 74 PFY--DKPMRIQYSKT 87
            Y    P  + YS +
Sbjct: 81 QIYIAGHPAFVNYSTS 96

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 52.5 bits (126), Expect = 2e-09
 Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
           P + ++ +  L +   E  L     +F     V ++P +   A VEFE+      A  A+
Sbjct: 19  PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKR-QALVEFEDV---LGACNAV 74

Query: 229 HGFKITPT----HAMKISFAK 245
           +           H   ++++ 
Sbjct: 75  NYAADNQIYIAGHPAFVNYST 95

>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 = 59.7 bits (145), Expect = 6e-12
 Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
           VY   I+S    + +   FS FGQIM+I   +    +G +FV F    SA +A+ S+ G 
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPFGQIMEI---RVFPEKGYSFVRFSTHESAAHAIVSVNGT 84

Query: 74  PFYDKPMRIQYSKTDSD 90
                 ++  + K   D
Sbjct: 85  TIEGHVVKCYWGKESPD 101

>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 = 52.3 bits (126), Expect = 3e-09
 Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 2/94 (2%)

Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIA 211
           S                P N  ++   +    ++ ++   F+ F    E+R+ P +   +
Sbjct: 6   SGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-YS 64

Query: 212 FVEFENEMQSAAAKLALHGFKITPTHAMKISFAK 245
           FV F     +A A ++++G  I   H +K  + K
Sbjct: 65  FVRFSTHESAAHAIVSVNGTTIE-GHVVKCYWGK 97

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 58.6 bits (142), Expect = 2e-11
 Identities = 12/75 (16%), Positives = 28/75 (37%), Gaps = 3/75 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          V    ++    +  L  +  ++G++ ++  L    T K  G A V+F     A   ++++
Sbjct: 9  VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68

Query: 71 QGFPFYDKPMRIQYS 85
                   +  Q  
Sbjct: 69 HLTSVMGNIIHAQLD 83

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 5/71 (7%)

Query: 168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSA 222
           Q P + +    L +   E  L  +  ++   +EV ++ +        +A V F +   + 
Sbjct: 3   QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62

Query: 223 AAKLALHGFKI 233
                LH   +
Sbjct: 63  ETVKNLHLTSV 73

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 61.2 bits (149), Expect = 3e-11
 Identities = 37/265 (13%), Positives = 77/265 (29%), Gaps = 50/265 (18%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
           V V ++  +  +  +Y  F   G I+ + VA    K    A + F     A  A+     
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 103

Query: 73  FPFYDKPMRIQYSK------------TDSDVISKIKGTFMERPKKVRKQPAPV------- 113
                  + + +                   I  +          +R             
Sbjct: 104 V-VGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFA 162

Query: 114 ----EDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQ-QPPVSQPAPPAPMATAGVPEQ 168
                   +A+   +K        +   + +   L  +   P+ +          G    
Sbjct: 163 YIDVTSKEDARYCVEK--------LNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGR--- 211

Query: 169 PPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENEMQS 221
                + + NL  E   E +L   F  F   +++ +   + +       AF+ FEN+  +
Sbjct: 212 ----EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSA 267

Query: 222 AAAKLALHGFKITPTHAMKISFAKK 246
             A L ++   +     + +S A K
Sbjct: 268 ERA-LQMNRSLLG-NREISVSLADK 290

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 57.1 bits (138), Expect = 4e-11
 Identities = 12/78 (15%), Positives = 28/78 (35%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          + + +I      + L ++  Q+G +     + T        V +     A  AL  + GF
Sbjct: 18 LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGF 77

Query: 74 PFYDKPMRIQYSKTDSDV 91
             +  +++ Y   +   
Sbjct: 78 QLENFTLKVAYIPDEMAA 95

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 51.7 bits (124), Expect = 4e-09
 Identities = 16/87 (18%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD--IAFVEFENE 218
           ++  VP++   + L + N+P      +L  L  Q+   +    V    +  +  V + ++
Sbjct: 5   SSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSK 64

Query: 219 MQSAAAKLALHGFKITPTHAMKISFAK 245
            Q+  A   L+GF++     +K+++  
Sbjct: 65  DQARQALDKLNGFQL-ENFTLKVAYIP 90

>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 = 57.5 bits (139), Expect = 4e-11
 Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 5/75 (6%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          V+V  +  + ++  L     +FG I  +     +  + QA V F+ I SA   +      
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYV---MMMPFKRQALVEFENIDSAKECVTFAADV 74

Query: 74 PFY--DKPMRIQYSK 86
          P Y   +     YS 
Sbjct: 75 PVYIAGQQAFFNYST 89

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 52.9 bits (127), Expect = 2e-09
 Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 4/82 (4%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFEN--EMQSAA 223
            +   + ++ +  L E   E  L     +F     V ++P +   A VEFEN    +   
Sbjct: 10  HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-QALVEFENIDSAKECV 68

Query: 224 AKLALHGFKITPTHAMKISFAK 245
              A     I        +++ 
Sbjct: 69  TFAADVPVYIAG-QQAFFNYST 89

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 56.9 bits (138), Expect = 4e-11
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          +YV ++  +  ++ +   F+           +  K+R  AFV F     A  A++++ G 
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVE---RVKKIRDYAFVHFSNREDAVEAMKALNGK 74

Query: 74 PFYDKPMRIQYSK 86
               P+ +  +K
Sbjct: 75 VLDGSPIEVTLAK 87

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 53.8 bits (130), Expect = 7e-10
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
              +IL++ NL   TSE M+   FN        R+   R D AFV F N   +  A  AL
Sbjct: 13  SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR-DYAFVHFSNREDAVEAMKAL 71

Query: 229 HGFKITPTHAMKISFAKK 246
           +G  +     ++++ AK 
Sbjct: 72  NGKVLD-GSPIEVTLAKP 88

>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 = 58.3 bits (141), Expect = 5e-11
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 3/80 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           +YV ++S    ++ +Y +FS+ G I  I+           G  FV +   A A NA+R +
Sbjct: 42  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101

Query: 71  QGFPFYDKPMRIQYSKTDSD 90
            G    D+ +R  +     +
Sbjct: 102 NGTRLDDRIIRTDWDAGFKE 121

>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 = 47.5 bits (113), Expect = 4e-07
 Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAA 223
             +  L++ NL   T+E  +  LF++    K++ +  ++         FVE+ +   +  
Sbjct: 37  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96

Query: 224 AKLALHGFKI 233
           A   ++G ++
Sbjct: 97  AMRYINGTRL 106

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 56.4 bits (137), Expect = 6e-11
 Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 6/77 (7%)

Query: 14 VYVTHISSTDLKKS-LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
          +++ ++   ++ K  L+ IFS +G IM I            F+ F    S  +A+     
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQIN-----IKNAFGFIQFDNPQSVRDAIECESQ 67

Query: 73 FPFYDKPMRIQYSKTDS 89
             + K + ++ S +++
Sbjct: 68 EMNFGKKLILEVSSSNA 84

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 55.7 bits (135), Expect = 9e-11
 Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 1/80 (1%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
            E      L++  L +  +E  L   F QF   + + +V  +   AF++F     +  A 
Sbjct: 7   GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ-CAFIQFATRQAAEVAA 65

Query: 226 LALHGFKITPTHAMKISFAK 245
                  I     + + + +
Sbjct: 66  EKSFNKLIVNGRRLNVKWGR 85

>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 = 55.7 bits (135), Expect = 9e-11
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 4/74 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM-QG 72
          +YV  +  T  +  L   F QFG+I  I     ++ +  AF+ F    +A  A       
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTI---TVVQRQQCAFIQFATRQAAEVAAEKSFNK 71

Query: 73 FPFYDKPMRIQYSK 86
               + + +++ +
Sbjct: 72 LIVNGRRLNVKWGR 85

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 56.0 bits (135), Expect = 1e-10
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          VYV ++        L     + G +   + L     R +AF+ + + A+A  A+  +QG 
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGSVP--LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGL 79

Query: 74 PFYDKPMRIQYSKTDSD 90
                +R+  ++   D
Sbjct: 80 RLGTDTLRVALARQQRD 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 46.7 bits (111), Expect = 2e-07
 Identities = 17/99 (17%), Positives = 35/99 (35%), Gaps = 9/99 (9%)

Query: 149 PPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH 208
              S P  P           P    +++ NLP +     L     +  G   +RL     
Sbjct: 3   SGSSGPGSPPGEGA------PLAADVYVGNLPRDARVSDLKRALREL-GSVPLRLTWQGP 55

Query: 209 D-IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
              AF+ + +   +  A   L G ++     ++++ A++
Sbjct: 56  RRRAFLHYPDSAAAQQAVSCLQGLRLGT-DTLRVALARQ 93

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 55.4 bits (134), Expect = 1e-10
 Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 14 VYVTHISSTDLKKS-LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
          +++ ++   ++ K  L+ IFS +G IM I            F+ F    S  +A+     
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-----KNAFGFIQFDNPQSVRDAIEXESQ 79

Query: 73 FPFYDKPMRIQYSK 86
             + K + ++ S 
Sbjct: 80 EMNFGKKLILEVSS 93

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.9 bits (133), Expect = 3e-10
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 1/64 (1%)

Query: 28 LYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK 86
          +  +FSQ G      +  +        FV F E   A  AL +M G     K +++ ++ 
Sbjct: 32 ILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT 91

Query: 87 TDSD 90
          T S 
Sbjct: 92 TPSS 95

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.3 bits (108), Expect = 9e-07
 Identities = 21/91 (23%), Positives = 45/91 (49%), Gaps = 4/91 (4%)

Query: 158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI---AFVE 214
           +  ++  + +    + L++ NL  + +E+++  LF+Q    K  +++          FVE
Sbjct: 2   SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVE 61

Query: 215 FENEMQSAAAKLALHGFKITPTHAMKISFAK 245
           F     +AAA  A++G KI     +K+++A 
Sbjct: 62  FYEHRDAAAALAAMNGRKIL-GKEVKVNWAT 91

>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 = 55.0 bits (133), Expect = 3e-10
 Identities = 16/73 (21%), Positives = 34/73 (46%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          +YV ++      K +  +F ++G I DI           AFV F++   A +A+    G+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84

Query: 74 PFYDKPMRIQYSK 86
           +    +R+++ +
Sbjct: 85 DYDGYRLRVEFPR 97

>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 = 43.1 bits (102), Expect = 6e-06
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 2/70 (2%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD--IAFVEFENEMQSAA 223
           P    +  +++ NLP +     +  +F ++   +++ L   R     AFVEFE+   +  
Sbjct: 17  PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAED 76

Query: 224 AKLALHGFKI 233
           A     G+  
Sbjct: 77  AVYGRDGYDY 86

>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 = 54.6 bits (132), Expect = 4e-10
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 28 LYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
          L+ +F Q G +++    K   T + +G  FV F     A  A++ M     Y KP+R+  
Sbjct: 32 LWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK 91

Query: 85 SKTDSD 90
          +   + 
Sbjct: 92 ASAHNK 97

>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 = 44.2 bits (105), Expect = 2e-06
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 5/81 (6%)

Query: 158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP----NRHD-IAF 212
           +  ++  + E+  +  +++  L E+ SE +L  LF Q        +       +H    F
Sbjct: 2   SSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF 61

Query: 213 VEFENEMQSAAAKLALHGFKI 233
           VEF +E  +  A   +   K+
Sbjct: 62  VEFLSEEDADYAIKIMDMIKL 82

>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 = 54.5 bits (131), Expect = 5e-10
 Identities = 14/89 (15%), Positives = 30/89 (33%), Gaps = 9/89 (10%)

Query: 8   ICVTNFVYVTHISSTDLKKSLYA---IFSQFGQIMDIVALK------TLKMRGQAFVIFK 58
           +   N V+V  +S       +      F +FG+I  +V         +      A+V + 
Sbjct: 12  VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYI 71

Query: 59  EIASATNALRSMQGFPFYDKPMRIQYSKT 87
               A  A++ +       + ++     T
Sbjct: 72  RSEDALRAIQCVNNVVVDGRTLKASLGTT 100

>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 = 55.2 bits (133), Expect = 8e-10
 Identities = 29/125 (23%), Positives = 50/125 (40%), Gaps = 8/125 (6%)

Query: 114 EDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQI 173
           +      + K+KA   + R   +     +A+   +   ++          G        I
Sbjct: 18  DGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELE---PGPQRSVEGWI 74

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAAKLAL 228
           LF+T++ EE  E  +   F  +   K + L  +R        A VE+E   Q+ AAK AL
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134

Query: 229 HGFKI 233
           +G +I
Sbjct: 135 NGAEI 139

>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 = 49.8 bits (119), Expect = 7e-08
 Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 3/77 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDI-VAL--KTLKMRGQAFVIFKEIASATNALRSM 70
           ++VT I     +  +   F  +G+I +I + L  +T   +G A V ++    A  A  ++
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134

Query: 71  QGFPFYDKPMRIQYSKT 87
            G     + +++ +   
Sbjct: 135 NGAEIMGQTIQVDWCFV 151

>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 = 53.7 bits (129), Expect = 1e-09
 Identities = 22/109 (20%), Positives = 42/109 (38%), Gaps = 12/109 (11%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
           +   ++ +  L   +   FS+FG +  ++  +       A V F E   A  A R +   
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG---GITAIVEFLEPLEARKAFRHLAYS 69

Query: 74  PFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKS 122
            F+  P+ ++++           G F   P+K   Q     + AE+  S
Sbjct: 70  KFHHVPLYLEWAP---------IGVFGAAPQKKDSQHEQPAEKAESGPS 109

>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 = 47.1 bits (112), Expect = 2e-07
 Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 1/63 (1%)

Query: 171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
             ++   NLP  T    +   F++F     V L       A VEF   +++  A   L  
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-ITAIVEFLEPLEARKAFRHLAY 68

Query: 231 FKI 233
            K 
Sbjct: 69  SKF 71

>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 = 56.8 bits (136), Expect = 1e-09
 Identities = 25/142 (17%), Positives = 54/142 (38%), Gaps = 19/142 (13%)

Query: 97  GTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAP 156
             ++   +  R  P P       ++ ++K  ++  R  Q  + +++       P + P  
Sbjct: 42  APYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWD----PHNDPNA 97

Query: 157 PAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IA 211
                     +    + LF+  +  +T+E  L   F  +   K + +V ++        A
Sbjct: 98  ----------QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYA 147

Query: 212 FVEFENEMQSAAAKLALHGFKI 233
           F+E+E+E    +A     G KI
Sbjct: 148 FIEYEHERDMHSAYKHADGKKI 169

>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 = 43.7 bits (102), Expect = 3e-05
 Identities = 14/102 (13%), Positives = 35/102 (34%), Gaps = 3/102 (2%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
           ++V  ++    +  L   F  +G I  I  +   ++ K RG AF+ ++      +A +  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 71  QGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAP 112
            G     + + +   +  +    + +          R     
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADV 206

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
           ++V        +  L  IF  FG + ++       + G AFV F+E  SA  A+  + G 
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVK-----ILNGFAFVEFEEAESAAKAIEEVHGK 88

Query: 74  PFYDKPMRIQYSK 86
            F ++P+ + YSK
Sbjct: 89  SFANQPLEVVYSK 101

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           LF+   P +  E  L+ +F  F   KEV+++   +  AFVEFE    +A A   +HG   
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSF 90

Query: 234 TPTHAMKISFAKK 246
                +++ ++K 
Sbjct: 91  A-NQPLEVVYSKL 102

>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 = 54.9 bits (133), Expect = 1e-09
 Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
           +   ++S    +  L  +F    +I   +  +  K +G A++ FK  A A   L   QG 
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEIR--LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 159

Query: 74  PFYDKPMRIQYSK 86
               + + + Y+ 
Sbjct: 160 EIDGRSVSLYYTG 172

>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 = 48.4 bits (116), Expect = 2e-07
 Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 3/79 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
          +++ +++       L    S+     D  +V ++T   R   +V F+       AL  + 
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELT 74

Query: 72 GFPFYDKPMRIQYSKTDSD 90
          G   +   ++++  K    
Sbjct: 75 GLKVFGNEIKLEKPKGRDS 93

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 5/71 (7%)

Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSA 222
           E      LF+ NL    S   L +  ++     ++ +V  R        +V+FE+  +  
Sbjct: 9   ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA-EDL 67

Query: 223 AAKLALHGFKI 233
              L L G K+
Sbjct: 68  EKALELTGLKV 78

>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 = 52.6 bits (127), Expect = 2e-09
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 4/74 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG- 72
          +Y+ ++S       L  +F      +     + L   G AFV + +   A  A+ ++ G 
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAG---QVLLKSGYAFVDYPDQNWAIRAIETLSGK 67

Query: 73 FPFYDKPMRIQYSK 86
             + K M + YS 
Sbjct: 68 VELHGKIMEVDYSV 81

>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 = 43.0 bits (102), Expect = 5e-06
 Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 1/72 (1%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           L++ NL    +   L  LF         +++      AFV++ ++  +  A   L G   
Sbjct: 11  LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-GYAFVDYPDQNWAIRAIETLSGKVE 69

Query: 234 TPTHAMKISFAK 245
                M++ ++ 
Sbjct: 70  LHGKIMEVDYSV 81

>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 = 53.3 bits (129), Expect = 4e-09
 Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 3/80 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          + V ++      + LYA+F   G I     ++   T    G AFV F     +  A++ +
Sbjct: 6  LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 71 QGFPFYDKPMRIQYSKTDSD 90
           G    +K +++ Y++   +
Sbjct: 66 NGITVRNKRLKVSYARPGGE 85

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 46.8 bits (112), Expect = 7e-07
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           +YVT++  T     L  IF ++G I+    L+   T + RG AFV + +   A  A+ ++
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

Query: 71  QG--FPFYDKPMRIQY 84
                    +P+ ++ 
Sbjct: 152 NNVIPEGGSQPLSVRL 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 = 42.2 bits (100), Expect = 3e-05
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           L +  LP++ ++  L  LF         R++ +         AFV+F +EM S  A   L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 229 HGFKITPTHAMKISFAKK 246
           +G  +     +K+S+A+ 
Sbjct: 66  NGITV-RNKRLKVSYARP 82

>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 = 39.9 bits (94), Expect = 2e-04
 Identities = 14/77 (18%), Positives = 34/77 (44%), Gaps = 6/77 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           L++TNLP   ++  L  +F ++    +  ++ ++       +AFV +    ++  A  AL
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

Query: 229 HGFKIT-PTHAMKISFA 244
           +       +  + +  A
Sbjct: 152 NNVIPEGGSQPLSVRLA 168

>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 = 51.4 bits (124), Expect = 4e-09
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 4/65 (6%)

Query: 26 KSLYAIFSQFGQIMD----IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
          K LY  FS FG I+     +    T   +G AF+ F    ++  A+ +M G    ++P+ 
Sbjct: 20 KLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPIT 79

Query: 82 IQYSK 86
          + Y+ 
Sbjct: 80 VSYAF 84

>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 = 51.2 bits (123), Expect = 7e-09
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 14 VYVTHISSTDLKKS-LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
          V++ ++++  +KKS +  IFS++G++    ++     +G AFV +     A  A+    G
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAG-CSVH----KGYAFVQYSNERHARAAVLGENG 84

Query: 73 FPFYDKPMRIQYSK 86
               + + I  + 
Sbjct: 85 RVLAGQTLDINMAG 98

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 51.3 bits (123), Expect = 7e-09
 Identities = 19/90 (21%), Positives = 36/90 (40%), Gaps = 8/90 (8%)

Query: 164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHD------IAFVEFE 216
           G      N  LF+  +P+      +     +   G  +V +  +  D       AFVE+E
Sbjct: 1   GSSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYE 60

Query: 217 NEMQSAAAKLALHGFKITP-THAMKISFAK 245
           +   +A A+  L   +I    H + + +A+
Sbjct: 61  SHRAAAMARRKLMPGRIQLWGHQIAVDWAE 90

>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 = 41.7 bits (98), Expect = 2e-05
 Identities = 15/96 (15%), Positives = 39/96 (40%), Gaps = 11/96 (11%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL-----KTLKMRGQAFVIFKEIASATNALR 68
           +++  I     ++ +    ++  + +  V +       +K RG AFV ++   +A  A R
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 69  SMQ--GFPFYDKPMRIQYSKT----DSDVISKIKGT 98
            +       +   + + +++     D DV+  + G 
Sbjct: 71  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGP 106

>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 = 53.1 bits (128), Expect = 8e-09
 Identities = 22/101 (21%), Positives = 42/101 (41%), Gaps = 2/101 (1%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
           +++ ++  +   K+LY  FS FG I+   V       +G  FV F+   +A  A+  M G
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165

Query: 73  FPFYDKPMRIQYSKTDSDVISKIKGTFME-RPKKVRKQPAP 112
               D+ + +   K+  +  +++     E  P  V      
Sbjct: 166 MLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGS 206

>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 = 50.0 bits (120), Expect = 1e-07
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 28 LYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
          LY  FS  G I+ I   +   T +  G A+V F++ A A  AL +M       KP+RI +
Sbjct: 32 LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW 91

Query: 85 SKTDS 89
          S+ D 
Sbjct: 92 SQRDP 96

>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 = 44.6 bits (106), Expect = 6e-06
 Identities = 18/100 (18%), Positives = 37/100 (37%), Gaps = 14/100 (14%)

Query: 150 PVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD 209
           P+    P AP          P   L++ +L  + +E ML   F+       +R+  +   
Sbjct: 2   PLGSMNPSAP--------SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMIT 53

Query: 210 -----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA 244
                 A+V F+    +  A   ++   I     ++I ++
Sbjct: 54  RRSLGYAYVNFQQPADAERALDTMNFDVI-KGKPVRIMWS 92

>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 = 40.7 bits (96), Expect = 2e-04
 Identities = 15/76 (19%), Positives = 28/76 (36%), Gaps = 4/76 (5%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLV--PNRH-DIAFVEFENEMQSAAAKLALHG 230
           +F+ NL +      L   F+ F      ++V   N      FV FE +  +  A   ++G
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165

Query: 231 FKITPTHAMKISFAKK 246
             +     + +   K 
Sbjct: 166 MLLN-DRKVFVGRFKS 180

>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 = 51.2 bits (123), Expect = 1e-08
 Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 5/75 (6%)

Query: 164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENE 218
           G        ILF+T + EE +E  +   F ++   K + L  +R          VE+E  
Sbjct: 15  GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74

Query: 219 MQSAAAKLALHGFKI 233
            ++ AA   L+G  +
Sbjct: 75  KEAQAAMEGLNGQDL 89

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 13/77 (16%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 14  VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
           ++VT +      ++ ++  F+++G+I +I       T  ++G   V ++    A  A+  
Sbjct: 25  LFVTGVHEEAT-EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 70  MQGFPFYDKPMRIQYSK 86
           + G     +P+ + +  
Sbjct: 84  LNGQDLMGQPISVDWCF 100

>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 = 51.3 bits (123), Expect = 1e-08
 Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 5/94 (5%)

Query: 145 SVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLV 204
            +      Q                PN  L +  L   T+E  L  +F+++    +V +V
Sbjct: 20  HMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV 79

Query: 205 PNRHD-----IAFVEFENEMQSAAAKLALHGFKI 233
            ++        AFV FEN   +  AK   +G ++
Sbjct: 80  YDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 113

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 49.7 bits (119), Expect = 4e-08
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           + V  +S    ++ L  +FS++G I D+  +    + + RG AFV F+ +  A  A    
Sbjct: 49  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108

Query: 71  QGFPFYDKPMRIQYSKT 87
            G     + +R+ +S T
Sbjct: 109 NGMELDGRRIRVDFSIT 125

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 49.7 bits (119), Expect = 1e-08
 Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 12 NFVYVTHISSTD------LKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASAT 64
          + + V ++          LK  ++ IFS+FG+I +     +  K +G  F+ +   A A 
Sbjct: 2  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61

Query: 65 NALRSMQGFPFYDK 78
          +A+++  G+    +
Sbjct: 62 DAVKNADGYKLDKQ 75

>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 = 50.3 bits (121), Expect = 1e-08
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
          + V  +S  T  ++ L  +FS++G I D+  +    + + RG AFV F+ +  A  A   
Sbjct: 18 LGVFGLSLYTT-ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 70 MQGFPFYDKPMRIQYSKT 87
            G     + +R+    +
Sbjct: 77 ANGMELDGRRIRVSGPSS 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 = 47.2 bits (113), Expect = 2e-07
 Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 5/79 (6%)

Query: 160 MATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVE 214
            ++       PN  L +  L   T+E  L  +F+++    +V +V ++        AFV 
Sbjct: 4   GSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63

Query: 215 FENEMQSAAAKLALHGFKI 233
           FEN   +  AK   +G ++
Sbjct: 64  FENVDDAKEAKERANGMEL 82

>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 = 51.8 bits (125), Expect = 1e-08
 Identities = 14/80 (17%), Positives = 35/80 (43%), Gaps = 3/80 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          + V ++     ++   ++F   G+I     ++   T +  G  FV + +   A  A+ ++
Sbjct: 5  LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 71 QGFPFYDKPMRIQYSKTDSD 90
           G     K +++ Y++  S 
Sbjct: 65 NGLRLQTKTIKVSYARPSSA 84

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 46.8 bits (112), Expect = 7e-07
 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 5/76 (6%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
           +YV+ +  T  +K L  +FSQ+G+I+    +V   T   RG  F+ F +   A  A++ +
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 71  QG--FPFYDKPMRIQY 84
            G       +P+ +++
Sbjct: 151 NGQKPSGATEPITVKF 166

>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 = 42.2 bits (100), Expect = 3e-05
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           L +  LP+  ++     LF      +  +LV ++         FV + +   +  A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 229 HGFKITPTHAMKISFAKK 246
           +G ++     +K+S+A+ 
Sbjct: 65  NGLRLQT-KTIKVSYARP 81

>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 = 38.7 bits (91), Expect = 5e-04
 Identities = 17/77 (22%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           L+++ LP+  ++  L  LF+Q+      R++ ++       + F+ F+  +++  A   L
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 229 HGFKIT-PTHAMKISFA 244
           +G K +  T  + + FA
Sbjct: 151 NGQKPSGATEPITVKFA 167

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 50.0 bits (120), Expect = 1e-08
 Identities = 14/93 (15%), Positives = 29/93 (31%), Gaps = 10/93 (10%)

Query: 164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQF--PGFKEVRLVPNRHD-----IAFVEFE 216
           G         + L N+   T    +    + +       +RL+ ++        AFV+  
Sbjct: 2   GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61

Query: 217 NEMQSAAAKLALHGFKITPT---HAMKISFAKK 246
           + M ++     L             + + FAK 
Sbjct: 62  SAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 42.3 bits (100), Expect = 8e-06
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 9/85 (10%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQ--IMDIVALK---TLKMRGQAFVIFKEIASATN 65
           + + + +I+   +  S+    S +    + +I  +K   T + RG AFV       A+ 
Sbjct: 9  MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQ 68

Query: 66 ALRSMQG----FPFYDKPMRIQYSK 86
           L+ +Q          K + + ++K
Sbjct: 69 LLQILQSLHPPLKIDGKTIGVDFAK 93

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 49.7 bits (119), Expect = 1e-08
 Identities = 12/76 (15%), Positives = 29/76 (38%), Gaps = 4/76 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          + V ++      + ++ +   +     +      + +  AFV       A NA++    +
Sbjct: 8  ILVKNLPQDSNCQEVHDLLKDYD----LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQY 63

Query: 74 PFYDKPMRIQYSKTDS 89
           F  K + +Q   TD+
Sbjct: 64 SFRGKDLIVQLQPTDA 79

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 48.6 bits (116), Expect = 4e-08
 Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 3/72 (4%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           + + NLP++++   +  L   +   K   +  N+   AFV   N  Q+  A    H +  
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKR-TAFVTLLNGEQAQNAIQMFHQYSF 65

Query: 234 TPTHAMKISFAK 245
                + +    
Sbjct: 66  R-GKDLIVQLQP 76

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 50.0 bits (120), Expect = 1e-08
 Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 4/74 (5%)

Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
          +   ++S +   +  L  +F    +I  +   +  K +G A++ FK  A A   L   QG
Sbjct: 19 LLAKNLSFNIT-EDELKEVFEDALEIRLVS--QDGKSKGIAYIEFKSEADAEKNLEEKQG 75

Query: 73 FPFYDKPMRIQYSK 86
               + + + Y+ 
Sbjct: 76 AEIDGRSVSLYYTG 89

>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 = 38.4 bits (90), Expect = 2e-04
 Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 10/73 (13%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
            +    + L   NL    +E  L  +F       E+RLV    D     IA++EF++E  
Sbjct: 11  KKVRAARTLLAKNLSFNITEDELKEVFEDA-L--EIRLV--SQDGKSKGIAYIEFKSEAD 65

Query: 221 SAAAKLALHGFKI 233
           +        G +I
Sbjct: 66  AEKNLEEKQGAEI 78

>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 = 49.9 bits (120), Expect = 2e-08
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 27 SLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
          ++ A F+ FG+I D   +K   T K +G  FV F     A NA++ M G     + +R  
Sbjct: 22 AIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN 81

Query: 84 YSK 86
          ++ 
Sbjct: 82 WAT 84

>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 = 40.6 bits (96), Expect = 3e-05
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           +F+ +L  E +   ++  F  F    + R+V +          FV F N+  +  A   +
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 229 HGFKITPTHAMKISFAKK 246
            G  +     ++ ++A +
Sbjct: 69  GGQWLG-GRQIRTNWATR 85

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 13/76 (17%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           ++VT +     ++ ++  F+++G+I +I       T  ++G   V ++    A  A+  +
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85

Query: 71  QGFPFYDKPMRIQYSK 86
            G     +P+ + +  
Sbjct: 86  NGQDLMGQPISVDWCF 101

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 49.2 bits (118), Expect = 3e-08
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAA 223
               ILF+T + EE +E  +   F ++   K + L  +R          VE+E   ++ A
Sbjct: 21  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 80

Query: 224 AKLALHGFKI 233
           A   L+G  +
Sbjct: 81  AMEGLNGQDL 90

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 49.5 bits (119), Expect = 2e-08
 Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQ 71
          ++V ++       K L   F++ G ++   + ++  K +G   V F+    A  A R M 
Sbjct: 11 IFVRNLPFDFT-WKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMN 69

Query: 72 GFPFYDKPMRIQ 83
          G     + + ++
Sbjct: 70 GMKLSGREIDVR 81

>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 = 50.0 bits (120), Expect = 2e-08
 Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
          V   ++V ++++T  ++ L   FSQFG++  +      K++  AF+ F E   A  A+  
Sbjct: 11 VKV-LFVRNLANTVTEEILEKAFSQFGKLERVK-----KLKDYAFIHFDERDGAVKAMEE 64

Query: 70 MQGFPFYDKPMRIQYSKTDSD 90
          M G     + + I ++K    
Sbjct: 65 MNGKDLEGENIEIVFAKPPDQ 85

>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 = 43.0 bits (102), Expect = 5e-06
 Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 4/86 (4%)

Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQ 220
            ++G       ++LF+ NL    +E +L   F+QF   + V+ +    D AF+ F+    
Sbjct: 1   GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDG 57

Query: 221 SAAAKLALHGFKITPTHAMKISFAKK 246
           +  A   ++G  +     ++I FAK 
Sbjct: 58  AVKAMEEMNGKDLE-GENIEIVFAKP 82

>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 = 49.1 bits (118), Expect = 2e-08
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          +YV  ++     K L+A F  FG I DI       T K RG AFV F+    A  A+ +M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69

Query: 71 QGFPFYDKPMRIQYSK 86
               + + +R+  +K
Sbjct: 70 NESELFGRTIRVNLAK 85

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAA 223
              ++L++  L EE  + +L   F  F    ++++  +         AFVEFE    +AA
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64

Query: 224 AKLALHGFKI 233
           A   ++  ++
Sbjct: 65  AIDNMNESEL 74

>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 = 49.5 bits (119), Expect = 2e-08
 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 3/80 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          + VT++S    +  L  +F  FG I  I   K   T + +G AF+ F     A  A+  +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77

Query: 71 QGFPFYDKPMRIQYSKTDSD 90
           GF +    + ++++K  ++
Sbjct: 78 SGFGYDHLILNVEWAKPSTN 97

>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 = 49.1 bits (118), Expect = 4e-08
 Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 5/71 (7%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
                N  + +TNL E+T E  L  LF  F     + L  ++        AF+ F     
Sbjct: 10  RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69

Query: 221 SAAAKLALHGF 231
           +A A   + GF
Sbjct: 70  AARAIAGVSGF 80

>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 = 50.6 bits (122), Expect = 3e-08
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 26  KSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
           ++L   F  F   +    +  ++T   RG  FV F     A NA+ SMQG     +P+RI
Sbjct: 102 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161

Query: 83  QYS 85
            ++
Sbjct: 162 NWA 164

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 49.8 bits (120), Expect = 6e-08
 Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 28 LYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
          L   F   G I +I  +  K  K    AFV + +   A  AL+++ G    +  ++I ++
Sbjct: 17 LKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWA 76

Query: 86 KTDS 89
              
Sbjct: 77 FQSQ 80

>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 = 41.7 bits (99), Expect = 4e-05
 Identities = 17/77 (22%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFENEMQSAAAKLALH 229
           L++ NL +  +E +L   F        ++++ ++++     AFVE+     +  A   L+
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 230 GFKITPTHAMKISFAKK 246
           G +I   + +KI++A +
Sbjct: 63  GKQI-ENNIVKINWAFQ 78

>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 = 38.3 bits (90), Expect = 7e-04
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           LF+ +L     +  L   F  FP +    ++ +          FV F ++  +  A  ++
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149

Query: 229 HGFKITPTHAMKISFAKK 246
            G  +     ++I++A K
Sbjct: 150 QGQDLN-GRPLRINWAAK 166

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 48.8 bits (117), Expect = 4e-08
 Identities = 16/76 (21%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          VY+  I     ++ +  + S  G ++++  +    T + +G AF+ F+++ S+ +A+R++
Sbjct: 5  VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64

Query: 71 QGFPFYDKPMRIQYSK 86
           G+    + ++  YS 
Sbjct: 65 NGYQLGSRFLKCGYSS 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 = 42.2 bits (100), Expect = 8e-06
 Identities = 14/69 (20%), Positives = 37/69 (53%), Gaps = 5/69 (7%)

Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAA 224
           P+++++L ++P + +E  +  L +       ++++ +         AF+EF +   SA+A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 225 KLALHGFKI 233
              L+G+++
Sbjct: 61  VRNLNGYQL 69

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 49.0 bits (117), Expect = 4e-08
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 8  ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASAT 64
          I V     +       LKK+L ++FS+ G+++++   +   T K +G  FV    +  A 
Sbjct: 9  IVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAK 68

Query: 65 NALRSMQGFPF 75
            ++S  G   
Sbjct: 69 KIIKSFHGKRL 79

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 48.8 bits (117), Expect = 4e-08
 Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 4/83 (4%)

Query: 155 APPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDI 210
                              LF++ LP   ++  L  +       K++RLV NR      +
Sbjct: 1   GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGL 60

Query: 211 AFVEFENEMQSAAAKLALHGFKI 233
           A+VE+ENE Q++ A + + G  I
Sbjct: 61  AYVEYENESQASQAVMKMDGMTI 83

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 48.8 bits (117), Expect = 5e-08
 Identities = 15/75 (20%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
          ++++ +  +  K+ L  I    G + D  +V  +  K +G A+V ++  + A+ A+  M 
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79

Query: 72 GFPFYDKPMRIQYSK 86
          G    +  +++  S 
Sbjct: 80 GMTIKENIIKVAISN 94

>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 = 4e-08
 Identities = 14/73 (19%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          ++V ++S+    + L ++F + G++++        ++  AFV  ++ A A  A+  + G 
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECD-----VVKDYAFVHMEKEADAKAAIAQLNGK 66

Query: 74 PFYDKPMRIQYSK 86
              K + ++ S 
Sbjct: 67 EVKGKRINVELST 79

>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 = 44.1 bits (105), Expect = 2e-06
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 3/57 (5%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
           +F+ N+    +   L  LF +     E  +V    D AFV  E E  + AA   L+G
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVK---DYAFVHMEKEADAKAAIAQLNG 65

>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 = 49.3 bits (118), Expect = 4e-08
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 19  ISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY 76
           +S  D+++    +F++FG +    +   ++ +  G A V F+  A A  A++  +G P  
Sbjct: 47  VSDADIQE----LFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLD 102

Query: 77  DKPMRIQYSKTDSD 90
            +PM IQ   +  D
Sbjct: 103 GRPMDIQLVASQID 116

>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 = 41.2 bits (97), Expect = 3e-05
 Identities = 21/114 (18%), Positives = 34/114 (29%), Gaps = 9/114 (7%)

Query: 141 MQALSVQQPPVSQPAPP----APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFP 196
           M +++  Q     P             G         L ++NL    S+  +  LF +F 
Sbjct: 1   MASMTGGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG 60

Query: 197 GFKEVRLVPNRHD----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
             K+  +  +R       A V FE    +  A     G  +     M I     
Sbjct: 61  TLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLD-GRPMDIQLVAS 113

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 49.0 bits (117), Expect = 5e-08
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 7/71 (9%)

Query: 12 NFVYVTHISSTD------LKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASAT 64
          + + V ++          LK  ++ IFS+FG+I +     +  K +G  F+ +   A A 
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 75

Query: 65 NALRSMQGFPF 75
          +A+++  G+  
Sbjct: 76 DAVKNADGYKL 86

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 50.8 bits (122), Expect = 5e-08
 Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           +YV  +        + ++F  FG+I      +   T K +G  F+ +++  S+ +A+ SM
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187

Query: 71  QGFPFYDKPMRIQYS 85
             F    + +R+  +
Sbjct: 188 NLFDLGGQYLRVGKA 202

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 48.1 bits (115), Expect = 4e-07
 Identities = 21/94 (22%), Positives = 34/94 (36%), Gaps = 3/94 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           VYV  I     + ++   F+ FG I  I       T+K +G AFV ++   +A  AL  M
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90

Query: 71  QGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPK 104
                  + +++            I     E   
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 16/105 (15%), Positives = 33/105 (31%), Gaps = 20/105 (19%)

Query: 134 MQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFN 193
                QQM     +     +    A M+            +++ ++  E  E  +   F 
Sbjct: 6   SMTGGQQMG----RGSAAQRQGALAIMSR-----------VYVGSIYYELGEDTIRQAFA 50

Query: 194 QFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKI 233
            F   K + +  +         AFVE+E    +  A   ++   +
Sbjct: 51  PFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVML 95

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 14/87 (16%), Positives = 32/87 (36%), Gaps = 5/87 (5%)

Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-- 209
           S      P+      E      +++ ++ ++ S+  +  +F  F   K   L  +     
Sbjct: 106 SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGK 165

Query: 210 ---IAFVEFENEMQSAAAKLALHGFKI 233
                F+E+E    S  A  +++ F +
Sbjct: 166 HKGYGFIEYEKAQSSQDAVSSMNLFDL 192

>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 = 5e-08
 Identities = 10/73 (13%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          +++ ++     ++ + ++F Q+G++++        ++   FV  ++  +A +A+R++  +
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECD-----IIKNYGFVHIEDKTAAEDAIRNLHHY 65

Query: 74 PFYDKPMRIQYSK 86
            +   + ++ SK
Sbjct: 66 KLHGVNINVEASK 78

>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 = 43.0 bits (102), Expect = 4e-06
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           LF+ NLP E +E  +  LF Q+    E  ++ N     FV  E++  +  A   LH +K+
Sbjct: 11  LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN---YGFVHIEDKTAAEDAIRNLHHYKL 67

>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 = 49.1 bits (117), Expect = 5e-08
 Identities = 17/109 (15%), Positives = 37/109 (33%), Gaps = 8/109 (7%)

Query: 141 MQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE 200
           M +        S   P             P++++ +  LP + +E  +  L   F     
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN 60

Query: 201 VRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPT----HAMKISFAK 245
           + ++  ++  AF+E   E    AA   ++ +           + I F+ 
Sbjct: 61  LLMLKGKNQ-AFIEMNTE---EAANTMVNYYTSVTPVLRGQPIYIQFSN 105

>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 = 47.2 bits (112), Expect = 3e-07
 Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
           +++  +     +  + ++   FG++ ++     LK + QAF+      +A   +      
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNL---LMLKGKNQAFIEMNTEEAANTMVNYYTSV 90

Query: 74  PFY--DKPMRIQYSK 86
                 +P+ IQ+S 
Sbjct: 91  TPVLRGQPIYIQFSN 105

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 50.2 bits (120), Expect = 5e-08
 Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
           + V+++        +  +F++FG +    +   ++ +  G A V F+  A A  A++  +
Sbjct: 91  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150

Query: 72  GFPFYDKPMRIQYSKTDSD 90
           G P   +PM IQ   +  D
Sbjct: 151 GVPLDGRPMDIQLVASQID 169

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 19/104 (18%), Positives = 30/104 (28%), Gaps = 5/104 (4%)

Query: 147 QQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN 206
           +  P             G         L ++NL    S+  +  LF +F   K+  +  +
Sbjct: 64  KPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD 123

Query: 207 RHD----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           R       A V FE    +  A     G  +     M I     
Sbjct: 124 RSGRSLGTADVHFERRADALKAMKQYKGVPLD-GRPMDIQLVAS 166

>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 = 48.4 bits (116), Expect = 6e-08
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
          + ++++S S   +++L  +F +   I  +   +  K +G AF+ F     A  AL S   
Sbjct: 18 LVLSNLSYSAT-EETLQEVFEKATFI-KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNK 75

Query: 73 FPFYDKPMRIQYSK 86
               + +R++   
Sbjct: 76 REIEGRAIRLELQG 89

>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 = 44.6 bits (106), Expect = 1e-06
 Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 9/73 (12%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
                ++ L L+NL    +E  L  +F +      ++ VP   +      AF+EF +   
Sbjct: 10  TWSGESKTLVLSNLSYSATEETLQEVFEK---ATFIK-VPQNQNGKSKGYAFIEFASFED 65

Query: 221 SAAAKLALHGFKI 233
           +  A  + +  +I
Sbjct: 66  AKEALNSCNKREI 78

>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 = 48.4 bits (116), Expect = 6e-08
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 28 LYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
          LY +F Q G +    I   +  K +   FV FK   S + A+  + G   Y +P+ +
Sbjct: 33 LYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV 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 = 41.8 bits (99), Expect = 1e-05
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 158 APMATAGVPEQPPNQI--LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IA 211
               ++G+          +F+ NL     E +L  LF Q     +V +  +R        
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60

Query: 212 FVEFENEMQSAAAKLALHGFKI 233
           FV F++    + A   L+G ++
Sbjct: 61  FVCFKHPESVSYAIALLNGIRL 82

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 48.9 bits (117), Expect = 6e-08
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 11/84 (13%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK-----------TLKMRGQAFVIFKEIAS 62
          ++V  +      +S+   F Q G I                  T K++G+A V F +  S
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69

Query: 63 ATNALRSMQGFPFYDKPMRIQYSK 86
          A  A+    G  F   P+++ ++ 
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFAT 93

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 14/93 (15%)

Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQF--------PGFKEVRLVPNRHD-----IAFV 213
           +   N  +F+  L E  +   ++  F Q          G   + L  +R        A V
Sbjct: 3   DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62

Query: 214 EFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
            F++   + AA     G + +  + +K+SFA +
Sbjct: 63  SFDDPPSAKAAIDWFDGKEFSG-NPIKVSFATR 94

>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 = 48.4 bits (116), Expect = 6e-08
 Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEF 215
              G        ILF+T++ EE  E  +   F  +   K + L  +R        A VE+
Sbjct: 16  LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 75

Query: 216 ENEMQSAAAKLALHGFKI 233
           E   Q+ AAK AL+G +I
Sbjct: 76  ETHKQALAAKEALNGAEI 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 = 48.4 bits (116), Expect = 8e-08
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 3/76 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           ++VT I     +  +   F  +G+I +I       T   +G A V ++    A  A  ++
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88

Query: 71  QGFPFYDKPMRIQYSK 86
            G     + +++ +  
Sbjct: 89  NGAEIMGQTIQVDWCF 104

>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 = 48.0 bits (115), Expect = 8e-08
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          ++V +IS T   + L A F ++G +++        ++  AFV  +    A  A+R +   
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECD-----IVKDYAFVHMERAEDAVEAIRGLDNT 67

Query: 74 PFYDKPMRIQYSK 86
           F  K M +Q S 
Sbjct: 68 EFQGKRMHVQLST 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 = 42.6 bits (101), Expect = 6e-06
 Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 4/70 (5%)

Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQ 220
            ++G   +   ++  + N+    +   L   F ++    E  +V    D AFV  E    
Sbjct: 1   GSSGSSGKASTKL-HVGNISPTCTNQELRAKFEEYGPVIECDIVK---DYAFVHMERAED 56

Query: 221 SAAAKLALHG 230
           +  A   L  
Sbjct: 57  AVEAIRGLDN 66

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 48.0 bits (115), Expect = 9e-08
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 9/75 (12%)

Query: 165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENE 218
           +P+ PP    FL NLP + +E  +   F        VRL     +        + EFE+ 
Sbjct: 14  LPKSPPY-TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDL 71

Query: 219 MQSAAAKLALHGFKI 233
             S  + L+L+   +
Sbjct: 72  -DSLLSALSLNEESL 85

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 48.0 bits (115), Expect = 9e-08
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 9/75 (12%)

Query: 165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENE 218
           +P+ PP    FL NLP + +E  +   F        VRL     +        + EFE+ 
Sbjct: 10  LPKSPPY-TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDL 67

Query: 219 MQSAAAKLALHGFKI 233
             S  + L+L+   +
Sbjct: 68  -DSLLSALSLNEESL 81

>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 = 36.9 bits (86), Expect = 7e-04
 Identities = 11/64 (17%), Positives = 27/64 (42%), Gaps = 6/64 (9%)

Query: 27 SLYAIFSQFGQIMDIVALK----TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
          S+   F     I  +   +      +++G  +  F+++ S  +AL S+      +K +R+
Sbjct: 31 SIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV 88

Query: 83 QYSK 86
            + 
Sbjct: 89 DVAD 92

>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 = 48.1 bits (115), Expect = 9e-08
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 25  KKSLYAIFSQFGQIMDIVALK----TLKMRGQAFVIFKEIASATNALRSM-QGFPFYDKP 79
           ++ +  +FS FG++  +   K    T   RG  FV F     A  A  ++      Y + 
Sbjct: 29  QREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR 88

Query: 80  MRIQYSKTDSDVIS 93
           + ++++ ++  V S
Sbjct: 89  LVLEWADSEVTVQS 102

>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 = 43.8 bits (104), Expect = 3e-06
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI------AFVE 214
           ++  VP++     + + N+P + ++  +  LF+ F   K VRL              FV+
Sbjct: 5   SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64

Query: 215 FENEMQSAAAKLAL-HGFKI 233
           F  +  +  A  AL H   +
Sbjct: 65  FITKQDAKKAFNALCHSTHL 84

>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 = 49.5 bits (119), Expect = 9e-08
 Identities = 14/92 (15%), Positives = 39/92 (42%), Gaps = 11/92 (11%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKTLKMRGQAFVIFKEIASATN 65
          +YV +I     ++++   F+   ++          ++A++  + +  AF+ F+ +   T 
Sbjct: 7  LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 66 ALRSMQGFPFYDKPMRIQYSK--TDSDVISKI 95
          A+ +  G  F  + ++I+            K+
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKL 97

>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 = 49.2 bits (118), Expect = 1e-07
 Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 11/83 (13%)

Query: 6   AHICVTNF-VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIA 61
             + +     Y+           +  + + FG +     +K   T   +G AF  + +I 
Sbjct: 95  HKLFIGGLPNYLND-------DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN 147

Query: 62  SATNALRSMQGFPFYDKPMRIQY 84
               A+  + G    DK + +Q 
Sbjct: 148 VTDQAIAGLNGMQLGDKKLLVQR 170

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 5/65 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           LF+  LP   ++  +  L   F   K   LV +         AF E+ +   +  A   L
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156

Query: 229 HGFKI 233
           +G ++
Sbjct: 157 NGMQL 161

>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 = 41.4 bits (98), Expect = 7e-05
 Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 11/70 (15%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP---------NRHD-IAFVEFENEMQSAA 223
           L++ N+P   +E  +   FN       +   P         N+    AF+EF +      
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV-DETT 65

Query: 224 AKLALHGFKI 233
             +A  G   
Sbjct: 66  QAMAFDGIIF 75

>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 = 48.0 bits (115), Expect = 1e-07
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 8/80 (10%)

Query: 10  VTNFVYVTHISSTDLKKSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNAL 67
           V+N  +   +S  D+++    +F++FG +    +   ++ +  G A V F+  A A  A+
Sbjct: 34  VSNLDF--GVSDADIQE----LFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAM 87

Query: 68  RSMQGFPFYDKPMRIQYSKT 87
           +   G P   +PM IQ   +
Sbjct: 88  KQYNGVPLDGRPMNIQLVTS 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 = 38.0 bits (89), Expect = 3e-04
 Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 4/77 (5%)

Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFE 216
              G         L ++NL    S+  +  LF +F   K+  +  +R       A V FE
Sbjct: 19  GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFE 78

Query: 217 NEMQSAAAKLALHGFKI 233
            +  +  A    +G  +
Sbjct: 79  RKADALKAMKQYNGVPL 95

>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 = 48.0 bits (115), Expect = 1e-07
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
          + V +++  T    SL  +F ++G++ D+   +   T   RG AFV F +   A +A  +
Sbjct: 16 LKVDNLTYRTS-PDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 70 MQGFPFYDKPMRIQYSK 86
          M G     + +R+Q ++
Sbjct: 75 MDGAELDGRELRVQVAR 91

>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 = 46.1 bits (110), Expect = 5e-07
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 5/73 (6%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
           P+      L + NL   TS   L  +F ++    +V +    H       AFV F +   
Sbjct: 8   PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67

Query: 221 SAAAKLALHGFKI 233
           +  A+ A+ G ++
Sbjct: 68  AQDAEAAMDGAEL 80

>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 = 49.5 bits (119), Expect = 1e-07
 Identities = 17/89 (19%), Positives = 40/89 (44%), Gaps = 8/89 (8%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK-----TLKMRGQAFVIFKEIASATNALR 68
          ++V  +  T  +K L  +F Q+G + +I  L+       + +G  FV F    +A  A  
Sbjct: 6  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 69 SMQG---FPFYDKPMRIQYSKTDSDVISK 94
          ++      P    P++++ + ++ +   +
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVE 94

>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 = 46.8 bits (112), Expect = 9e-07
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQ 71
           +++  IS    +  +  +FS FGQI +   L+      RG AFV F   A A  A+++M 
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157

Query: 72  G---FPFYDKPMRIQY 84
                     PM +++
Sbjct: 158 QAQTMEGCSSPMVVKF 173

>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 = 42.2 bits (100), Expect = 3e-05
 Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 7/72 (9%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-------IAFVEFENEMQSAAAKL 226
           +F+  +P   SE  L  LF Q+    E+ ++ +R           FV F     +  A+ 
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 227 ALHGFKITPTHA 238
           ALH  K+ P   
Sbjct: 66  ALHNMKVLPGMH 77

>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 = 39.1 bits (92), Expect = 4e-04
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 10/79 (12%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENEMQSAAAKLA 227
           LF+  + ++ +E  + ++F+ F   +E R++  R         AFV F     +  A  A
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAMAQTAIKA 155

Query: 228 LHGFKITP--THAMKISFA 244
           +H  +     +  M + FA
Sbjct: 156 MHQAQTMEGCSSPMVVKFA 174

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 50.1 bits (119), Expect = 1e-07
 Identities = 16/151 (10%), Positives = 42/151 (27%), Gaps = 11/151 (7%)

Query: 26  KSLYAIFSQFGQIMDIVALK------TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKP 79
           + L       G + DI+ +K        + +G A V     AS+   +  +     + + 
Sbjct: 83  EDLTEAVHSLG-VNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQN 141

Query: 80  MRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQ 139
             +           +++     +  ++  +         ++ +  +  + + R   A   
Sbjct: 142 PVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPG 201

Query: 140 QMQALSVQQPPVSQPAPPAPMATAGVPEQPP 170
             +       P     PP P           
Sbjct: 202 GDRF----PGPAGPGGPPPPFPAGQTHHHHH 228

>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 = 47.0 bits (111), Expect = 1e-06
 Identities = 16/119 (13%), Positives = 32/119 (26%), Gaps = 8/119 (6%)

Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQ 194
               +    +    P V                      L++ NL   T++  L+   + 
Sbjct: 32  GDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHS 91

Query: 195 F--PGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
                  E++   NR +      A V   +E  S      L   ++       ++   K
Sbjct: 92  LGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG-QNPVVTPVNK 149

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          VYV ++ +   K  L   FS +G +   V +      G AFV F++   A +A+R + G 
Sbjct: 3  VYVGNLGTGAGKGELERAFSYYGPLRT-VWIAR-NPPGFAFVEFEDPRDAEDAVRGLDGK 60

Query: 74 PFYDKPMRIQYSK 86
                +R++ S 
Sbjct: 61 VICGSRVRVELST 73

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 16/60 (26%), Positives = 26/60 (43%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           +++ NL     +  L   F+ +   + V +  N    AFVEFE+   +  A   L G  I
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62

>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 = 47.9 bits (114), Expect = 1e-07
 Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 8/85 (9%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
            +  P+++L +  LP E +E  +  L   F     + ++  ++  AF+E   E    AA 
Sbjct: 10  MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQ-AFLELATE---EAAI 65

Query: 226 LALHGFKITPT----HAMKISFAKK 246
             ++ +           + I ++  
Sbjct: 66  TMVNYYSAVTPHLRNQPIYIQYSNH 90

>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 = 47.5 bits (113), Expect = 1e-07
 Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 5/75 (6%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          +++  +     +  + A+   FG++ +I     LK + QAF+      +A   +      
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNI---LMLKGKNQAFLELATEEAAITMVNYYSAV 74

Query: 74 PFY--DKPMRIQYSK 86
            +  ++P+ IQYS 
Sbjct: 75 TPHLRNQPIYIQYSN 89

>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 = 47.3 bits (113), Expect = 1e-07
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 11/82 (13%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK-----------TLKMRGQAFVIFKEIAS 62
          ++V  +      +S+   F Q G I                  T K++G+A V F +  S
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75

Query: 63 ATNALRSMQGFPFYDKPMRIQY 84
          A  A+    G  F   P+++ +
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSF 97

>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 = 39.2 bits (92), Expect = 1e-04
 Identities = 19/92 (20%), Positives = 34/92 (36%), Gaps = 14/92 (15%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQF--------PGFKEVRLVPNRHD-----IAF 212
                N  +F+  L E  +   ++  F Q          G   + L  +R        A 
Sbjct: 8   HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 67

Query: 213 VEFENEMQSAAAKLALHGFKITPTHAMKISFA 244
           V F++   + AA     G + +  + +K+SFA
Sbjct: 68  VSFDDPPSAKAAIDWFDGKEFSG-NPIKVSFA 98

>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 = 47.7 bits (114), Expect = 1e-07
 Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
           +++ H+      + L  +F  FG ++     +  +T   +   FV +    SA  A++SM
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 71  QGFPFYDKPMRIQYSK 86
            GF    K +++Q  +
Sbjct: 88  NGFQIGMKRLKVQLKR 103

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 21/100 (21%), Positives = 42/100 (42%), Gaps = 6/100 (6%)

Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-- 209
           S     +  A     E P    LF+ +LP+E  +  L  +F  F      ++  ++    
Sbjct: 6   SGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNL 65

Query: 210 ---IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
                FV ++N + + AA  +++GF+I     +K+   + 
Sbjct: 66  SKCFGFVSYDNPVSAQAAIQSMNGFQIG-MKRLKVQLKRS 104

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 3/78 (3%)

Query: 168 QPPNQILFLTN--LPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
               Q L + N  L    S   L  +  +      + + PN+   +F  +    +S  A 
Sbjct: 22  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP-YSFARYRTTEESKRAY 80

Query: 226 LALHGFKITPTHAMKISF 243
           + L+G ++      KI+ 
Sbjct: 81  VTLNGKEVVDDLGQKITL 98

>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 = 45.3 bits (107), Expect = 1e-06
 Identities = 7/65 (10%), Positives = 22/65 (33%), Gaps = 3/65 (4%)

Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
           V    + +   +  L  +  + G +  ++       +  +F  ++    +  A  ++ G
Sbjct: 29 VVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN---KPYSFARYRTTEESKRAYVTLNG 85

Query: 73 FPFYD 77
              D
Sbjct: 86 KEVVD 90

>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 = 47.3 bits (113), Expect = 2e-07
 Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 2/78 (2%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
                LF+ NLP + +E  +  LF ++    EV +  ++    F+  E    +  AK+ L
Sbjct: 13  TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-FGFIRLETRTLAEIAKVEL 71

Query: 229 HGFKITPTHAMKISFAKK 246
               +     +++ FA  
Sbjct: 72  DNMPLR-GKQLRVRFACH 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 = 46.5 bits (111), Expect = 3e-07
 Identities = 14/84 (16%), Positives = 37/84 (44%), Gaps = 11/84 (13%)

Query: 14 VYV----THISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
          ++V      I+  +++K    +F ++G+  ++      K +G  F+  +    A  A   
Sbjct: 18 LFVGNLPPDITEEEMRK----LFEKYGKAGEV---FIHKDKGFGFIRLETRTLAEIAKVE 70

Query: 70 MQGFPFYDKPMRIQYSKTDSDVIS 93
          +   P   K +R++++   + + S
Sbjct: 71 LDNMPLRGKQLRVRFACHSASLTS 94

>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 = 47.3 bits (112), Expect = 2e-07
 Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 2/85 (2%)

Query: 6  AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATN 65
          A + V+N  Y   +S  +L++ L   F++ G++  +        + +A V  + +  A  
Sbjct: 10 ADVQVSNIDY--RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIG 67

Query: 66 ALRSMQGFPFYDKPMRIQYSKTDSD 90
          A+ S+  +    K + +  +   S 
Sbjct: 68 AVNSLHRYKIGSKKILVSLATGASG 92

>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 = 47.6 bits (114), Expect = 2e-07
 Identities = 22/90 (24%), Positives = 41/90 (45%), Gaps = 3/90 (3%)

Query: 14  VYVTHIS-STDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQ 71
           +++ ++  S D  K+LY  FS FG I+   V       +G  FV F+   +A  A+  M 
Sbjct: 8   IFIKNLDKSID-NKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 66

Query: 72  GFPFYDKPMRIQYSKTDSDVISKIKGTFME 101
           G    D+ + +   K+  +  +++     E
Sbjct: 67  GMLLNDRKVFVGRFKSRKEREAELGARAKE 96

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 27/114 (23%), Positives = 46/114 (40%), Gaps = 6/114 (5%)

Query: 137 QQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFP 196
           Q     ALS         +  A  A     E P    LF+ +LP+E ++  L+  F  F 
Sbjct: 6   QFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFG 65

Query: 197 GFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK 245
                ++  ++         FV F+N   +  A  A++GF++  T  +K+   K
Sbjct: 66  NVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVG-TKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
           +++ H+        L + F  FG ++     +  +T   +   FV F    SA  A+++M
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 71  QGFPFYDKPMRIQYSK 86
            GF    K +++Q  K
Sbjct: 103 NGFQVGTKRLKVQLKK 118

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           +YV  ++     K L+A F  FG I DI       T K RG AFV F+    A  A+ +M
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125

Query: 71  QGFPFYDKPMRI 82
                + + +R+
Sbjct: 126 NESELFGRTIRV 137

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 5/98 (5%)

Query: 141 MQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE 200
             A +            +  +          ++L++  L EE  + +L   F  F    +
Sbjct: 33  SVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITD 92

Query: 201 VRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKI 233
           +++  +         AFVEFE    +AAA   ++  ++
Sbjct: 93  IQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL 130

>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 = 47.2 bits (113), Expect = 2e-07
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          +YV  ++     K L+A F  FG I DI       T K RG AFV F+    A  A+ +M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74

Query: 71 QGFPFYDKPMRIQYSK 86
               + + +R+  +K
Sbjct: 75 NESELFGRTIRVNLAK 90

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEF 215
           ++         ++L++  L EE  + +L   F  F    ++++  +         AFVEF
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61

Query: 216 ENEMQSAAAKLALHGFKI 233
           E    +AAA   ++  ++
Sbjct: 62  ELAEDAAAAIDNMNESEL 79

>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 = 47.3 bits (113), Expect = 2e-07
 Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQ 71
          ++V  ++    ++ +  +F  FG I +   L+      +G AFV F     A  A+ ++ 
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77

Query: 72 G---FPFYDKPMRIQYSKTDSD 90
          G    P     + ++++ TD +
Sbjct: 78 GSQTMPGASSSLVVKFADTDKE 99

>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 = 43.8 bits (104), Expect = 3e-06
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 6/92 (6%)

Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFE 216
           ++        ++ LF+  L ++ SE  +  LF  F    E  ++          AFV+F 
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFS 64

Query: 217 NEMQSAAAKLALHGFKITP--THAMKISFAKK 246
           +  ++ AA  ALHG +  P  + ++ + FA  
Sbjct: 65  SHTEAQAAIHALHGSQTMPGASSSLVVKFADT 96

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 5/87 (5%)

Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-- 209
            Q    +       P+      L + NL   TS   L  +F ++    +V +  +R+   
Sbjct: 28  QQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 87

Query: 210 ---IAFVEFENEMQSAAAKLALHGFKI 233
               AFV F ++  +  A  A+ G  +
Sbjct: 88  SRGFAFVRFHDKRDAEDAMDAMDGAVL 114

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           + V +++      +L  +F ++G++ D+   +   T + RG AFV F +   A +A+ +M
Sbjct: 50  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109

Query: 71  QGFPFYDKPMRIQYSKTD 88
            G     + +R+Q ++  
Sbjct: 110 DGAVLDGRELRVQMARYG 127

>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 = 46.9 bits (112), Expect = 2e-07
 Identities = 14/84 (16%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 155 APPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----- 209
           +  +  +++G   +P   ++ + N+P   S   +   F  +        +          
Sbjct: 2   SSGSSGSSSG---KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG 58

Query: 210 IAFVEFENEMQSAAAKLALHGFKI 233
            A V FE+  ++ AA + L+   I
Sbjct: 59  EAMVAFESRDEATAAVIDLNDRPI 82

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 3/66 (4%)

Query: 25 KKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
             +   F  +  I   V LK        G+A V F+    AT A+  +   P   + ++
Sbjct: 29 IDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK 88

Query: 82 IQYSKT 87
          +    +
Sbjct: 89 LSGPSS 94

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 8/93 (8%)

Query: 161 ATAGVPEQPPNQI-LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVE 214
           ++     +  + I LF+  +P    E  L  LF +F    E+ ++ +R        AF+ 
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 215 FENEMQSAAAKLALHGFKITP--THAMKISFAK 245
           +     +  A+ ALH  K  P     +++  A 
Sbjct: 62  YCERESALKAQSALHEQKTLPGMNRPIQVKPAD 94

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 20/84 (23%), Positives = 43/84 (51%), Gaps = 6/84 (7%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          +++  I     +K L  +F +FG+I ++  LK   T   +G AF+ + E  SA  A  ++
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75

Query: 71 QG---FPFYDKPMRIQYSKTDSDV 91
                P  ++P++++ + ++S  
Sbjct: 76 HEQKTLPGMNRPIQVKPADSESRG 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 = 47.8 bits (114), Expect = 2e-07
 Identities = 28/121 (23%), Positives = 48/121 (39%), Gaps = 8/121 (6%)

Query: 130 QARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLS 189
           Q  L+       Q   +QQ    Q     P      P+   N  L +  +P    E+ L 
Sbjct: 3   QIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRN--LMVNYIPTTVDEVQLR 60

Query: 190 MLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA 244
            LF ++   + V++V +R         FV+F++   +  A   L+GF I     +K++ A
Sbjct: 61  QLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI-LNKRLKVALA 119

Query: 245 K 245
            
Sbjct: 120 A 120

>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 = 42.8 bits (101), Expect = 1e-05
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 3/76 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
           + V +I +T  +  L  +F ++G I     +   +T + RG  FV F+  +SA  A+  +
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104

Query: 71  QGFPFYDKPMRIQYSK 86
            GF   +K +++  + 
Sbjct: 105 NGFNILNKRLKVALAA 120

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 49.0 bits (116), Expect = 2e-07
 Identities = 14/83 (16%), Positives = 32/83 (38%), Gaps = 3/83 (3%)

Query: 10  VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
           +   +   H+    ++  +  +FS+ G I  I   + ++ +   FV FK  A+A  A  +
Sbjct: 142 IDGALNSKHLKPAQIESRIRFVFSRLGDIDRI---RYVESKNCGFVKFKYQANAEFAKEA 198

Query: 70  MQGFPFYDKPMRIQYSKTDSDVI 92
           M          +    + +   +
Sbjct: 199 MSNQTLLLPSDKEWDDRREGTGL 221

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 43.6 bits (102), Expect = 2e-05
 Identities = 14/86 (16%), Positives = 34/86 (39%), Gaps = 11/86 (12%)

Query: 157 PAPMATAGVPEQPPNQILFLTNLPEETS---------EMMLSMLFNQFPGFKEVRLVPNR 207
              M   G   +  N+ L++  +    +         E  +  +F++      +R V ++
Sbjct: 121 REDMGGIG-SFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK 179

Query: 208 HDIAFVEFENEMQSAAAKLALHGFKI 233
           +   FV+F+ +  +  AK A+    +
Sbjct: 180 N-CGFVKFKYQANAEFAKEAMSNQTL 204

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 9/86 (10%)

Query: 165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEM 219
           +P +PP    ++ NLP  T +  +  +F      + VRLV ++         +VEF+   
Sbjct: 10  LPTEPPY-TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEV- 66

Query: 220 QSAAAKLALHGFKITPTHAMKISFAK 245
            S    L   G  +    ++++  A+
Sbjct: 67  DSLKEALTYDGALLG-DRSLRVDIAE 91

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 48.0 bits (114), Expect = 3e-07
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
           VYV ++ +   K  L   F  +G +  +   +     G AFV F++   A +A+R + G 
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVAR--NPPGFAFVEFEDPRDAADAVRELDGR 133

Query: 74  PFYDKPMRIQYSK 86
                 +R++ S 
Sbjct: 134 TLCGCRVRVELSN 146

>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 = 46.8 bits (111), Expect = 6e-07
 Identities = 17/65 (26%), Positives = 29/65 (44%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
           P +  +++ NL    ++  L   F  +   + V +  N    AFVEFE+   +A A   L
Sbjct: 71  PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVREL 130

Query: 229 HGFKI 233
            G  +
Sbjct: 131 DGRTL 135

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 2/91 (2%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
           V+V ++      K L  +FS  G ++  DI+  K  K RG   V F++   A  A+    
Sbjct: 18  VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFN 77

Query: 72  GFPFYDKPMRIQYSKTDSDVISKIKGTFMER 102
           G   +D+PM ++  +              ++
Sbjct: 78  GQLLFDRPMHVKMDERALPKGDFFPPERPQQ 108

>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 = 47.9 bits (114), Expect = 3e-07
 Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 5/86 (5%)

Query: 150 PVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD 209
             +              +      L + NL   TS   L  +F ++    +V +  +R+ 
Sbjct: 49  TKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT 108

Query: 210 -----IAFVEFENEMQSAAAKLALHG 230
                 AFV F ++  +  A  A+ G
Sbjct: 109 KESRGFAFVRFHDKRDAEDAMDAMDG 134

>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 = 44.8 bits (106), Expect = 4e-06
 Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 14  VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
           + V +++  T    +L  +F ++G++ D+   +   T + RG AFV F +   A +A+ +
Sbjct: 73  LKVDNLTYRTS-PDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131

Query: 70  MQGFPFYDKPMRIQYSKT 87
           M G     + +R+Q ++ 
Sbjct: 132 MDGAVLDGRELRVQMARY 149

>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 = 46.0 bits (110), Expect = 4e-07
 Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 4/77 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIV----ALKTLKMRGQAFVIFKEIASATNALRS 69
          V++  ++    K  +  IFS +G+I  I      +     +G A+V F+    A  AL+ 
Sbjct: 7  VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66

Query: 70 MQGFPFYDKPMRIQYSK 86
          M G     + +      
Sbjct: 67 MDGGQIDGQEITATAVL 83

>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 = 43.7 bits (104), Expect = 2e-06
 Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 6/66 (9%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENEMQSAAAKLA 227
           + +  L    ++  +  +F+ +   K + +   R         A+VEFEN  ++  A   
Sbjct: 7   VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66

Query: 228 LHGFKI 233
           + G +I
Sbjct: 67  MDGGQI 72

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 27/102 (26%), Positives = 51/102 (50%), Gaps = 15/102 (14%)

Query: 14  VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSM 70
           +++  ++  T+ +K L A+F + G I +++ +K  T K RG AF+ F+  A A NA + M
Sbjct: 10  LFIGGLNRETN-EKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68

Query: 71  QGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAP 112
            G   + K ++++ +K  S            +    R+ PA 
Sbjct: 69  NGKSLHGKAIKVEQAKKPS-----------FQSGGRRRPPAS 99

>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 = 40.0 bits (94), Expect = 8e-05
 Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 4/64 (6%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFENEMQSAAAKLALH 229
           LF+  L  ET+E ML  +F +     EV L+ +R       AF+ FEN   +  A   ++
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69

Query: 230 GFKI 233
           G  +
Sbjct: 70  GKSL 73

>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 = 46.6 bits (111), Expect = 4e-07
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 27 SLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
           + A F+ FG+I D   +K   T K +G  FV F     A NA++ M G     + +R  
Sbjct: 31 DIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN 90

Query: 84 YSK 86
          ++ 
Sbjct: 91 WAT 93

>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 = 40.8 bits (96), Expect = 4e-05
 Identities = 16/95 (16%), Positives = 36/95 (37%), Gaps = 10/95 (10%)

Query: 161 ATAGVPEQPPNQI----LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IA 211
            ++G   Q  +      +F+ +L  E +   +   F  F    + R+V +          
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60

Query: 212 FVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           FV F N+  +  A   + G  +     ++ ++A +
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLG-GRQIRTNWATR 94

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 45.6 bits (109), Expect = 5e-07
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
          +YV  +  +   +  L  IF  FG+I +IV +K   T + +G  F+ F +   A  AL  
Sbjct: 8  LYVGSLHFNIT-EDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 70 MQGFPFYDKPMRIQYSK 86
          + GF    +PMR+ +  
Sbjct: 67 LNGFELAGRPMRVGHVT 83

>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 = 41.4 bits (98), Expect = 2e-05
 Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 5/70 (7%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAA 223
             +  L++ +L    +E ML  +F  F     + L+ +          F+ F +   +  
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 224 AKLALHGFKI 233
           A   L+GF++
Sbjct: 63  ALEQLNGFEL 72

>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 = 45.3 bits (108), Expect = 6e-07
 Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 7/77 (9%)

Query: 14 VYVTHIS--STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALR 68
          VYV+++    T+    LY IFS++G+++ +  +K   T K +G AF++F +  SA N  R
Sbjct: 19 VYVSNLPFSLTN--NDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 69 SMQGFPFYDKPMRIQYS 85
          ++     + + ++   +
Sbjct: 77 AINNKQLFGRVIKASIA 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 11/73 (15%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQ 220
              P    ++++NLP   +   L  +F+++    +V ++ ++       +AF+ F ++  
Sbjct: 11  GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70

Query: 221 SAAAKLALHGFKI 233
           +     A++  ++
Sbjct: 71  AQNCTRAINNKQL 83

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 46.8 bits (111), Expect = 7e-07
 Identities = 14/107 (13%), Positives = 32/107 (29%), Gaps = 9/107 (8%)

Query: 134 MQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFN 193
            Q+ +          P  +   P      +G+  +     +++ +    T++  L  +  
Sbjct: 20  FQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAA--VYVGSFSWWTTDQQLIQVIR 77

Query: 194 QF--PGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKI 233
                   E++   NR +      A V   +E         L G  +
Sbjct: 78  SIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVL 124

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 44.5 bits (105), Expect = 5e-06
 Identities = 20/106 (18%), Positives = 35/106 (33%), Gaps = 15/106 (14%)

Query: 14  VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK------TLKMRGQAFVIFKEIASATNA 66
           VYV   S  T   + L  +    G   D+V LK        + +G A V+     S    
Sbjct: 58  VYVGSFSWWTT-DQQLIQVIRSIGVY-DVVELKFAENRANGQSKGYAEVVVASENSVHKL 115

Query: 67  LRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAP 112
           L  + G     + + ++ +        +    F  + +K      P
Sbjct: 116 LELLPGKVLNGEKVDVRPAT------RQNLSQFEAQARKRECVRVP 155

>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 = 44.8 bits (107), Expect = 7e-07
 Identities = 13/71 (18%), Positives = 31/71 (43%), Gaps = 3/71 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          +Y+  +      + L  +   +G+I+   A+    T K +G  FV F   ++A  A+ ++
Sbjct: 8  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 71 QGFPFYDKPMR 81
          +      +  +
Sbjct: 68 KASGVQAQMAK 78

>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 = 39.4 bits (93), Expect = 7e-05
 Identities = 11/65 (16%), Positives = 25/65 (38%), Gaps = 5/65 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           L++  L   T++  L  L   +      + + ++         FV+F++   +  A  AL
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 229 HGFKI 233
               +
Sbjct: 68  KASGV 72

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.4 bits (108), Expect = 8e-07
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 160 MATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD---IAFVEFE 216
            ++     +   + L ++N+P    +  L  +F QF    +V ++ N        FV FE
Sbjct: 4   GSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFE 63

Query: 217 NEMQSAAAKLALHGFKI 233
           N   +  A+  LHG  +
Sbjct: 64  NSADADRAREKLHGTVV 80

>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 = 40.7 bits (96), Expect = 3e-05
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQ 71
          ++V++I         L  +F QFG+I+D+ +       +G  FV F+  A A  A   + 
Sbjct: 18 LHVSNIPFRFR-DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 76

Query: 72 GFPFYDKPMRIQYSK 86
          G     + + +  + 
Sbjct: 77 GTVVEGRKIEVNNAT 91

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 45.6 bits (108), Expect = 8e-07
 Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          +++  +     +  + ++   FG++ ++     LK + QAF+      +A   +      
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNL---LMLKGKNQAFIEMNTEEAANTMVNYYTSV 75

Query: 74 P--FYDKPMRIQYSK 86
                +P+ IQ+S 
Sbjct: 76 TPVLRGQPIYIQFSN 90

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 45.2 bits (107), Expect = 9e-07
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLA 227
             P++++ +  LP + +E  +  L   F     + ++  ++  AF+E   E    AA   
Sbjct: 13  GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQ-AFIEMNTE---EAANTM 68

Query: 228 LHGFKITPT----HAMKISFAK 245
           ++ +           + I F+ 
Sbjct: 69  VNYYTSVTPVLRGQPIYIQFSN 90

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 48.7 bits (115), Expect = 9e-07
 Identities = 37/235 (15%), Positives = 66/235 (28%), Gaps = 76/235 (32%)

Query: 8   ICVTNFV---YVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASAT 64
             VT+F+     THIS      +L        ++  ++  K L  R Q           T
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTP-----DEVKSLLL-KYLDCRPQDL---PREVLTT 325

Query: 65  NALR-SMQGFPFYDKPMRIQYSKT-DSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKS 122
           N  R S+      D        K  + D ++ I  + +            V +PAE    
Sbjct: 326 NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN-----------VLEPAE---- 370

Query: 123 KKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFL--TNLP 180
                          ++    LSV  P               +P      +L L   ++ 
Sbjct: 371 --------------YRKMFDRLSVFPPSAH------------IPTI----LLSLIWFDVI 400

Query: 181 EETSEMML------SMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH 229
           +    +++      S++  Q      + +      I              + ALH
Sbjct: 401 KSDVMVVVNKLHKYSLVEKQPKEST-ISI----PSIYL----ELKVKLENEYALH 446

>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 = 45.3 bits (108), Expect = 1e-06
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
          +YV ++      + L   FS FG I    V ++  + +G  FV F     AT A+  M G
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77

Query: 73 FPFYDKPMRIQYSK 86
               KP+ +  ++
Sbjct: 78 RIVATKPLYVALAQ 91

>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 = 44.9 bits (107), Expect = 1e-06
 Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 27 SLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
           L  +FS +G + ++       T K +G AFV F     A  A   + G  F  + + + 
Sbjct: 24 DLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL 83

Query: 84 YSK 86
           S 
Sbjct: 84 PST 86

>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 = 44.5 bits (106), Expect = 1e-06
 Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 5/72 (6%)

Query: 164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENE 218
           G      +  LF+ NL   +SE  L  LF+ +    E+    +         AFV F   
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 219 MQSAAAKLALHG 230
             +  A   + G
Sbjct: 61  EHAVKAYAEVDG 72

>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 = 44.2 bits (105), Expect = 2e-06
 Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 3/68 (4%)

Query: 25 KKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
             +   F  +  I   V LK        G+A V F+    AT A+  +   P   + ++
Sbjct: 29 IDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK 88

Query: 82 IQYSKTDS 89
          +      S
Sbjct: 89 LVLGSGPS 96

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 155 APPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----- 209
           +  +  A++G   +P   I+ + N+P   S   +   F  +        +          
Sbjct: 2   SSGSSGASSG---KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG 58

Query: 210 IAFVEFENEMQSAAAKLALHGFKI 233
            A V FE+  ++ AA + L+   I
Sbjct: 59  EAMVAFESRDEATAAVIDLNDRPI 82

>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 = 44.2 bits (105), Expect = 2e-06
 Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 8/80 (10%)

Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQI------MDIVALKTLKMRGQAFVIFKEIASATNA 66
          +++ +++ ST  +++L  +FS+ G I              L   G  FV +K+   A  A
Sbjct: 8  LFIKNLNFSTT-EETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 67 LRSMQGFPFYDKPMRIQYSK 86
          L+ +QG       + ++ S+
Sbjct: 67 LKQLQGHTVDGHKLEVRISE 86

>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 = 44.2 bits (105), Expect = 2e-06
 Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 9/81 (11%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI--------AFVEFENEMQSAAAK 225
           LF+ NL   T+E  L  +F++    K   +   ++           FVE++   Q+  A 
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67

Query: 226 LALHGFKITPTHAMKISFAKK 246
             L G  +   H +++  +++
Sbjct: 68  KQLQGHTVD-GHKLEVRISER 87

>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 = 44.5 bits (106), Expect = 2e-06
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEF 215
           ++           LF+  L  +T+E  L  +F+++    EV +V +R         FV F
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 216 ENEMQSAAAKLALHGFKI 233
           EN   +  A +A++G  +
Sbjct: 62  ENIDDAKDAMMAMNGKSV 79

>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 = 44.2 bits (105), Expect = 2e-06
 Identities = 26/81 (32%), Positives = 47/81 (58%), Gaps = 5/81 (6%)

Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
          ++V  +S  T+ ++SL  +FS++GQI ++V +K   T + RG  FV F+ I  A +A+ +
Sbjct: 15 LFVGGLSFDTN-EQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73

Query: 70 MQGFPFYDKPMRIQYSKTDSD 90
          M G     + +R+  +   SD
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSD 94

>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 = 43.6 bits (104), Expect = 2e-06
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 26 KSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
          ++L   F  F   +    +  ++T   RG  FV F     A NA+ SMQG     +P+RI
Sbjct: 16 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 75

Query: 83 QYSK 86
           ++ 
Sbjct: 76 NWAA 79

>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 = 40.6 bits (96), Expect = 3e-05
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           LF+ +L     +  L   F  FP +    ++ +          FV F ++  +  A  ++
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 229 HGFKITPTHAMKISFAKK 246
            G  +     ++I++A K
Sbjct: 64  QGQDLN-GRPLRINWAAK 80

>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 = 44.2 bits (105), Expect = 2e-06
 Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 8/81 (9%)

Query: 158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAF 212
           +  ++       P++ LF+  L E+T+E  L   F+        R+V +R         F
Sbjct: 2   SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGF 58

Query: 213 VEFENEMQSAAAKLALHGFKI 233
           V+F +E  + AAK A+   +I
Sbjct: 59  VDFNSEEDAKAAKEAMEDGEI 79

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 14/74 (18%), Positives = 30/74 (40%), Gaps = 2/74 (2%)

Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
          ++V  +S  T  +++L   F    +   +   +T   +G  FV F     A  A  +M+ 
Sbjct: 18 LFVKGLSEDTT-EETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMED 76

Query: 73 FPFYDKPMRIQYSK 86
                 + + ++K
Sbjct: 77 GEIDGNKVTLDWAK 90

>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 = 44.4 bits (105), Expect = 2e-06
 Identities = 11/80 (13%), Positives = 27/80 (33%), Gaps = 6/80 (7%)

Query: 158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFV 213
           +  +   +P  P +  + +  +P    E  +   F+       V L+ +          V
Sbjct: 3   SGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLV 61

Query: 214 EFENEMQSAAAKLALHGFKI 233
           +F +   +  A L  +   +
Sbjct: 62  KFLSPQDTFEA-LKRNRMLM 80

>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 = 44.2 bits (105), Expect = 3e-06
 Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 4/77 (5%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           V+   +++    + L   FS  G++ D+  +    + + +G A+V F EI S   A+  +
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86

Query: 71  QGFPFYDKPMRIQYSKT 87
            G      P+ +Q S+ 
Sbjct: 87  TGQRLLGVPIIVQASQA 103

>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 = 40.4 bits (95), Expect = 7e-05
 Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 12/91 (13%)

Query: 148 QPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR 207
           + PV +P           PE+   + +F   L        L   F+     ++VR++ +R
Sbjct: 8   KSPVREPVDNLS------PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 61

Query: 208 HD-----IAFVEFENEMQSAAAKLALHGFKI 233
           +      IA+VEF    QS    + L G ++
Sbjct: 62  NSRRSKGIAYVEFCEI-QSVPLAIGLTGQRL 91

>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 = 45.8 bits (109), Expect = 3e-06
 Identities = 12/72 (16%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          ++V ++ +   ++    +F ++G+  ++      + RG  F+  +    A  A   + G 
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEV---FINRDRGFGFIRLESRTLAEIAKAELDGT 81

Query: 74 PFYDKPMRIQYS 85
              +P+RI+++
Sbjct: 82 ILKSRPLRIRFA 93

>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 = 44.3 bits (105), Expect = 1e-05
 Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 4/83 (4%)

Query: 166 PEQPPNQI--LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAA 223
            E+   Q   LF+ NLP + +E     LF ++    EV +  +R    F+  E+   +  
Sbjct: 15  GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG-FGFIRLESRTLAEI 73

Query: 224 AKLALHGFKITPTHAMKISFAKK 246
           AK  L G  +     ++I FA  
Sbjct: 74  AKAELDGTILKS-RPLRIRFATH 95

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 40.1 bits (94), Expect = 3e-04
 Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 2/61 (3%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASATNALRSMQ 71
           + V ++S     + L   FSQFG +   V +     +  G+ FV F     A  AL    
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCG 158

Query: 72  G 72
            
Sbjct: 159 D 159

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 43.6 bits (102), Expect = 4e-06
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 4/60 (6%)

Query: 25 KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
          K  L  +  ++G+++++V     K  G A V F  + +A  A+++  G    D P++I +
Sbjct: 31 KDVLLRLLQKYGEVLNLVLSS--KKPGTAVVEFATVKAAELAVQNEVGLV--DNPLKISW 86

>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 = 43.6 bits (103), Expect = 4e-06
 Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 11/84 (13%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK-----------TLKMRGQAFVIFKEIAS 62
           +YV  ++ +     L   F Q G +                  T K +G A V +++  +
Sbjct: 18  IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77

Query: 63  ATNALRSMQGFPFYDKPMRIQYSK 86
           A  A+    G  F    +++  ++
Sbjct: 78  AKAAVEWFDGKDFQGSKLKVSLAR 101

>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 = 37.8 bits (88), Expect = 6e-04
 Identities = 18/103 (17%), Positives = 38/103 (36%), Gaps = 15/103 (14%)

Query: 158 APMATAGVPEQPP-NQILFLTNLPEETSEMMLSMLFNQF--------PGFKEVRLVPNRH 208
               ++G P++   N  +++  L +  +   L+  F Q          G   + +  ++ 
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 209 D-----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
                  A V +E+   + AA     G        +K+S A+K
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG-SKLKVSLARK 102

>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 = 43.2 bits (102), Expect = 7e-06
 Identities = 14/100 (14%), Positives = 36/100 (36%), Gaps = 6/100 (6%)

Query: 136 AQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF 195
           A    MQ    +    +    P    +A   ++   + +++ N+   ++   L   F+  
Sbjct: 1   AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60

Query: 196 PGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHG 230
                + ++ ++        A++EF     S  A +A+  
Sbjct: 61  GSINRITILCDKFSGHPKGYAYIEFAER-NSVDAAVAMDE 99

>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 = 37.8 bits (88), Expect = 5e-04
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 4/77 (5%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           VYV ++      + L A FS  G I  I  L    +   +G A++ F E  S   A+ +M
Sbjct: 39  VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AM 97

Query: 71  QGFPFYDKPMRIQYSKT 87
               F  + +++   +T
Sbjct: 98  DETVFRGRTIKVLPKRT 114

>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 = 42.6 bits (101), Expect = 8e-06
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 3/62 (4%)

Query: 27 SLYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
           L    S+     D+  +  +T   R   +V F+       AL  + G   +   ++++ 
Sbjct: 33 ELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK 91

Query: 85 SK 86
           K
Sbjct: 92 PK 93

>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 = 40.7 bits (96), Expect = 4e-05
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 8/78 (10%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           LF+ NL    S   L +  ++     ++  V +          +V+FE+      A L L
Sbjct: 20  LFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAEDLEKA-LEL 77

Query: 229 HGFKITPTHAMKISFAKK 246
            G K+   + +K+   K 
Sbjct: 78  TGLKVF-GNEIKLEKPKG 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 = 42.2 bits (100), Expect = 1e-05
 Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 7/81 (8%)

Query: 11 TNFVYVTHIS--STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATN 65
             V+V +I   +T+  + L  IFS+ G ++    +    T K +G  F  +++  +A +
Sbjct: 8  LRSVFVGNIPYEATE--EQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 66 ALRSMQGFPFYDKPMRIQYSK 86
          A+R++ G  F  + +R+  + 
Sbjct: 66 AMRNLNGREFSGRALRVDNAA 86

>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 = 37.6 bits (88), Expect = 5e-04
 Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 16/86 (18%)

Query: 153 QPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH---- 208
            PA    + +           +F+ N+P E +E  L  +F++       RLV +R     
Sbjct: 1   DPAVDRSLRS-----------VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKP 49

Query: 209 -DIAFVEFENEMQSAAAKLALHGFKI 233
               F E++++  + +A   L+G + 
Sbjct: 50  KGYGFCEYQDQETALSAMRNLNGREF 75

>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 = 42.0 bits (99), Expect = 1e-05
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 6/73 (8%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
           P+   +  + L  LP   S+  +   F+          +P          AFV+F ++  
Sbjct: 10  PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI 69

Query: 221 SAAAKLALHGFKI 233
           +  A L  H  +I
Sbjct: 70  AEKA-LKKHKERI 81

>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 = 42.1 bits (99), Expect = 1e-05
 Identities = 18/80 (22%), Positives = 26/80 (32%), Gaps = 10/80 (12%)

Query: 158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF--PGFKEVRLVPNRHDIAFVEF 215
           AP    G P +     + ++ LP   S   L     +     + +V     R     VEF
Sbjct: 3   APRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV----YRDGTGVVEF 58

Query: 216 EN--EMQSAAAKLALHGFKI 233
               +M  A  K  L   K 
Sbjct: 59  VRKEDMTYAVRK--LDNTKF 76

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 15/81 (18%), Positives = 24/81 (29%), Gaps = 12/81 (14%)

Query: 14 VYVTHISST----DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
          V V+ +  +    DLK        + G +      +     G   V F      T A+R 
Sbjct: 19 VVVSGLPPSGSWQDLKD----HMREAGDVCYADVYR----DGTGVVEFVRKEDMTYAVRK 70

Query: 70 MQGFPFYDKPMRIQYSKTDSD 90
          +    F        Y +   D
Sbjct: 71 LDNTKFRSHEGETAYIRVKVD 91

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 14  VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
           +YV  +  +   +  L  IF  FG+I  I  +    T + +G  F+ F +   A  AL  
Sbjct: 29  LYVGSLHFNIT-EDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

Query: 70  MQGFPFYDKPMRIQYSK 86
           + GF    +PM++ +  
Sbjct: 88  LNGFELAGRPMKVGHVT 104

>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 = 41.1 bits (97), Expect = 2e-05
 Identities = 15/101 (14%), Positives = 31/101 (30%), Gaps = 16/101 (15%)

Query: 136 AQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF 195
                  +        +     A               L++ +L    +E ML  +F  F
Sbjct: 2   GHHHHHHSHMAAAMANNLQKGSAGPMR-----------LYVGSLHFNITEDMLRGIFEPF 50

Query: 196 PGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGF 231
              + ++L+ +          F+ F +   +  A   L+GF
Sbjct: 51  GRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGF 91

>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 = 42.5 bits (100), Expect = 2e-05
 Identities = 12/92 (13%), Positives = 27/92 (29%), Gaps = 6/92 (6%)

Query: 146 VQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP 205
           +      Q        +    +      + +  LP + +E  +   F+       V +  
Sbjct: 21  MASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-NPVRVHIEI 79

Query: 206 NRHD----IAFVEFENEMQSAAAKLALHGFKI 233
                    A VEF    ++ AA ++     +
Sbjct: 80  GPDGRVTGEADVEFATHEEAVAA-MSKDRANM 110

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD---IAFVEFENEMQSAAAKLALHG 230
           L ++N+P    +  L  +F QF    +V ++ N        FV FEN   +  A+  LHG
Sbjct: 32  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91

Query: 231 FKI 233
             +
Sbjct: 92  TVV 94

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 14  VYVTHIS-STDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQ 71
           ++V++I         L  +F QFG+I+D+ +       +G  FV F+  A A  A   + 
Sbjct: 32  LHVSNIPFRFR-DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 90

Query: 72  GFPFYDKPMRIQYSK 86
           G     + + +  + 
Sbjct: 91  GTVVEGRKIEVNNAT 105

>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 = 42.0 bits (99), Expect = 2e-05
 Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 6/70 (8%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKE-VRLVPNRHD----IAFVEFENEMQSAA 223
                  +TN+P   ++M +       P  +  V ++ + +      A V+F+NE  +  
Sbjct: 13  SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 72

Query: 224 AKLALHGFKI 233
           +   LH  K+
Sbjct: 73  S-ERLHRKKL 81

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 15/92 (16%), Positives = 36/92 (39%), Gaps = 8/92 (8%)

Query: 20  SSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKP 79
           S ++ +    ++F  + +       K+ K   +  + F    SA +A   +    F  K 
Sbjct: 19  SESETRAKFESLFRTYDKDTTFQYFKSFK---RVRINFSNPLSAADARLRLHKTEFLGKE 75

Query: 80  MRIQYSKTDSDVISKIKGTFMERPKKVRKQPA 111
           M++ +++T       I  + +  P   +  P+
Sbjct: 76  MKLYFAQT-----LHIGSSHLAPPNPDKSGPS 102

>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 = 41.0 bits (97), Expect = 3e-05
 Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 7/64 (10%)

Query: 174 LFLTNLPEETSEMMLSMLFNQF--PGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKL 226
           L++ NL   T++  L+   +        E++   NR +      A V   +E  S     
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 227 ALHG 230
            L  
Sbjct: 64  LLPK 67

>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 = 36.8 bits (86), Expect = 7e-04
 Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 11/81 (13%)

Query: 14 VYVTHIS--STDLKKSLYAIFSQFGQIMDIVALK------TLKMRGQAFVIFKEIASATN 65
          +Y+ +++  +TD  + L       G + DI+ +K        + +G A V     AS+  
Sbjct: 4  LYIGNLTWWTTD--EDLTEAVHSLG-VNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60

Query: 66 ALRSMQGFPFYDKPMRIQYSK 86
           +  +     + +   +  S 
Sbjct: 61 LMDLLPKRELHGQNPVVTPSN 81

>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 = 41.1 bits (97), Expect = 3e-05
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 3/78 (3%)

Query: 11  TNFVYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALR 68
           TN +Y++++  +  ++ L  +   FGQ++   I+   +   RG  F   +        + 
Sbjct: 26  TN-LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIG 84

Query: 69  SMQGFPFYDKPMRIQYSK 86
              G      P     ++
Sbjct: 85  HFNGKFIKTPPGVSAPTE 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 = 5e-05
 Identities = 17/87 (19%), Positives = 27/87 (31%), Gaps = 6/87 (6%)

Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHD- 209
           S  +P     +           ++L  LP E     +   F +       + +    +  
Sbjct: 6   SGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK 65

Query: 210 ---IAFVEFENEMQSAAAKLALHGFKI 233
                FVEF NE    AA L  H   +
Sbjct: 66  ATGEGFVEFRNEADYKAA-LCRHKQYM 91

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 11/75 (14%)

Query: 163 AGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF--PGFKEVRLVPNRHDIAFVEFEN--E 218
                +  N++  ++ LP   S   L     +     + +V     R     VEF    +
Sbjct: 8   GPPSRRSENRV-VVSGLPPSGSWQDLKDHMREAGDVCYADVY----RDGTGVVEFVRKED 62

Query: 219 MQSAAAKLALHGFKI 233
           M  A  K  L   K 
Sbjct: 63  MTYAVRK--LDNTKF 75

>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 = 39.4 bits (92), Expect = 1e-04
 Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 4/77 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          V V+ +  +   + L     + G +      +     G   V F      T A+R +   
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----DGTGVVEFVRKEDMTYAVRKLDNT 73

Query: 74 PFYDKPMRIQYSKTDSD 90
           F        Y +   D
Sbjct: 74 KFRSHEGETAYIRVKVD 90

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 39.5 bits (93), Expect = 7e-05
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 3/49 (6%)

Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          KK L   F++FG+++D        T + RG  F++FK+ AS    L   
Sbjct: 25 KKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 40.3 bits (94), Expect = 8e-05
 Identities = 17/75 (22%), Positives = 24/75 (32%), Gaps = 8/75 (10%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFP---GFKEVRLVPNRHD----IAFVEFENE 218
           PE     ++ L  LP   S   +    +      G   V  +  R       AFVE E+E
Sbjct: 12  PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESE 71

Query: 219 MQSAAAKLALHGFKI 233
                A L      +
Sbjct: 72  DDVKLA-LKKDRESM 85

>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 = 40.2 bits (94), Expect = 8e-05
 Identities = 14/87 (16%), Positives = 29/87 (33%), Gaps = 6/87 (6%)

Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-- 209
           S          +   +   +  + L  LP   ++  +   F+          +P   +  
Sbjct: 23  SMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK 82

Query: 210 ---IAFVEFENEMQSAAAKLALHGFKI 233
               AFV+F ++  +  A L  H  +I
Sbjct: 83  ITGEAFVQFASQELAEKA-LGKHKERI 108

>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 = 39.4 bits (93), Expect = 9e-05
 Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 6/62 (9%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           +++ N+    +   L   F+       V ++ ++        A++EF ++ +S    LAL
Sbjct: 9   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLAL 67

Query: 229 HG 230
             
Sbjct: 68  DE 69

>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 = 38.3 bits (90), Expect = 2e-04
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          +YV ++      + L A F   G +  +  L    +   +G A++ F +  S   +L ++
Sbjct: 9  IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67

Query: 71 QGFPFYDKPMRIQYSKT 87
              F  + +++   +T
Sbjct: 68 DESLFRGRQIKVIPKRT 84

>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 = 39.6 bits (93), Expect = 9e-05
 Identities = 15/84 (17%), Positives = 36/84 (42%), Gaps = 11/84 (13%)

Query: 14  VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
           V++ ++S  ++ +++L  +  QFG +  +  +    T   +G AF  F    +A   L +
Sbjct: 18  VFIRNLSFDSE-EEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76

Query: 70  MQ------GFPFYDKPMRIQYSKT 87
                   G     + +++  + T
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 = 38.9 bits (91), Expect = 2e-04
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 9/74 (12%)

Query: 161 ATAGVPEQPPNQI-LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVE 214
            ++G+P        +F+ NL  ++ E  L  +  QF   K VR+V +         AF +
Sbjct: 4   GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQ 63

Query: 215 FENEMQSAAAKLAL 228
           F  +    AA+  L
Sbjct: 64  FMTQ---EAAQKCL 74

>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 = 39.5 bits (92), Expect = 1e-04
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 9/77 (11%)

Query: 16 VTHIS----STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
          V HI       +L+  L  +   FG I + +    L    +AF+       A  A+    
Sbjct: 17 VVHIMDFQRGKNLRYQLLQLVEPFGVISNHL---ILNKINEAFIEMATTEDAQAAVDYYT 73

Query: 72 GFP--FYDKPMRIQYSK 86
            P   + KP+R+  S+
Sbjct: 74 TTPALVFGKPVRVHLSQ 90

>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 = 39.3 bits (92), Expect = 1e-04
 Identities = 12/69 (17%), Positives = 21/69 (30%), Gaps = 6/69 (8%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSAAA 224
                + +  LP   +E  +   F+       V +           A VEF     + AA
Sbjct: 13  TTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADVEFATHEDAVAA 71

Query: 225 KLALHGFKI 233
            +A     +
Sbjct: 72  -MAKDKANM 79

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 38.2 bits (90), Expect = 1e-04
 Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 3/47 (6%)

Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALR 68
          ++ L   F QFG++ + + ++   T + RG  FV F + A     L 
Sbjct: 14 QEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>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 = 40.2 bits (95), Expect = 1e-04
 Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           ++V  I      K     FSQ+G I+D   +    T + RG  FV +    +        
Sbjct: 90  IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QN 148

Query: 71  QGFPFYDKPMRIQYS 85
           +   F D+ + I+ +
Sbjct: 149 KFIDFKDRKIEIKRA 163

>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 = 38.3 bits (90), Expect = 7e-04
 Identities = 11/50 (22%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQ 71
          + +L   F ++G + D+  +K   T + RG  F+ F++ +S    +++  
Sbjct: 17 EDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH 66

>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 = 38.6 bits (90), Expect = 1e-04
 Identities = 13/77 (16%), Positives = 36/77 (46%), Gaps = 9/77 (11%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKTLKMRGQAFVIFKEIASATN 65
          +YV +I     ++++   F+   ++          ++A++  + +  AF+ F+ +   T 
Sbjct: 9  LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 66 ALRSMQGFPFYDKPMRI 82
          A+ +  G  F  + ++I
Sbjct: 69 AM-AFDGIIFQGQSLKI 84

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 20/98 (20%), Positives = 36/98 (36%), Gaps = 14/98 (14%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQ 71
           VY+    +      +       GQ+++I   +TL    +G  FV+F  I SA   +    
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ETP 72

Query: 72  GFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQ 109
           G  + +  + I             K  +  +  + RKQ
Sbjct: 73  GQKYKETDLLI-----------LFKDDYFAKKNEERKQ 99

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 9/64 (14%), Positives = 22/64 (34%), Gaps = 5/64 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSAAAKLALH 229
           +++   P + +   +            +++    H       FV F++  +SA   +   
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSI-ESAKKFVETP 72

Query: 230 GFKI 233
           G K 
Sbjct: 73  GQKY 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 = 37.8 bits (89), Expect = 2e-04
 Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 3/47 (6%)

Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALR 68
           + +   F QFG++ D + +    T + RG  FV F+          
Sbjct: 13 VEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

>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 = 39.2 bits (91), Expect = 2e-04
 Identities = 9/61 (14%), Positives = 26/61 (42%), Gaps = 5/61 (8%)

Query: 28  LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFP--FYDKPMRIQYS 85
           +  +   +G+I + +    ++M+ QAF+  +    A   +         F  + +++  S
Sbjct: 43  VLKLAEPYGKIKNYI---LMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS 99

Query: 86  K 86
           +
Sbjct: 100 E 100

>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 = 37.2 bits (86), Expect = 7e-04
 Identities = 18/102 (17%), Positives = 34/102 (33%), Gaps = 9/102 (8%)

Query: 150 PVSQPAPPAPMATAGVPEQPPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRH 208
             S   P          +Q   +++ L+NLP    S+  +  L   +   K   L+  + 
Sbjct: 4   GSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS 63

Query: 209 DIAFVEFENEMQSAAAKLALHGFKITPT----HAMKISFAKK 246
             AF+E E       A   +              +K+  ++K
Sbjct: 64  -QAFIEMETR---EDAMAMVDHCLKKALWFQGRCVKVDLSEK 101

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 26 KSLYAIFSQ-FGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD-KPMR 81
            LY  F + +       +V  +T   +G  FV F +      AL   QG      KP+R
Sbjct: 24 GMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR 83

Query: 82 IQYS 85
          +  +
Sbjct: 84 LSVA 87

>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 = 38.1 bits (89), Expect = 3e-04
 Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 12/71 (16%)

Query: 26 KSLYAIFSQFGQIMDIVALK------TLKMRGQAFVIFKEIASATNALRSMQGFPF---- 75
            +   F+  G+   ++++K      T    G  FV F ++A+A   L  + G P     
Sbjct: 24 NFISRAFATMGE--TVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGAT 81

Query: 76 YDKPMRIQYSK 86
            K  ++ Y+ 
Sbjct: 82 PAKRFKLNYAT 92

>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 = 36.9 bits (86), Expect = 7e-04
 Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 9/90 (10%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHD-----IAFVEFENEM 219
                   L++ +L     E  +S  F         V+++ NR         FVEF +  
Sbjct: 4   GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63

Query: 220 QSAAAKLALHGFKI---TPTHAMKISFAKK 246
            +      ++G  +   TP    K+++A  
Sbjct: 64  TAEKCLHKINGKPLPGATPAKRFKLNYATY 93

>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 = 37.6 bits (88), Expect = 4e-04
 Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 2/58 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
          V+V   +    +  L   FSQ+G +MD+   K    R  AFV F +   A +      
Sbjct: 8  VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK--PFRAFAFVTFADDQIAQSLCGEDL 63

>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 = 37.6 bits (88), Expect = 4e-04
 Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 3/43 (6%)

Query: 32 FSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQ 71
          FS FG+++ +   K   T   +G  FV F E  +    +    
Sbjct: 36 FSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH 78

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 3/48 (6%)

Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
          +++L + FSQ+G+++D V +K   T + RG  FV FK+       L S
Sbjct: 30 QETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 37.3 bits (87), Expect = 5e-04
 Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 1/60 (1%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           +F++  P       LS  F  F     V +  ++   A VE  +   +  A L+     +
Sbjct: 11  VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDV-GAREAVLSQSQHSL 69

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 3/49 (6%)

Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
            SL   F  FG I + V +    T K RG  FV   + A+A  A +  
Sbjct: 31 DASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79

>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 = 36.7 bits (86), Expect = 5e-04
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 3/58 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALR 68
          ++V  +S    ++ +   F  FG++  I       T K RG  F+ FKE       + 
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

>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 = 36.9 bits (86), Expect = 7e-04
 Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 7/77 (9%)

Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFE 216
            ++G      +  + L   P   +E  +            +R+V N H       FV+F 
Sbjct: 1   GSSGSSGTTCH-TVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFS 58

Query: 217 NEMQSAAAKLALHGFKI 233
           NE +   A L  +   +
Sbjct: 59  NEEEVKQA-LKCNREYM 74

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 37.2 bits (86), Expect = 9e-04
 Identities = 16/89 (17%), Positives = 25/89 (28%), Gaps = 9/89 (10%)

Query: 153 QPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF----PGFKEVRLVPNRH 208
                     A    +    I+ +  LP   +   +   F Q      G + +  V    
Sbjct: 5   SSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD 64

Query: 209 D----IAFVEFENEMQSAAAKLALHGFKI 233
                 AFV F  E  +  A L  H   +
Sbjct: 65  GRPTGDAFVLFACEEYAQNA-LRKHKDLL 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	246
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	100.0
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
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	100.0
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	100.0
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.92
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.92
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.91
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.87
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.86
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.86
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.86
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.86
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.85
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.85
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.84
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.84
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.84
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.84
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.84
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.84
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.83
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.83
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.83
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.83
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.83
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.83
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.83
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.83
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.82
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.82
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.82
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.82
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.82
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.82
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.82
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.82
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.82
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.82
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.82
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.82
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.82
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.82
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.82
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.82
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.82
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.81
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.81
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.81
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.81
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.81
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.81
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.81
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.81
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.81
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.81
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.81
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.81
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.81
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.81
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.81
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.81
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.81
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.81
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.81
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.81
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.81
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.81
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.81
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.81
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.81
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.81
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.81
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.81
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.81
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.81
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.81
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.81
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.81
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.8
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.8
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.8
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.8
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.8
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.8
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.8
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.8
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.8
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.8
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.8
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.8
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.8
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.8
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.8
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.8
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.8
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.8
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.8
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.8
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.8
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.8
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.8
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.8
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.8
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.8
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.8
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.8
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.8
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.8
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.8
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.8
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.79
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.79
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.79
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.79
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.79
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.79
2div_A	99	TRNA selenocysteine associated protein; structural	99.79
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.79
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.79
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.79
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.79
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.79
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.79
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.79
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.79
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.79
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.79
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.79
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.79
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.79
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.79
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.79
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.79
2div_A	99	TRNA selenocysteine associated protein; structural	99.79
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.79
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.79
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.79
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.78
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.78
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.78
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.78
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.78
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.78
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.78
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.78
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.78
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.78
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.78
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.78
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.78
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.78
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.78
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.78
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.78
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.78
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.78
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.78
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.78
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.78
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.78
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.78
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.78
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.78
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.78
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.78
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.77
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.77
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.77
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.77
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.77
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.77
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.77
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.77
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.77
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.77
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.77
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.77
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.77
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.77
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.77
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.77
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.77
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.77
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.77
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.77
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.77
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.77
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.77
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.77
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.77
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.77
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.77
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.77
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.77
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.77
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.77
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.77
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.77
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.77
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.77
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.76
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.76
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.76
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.76
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.76
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.76
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.76
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.76
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.76
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.76
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.76
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.76
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.76
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.76
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.76
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.76
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.75
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.75
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.75
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.75
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.75
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.75
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.75
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.75
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.75
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.75
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.75
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.75
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.75
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.75
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.75
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.75
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.75
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.75
1x5p_A	97	Negative elongation factor E; structure genomics,	99.75
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.75
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.75
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.74
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.74
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.74
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.74
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.74
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.74
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.74
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.74
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.74
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.74
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.74
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.74
1x5p_A	97	Negative elongation factor E; structure genomics,	99.74
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.74
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.74
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.74
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.73
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.73
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.73
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.73
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.73
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.73
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.73
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.73
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.73
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.73
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.73
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.72
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.72
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.72
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.72
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.72
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.72
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.72
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.72
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.72
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.72
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.72
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.56
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.71
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.71
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.71
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.71
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.71
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.71
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.71
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.71
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.71
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.71
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.71
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.71
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.7
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.7
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.7
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.7
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.7
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.7
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.7
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.7
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.69
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.69
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.69
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.69
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.69
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.52
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.69
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.69
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.68
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.68
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.68
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.68
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.67
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.67
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.67
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.67
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.66
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.66
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.66
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.66
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.66
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.66
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.66
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.66
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.65
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.65
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.65
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.65
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.65
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.64
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.64
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.64
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.63
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.63
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.63
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.62
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.61
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.6
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.58
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.58
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.58
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.58
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.58
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.56
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.56
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.56
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.53
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.51
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.44
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.39
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.38
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.29
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.26
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.26
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.05
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.05
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.93
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.76
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.46
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.33
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.3
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.01
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.99
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.81
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.66
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.48
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.44
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.42
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.33
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.24
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.11
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.84
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.76
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.53
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.0
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.87
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	93.53
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	92.07
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	89.34

>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=100.00  E-value=8.7e-39  Score=262.68  Aligned_cols=239  Identities=60%  Similarity=0.922  Sum_probs=167.0

Q ss_pred             CCCCCcEEEecCCChhhhHHHHH----HHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLY----AIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~----~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ..+++++|||+|||.++++++|+    ++|++||.|.+|.+.++++++|||||+|.+.++|.+|++.|||..+.|++|+|
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   84 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   84 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            57889999999999999999966    99999999999999998899999999999999999999999999999999999


Q ss_pred             EEccCCccccccccCccccccccccC-CCCCCCChhHHhhhhhhhHHHH-----------HHHHHHHHHHHhcccccCCC
Q psy4057          83 QYSKTDSDVISKIKGTFMERPKKVRK-QPAPVEDPAEAKKSKKKAAKEQ-----------ARLMQAQQQQMQALSVQQPP  150 (246)
Q Consensus        83 ~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~  150 (246)
                      .+++...+......+.+..+...... +.....................           ...... ........+..+.
T Consensus        85 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~  163 (282)
T 3pgw_A           85 QYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQA-PRIMHHMPGQPPY  163 (282)
T ss_pred             EEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCccccc-ccccccCCCCCCC
Confidence            99977765555444544433332222 1111111100000000000000           000000 0000000000000


Q ss_pred             CCCCC-CCCC----------------------CCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC
Q psy4057         151 VSQPA-PPAP----------------------MATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR  207 (246)
Q Consensus       151 ~~~~~-~~~~----------------------~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~  207 (246)
                      ...+. .+.+                      .........+++++|||+|||.++++++|+++|++||.|.+++++.++
T Consensus       164 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~  243 (282)
T 3pgw_A          164 MPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR  243 (282)
T ss_pred             CCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC
Confidence            00000 0000                      000112345578999999999999999999999999999999999998


Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         208 HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       208 ~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      +|||||+|.+.++|.+|+..|||+.|++|+.|+|+||||
T Consensus       244 ~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~akk  282 (282)
T 3pgw_A          244 HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK  282 (282)
T ss_pred             CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEecC
Confidence            899999999999999999999999998789999999997

>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=8.8e-38  Score=246.66  Aligned_cols=162  Identities=23%  Similarity=0.341  Sum_probs=145.2

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..|+++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.+|+..+.|+.|++.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            4578999999999999999999999999999999998764   7889999999999999999999999999999999999


Q ss_pred             ccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCC
Q psy4057          85 SKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAG  164 (246)
Q Consensus        85 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (246)
                      +.....                                                  .                       
T Consensus        92 ~~~~~~--------------------------------------------------~-----------------------   98 (213)
T 4f02_A           92 SQRDPS--------------------------------------------------L-----------------------   98 (213)
T ss_dssp             CCCCTH--------------------------------------------------H-----------------------
T ss_pred             cccccc--------------------------------------------------c-----------------------
Confidence            754421                                                  0                       


Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       165 ~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                        ......+|||+|||.++|+++|+++|+.||.|.+++++.+.   +|||||+|.+.++|.+|++.|||+.|+ |++|+|
T Consensus        99 --~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~-g~~i~V  175 (213)
T 4f02_A           99 --RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN-DRKVFV  175 (213)
T ss_dssp             --HHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEE
T ss_pred             --cccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEEC-CEEEEE
Confidence              01135689999999999999999999999999999999865   689999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .||+
T Consensus       176 ~~a~  179 (213)
T 4f02_A          176 GRFK  179 (213)
T ss_dssp             EECC
T ss_pred             EEcC
Confidence            9986

>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=3e-37  Score=233.71  Aligned_cols=159  Identities=19%  Similarity=0.313  Sum_probs=146.3

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDS   89 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~   89 (246)
                      ++|||+|||.++++++|+++|++||.|.+|.++++.  +++|||||+|.+.++|.+|++.|||..+.|++|.|.++....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            689999999999999999999999999999998765  678999999999999999999999999999999999975442


Q ss_pred             cccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCC
Q psy4057          90 DVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQP  169 (246)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (246)
                      .                                                                           ....
T Consensus        81 ~---------------------------------------------------------------------------~~~~   85 (166)
T 3md3_A           81 Q---------------------------------------------------------------------------SSSD   85 (166)
T ss_dssp             C---------------------------------------------------------------------------CCCT
T ss_pred             C---------------------------------------------------------------------------CCCC
Confidence            1                                                                           1334


Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      +.++|||+|||.++|+++|+++|++||.|.++.++.+.     +|+|||+|.+.++|.+|+..|||..++ |++|+|+||
T Consensus        86 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~a  164 (166)
T 3md3_A           86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN-GRPLRINWA  164 (166)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEET-TEECEEEES
T ss_pred             CCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEEEEec
Confidence            68899999999999999999999999999999999874     579999999999999999999999999 999999999


Q ss_pred             cC
Q psy4057         245 KK  246 (246)
Q Consensus       245 k~  246 (246)
                      +|
T Consensus       165 ~~  166 (166)
T 3md3_A          165 AK  166 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            86

>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=1.5e-36  Score=230.54  Aligned_cols=157  Identities=20%  Similarity=0.396  Sum_probs=145.1

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      |+++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|+|..+.|++|.|.++.
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            68999999999999999999999999999999998754   578999999999999999999999999999999999985


Q ss_pred             CCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                      ...                                                                             
T Consensus        82 ~~~-----------------------------------------------------------------------------   84 (168)
T 1b7f_A           82 PGG-----------------------------------------------------------------------------   84 (168)
T ss_dssp             CCS-----------------------------------------------------------------------------
T ss_pred             CCc-----------------------------------------------------------------------------
Confidence            442                                                                             


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCC--Cce
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPT--HAM  239 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g--~~l  239 (246)
                      ...+.++|+|+|||.++++++|+++|++||.|..++++.++     +|+|||+|.+.++|.+|++.|||..+. |  ++|
T Consensus        85 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~~~l  163 (168)
T 1b7f_A           85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPE-GGSQPL  163 (168)
T ss_dssp             STTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCT-TCSSCC
T ss_pred             ccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEec-CCCeEE
Confidence            22357899999999999999999999999999999999876     589999999999999999999999997 6  999


Q ss_pred             EEEee
Q psy4057         240 KISFA  244 (246)
Q Consensus       240 ~v~~a  244 (246)
                      +|+||
T Consensus       164 ~V~~A  168 (168)
T 1b7f_A          164 SVRLA  168 (168)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99997

>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=2.9e-36  Score=228.49  Aligned_cols=157  Identities=18%  Similarity=0.405  Sum_probs=143.6

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      |+++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|.|.++.
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            57999999999999999999999999999999998754   678999999999999999999999999999999999985


Q ss_pred             CCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                      ...                                                                             
T Consensus        81 ~~~-----------------------------------------------------------------------------   83 (167)
T 1fxl_A           81 PSS-----------------------------------------------------------------------------   83 (167)
T ss_dssp             CCC-----------------------------------------------------------------------------
T ss_pred             CCc-----------------------------------------------------------------------------
Confidence            442                                                                             


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCC--ce
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTH--AM  239 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~--~l  239 (246)
                      .....++|||+|||.++++++|+++|++||.|..++++.++     +|+|||+|.+.++|.+|++.|||..++ |+  +|
T Consensus        84 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~~~i  162 (167)
T 1fxl_A           84 ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPS-GATEPI  162 (167)
T ss_dssp             GGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCT-TCSSCC
T ss_pred             ccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccC-CCccce
Confidence            12246789999999999999999999999999999999875     689999999999999999999999999 64  59


Q ss_pred             EEEee
Q psy4057         240 KISFA  244 (246)
Q Consensus       240 ~v~~a  244 (246)
                      +|+||
T Consensus       163 ~v~~A  167 (167)
T 1fxl_A          163 TVKFA  167 (167)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99997

>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=100.00  E-value=4.9e-36  Score=239.19  Aligned_cols=196  Identities=20%  Similarity=0.308  Sum_probs=153.1

Q ss_pred             CCCCCcEEEecCCCh-hhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           7 HICVTNFVYVTHISS-TDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~-~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ..+++++|||+|||. ++++++|+++|++||.|.+|.++++.  +|||||+|.+.++|.+|++.|||..+.|++|.|.++
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~--~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  107 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS  107 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT--SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC--CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            456789999999999 99999999999999999999998874  899999999999999999999999999999999998


Q ss_pred             cCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCC
Q psy4057          86 KTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV  165 (246)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (246)
                      ........+.........+.....                                       +.   .....+......
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~---------------------------------------~~---~~~~~~~~~~~~  145 (229)
T 2adc_A          108 KHQNVQLPREGQEDQGLTKDYGNS---------------------------------------PL---HRFKKPGSKNFQ  145 (229)
T ss_dssp             SCCCCCCCCSSSSTTTTEEECTTC---------------------------------------SS---CCCCSTTSGGGT
T ss_pred             cCccccCccccccccccccccccC---------------------------------------cc---cccCCccccccc
Confidence            765432111110000000000000                                       00   000000000011


Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCC-CceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFP-GFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G-~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ...+++++|||+|||.++++++|+++|++|| .|..++++++.+|+|||+|.+.++|.+|++.|||..+.+|+.|+|+||
T Consensus       146 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a  225 (229)
T 2adc_A          146 NIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS  225 (229)
T ss_dssp             TCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             cCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEe
Confidence            2345789999999999999999999999999 999999988677999999999999999999999999976899999999


Q ss_pred             cC
Q psy4057         245 KK  246 (246)
Q Consensus       245 k~  246 (246)
                      +.
T Consensus       226 ~~  227 (229)
T 2adc_A          226 KS  227 (229)
T ss_dssp             SS
T ss_pred             cC
Confidence            73

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=100.00  E-value=7.1e-36  Score=233.03  Aligned_cols=193  Identities=20%  Similarity=0.327  Sum_probs=151.3

Q ss_pred             CCcEEEecCCCh-hhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          10 VTNFVYVTHISS-TDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        10 ~~~~l~V~nl~~-~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      .+++|||+|||. ++++++|+++|++||.|.+|.++++.  +|||||+|.+.++|.+|++.|||..+.|++|.|.++...
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~--~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~   79 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   79 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC--SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC--CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCC
Confidence            468999999999 99999999999999999999998874  899999999999999999999999999999999998765


Q ss_pred             ccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCC
Q psy4057          89 SDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQ  168 (246)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (246)
                      .....+......        .       ..                       .... ..+. .....  +.........
T Consensus        80 ~~~~~~~~~~~~--------~-------~~-----------------------~~~~-~~~~-~r~~~--~~~~~~~~~~  117 (198)
T 1qm9_A           80 NVQLPREGQEDQ--------G-------LT-----------------------KDYG-NSPL-HRFKK--PGSKNFQNIF  117 (198)
T ss_dssp             SCCCSSSSSSSS--------S-------CE-----------------------EESS-CCCT-TSSSS--CCCCCCSCCC
T ss_pred             CcCCCCcCCccc--------c-------cc-----------------------cccc-CCch-hhccC--ccccccccCC
Confidence            422111000000        0       00                       0000 0000 00000  0001112235


Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCC-CceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFP-GFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G-~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      +++++|||+|||.++++++|+++|+.|| .|..++++++.+|+|||+|.+.++|.+|+..|||..+++|++|+|+||+.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence            6799999999999999999999999999 99999998877899999999999999999999999997689999999973

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=100.00  E-value=1.4e-35  Score=232.18  Aligned_cols=193  Identities=13%  Similarity=0.168  Sum_probs=145.1

Q ss_pred             CCCcEEEecCCC-hhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           9 CVTNFVYVTHIS-STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         9 ~~~~~l~V~nl~-~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      +++++|||+||+ ..+++++|+++|++||.|.+|+++++  .+|||||+|.+.++|+.|++.|||..+.|++|+|.+++.
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~--~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~   79 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS--KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ   79 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT--STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC--CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccC
Confidence            578999999999 89999999999999999999999876  589999999999999999999999999999999999875


Q ss_pred             CccccccccCccccccccccCCCCCCCChh-HHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          88 DSDVISKIKGTFMERPKKVRKQPAPVEDPA-EAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                      .....  .........  .  ....+.... ..+...+               ...                    ....
T Consensus        80 ~~~~p--~~~~~~~~~--~--~~~~~~~~~~~~r~~~~---------------~~~--------------------~~~~  118 (205)
T 3tyt_A           80 PAIMP--GQSYGLEDG--S--CSYKDFSESRNNRFSTP---------------EQA--------------------AKNR  118 (205)
T ss_dssp             SCCCC--CSCCBCTTS--C--BSEEECTTCTTCSCSSH---------------HHH--------------------TTSC
T ss_pred             CccCC--CcccccccC--C--ccccccCCCccccccCc---------------ccc--------------------cccc
Confidence            43210  000000000  0  000000000 0000000               000                    0011


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCc--eEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCC---Cc
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGF--KEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPT---HA  238 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i--~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g---~~  238 (246)
                      ..+++++|||+|||.++|+++|+++|++||.|  .++++..++   +|+|||+|.+.++|..|+..|||+.|.+.   .+
T Consensus       119 ~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          119 IQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             cCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            34678999999999999999999999999999  899998863   58999999999999999999999999831   36


Q ss_pred             eEEEee
Q psy4057         239 MKISFA  244 (246)
Q Consensus       239 l~v~~a  244 (246)
                      +.|.||
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            777775

>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=2.2e-35  Score=225.39  Aligned_cols=160  Identities=21%  Similarity=0.386  Sum_probs=141.9

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-----CCccEEEEEEcCHHHHHHHHHHhcCCccC---CeeEE
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-----KMRGQAFVIFKEIASATNALRSMQGFPFY---DKPMR   81 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-----~~kg~aFV~f~~~~~A~~Ai~~lng~~~~---g~~l~   81 (246)
                      .+++|||+|||.++++++|+++|++||.|.+|.++++.     +++|||||+|.+.++|.+|++.|||..+.   ++++.
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            57899999999999999999999999999999998765     57899999999999999999999998875   67788


Q ss_pred             EEEccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCC
Q psy4057          82 IQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMA  161 (246)
Q Consensus        82 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (246)
                      +.++.....                                                                       
T Consensus        82 ~~~~~~~~~-----------------------------------------------------------------------   90 (175)
T 3nmr_A           82 MKPADSEKN-----------------------------------------------------------------------   90 (175)
T ss_dssp             EEECGGGCC-----------------------------------------------------------------------
T ss_pred             Ecccccccc-----------------------------------------------------------------------
Confidence            877643210                                                                       


Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCC-
Q psy4057         162 TAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPT-  236 (246)
Q Consensus       162 ~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g-  236 (246)
                           ...+.++|||+|||.++|+++|+++|++||.|.+++++.++    +|||||+|.+.++|.+|++.|||..+.+| 
T Consensus        91 -----~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~  165 (175)
T 3nmr_A           91 -----NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGC  165 (175)
T ss_dssp             -----SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTC
T ss_pred             -----ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCC
Confidence                 22357899999999999999999999999999999999974    57999999999999999999999988753 


Q ss_pred             -CceEEEeec
Q psy4057         237 -HAMKISFAK  245 (246)
Q Consensus       237 -~~l~v~~ak  245 (246)
                       ++|+|+||.
T Consensus       166 ~~~l~V~~ad  175 (175)
T 3nmr_A          166 SSPMVVKFAD  175 (175)
T ss_dssp             SSCCEEEECC
T ss_pred             CCCeEEEecC
Confidence             999999983

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=1.1e-35  Score=234.71  Aligned_cols=170  Identities=19%  Similarity=0.259  Sum_probs=145.7

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .++++|||+|||.++++++|+++|+.||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|.|.++
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            456899999999999999999999999999999998754   68999999999999999999999999999999999887


Q ss_pred             cCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCC
Q psy4057          86 KTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV  165 (246)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (246)
                      ........                                   .....      ..                        
T Consensus       106 ~~~~~~~~-----------------------------------~~~~~------~~------------------------  120 (216)
T 2qfj_A          106 SNIGQAQP-----------------------------------IIDQL------AE------------------------  120 (216)
T ss_dssp             SCCGGGHH-----------------------------------HHHHH------HH------------------------
T ss_pred             CCccccch-----------------------------------hhhhh------hc------------------------
Confidence            54421000                                   00000      00                        


Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                       .....++|||+|||.++|+++|+++|+.||.|.+++++.+.     +|||||+|.+.++|.+|+..|||..|+ |+.|+
T Consensus       121 -~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~i~  198 (216)
T 2qfj_A          121 -EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLG-GQYLR  198 (216)
T ss_dssp             -HHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCS-SSBCE
T ss_pred             -ccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeC-CcEEE
Confidence             12257899999999999999999999999999999999874     589999999999999999999999999 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.||+
T Consensus       199 V~~a~  203 (216)
T 2qfj_A          199 VGKAV  203 (216)
T ss_dssp             EEECS
T ss_pred             EEEec
Confidence            99986

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=100.00  E-value=1.2e-34  Score=220.86  Aligned_cols=154  Identities=19%  Similarity=0.346  Sum_probs=139.8

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhcc----C-------CeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQF----G-------QIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD   77 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~f----G-------~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (246)
                      .++++|||+|||.++++++|+++|++|    |       .|.++.+.   +++|||||+|.+.++|.+|+ .+||..+.|
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~---~~~g~afV~f~~~~~A~~A~-~~~~~~~~g   77 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN---QDKNFAFLEFRSVDETTQAM-AFDGIIFQG   77 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE---TTTTEEEEEESSHHHHHHHG-GGTTCEETT
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec---CCCCEEEEEeCCHHHHHHHH-HhCCcEecC
Confidence            578999999999999999999999999    6       67777654   46899999999999999999 899999999


Q ss_pred             eeEEEEEccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCC
Q psy4057          78 KPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPP  157 (246)
Q Consensus        78 ~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (246)
                      ++|.|.++....                                                                    
T Consensus        78 ~~i~v~~~~~~~--------------------------------------------------------------------   89 (172)
T 2g4b_A           78 QSLKIRRPHDYQ--------------------------------------------------------------------   89 (172)
T ss_dssp             EECEEECCSSCC--------------------------------------------------------------------
T ss_pred             ceeeecCCcccC--------------------------------------------------------------------
Confidence            999999864331                                                                    


Q ss_pred             CCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCc
Q psy4057         158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFK  232 (246)
Q Consensus       158 ~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~  232 (246)
                               ..+..++|||+|||.++|+++|+++|++||.|..++++.++     +|+|||+|.+.++|.+|++.|||..
T Consensus        90 ---------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~  160 (172)
T 2g4b_A           90 ---------PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ  160 (172)
T ss_dssp             ---------CCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCE
T ss_pred             ---------CCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCE
Confidence                     12247899999999999999999999999999999999985     5899999999999999999999999


Q ss_pred             cCCCCceEEEee
Q psy4057         233 ITPTHAMKISFA  244 (246)
Q Consensus       233 i~~g~~l~v~~a  244 (246)
                      ++ |++|+|+||
T Consensus       161 ~~-g~~l~V~~A  171 (172)
T 2g4b_A          161 LG-DKKLLVQRA  171 (172)
T ss_dssp             ET-TEECEEEEC
T ss_pred             EC-CeEEEEEeC
Confidence            99 999999997

>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=1.3e-34  Score=225.18  Aligned_cols=166  Identities=17%  Similarity=0.282  Sum_probs=143.7

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ....++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++. ++..+.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v   86 (196)
T 1l3k_A            8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEP   86 (196)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeee
Confidence            355678999999999999999999999999999999998764   6789999999999999999985 999999999999


Q ss_pred             EEccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCC
Q psy4057          83 QYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMAT  162 (246)
Q Consensus        83 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (246)
                      .++.......                                                                      
T Consensus        87 ~~~~~~~~~~----------------------------------------------------------------------   96 (196)
T 1l3k_A           87 KRAVSREDSQ----------------------------------------------------------------------   96 (196)
T ss_dssp             EECCC---------------------------------------------------------------------------
T ss_pred             ecccCccccc----------------------------------------------------------------------
Confidence            9975442100                                                                      


Q ss_pred             CCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCC
Q psy4057         163 AGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTH  237 (246)
Q Consensus       163 ~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~  237 (246)
                       ......+.++|||+|||.++|+++|+++|+.||.|..++++.++     +|||||+|.+.++|.+|+.. +|..++ |+
T Consensus        97 -~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~-G~  173 (196)
T 1l3k_A           97 -RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVN-GH  173 (196)
T ss_dssp             -------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEET-TE
T ss_pred             -ccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEEC-CE
Confidence             00123357899999999999999999999999999999999874     58999999999999999986 899999 99


Q ss_pred             ceEEEeec
Q psy4057         238 AMKISFAK  245 (246)
Q Consensus       238 ~l~v~~ak  245 (246)
                      .|.|.||.
T Consensus       174 ~i~v~~a~  181 (196)
T 1l3k_A          174 NCEVRKAL  181 (196)
T ss_dssp             ECEEEECC
T ss_pred             EEEEEecC
Confidence            99999985

>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=4e-35  Score=222.51  Aligned_cols=156  Identities=13%  Similarity=0.246  Sum_probs=140.2

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .++++|||+|||.++++++|+++|++||.|.+|.++++   ++++|||||+|.+.++|..|++.  +..+.|+.|.|.++
T Consensus         1 k~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRA   78 (167)
T ss_dssp             CGGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccc
Confidence            36899999999999999999999999999999999876   47899999999999999999994  67899999999887


Q ss_pred             cCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCC
Q psy4057          86 KTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV  165 (246)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (246)
                      .....                                                                           
T Consensus        79 ~~~~~---------------------------------------------------------------------------   83 (167)
T 2cjk_A           79 IPRDE---------------------------------------------------------------------------   83 (167)
T ss_dssp             CCHHH---------------------------------------------------------------------------
T ss_pred             cchhh---------------------------------------------------------------------------
Confidence            43310                                                                           


Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                        ..+.++|||+|||.++|+++|+++|++||.|..++++.++     +|||||+|.+.++|.+|++ |||..++ |++|+
T Consensus        84 --~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~-g~~i~  159 (167)
T 2cjk_A           84 --QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFK-DRKIE  159 (167)
T ss_dssp             --HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSS-SSCEE
T ss_pred             --ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeC-CeEEE
Confidence              1136789999999999999999999999999999999864     5899999999999999998 9999999 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.||+
T Consensus       160 V~~a~  164 (167)
T 2cjk_A          160 IKRAE  164 (167)
T ss_dssp             EEECC
T ss_pred             EeecC
Confidence            99986

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=100.00  E-value=1.2e-33  Score=220.12  Aligned_cols=175  Identities=17%  Similarity=0.296  Sum_probs=141.9

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhcc----C-------CeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQF----G-------QIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD   77 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~f----G-------~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (246)
                      ..+++|||+|||.++++++|+++|++|    |       .|.++.+   ++++|||||+|.+.++|.+|+ .|||..+.|
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~---~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g   77 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI---NQDKNFAFLEFRSVDETTQAM-AFDGIIFQG   77 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE---ETTTTEEEEEESCSHHHHHHG-GGTTEEETT
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe---cCCCCEEEEEeCCHHHHHHHH-HhcCCEEcC
Confidence            457999999999999999999999999    5       5666554   457999999999999999999 799999999


Q ss_pred             eeEEEEEccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCC
Q psy4057          78 KPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPP  157 (246)
Q Consensus        78 ~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (246)
                      ++|+|.++...........                                                   .+.   ..  
T Consensus        78 ~~i~v~~~~~~~~~~~~~~---------------------------------------------------~~~---~~--  101 (198)
T 2yh0_A           78 QSLKIRRPHDYQPLPGMSE---------------------------------------------------NPS---VY--  101 (198)
T ss_dssp             EEEEEECCCCCCCCCCSSS---------------------------------------------------CSS---CC--
T ss_pred             ceEEEeCCCCCCCCCCCcC---------------------------------------------------CCc---CC--
Confidence            9999999765421100000                                                   000   00  


Q ss_pred             CCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCc
Q psy4057         158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFK  232 (246)
Q Consensus       158 ~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~  232 (246)
                       .+.........+.++|||+|||.++++++|+++|++||.|.++++..++     +|||||+|.+.++|..|++.|||..
T Consensus       102 -~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~  180 (198)
T 2yh0_A          102 -VPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ  180 (198)
T ss_dssp             -CTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCE
T ss_pred             -CCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCE
Confidence             0000111233578999999999999999999999999999999999875     6899999999999999999999999


Q ss_pred             cCCCCceEEEeec
Q psy4057         233 ITPTHAMKISFAK  245 (246)
Q Consensus       233 i~~g~~l~v~~ak  245 (246)
                      ++ |+.|+|+||+
T Consensus       181 ~~-g~~l~v~~a~  192 (198)
T 2yh0_A          181 LG-DKKLLVQRAS  192 (198)
T ss_dssp             ET-TEECEEEESC
T ss_pred             EC-CEEEEEEECC
Confidence            99 9999999986

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=100.00  E-value=1.5e-34  Score=221.06  Aligned_cols=162  Identities=15%  Similarity=0.240  Sum_probs=139.3

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEc--cCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~--~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ...++++|||+|||.++++++|+++|+.||.+..+.+.  .+++++|||||+|.+.++|.+|++ |||..+.|++|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            56778999999999999999999999999987663222  345889999999999999999995 999999999999999


Q ss_pred             ccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCC
Q psy4057          85 SKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAG  164 (246)
Q Consensus        85 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (246)
                      +.....                                                                          
T Consensus        88 ~~~~~~--------------------------------------------------------------------------   93 (175)
T 1fje_B           88 PKGRDS--------------------------------------------------------------------------   93 (175)
T ss_dssp             CCCSSC--------------------------------------------------------------------------
T ss_pred             CCCccc--------------------------------------------------------------------------
Confidence            864421                                                                          


Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       165 ~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                       ....+.++|||+|||.++|+++|+++|++||.|..+......+|||||+|.+.++|.+|+..|||..++ |+.|+|+||
T Consensus        94 -~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~a  171 (175)
T 1fje_B           94 -KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID-GRSVSLYYT  171 (175)
T ss_dssp             -STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEET-TEEEEEEEC
T ss_pred             -cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEEC-CeEEEEEec
Confidence             122358899999999999999999999999999877111123689999999999999999999999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus       172 ~  172 (175)
T 1fje_B          172 G  172 (175)
T ss_dssp             S
T ss_pred             C
Confidence            6

>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=5.2e-33  Score=228.47  Aligned_cols=163  Identities=14%  Similarity=0.237  Sum_probs=147.2

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      .+++++|||+|||.++++++|+++|++||.|.++.++.+   ++++|||||+|.+.++|.+|++.|||..+.|++|.|.+
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~  171 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW  171 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            567899999999999999999999999999999998865   36789999999999999999999999999999999999


Q ss_pred             ccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCC
Q psy4057          85 SKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAG  164 (246)
Q Consensus        85 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (246)
                      +.....                                                                          
T Consensus       172 a~~~~~--------------------------------------------------------------------------  177 (284)
T 3smz_A          172 TDAGQL--------------------------------------------------------------------------  177 (284)
T ss_dssp             CCGGGC--------------------------------------------------------------------------
T ss_pred             CCCCCC--------------------------------------------------------------------------
Confidence            854321                                                                          


Q ss_pred             CCCCCCCcEEEEcCCCCCC-CHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         165 VPEQPPNQILFLTNLPEET-SEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       165 ~~~~~~~~~l~v~nL~~~~-t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                      .....+.++|||+|||.++ ++++|+++|+.||.|..++++.+.    +|+|||+|.+.++|.+|+..|||..++ |++|
T Consensus       178 ~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l  256 (284)
T 3smz_A          178 TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLG-GSHL  256 (284)
T ss_dssp             CTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEET-TEEC
T ss_pred             CcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccC-CeEE
Confidence            0123468899999999995 999999999999999999999974    589999999999999999999999999 9999


Q ss_pred             EEEeec
Q psy4057         240 KISFAK  245 (246)
Q Consensus       240 ~v~~ak  245 (246)
                      +|+||+
T Consensus       257 ~v~~a~  262 (284)
T 3smz_A          257 RVSFCA  262 (284)
T ss_dssp             EEEECC
T ss_pred             EEEEec
Confidence            999986

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=100.00  E-value=1.8e-32  Score=226.05  Aligned_cols=166  Identities=14%  Similarity=0.206  Sum_probs=143.2

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccC-CeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFG-QIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG-~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .++++|||+|||.++++++|+++|++|| .|..|.++++.  +++|||||+|.+.++|.+|++.|||..+.|++|.|.++
T Consensus       115 ~~~~~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          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            4689999999999999999999999999 99999998765  68899999999999999999999999999999999998


Q ss_pred             cCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCC
Q psy4057          86 KTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV  165 (246)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (246)
                      .+......                                                                      ..
T Consensus       195 ~~~~~~~~----------------------------------------------------------------------~~  204 (292)
T 2ghp_A          195 NPLEKSKR----------------------------------------------------------------------TD  204 (292)
T ss_dssp             CCC-----------------------------------------------------------------------------
T ss_pred             CCCccccc----------------------------------------------------------------------cc
Confidence            65421000                                                                      00


Q ss_pred             CCCCCCcEEEEcCCCCC-CCHHHHHHHHccCCCceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCc
Q psy4057         166 PEQPPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNR------HDIAFVEFENEMQSAAAKLALHGFKITPTHA  238 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~-~t~e~l~~~f~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~  238 (246)
                      ....+.++|||+|||.+ +|+++|+++|+.||.|..++++.+.      +|||||+|.+.++|.+|+ .|||+.|+ |++
T Consensus       205 ~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~-g~~  282 (292)
T 2ghp_A          205 SATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLG-NRE  282 (292)
T ss_dssp             --CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEET-TEE
T ss_pred             ccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEEC-CcE
Confidence            13446899999999999 9999999999999999999998864      489999999999999999 99999999 999


Q ss_pred             eEEEeecC
Q psy4057         239 MKISFAKK  246 (246)
Q Consensus       239 l~v~~ak~  246 (246)
                      |+|+||+.
T Consensus       283 i~V~~a~~  290 (292)
T 2ghp_A          283 ISVSLADK  290 (292)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEecC
Confidence            99999974

>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=9.3e-32  Score=220.99  Aligned_cols=150  Identities=16%  Similarity=0.276  Sum_probs=140.1

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      ..++++|||+|||.++++++|+++|+.|| |.++.+   ++++|||||+|.+.++|.+|++.|||..+.|++|.|.++. 
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~-   93 (284)
T 3smz_A           19 FRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV---DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP-   93 (284)
T ss_dssp             HHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE---ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC-
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE---ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC-
Confidence            45789999999999999999999999999 999887   5689999999999999999999999999999999999841 


Q ss_pred             CccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCC
Q psy4057          88 DSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE  167 (246)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (246)
                                                                                                      
T Consensus        94 --------------------------------------------------------------------------------   93 (284)
T 3smz_A           94 --------------------------------------------------------------------------------   93 (284)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                        +.++|||+|||.++|+++|+++|+.||.|..++++.++     +|||||+|.+.++|..|+..|||..++ |++|.|.
T Consensus        94 --~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~-g~~i~v~  170 (284)
T 3smz_A           94 --TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLG-PRTLYVH  170 (284)
T ss_dssp             --CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEEE
T ss_pred             --CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeC-CcEEEEE
Confidence              35789999999999999999999999999999999865     579999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      |++
T Consensus       171 ~a~  173 (284)
T 3smz_A          171 WTD  173 (284)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            985

>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=100.00  E-value=5.6e-32  Score=219.76  Aligned_cols=152  Identities=17%  Similarity=0.266  Sum_probs=137.5

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      ..++++|||+|||.++++++|+++|++||.|.+|.+.+   ++|||||+|.+.++|.+|+..|||..+.|++|.|.++. 
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~---~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~-   94 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR---DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT-   94 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC-
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC---CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecc-
Confidence            45678999999999999999999999999999998865   68999999999999999999999999999999999962 


Q ss_pred             CccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCC
Q psy4057          88 DSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE  167 (246)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (246)
                                                                                                      
T Consensus        95 --------------------------------------------------------------------------------   94 (261)
T 3sde_A           95 --------------------------------------------------------------------------------   94 (261)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCC-CccC--CCCceE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHG-FKIT--PTHAMK  240 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g-~~i~--~g~~l~  240 (246)
                        ++.+|||+|||..+|+++|+++|+.||.|.+++++.+.    +|||||+|.+.++|.+|+..||+ ..+.  .+++|.
T Consensus        95 --~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           95 --HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             --CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             --cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEE
Confidence              35689999999999999999999999999999999874    58999999999999999999955 3332  179999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.+++
T Consensus       173 v~~~~  177 (261)
T 3sde_A          173 VEPME  177 (261)
T ss_dssp             EEECC
T ss_pred             Eeecc
Confidence            99975

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=100.00  E-value=4.7e-32  Score=223.59  Aligned_cols=155  Identities=17%  Similarity=0.211  Sum_probs=137.7

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      +...+++++|||+|||.++++++|+++|+.||.|.+|.++++. .++|||||+|.+.++|.+|++ +||..+.|++|.|.
T Consensus        35 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~  113 (292)
T 2ghp_A           35 LTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVS  113 (292)
T ss_dssp             -------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEE
Confidence            3456789999999999999999999999999999999999865 458999999999999999995 99999999999999


Q ss_pred             EccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCC
Q psy4057          84 YSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATA  163 (246)
Q Consensus        84 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (246)
                      ++                                                                              
T Consensus       114 ~~------------------------------------------------------------------------------  115 (292)
T 2ghp_A          114 HL------------------------------------------------------------------------------  115 (292)
T ss_dssp             EC------------------------------------------------------------------------------
T ss_pred             EC------------------------------------------------------------------------------
Confidence            85                                                                              


Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCC-CceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCc
Q psy4057         164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFP-GFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHA  238 (246)
Q Consensus       164 ~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G-~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~  238 (246)
                            ..++|||+|||.++++++|+++|+.|| .|..++++.++    +|||||+|.+.++|..|+..|||..+. |+.
T Consensus       116 ------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~  188 (292)
T 2ghp_A          116 ------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIE-GYT  188 (292)
T ss_dssp             ------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEET-TEE
T ss_pred             ------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeC-CcE
Confidence                  367899999999999999999999999 99999998855    689999999999999999999999999 999


Q ss_pred             eEEEeec
Q psy4057         239 MKISFAK  245 (246)
Q Consensus       239 l~v~~ak  245 (246)
                      |.|.||+
T Consensus       189 l~v~~a~  195 (292)
T 2ghp_A          189 LVTKVSN  195 (292)
T ss_dssp             CEEEECC
T ss_pred             EEEEECC
Confidence            9999975

>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=99.92  E-value=9.4e-25  Score=162.65  Aligned_cols=135  Identities=16%  Similarity=0.201  Sum_probs=112.8

Q ss_pred             CCccEEEEEEcCHHHHHHHHHHh-cCCccCCeeEEEEEccCCccccccccCccccccccccCCCCCCCChhHHhhhhhhh
Q psy4057          48 KMRGQAFVIFKEIASATNALRSM-QGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKA  126 (246)
Q Consensus        48 ~~kg~aFV~f~~~~~A~~Ai~~l-ng~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (246)
                      ..+|+++|+|.+.++|++|++.+ ||..+.| .+.+.++............                             
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~-----------------------------   60 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHH-----------------------------   60 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSS-----------------------------
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccccc-----------------------------
Confidence            77899999999999999999999 9999999 9999987543211000000                             


Q ss_pred             HHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC
Q psy4057         127 AKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN  206 (246)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~  206 (246)
                                                      ...........+.++|||+|||.++|+++|+++|++||.|.+++++.+
T Consensus        61 --------------------------------~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~  108 (150)
T 2i2y_A           61 --------------------------------HHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN  108 (150)
T ss_dssp             --------------------------------CCCCSCSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS
T ss_pred             --------------------------------ccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC
Confidence                                            000011224457899999999999999999999999999999999999


Q ss_pred             CccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         207 RHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       207 ~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .+|||||+|.+.++|..|+..|||..++ |++|+|+||+
T Consensus       109 ~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~a~  146 (150)
T 2i2y_A          109 PPGFAFVEFEDPRDAADAVRELDGRTLC-GCRVRVELSN  146 (150)
T ss_dssp             SCSEEEEEESSHHHHHHHHHHHSSSCSS-SSCCEEEECC
T ss_pred             CCcEEEEEECCHHHHHHHHHHcCCCEEC-CeEEEEEEcC
Confidence            8899999999999999999999999999 9999999986

>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=99.92  E-value=2.9e-24  Score=161.36  Aligned_cols=140  Identities=16%  Similarity=0.173  Sum_probs=106.5

Q ss_pred             EEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCccccccccCccccccccccCCCCCCCChhHH
Q psy4057          41 IVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEA  119 (246)
Q Consensus        41 v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (246)
                      +.+..++ +++|||||+|.+.++|++|++.+++....+..+.+.........   ..                       
T Consensus         3 ~kl~ln~~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~---~~-----------------------   56 (158)
T 2kn4_A            3 YKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTV---TE-----------------------   56 (158)
T ss_dssp             EEEEEECSSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEE---EC-----------------------
T ss_pred             EEEEecCccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccc---cc-----------------------
Confidence            4555555 78999999999999999999988874443333333321111000   00                       


Q ss_pred             hhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCce
Q psy4057         120 KKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFK  199 (246)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~  199 (246)
                                                  .+.          .........+.++|||+|||.++|+++|+++|++||.|.
T Consensus        57 ----------------------------~~~----------~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~   98 (158)
T 2kn4_A           57 ----------------------------GSH----------HHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG   98 (158)
T ss_dssp             ----------------------------CCC----------CSSCCCCCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEE
T ss_pred             ----------------------------ccc----------ccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE
Confidence                                        000          001112345689999999999999999999999999999


Q ss_pred             EEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         200 EVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       200 ~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .++++.++     +|||||+|.+.++|..|++.|||..+. |++|+|.||+
T Consensus        99 ~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~a~  148 (158)
T 2kn4_A           99 DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD-GRELRVQMAR  148 (158)
T ss_dssp             EEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESS-SSEEEEEEEC
T ss_pred             EEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEEC-CeEEEEEECC
Confidence            99999874     589999999999999999999999999 9999999997

>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=99.91  E-value=8.2e-25  Score=155.63  Aligned_cols=79  Identities=23%  Similarity=0.395  Sum_probs=73.5

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      .+.+|||+|||.++++++|+++|++||.|.+|+++++. .++|||||+|.+.++|++|++.|||..+.|++|+|.++..+
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            46789999999999999999999999999999998875 57899999999999999999999999999999999998655

>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=99.87  E-value=7.3e-22  Score=136.41  Aligned_cols=78  Identities=17%  Similarity=0.357  Sum_probs=73.1

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      .+++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.+|+
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            36789999999999999999999999999999998764   788999999999999999999999999999999999985


Q ss_pred             C
Q psy4057          87 T   87 (246)
Q Consensus        87 ~   87 (246)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            3

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.86  E-value=1.3e-21  Score=134.05  Aligned_cols=81  Identities=19%  Similarity=0.292  Sum_probs=73.3

Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCc--cCCCCceEE
Q psy4057         164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK--ITPTHAMKI  241 (246)
Q Consensus       164 ~~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~--i~~g~~l~v  241 (246)
                      .....+|+++|||+|||.++|+++|+++|++||.|.++++++++ |+|||+|.+.++|.+|++.|||..  +. |++|+|
T Consensus        14 ~~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~k-g~AFVef~~~~~A~~Av~~ln~~~~~i~-Gr~i~V   91 (100)
T 3r27_A           14 DPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK-RQALVEFEDVLGACNAVNYAADNQIYIA-GHPAFV   91 (100)
T ss_dssp             ---CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHHHSCEEET-TEEEEE
T ss_pred             ccccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCC-CEEEEEECCHHHHHHHHHHhcCCCceeC-CcEEEE
Confidence            34467789999999999999999999999999999999999765 899999999999999999999986  77 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      +|||.
T Consensus        92 ~~S~~   96 (100)
T 3r27_A           92 NYSTS   96 (100)
T ss_dssp             EECSC
T ss_pred             Eeccc
Confidence            99974

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.86  E-value=1.5e-21  Score=134.85  Aligned_cols=76  Identities=20%  Similarity=0.413  Sum_probs=71.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ..+++|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|++.|||..++ |++|+|+|
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~-gr~l~V~~   95 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQ-SKTIKVSY   95 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEE
Confidence            357899999999999999999999999999999999865     579999999999999999999999999 99999999


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      ||
T Consensus        96 Ak   97 (99)
T 4fxv_A           96 AR   97 (99)
T ss_dssp             CC
T ss_pred             ee
Confidence            97

>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=99.86  E-value=4.6e-22  Score=141.36  Aligned_cols=81  Identities=25%  Similarity=0.488  Sum_probs=76.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.+++++.++|||||+|.+.++|..|++.|||..+.|++|.|.++.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            45678999999999999999999999999999999999998899999999999999999999999999999999999985


Q ss_pred             C
Q psy4057          87 T   87 (246)
Q Consensus        87 ~   87 (246)
                      .
T Consensus        84 ~   84 (115)
T 3lqv_A           84 A   84 (115)
T ss_dssp             H
T ss_pred             C
Confidence            3

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.86  E-value=2.4e-21  Score=132.67  Aligned_cols=80  Identities=20%  Similarity=0.306  Sum_probs=73.7

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCc--cCCeeEEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFP--FYDKPMRIQ   83 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~--~~g~~l~v~   83 (246)
                      ...+|+++|||+|||+++++++|+++|++||.|.+|.+++   +||+|||+|.+.++|..|++.||+..  +.|++|+|.
T Consensus        16 ~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~---~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP---KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             -CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             ccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc---CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            3568999999999999999999999999999999999875   68999999999999999999999876  789999999


Q ss_pred             EccCC
Q psy4057          84 YSKTD   88 (246)
Q Consensus        84 ~a~~~   88 (246)
                      ||+.+
T Consensus        93 ~S~~k   97 (100)
T 3r27_A           93 YSTSQ   97 (100)
T ss_dssp             ECSCS
T ss_pred             ecccc
Confidence            99765

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.85  E-value=2.9e-21  Score=139.07  Aligned_cols=91  Identities=29%  Similarity=0.451  Sum_probs=80.8

Q ss_pred             CCCCCcEEEecCCChhhhHHHHH----HHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLY----AIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~----~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ..+|+++|||+|||..+++++|+    ++|++||.|.+|.+.++++++|||||+|.+.++|..|++.|||..+.|++|+|
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            45788999999999999998865    79999999999999888899999999999999999999999999999999999


Q ss_pred             EEccCCccccccccC
Q psy4057          83 QYSKTDSDVISKIKG   97 (246)
Q Consensus        83 ~~a~~~~~~~~~~~~   97 (246)
                      .|++.+........+
T Consensus       105 ~~a~~~~~~~~~~~~  119 (127)
T 2a3j_A          105 TFSETPQSQVAEDGS  119 (127)
T ss_dssp             EECCCCCHHHHCC--
T ss_pred             EEccCcchhcccccc
Confidence            999887765544433

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.85  E-value=4.2e-21  Score=135.06  Aligned_cols=82  Identities=13%  Similarity=0.154  Sum_probs=76.5

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..+|.++|||+||++++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus         2 g~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~   81 (110)
T 3s8s_A            2 GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQ   81 (110)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            35788999999999999999999999999999999998764   788999999999999999999999999999999999


Q ss_pred             EccCC
Q psy4057          84 YSKTD   88 (246)
Q Consensus        84 ~a~~~   88 (246)
                      ++...
T Consensus        82 ~a~~~   86 (110)
T 3s8s_A           82 LDIKG   86 (110)
T ss_dssp             ECSTT
T ss_pred             ECCCC
Confidence            98654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=6.1e-21  Score=131.94  Aligned_cols=80  Identities=15%  Similarity=0.267  Sum_probs=73.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcC--CccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG--FPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng--~~~~g~~l~v~~   84 (246)
                      ..+++++|||+|||+++++++|+++|++||.|.+|.++++   ||||||+|.+.++|..|++.|++  ..+.|++|+|.+
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~---kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   88 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF   88 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC---CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            5678999999999999999999999999999999999874   89999999999999999998864  789999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      +..+.
T Consensus        89 A~~~~   93 (105)
T 1sjq_A           89 SNHKE   93 (105)
T ss_dssp             CSSSS
T ss_pred             cCCCC
Confidence            87653

>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=99.84  E-value=2.3e-20  Score=129.76  Aligned_cols=78  Identities=18%  Similarity=0.197  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCC--ccCCCCceEEEee
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF--KITPTHAMKISFA  244 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~--~i~~g~~l~v~~a  244 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|++++++ |||||+|.+.++|..|++.|++.  .+. |++|+|.||
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~k-g~aFVef~~~~~A~~Ai~~l~~~~~~i~-Gr~l~V~~a   88 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK-RQALVEFENIDSAKECVTFAADVPVYIA-GQQAFFNYS   88 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHHHSCCBSS-SSBCEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCC-CEEEEEECCHHHHHHHHHHhccCCceEC-CEEEEEEEc
Confidence            56689999999999999999999999999999999998874 89999999999999999999775  488 999999999


Q ss_pred             cC
Q psy4057         245 KK  246 (246)
Q Consensus       245 k~  246 (246)
                      +.
T Consensus        89 ~~   90 (104)
T 1wex_A           89 TS   90 (104)
T ss_dssp             SS
T ss_pred             cC
Confidence            73

>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=99.84  E-value=7.3e-21  Score=131.41  Aligned_cols=77  Identities=12%  Similarity=0.184  Sum_probs=71.7

Q ss_pred             CCCCcEEEEcCCCC-CCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCC--ccCCCCceEEEee
Q psy4057         168 QPPNQILFLTNLPE-ETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF--KITPTHAMKISFA  244 (246)
Q Consensus       168 ~~~~~~l~v~nL~~-~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~--~i~~g~~l~v~~a  244 (246)
                      ..++++|||+|||. ++|+++|+++|++||.|.+|++++++ |||||+|.+.++|..|++.|||.  .|. |++|+|.||
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k-g~aFVef~~~~~A~~Ai~~l~~~~~~~~-Gr~l~V~~a   89 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI-NEAFIEMATTEDAQAAVDYYTTTPALVF-GKPVRVHLS   89 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS-SCEEEEESSHHHHHHHHHHHHHSCCEET-TEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC-CEEEEEECCHHHHHHHHHHHcCCCceEC-CcEEEEEEC
Confidence            44799999999999 99999999999999999999999886 89999999999999999999975  488 999999999


Q ss_pred             cC
Q psy4057         245 KK  246 (246)
Q Consensus       245 k~  246 (246)
                      ++
T Consensus        90 ~~   91 (102)
T 1x4d_A           90 QK   91 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            84

>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=99.84  E-value=2.5e-20  Score=128.75  Aligned_cols=79  Identities=16%  Similarity=0.287  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhC--CCccCCCCceEEEe
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH--GFKITPTHAMKISF  243 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~--g~~i~~g~~l~v~~  243 (246)
                      ...+++++|||+|||.++++++|+++|++||.|.+++++++ +|||||+|.+.++|..|++.|+  +..+. |++|+|.|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-kg~aFVef~~~~~A~~Ai~~l~~~~~~~~-Gr~l~V~~   87 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-KNQAFLELATEEAAITMVNYYSAVTPHLR-NQPIYIQY   87 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHHHSCCEET-TEECEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-CCEEEEEECCHHHHHHHHHHhccCCceEC-CcEEEEEE
Confidence            35668999999999999999999999999999999999987 4999999999999999999874  67899 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |+.
T Consensus        88 a~~   90 (101)
T 2cq1_A           88 SNH   90 (101)
T ss_dssp             CSC
T ss_pred             cCc
Confidence            973

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.84  E-value=2.2e-20  Score=131.39  Aligned_cols=78  Identities=17%  Similarity=0.214  Sum_probs=73.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .++.++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|++.|||+.++ |+.|+|.
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~-gr~i~V~   81 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVM-GNIIHAQ   81 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEEC-CeEEEEE
Confidence            3578999999999999999999999999999999999875     589999999999999999999999999 9999999


Q ss_pred             eecC
Q psy4057         243 FAKK  246 (246)
Q Consensus       243 ~ak~  246 (246)
                      +|++
T Consensus        82 ~a~~   85 (110)
T 3s8s_A           82 LDIK   85 (110)
T ss_dssp             ECST
T ss_pred             ECCC
Confidence            9864

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.84  E-value=2.3e-21  Score=131.81  Aligned_cols=79  Identities=19%  Similarity=0.362  Sum_probs=72.2

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccC-CeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhc-CCccCCeeEEEEEc
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFG-QIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQ-GFPFYDKPMRIQYS   85 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG-~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~ln-g~~~~g~~l~v~~a   85 (246)
                      +++|||+|||.++++++|+++|++|| .|.+|+++++.   +++|||||+|.+.++|.+|++.++ +..+.|++|+|.+|
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            58999999999999999999999999 89999998764   789999999999999999999874 57899999999999


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      .++.
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=6e-21  Score=131.97  Aligned_cols=78  Identities=15%  Similarity=0.260  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCC--CccCCCCceEEEee
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG--FKITPTHAMKISFA  244 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g--~~i~~g~~l~v~~a  244 (246)
                      ..+++++|||+|||.++|+++|+++|++||.|.+|++++++ |||||+|.+.++|..|++.|++  ..+. |++|+|.||
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~k-GfaFVeF~~~~~A~~Ai~~l~~~~~~l~-Gr~l~V~~A   89 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVTPVLR-GQPIYIQFS   89 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHTTSCCEET-TEECCBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCC-CEEEEEECCHHHHHHHHHHhccCCceEC-CEEEEEEEc
Confidence            34579999999999999999999999999999999999985 9999999999999999999874  7899 999999998


Q ss_pred             cC
Q psy4057         245 KK  246 (246)
Q Consensus       245 k~  246 (246)
                      +.
T Consensus        90 ~~   91 (105)
T 1sjq_A           90 NH   91 (105)
T ss_dssp             SS
T ss_pred             CC
Confidence            73

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.83  E-value=1.4e-20  Score=124.50  Aligned_cols=75  Identities=9%  Similarity=0.149  Sum_probs=71.3

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ...+..|||+||+++++|++|+++|.+||+|.++.+..   +||||||+|.+.++|.+|++.||+..+.|++|+|.+|
T Consensus         4 ~~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~---~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            4 AWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL---NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC---CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            35688999999999999999999999999999999865   8999999999999999999999999999999999998

>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=99.83  E-value=2.2e-20  Score=132.27  Aligned_cols=80  Identities=15%  Similarity=0.237  Sum_probs=73.5

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCC--CccCCCCceEEE
Q psy4057         165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG--FKITPTHAMKIS  242 (246)
Q Consensus       165 ~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g--~~i~~g~~l~v~  242 (246)
                      ....+++++|||+|||.++|+++|+++|++||.|.+|+++++ +|||||+|.+.++|.+|++.|++  ..+. |++|+|.
T Consensus        25 ~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~-Gr~l~V~  102 (119)
T 2ad9_A           25 RSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-KNQAFIEMNTEEAANTMVNYYTSVTPVLR-GQPIYIQ  102 (119)
T ss_dssp             TSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-GTEEEEECSCHHHHHHHHHHHHHHCCCBT-TBCCEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-CCEEEEEECCHHHHHHHHHHhccCCceEC-CeEEEEE
Confidence            345668999999999999999999999999999999999988 49999999999999999999984  6899 9999999


Q ss_pred             eecC
Q psy4057         243 FAKK  246 (246)
Q Consensus       243 ~ak~  246 (246)
                      ||+.
T Consensus       103 ~a~~  106 (119)
T 2ad9_A          103 FSNH  106 (119)
T ss_dssp             ECSS
T ss_pred             EccC
Confidence            9973

>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=99.83  E-value=8e-21  Score=130.75  Aligned_cols=87  Identities=62%  Similarity=0.987  Sum_probs=78.3

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHH----HHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeE
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLY----AIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPM   80 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~----~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (246)
                      +...+|+++|||+|||.++++++|+    ++|++||.|.+|.+.++++++|||||+|.+.++|..|++.|||..+.|++|
T Consensus         2 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            2 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             ----CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3467899999999999999999999    999999999999998777889999999999999999999999999999999


Q ss_pred             EEEEccCCccc
Q psy4057          81 RIQYSKTDSDV   91 (246)
Q Consensus        81 ~v~~a~~~~~~   91 (246)
                      +|.++......
T Consensus        82 ~v~~a~~~~~~   92 (97)
T 1nu4_A           82 RIQYAKTDSDI   92 (97)
T ss_dssp             EEEECSSCCTH
T ss_pred             EEEEccCCCcc
Confidence            99999876543

>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=99.83  E-value=2.9e-20  Score=127.70  Aligned_cols=81  Identities=19%  Similarity=0.436  Sum_probs=76.0

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      |+++|||+|||.++++++|+++|++||.|.+|.+.++   ++++|||||+|.+.++|.+|++.|||..+.|++|+|.++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            6899999999999999999999999999999999876   4779999999999999999999999999999999999997


Q ss_pred             CCcc
Q psy4057          87 TDSD   90 (246)
Q Consensus        87 ~~~~   90 (246)
                      ....
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7653

>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=99.83  E-value=2.3e-20  Score=125.77  Aligned_cols=82  Identities=26%  Similarity=0.374  Sum_probs=72.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus         2 p~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   81 (87)
T 3bs9_A            2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   81 (87)
T ss_dssp             ----CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34678999999999999999999999999999999998753   678999999999999999999999999999999999


Q ss_pred             EccCC
Q psy4057          84 YSKTD   88 (246)
Q Consensus        84 ~a~~~   88 (246)
                      ++..+
T Consensus        82 ~a~~k   86 (87)
T 3bs9_A           82 WATRK   86 (87)
T ss_dssp             EEC--
T ss_pred             ecCCC
Confidence            98654

>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=99.83  E-value=5e-20  Score=129.52  Aligned_cols=83  Identities=19%  Similarity=0.295  Sum_probs=78.0

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.+..+++++|||||+|.+.++|.+|++.||+..+.|++|+|.+++
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   97 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   97 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcc
Confidence            45678999999999999999999999999999999998888899999999999999999999999999999999999987


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      ...
T Consensus        98 ~~~  100 (109)
T 1x4a_A           98 SGR  100 (109)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            653

>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=99.83  E-value=3.2e-20  Score=124.52  Aligned_cols=80  Identities=29%  Similarity=0.405  Sum_probs=74.5

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.
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            35688999999999999999999999999999999998763   678999999999999999999999999999999999


Q ss_pred             Ecc
Q psy4057          84 YSK   86 (246)
Q Consensus        84 ~a~   86 (246)
                      +++
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            974

>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=99.83  E-value=4.1e-20  Score=124.00  Aligned_cols=77  Identities=23%  Similarity=0.412  Sum_probs=72.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .++.++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||..++ |++|+|+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~   82 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF-GRTIRVN   82 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEET-TEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEEC-CcEEEEE
Confidence            4578999999999999999999999999999999998863     589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      |||
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            997

>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=99.82  E-value=4.3e-20  Score=127.60  Aligned_cols=81  Identities=19%  Similarity=0.288  Sum_probs=74.0

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhc--CCccCCeeEEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ--GFPFYDKPMRIQ   83 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~ln--g~~~~g~~l~v~   83 (246)
                      ...+|+++|||+|||.++++++|+++|++||.|.+|.++++   ||||||+|.+.++|..|++.|+  +..+.|++|+|.
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC---CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            35678999999999999999999999999999999988774   8999999999999999999774  678999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      |+..+.
T Consensus        87 ~a~~~~   92 (101)
T 2cq1_A           87 YSNHKE   92 (101)
T ss_dssp             ECSCSS
T ss_pred             EcCccc
Confidence            997654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=6.8e-20  Score=125.57  Aligned_cols=83  Identities=28%  Similarity=0.463  Sum_probs=77.2

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      .+++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            4678999999999999999999999999999999998863   6889999999999999999999999999999999999


Q ss_pred             ccCCcc
Q psy4057          85 SKTDSD   90 (246)
Q Consensus        85 a~~~~~   90 (246)
                      +..+..
T Consensus        82 a~~~~~   87 (95)
T 2dnz_A           82 VTERLD   87 (95)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            976643

>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=99.82  E-value=3e-20  Score=131.60  Aligned_cols=80  Identities=15%  Similarity=0.258  Sum_probs=73.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhc--CCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ--GFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~ln--g~~~~g~~l~v~~   84 (246)
                      ..+|+++|||+|||+++++++|+++|++||.|.+|.++++   ||||||+|.+.++|.+|++.|+  +..+.|++|+|.+
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~---kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~  103 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF  103 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG---GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEE
Confidence            5678999999999999999999999999999999999874   8999999999999999999887  4789999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      +..+.
T Consensus       104 a~~k~  108 (119)
T 2ad9_A          104 SNHKE  108 (119)
T ss_dssp             CSSSS
T ss_pred             ccCCC
Confidence            97653

>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=99.82  E-value=2.7e-20  Score=128.56  Aligned_cols=80  Identities=19%  Similarity=0.316  Sum_probs=72.9

Q ss_pred             CCCCCcEEEecCCCh-hhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcC--CccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISS-TDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG--FPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~-~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng--~~~~g~~l~v~   83 (246)
                      ...|+++|||+|||. ++++++|+++|++||.|.+|.+++   .+|||||+|.+.++|..|++.||+  ..+.|++|+|.
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~---~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN---KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS---SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEc---CCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            467899999999999 999999999999999999999976   469999999999999999999986  45999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      +|....
T Consensus        88 ~a~~~~   93 (102)
T 1x4d_A           88 LSQKYK   93 (102)
T ss_dssp             EECCCT
T ss_pred             ECCCCC
Confidence            997543

>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=99.82  E-value=7.9e-20  Score=127.17  Aligned_cols=85  Identities=22%  Similarity=0.286  Sum_probs=78.4

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      +....+.++|||+|||.++++++|+++|++||.|.+|.++++. .++|||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A            9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            3456788999999999999999999999999999999998875 578999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++....
T Consensus        89 ~a~~~~   94 (103)
T 2cqi_A           89 WATTPS   94 (103)
T ss_dssp             ECCCTT
T ss_pred             ECCCCc
Confidence            987654

>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=99.82  E-value=3.7e-20  Score=128.68  Aligned_cols=81  Identities=20%  Similarity=0.313  Sum_probs=73.8

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcC--CccCCeeEEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG--FPFYDKPMRIQ   83 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng--~~~~g~~l~v~   83 (246)
                      ...+|+++|||+|||.++++++|+++|++||.|.+|.+++   .||||||+|.+.++|.+|++.|++  ..+.|++|+|.
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~---~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP---FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC---CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            4578899999999999999999999999999999999876   489999999999999999998876  45899999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      |+..+.
T Consensus        87 ~a~~~~   92 (104)
T 1wex_A           87 YSTSKR   92 (104)
T ss_dssp             ECSSSS
T ss_pred             EccCcc
Confidence            997654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.82  E-value=2.6e-20  Score=127.31  Aligned_cols=81  Identities=20%  Similarity=0.354  Sum_probs=73.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCC--eeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCC----ccCC
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQ--IMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGF----PFYD   77 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~--i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~----~~~g   77 (246)
                      ....=++|||+|||+++++++|+++|++||.  |.+|+++++.   ++||||||+|.+.++|.+|++.|||.    .+.|
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            5566789999999999999999999999995  6789988764   78999999999999999999999996    4899


Q ss_pred             eeEEEEEccC
Q psy4057          78 KPMRIQYSKT   87 (246)
Q Consensus        78 ~~l~v~~a~~   87 (246)
                      |+|.|.||+.
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            9999999863

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.82  E-value=3.2e-20  Score=122.77  Aligned_cols=74  Identities=18%  Similarity=0.209  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .+.-|||+||+..+|+++|+++|.+||+|.++++... +|||||+|.+.++|..|++.|||..++ |++|+|.+|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~-kGfaFVey~~~~eA~~Ai~~Ln~~~l~-gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN-QGIALCKYTTREEANKAQMALNNCVLA-NTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTEEET-TEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCC-CcEEEEEECCHHHHHHHHHHhcCCEEC-CcEEEEEECC
Confidence            5788999999999999999999999999999999885 599999999999999999999999999 9999999985

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.82  E-value=1.6e-20  Score=128.32  Aligned_cols=76  Identities=20%  Similarity=0.387  Sum_probs=69.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCC--ceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCC----ccCCCC
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPG--FKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGF----KITPTH  237 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~--i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~----~i~~g~  237 (246)
                      ..-.+|||+|||+++|+++|+++|++||.  +.+|++++|+     +|||||+|.+.++|.+|++.|||.    .|+ |+
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~-Gr   85 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKID-GK   85 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEET-TE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceEC-CE
Confidence            35678999999999999999999999995  6799999875     589999999999999999999997    488 99


Q ss_pred             ceEEEeec
Q psy4057         238 AMKISFAK  245 (246)
Q Consensus       238 ~l~v~~ak  245 (246)
                      +|.|+|||
T Consensus        86 ~i~V~~Ak   93 (95)
T 2lkz_A           86 TIGVDFAK   93 (95)
T ss_dssp             EEEEEECC
T ss_pred             EEEEEEcc
Confidence            99999998

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=7.9e-20  Score=124.98  Aligned_cols=78  Identities=18%  Similarity=0.346  Sum_probs=73.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ..++.++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|++.|||..+. |++|+|
T Consensus        12 ~~~~~~~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           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLF-GRVIKA   90 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEET-TEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeC-CcEEEE
Confidence            45678999999999999999999999999999999999864     479999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      +|||
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9997

>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=99.82  E-value=6.3e-20  Score=126.03  Aligned_cols=83  Identities=17%  Similarity=0.190  Sum_probs=76.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHH----HHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLY----AIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~----~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      .....++|||+|||.++++++|+    ++|++||.|.+|.++.+...+|||||+|.+.++|.+|++.|||..+.|++|+|
T Consensus         5 ~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             CCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34567899999999999999999    99999999999999987755999999999999999999999999999999999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .++....
T Consensus        85 ~~a~~~~   91 (96)
T 2dgx_A           85 SLATGAS   91 (96)
T ss_dssp             EECCCSS
T ss_pred             EEcCCCC
Confidence            9987653

>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=99.82  E-value=5.1e-20  Score=130.70  Aligned_cols=75  Identities=19%  Similarity=0.294  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .+.+|||+|||.++|+++|+++|++||.|.+|+++.+.   +|||||+|.+.++|.+|++.|||..|+ |+.|+|.+|+
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 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN-DRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEET-TEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEEC-CEEEEEEECC
Confidence            36789999999999999999999999999999999875   589999999999999999999999999 9999999986

>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=99.82  E-value=8.8e-20  Score=129.65  Aligned_cols=85  Identities=26%  Similarity=0.431  Sum_probs=78.5

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      |.+..+.++|||+|||.++++++|+++|++||.|.+|.+..+.  +++|||||+|.+.++|++|++.|||..+.|++|+|
T Consensus         1 m~e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V   80 (116)
T 2fy1_A            1 MVEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKV   80 (116)
T ss_dssp             CCTTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3456788999999999999999999999999999999998854  78899999999999999999999999999999999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .++....
T Consensus        81 ~~a~~~~   87 (116)
T 2fy1_A           81 EQAKKPS   87 (116)
T ss_dssp             EECCCSS
T ss_pred             EECCCCC
Confidence            9997654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.1e-19  Score=124.48  Aligned_cols=80  Identities=25%  Similarity=0.331  Sum_probs=74.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ...+++++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|+..|||..+. |++|+
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~   88 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD-GRRIR   88 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEET-TEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC-CEEEE
Confidence            355679999999999999999999999999999999999864     479999999999999999999999999 99999


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |+||+.
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999973

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=6.8e-20  Score=125.32  Aligned_cols=80  Identities=24%  Similarity=0.472  Sum_probs=75.0

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45778999999999999999999999999999999998864   678999999999999999999999999999999999


Q ss_pred             Ecc
Q psy4057          84 YSK   86 (246)
Q Consensus        84 ~a~   86 (246)
                      +|+
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            974

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.82  E-value=2.3e-19  Score=123.89  Aligned_cols=78  Identities=24%  Similarity=0.339  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceE--------EEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCcc
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE--------VRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKI  233 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~--------v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i  233 (246)
                      ..++.++|||+|||.++++++|+++|++||.|..        ++++.++     +|||||+|.+.++|..|++.|||..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            4557999999999999999999999999999999        9999874     58999999999999999999999999


Q ss_pred             CCCCceEEEeec
Q psy4057         234 TPTHAMKISFAK  245 (246)
Q Consensus       234 ~~g~~l~v~~ak  245 (246)
                      . |+.|+|+||+
T Consensus        89 ~-g~~l~V~~A~   99 (99)
T 2la6_A           89 S-GNPIKVSFAT   99 (99)
T ss_dssp             S-SSBCEEEECC
T ss_pred             C-CcEEEEEecC
Confidence            9 9999999986

>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=99.82  E-value=5e-20  Score=129.24  Aligned_cols=86  Identities=22%  Similarity=0.388  Sum_probs=78.5

Q ss_pred             cccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeE
Q psy4057           4 ILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPM   80 (246)
Q Consensus         4 ~~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (246)
                      +....+++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|
T Consensus        19 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l   98 (108)
T 2jrs_A           19 LQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM   98 (108)
T ss_dssp             SCCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             cccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34556778999999999999999999999999999999998763   678999999999999999999999999999999


Q ss_pred             EEEEccCCc
Q psy4057          81 RIQYSKTDS   89 (246)
Q Consensus        81 ~v~~a~~~~   89 (246)
                      +|.++.++.
T Consensus        99 ~V~~a~~k~  107 (108)
T 2jrs_A           99 KVGHVTERT  107 (108)
T ss_dssp             EEECSCSSC
T ss_pred             EEEEcccCC
Confidence            999987654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.82  E-value=3.2e-20  Score=128.69  Aligned_cols=76  Identities=25%  Similarity=0.350  Sum_probs=72.2

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDS   89 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~   89 (246)
                      ++|||+|||.++++++|+++|++||.|.+|.+.++  ++|||||+|.+.++|.+|++.|||..+.|++|+|.++....
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN--PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS--SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            48999999999999999999999999999999887  89999999999999999999999999999999999987653

>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=99.81  E-value=1.6e-19  Score=124.75  Aligned_cols=79  Identities=22%  Similarity=0.399  Sum_probs=74.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ...++.++|||+|||.++++++|+++|++||.|..+++.+++ |||||+|.+.++|.+|++.|||..+. |++|+|.||+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~k-g~afV~f~~~~~a~~a~~~l~g~~~~-g~~l~v~~a~   87 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-GFGFIRLETRTLAEIAKVELDNMPLR-GKQLRVRFAC   87 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT-TEEEEECSSSHHHHHHHHHHTTCCBT-TBCCEEEESS
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCC-CEEEEEECCHHHHHHHHHHhCCCEeC-CceEEEEEcC
Confidence            345678999999999999999999999999999999999875 89999999999999999999999999 9999999987


Q ss_pred             C
Q psy4057         246 K  246 (246)
Q Consensus       246 ~  246 (246)
                      .
T Consensus        88 ~   88 (99)
T 2cpj_A           88 H   88 (99)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.81  E-value=1.8e-19  Score=125.29  Aligned_cols=83  Identities=20%  Similarity=0.303  Sum_probs=77.3

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ...+.++|||+|||.++++++|+++|++||.|.+|.++++. .++|||||+|.+.++|.+|++.|||..+.|++|+|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45678999999999999999999999999999999998775 57899999999999999999999999999999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ..+.
T Consensus        91 ~~~~   94 (103)
T 2cq3_A           91 TARV   94 (103)
T ss_dssp             CSSC
T ss_pred             ccCC
Confidence            7654

>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=1.1e-19  Score=125.40  Aligned_cols=84  Identities=21%  Similarity=0.287  Sum_probs=77.5

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.
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            45678999999999999999999999999999999998754   788999999999999999999999999999999999


Q ss_pred             EccCCcc
Q psy4057          84 YSKTDSD   90 (246)
Q Consensus        84 ~a~~~~~   90 (246)
                      ++..+..
T Consensus        84 ~a~~~~~   90 (99)
T 1whw_A           84 PSTIKKE   90 (99)
T ss_dssp             ECCCCST
T ss_pred             EcCCCcc
Confidence            9976643

>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=9.8e-20  Score=121.56  Aligned_cols=78  Identities=26%  Similarity=0.351  Sum_probs=73.0

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      +.+|||+|||.++++++|+++|++||.|.++.++++   ++++|||||+|.+.++|.+|++.|||..+.|++|+|.++.+
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            468999999999999999999999999999999876   37789999999999999999999999999999999999875


Q ss_pred             C
Q psy4057          88 D   88 (246)
Q Consensus        88 ~   88 (246)
                      +
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=1.2e-19  Score=122.32  Aligned_cols=77  Identities=18%  Similarity=0.330  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ++.++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||..++ |+.|+|.|
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v~~   82 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG-GRQIRTNW   82 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC-CeEEEEEe
Confidence            468899999999999999999999999999999999875     589999999999999999999999999 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |+.
T Consensus        83 a~~   85 (87)
T 3bs9_A           83 ATR   85 (87)
T ss_dssp             EC-
T ss_pred             cCC
Confidence            974

>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=99.81  E-value=7.4e-20  Score=122.74  Aligned_cols=77  Identities=17%  Similarity=0.336  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHh-CCCccCCCCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL-HGFKITPTHAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l-~g~~i~~g~~l~v~~ak  245 (246)
                      ..++.++|||+|||.++++++|+++|++||.|.++++++++ |||||+|.+.++|..|+..| ||..+. |++|+|.|||
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~k-g~afV~f~~~~~A~~a~~~l~~~~~~~-g~~l~v~~ak   85 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ-QCAFIQFATRQAAEVAAEKSFNKLIVN-GRRLNVKWGR   85 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGG-TEEEEEESSHHHHHHHHHTTTTTCEET-TEECCEEECC
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCC-CEEEEEECCHHHHHHHHHHhcCCeeEC-CCEEEEEecC
Confidence            45578999999999999999999999999999999999864 89999999999999999999 999999 9999999997

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=1.1e-19  Score=125.71  Aligned_cols=84  Identities=17%  Similarity=0.312  Sum_probs=77.3

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ....++++|||+|||.++++++|+++|++||.|.+|.+..+.  +++|||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus        12 ~~~~~~~~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           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            355678999999999999999999999999999999998765  678999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++.++.
T Consensus        92 ~a~~~~   97 (100)
T 2do4_A           92 ISNSGP   97 (100)
T ss_dssp             ECCCCS
T ss_pred             ECCCCC
Confidence            987653

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.81  E-value=7.1e-20  Score=126.70  Aligned_cols=79  Identities=20%  Similarity=0.267  Sum_probs=73.9

Q ss_pred             CCCcEEEecCCCh------hhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCC-e
Q psy4057           9 CVTNFVYVTHISS------TDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYD-K   78 (246)
Q Consensus         9 ~~~~~l~V~nl~~------~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g-~   78 (246)
                      ..+++|||+|||.      ++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            4578999999999      99999999999999999999998764   688999999999999999999999999999 9


Q ss_pred             eEEEEEccC
Q psy4057          79 PMRIQYSKT   87 (246)
Q Consensus        79 ~l~v~~a~~   87 (246)
                      +|+|.++.+
T Consensus        84 ~l~V~~a~~   92 (100)
T 3ns6_A           84 RLFLYTMKD   92 (100)
T ss_dssp             BCEEEESHH
T ss_pred             EEEEEECch
Confidence            999999854

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.81  E-value=1.1e-19  Score=130.81  Aligned_cols=80  Identities=19%  Similarity=0.353  Sum_probs=72.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHH----HHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLS----MLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~----~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                      ...+++++|||+|||..+++++|+    ++|++||.|.+|.+..+.  +|||||+|.+.++|..|+..|||..|. |++|
T Consensus        24 ~~~~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           24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQ-GNPL  102 (127)
T ss_dssp             CCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCT-TSCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeC-CCEE
Confidence            345678999999999999999876    699999999999987643  699999999999999999999999999 9999


Q ss_pred             EEEeecC
Q psy4057         240 KISFAKK  246 (246)
Q Consensus       240 ~v~~ak~  246 (246)
                      +|.||+.
T Consensus       103 ~V~~a~~  109 (127)
T 2a3j_A          103 VITFSET  109 (127)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999973

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=7.1e-20  Score=125.43  Aligned_cols=82  Identities=23%  Similarity=0.352  Sum_probs=76.1

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ...+++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            356789999999999999999999999999999999998764   67899999999999999999999999999999999


Q ss_pred             EEccC
Q psy4057          83 QYSKT   87 (246)
Q Consensus        83 ~~a~~   87 (246)
                      .+++.
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99853

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.1e-19  Score=126.17  Aligned_cols=83  Identities=28%  Similarity=0.450  Sum_probs=77.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.
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 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            45678999999999999999999999999999999998864   678999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++....
T Consensus        88 ~a~~~~   93 (102)
T 1x5s_A           88 QAGKSS   93 (102)
T ss_dssp             EEECCC
T ss_pred             ECCCCC
Confidence            997664

>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=99.81  E-value=3.7e-20  Score=129.70  Aligned_cols=78  Identities=21%  Similarity=0.289  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEcCCCCC-CCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCC--CccCCCCceEEEe
Q psy4057         167 EQPPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG--FKITPTHAMKISF  243 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~-~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g--~~i~~g~~l~v~~  243 (246)
                      ..+++++|||+|||.+ +|+++|+++|++||.|.+|++++.+ |||||+|.+.++|..|++.||+  ..|. |++|+|.|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~k-g~aFVef~~~~~A~~Ai~~l~~~~~~l~-Gr~l~V~~   98 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK-SQAFIEMETREDAMAMVDHCLKKALWFQ-GRCVKVDL   98 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT-TEEEEECSSHHHHHHHHHHHHHSCCCSS-SSCCEEEE
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCC-CEEEEEECCHHHHHHHHHHhccCCceEC-CEEEEEEE
Confidence            3567999999999998 9999999999999999999998765 8999999999999999999865  5688 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |++
T Consensus        99 a~~  101 (112)
T 1x4f_A           99 SEK  101 (112)
T ss_dssp             ECS
T ss_pred             Ccc
Confidence            974

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.2e-19  Score=126.30  Aligned_cols=84  Identities=21%  Similarity=0.326  Sum_probs=77.6

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ....++++|||+|||.++++++|+++|++||.|.+|.++.+   ++++|||||+|.+.++|.+|++.|||..+.|++|+|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            45667899999999999999999999999999999999876   468899999999999999999999999999999999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .++....
T Consensus        88 ~~a~~~~   94 (103)
T 2dnm_A           88 QVARYGR   94 (103)
T ss_dssp             EECSSCC
T ss_pred             EECCcCC
Confidence            9987553

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.9e-19  Score=124.26  Aligned_cols=83  Identities=19%  Similarity=0.331  Sum_probs=76.7

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ....++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++ ||+..+.|++|.|
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            345788999999999999999999999999999999998764   689999999999999999999 9999999999999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .++..+.
T Consensus        84 ~~a~~~~   90 (99)
T 2dgs_A           84 KRAEPRD   90 (99)
T ss_dssp             EECCCCC
T ss_pred             EECCCCc
Confidence            9997654

>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=1.5e-19  Score=126.12  Aligned_cols=84  Identities=23%  Similarity=0.347  Sum_probs=77.9

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ....++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            356778999999999999999999999999999999998854   78899999999999999999999999999999999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .++....
T Consensus        90 ~~a~~~~   96 (105)
T 1x5u_A           90 NKASAHN   96 (105)
T ss_dssp             EETTTTS
T ss_pred             EECCCCC
Confidence            9997664

>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=99.81  E-value=2.2e-19  Score=124.93  Aligned_cols=79  Identities=27%  Similarity=0.466  Sum_probs=74.2

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ....+.++|||+|||.++++++|+++|++||.|..|+++.++   +|||||+|.+.++|.+|+..|||..|. |++|+|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~V~   88 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKIL-GKEVKVN   88 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEET-TEEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcC-CCeEEEE
Confidence            355679999999999999999999999999999999999964   589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus        89 ~a~   91 (103)
T 2cqi_A           89 WAT   91 (103)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            986

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.81  E-value=4.1e-19  Score=123.94  Aligned_cols=80  Identities=28%  Similarity=0.405  Sum_probs=73.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCC--Cce
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPT--HAM  239 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g--~~l  239 (246)
                      ...+++++|||+|||.++++++|+++|++||.|..++++.++    +|||||+|.+.++|.+|++.|||..+.+|  ++|
T Consensus        10 ~~~~~~~~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           10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             CSCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            345679999999999999999999999999999999999975    58999999999999999999999999833  999


Q ss_pred             EEEeec
Q psy4057         240 KISFAK  245 (246)
Q Consensus       240 ~v~~ak  245 (246)
                      +|.||+
T Consensus        90 ~V~~a~   95 (105)
T 2dnh_A           90 VVKFAD   95 (105)
T ss_dssp             EEEESC
T ss_pred             EEEECc
Confidence            999986

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=8.1e-20  Score=125.43  Aligned_cols=82  Identities=21%  Similarity=0.434  Sum_probs=76.1

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEE-EEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v-~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..++++|||+|||.++++++|+++|++||.|.++ .++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus         2 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   81 (96)
T 1x5t_A            2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVS   81 (96)
T ss_dssp             CSCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3578999999999999999999999999999999 888763   678999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++....
T Consensus        82 ~a~~~~   87 (96)
T 1x5t_A           82 YAFKKD   87 (96)
T ss_dssp             ESCCCC
T ss_pred             EecccC
Confidence            987654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=3.6e-19  Score=123.13  Aligned_cols=79  Identities=28%  Similarity=0.503  Sum_probs=74.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ....+.++|||+|||.++|+++|+++|++||.|.+++++.++    +|||||+|.+.++|..|++.|||..+. |++|+|
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v   90 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIK-ENIIKV   90 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESS-SCEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEEC-CEEEEE
Confidence            345678999999999999999999999999999999999876    489999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .||+
T Consensus        91 ~~a~   94 (100)
T 2do4_A           91 AISN   94 (100)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9986

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.81  E-value=1.5e-20  Score=127.84  Aligned_cols=74  Identities=23%  Similarity=0.354  Sum_probs=68.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCC-CceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhC-CCccCCCCceEEEe
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFP-GFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALH-GFKITPTHAMKISF  243 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G-~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~-g~~i~~g~~l~v~~  243 (246)
                      +.+|||+|||.++|+++|+++|++|| .|.+|++++++     +|||||+|.+.++|.+|++.|+ +..++ |++|+|.|
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~-gr~i~V~~   79 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNIL-GQKVSMHY   79 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEET-TEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEEC-CEEEEEEE
Confidence            57899999999999999999999999 89999999864     5899999999999999999885 56788 99999999


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      |+
T Consensus        80 a~   81 (91)
T 2lxi_A           80 SD   81 (91)
T ss_dssp             CC
T ss_pred             cC
Confidence            86

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.81  E-value=1.8e-20  Score=136.74  Aligned_cols=78  Identities=22%  Similarity=0.317  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..+.++|||+|||.++|+++|+++|+.||.|..|+++.++     +|||||+|.+.++|.+|+..|||..|. |++|+|.
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~-g~~l~V~  122 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD-GRELRVQ  122 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSS-SSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC-CEEEEEE
Confidence            3458899999999999999999999999999999998864     579999999999999999999999999 9999999


Q ss_pred             eecC
Q psy4057         243 FAKK  246 (246)
Q Consensus       243 ~ak~  246 (246)
                      ||+.
T Consensus       123 ~a~~  126 (135)
T 2lea_A          123 MARY  126 (135)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9973

>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=99.81  E-value=1.1e-19  Score=124.46  Aligned_cols=80  Identities=23%  Similarity=0.388  Sum_probs=75.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.+.++.  +++|||||+|.+.++|.+|++.|||..+.|++|+|.+
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            45678999999999999999999999999999999998764  6789999999999999999999999999999999999


Q ss_pred             cc
Q psy4057          85 SK   86 (246)
Q Consensus        85 a~   86 (246)
                      ++
T Consensus        92 a~   93 (95)
T 2ywk_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.81  E-value=3e-19  Score=125.23  Aligned_cols=80  Identities=20%  Similarity=0.359  Sum_probs=74.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ...+++++|||+|||.++++++|+++|++||.|..++++.++     +|||||+|.+.++|..|++.|||..|. |++|+
T Consensus        21 ~~~~~~~~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           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELA-GRPMK   99 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSS-SSCCE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC-CEEEE
Confidence            345678999999999999999999999999999999999864     589999999999999999999999999 99999


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |+||+.
T Consensus       100 V~~a~~  105 (108)
T 2jrs_A          100 VGHVTE  105 (108)
T ss_dssp             EECSCS
T ss_pred             EEEccc
Confidence            999874

>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=3e-19  Score=124.63  Aligned_cols=79  Identities=23%  Similarity=0.301  Sum_probs=73.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ....+.++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|+..|||..|. |++|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~   88 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY-GKPIR   88 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCS-SCBCE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeEC-CeEEE
Confidence            355678999999999999999999999999999999999875     479999999999999999999999999 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.||+
T Consensus        89 v~~a~   93 (105)
T 1x5u_A           89 VNKAS   93 (105)
T ss_dssp             EEETT
T ss_pred             EEECC
Confidence            99986

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.3e-19  Score=126.76  Aligned_cols=82  Identities=15%  Similarity=0.311  Sum_probs=75.6

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.+..+   ++++|||||+|.+.++|.+|++.|||..+.|++|.|.
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            3456789999999999999999999999999999999876   4678999999999999999999999999999999999


Q ss_pred             EccCC
Q psy4057          84 YSKTD   88 (246)
Q Consensus        84 ~a~~~   88 (246)
                      ++..+
T Consensus        99 ~a~~~  103 (106)
T 1p27_B           99 WCFVR  103 (106)
T ss_dssp             ESEES
T ss_pred             eecCC
Confidence            98654

>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=2.3e-19  Score=119.71  Aligned_cols=75  Identities=20%  Similarity=0.371  Sum_probs=70.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      +.+|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|..|+..|||..++ |++|+|.||+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~-g~~l~v~~a~   79 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN-GRPLRINWAA   79 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEET-TEECEEEECC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeC-CcEEEEEecC
Confidence            4689999999999999999999999999999999874     589999999999999999999999999 9999999997


Q ss_pred             C
Q psy4057         246 K  246 (246)
Q Consensus       246 ~  246 (246)
                      .
T Consensus        80 ~   80 (83)
T 3md1_A           80 K   80 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=3.4e-19  Score=124.74  Aligned_cols=80  Identities=23%  Similarity=0.405  Sum_probs=74.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHh-CCCccCCCCc
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR------HDIAFVEFENEMQSAAAKLAL-HGFKITPTHA  238 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l-~g~~i~~g~~  238 (246)
                      ...++.++|||+|||..+++++|+++|++||.|..|+++.+.      +|||||+|.+.++|.+|+..| ||..|. |++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~-g~~   88 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY-GRR   88 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS-SCB
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeEC-CCE
Confidence            345679999999999999999999999999999999999883      689999999999999999999 999999 999


Q ss_pred             eEEEeecC
Q psy4057         239 MKISFAKK  246 (246)
Q Consensus       239 l~v~~ak~  246 (246)
                      |+|.||+.
T Consensus        89 l~v~~a~~   96 (107)
T 2cph_A           89 LVLEWADS   96 (107)
T ss_dssp             CEEEECCC
T ss_pred             EEEEeCCC
Confidence            99999873

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.5e-19  Score=120.67  Aligned_cols=80  Identities=16%  Similarity=0.267  Sum_probs=72.0

Q ss_pred             CCCCCcE-EEecCCChhhhHHH----HHHHhhcc-CCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeE
Q psy4057           7 HICVTNF-VYVTHISSTDLKKS----LYAIFSQF-GQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPM   80 (246)
Q Consensus         7 ~~~~~~~-l~V~nl~~~~~e~~----l~~~F~~f-G~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (246)
                      .++|+.+ |||+|||..+++++    |+++|++| |+|.+|       ..|+|||.|.+.++|++|++.|||..+.||+|
T Consensus         4 ~~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tgG~AfV~F~~~esA~~A~~~l~G~~l~gr~i   76 (96)
T 2diu_A            4 GSSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TGCSAILRFINQDSAERAQKRMENEDVFGNRI   76 (96)
T ss_dssp             SCCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CTTCEEEEESSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ecCEEEEEECCHHHHHHHHHHhcCCccCCceE
Confidence            4678888 99999999999887    66899999 599998       23999999999999999999999999999999


Q ss_pred             EEEEccCCccccc
Q psy4057          81 RIQYSKTDSDVIS   93 (246)
Q Consensus        81 ~v~~a~~~~~~~~   93 (246)
                      +|.||+.+++...
T Consensus        77 ~v~~A~~~sd~~~   89 (96)
T 2diu_A           77 IVSFTPKNRELCE   89 (96)
T ss_dssp             EEESSCCSCCCCC
T ss_pred             EEEecCCCcceeE
Confidence            9999998877654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.81  E-value=2.3e-19  Score=127.94  Aligned_cols=79  Identities=27%  Similarity=0.452  Sum_probs=73.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ...++.++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||..++ |++|+
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~  113 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVG-TKRLK  113 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEET-TEECC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEEC-CEEEE
Confidence            455678999999999999999999999999999999999864     589999999999999999999999999 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |+|||
T Consensus       114 V~~ak  118 (118)
T 2khc_A          114 VQLKK  118 (118)
T ss_dssp             EEEC-
T ss_pred             EEecC
Confidence            99997

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.1e-19  Score=127.66  Aligned_cols=82  Identities=21%  Similarity=0.311  Sum_probs=76.3

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.+.++. .++|||||+|.+.++|.+|++.|||..+.|++|+|.++
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  104 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA  104 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45678999999999999999999999999999999998765 67899999999999999999999999999999999998


Q ss_pred             cCC
Q psy4057          86 KTD   88 (246)
Q Consensus        86 ~~~   88 (246)
                      ..+
T Consensus       105 ~~~  107 (109)
T 2err_A          105 TAR  107 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.81  E-value=1.3e-19  Score=125.07  Aligned_cols=82  Identities=23%  Similarity=0.346  Sum_probs=75.8

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeE--------EEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCC
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKT---LKMRGQAFVIFKEIASATNALRSMQGF   73 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~--------v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~   73 (246)
                      ....++.++|||+|||.++++++|+++|++||.|.+        |.+..+   ++++|||||+|.+.++|.+|++.|||.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            346678999999999999999999999999999999        888876   377899999999999999999999999


Q ss_pred             ccCCeeEEEEEcc
Q psy4057          74 PFYDKPMRIQYSK   86 (246)
Q Consensus        74 ~~~g~~l~v~~a~   86 (246)
                      .+.|++|+|.+|+
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999973

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.81  E-value=1.7e-19  Score=122.83  Aligned_cols=83  Identities=18%  Similarity=0.206  Sum_probs=76.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC-CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT-LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~-~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.+.++ ++++|||||+|.+.++|.+|++.|||..+.|++|+|.++
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            4578899999999999999999999999999999998874 378899999999999999999999999999999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ....
T Consensus        84 ~~~~   87 (92)
T 2dgv_A           84 RNAS   87 (92)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            7654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=3.7e-19  Score=121.86  Aligned_cols=77  Identities=19%  Similarity=0.371  Sum_probs=72.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      +++++|||+|||.++++++|+++|++||.|..++++.++     +|||||+|.+.++|..|++.|||..+. |++|+|.|
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~V~~   81 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELA-GRPMRVGH   81 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSS-SSCCEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeC-CcEEEEEE
Confidence            468999999999999999999999999999999999874     579999999999999999999999999 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |+.
T Consensus        82 a~~   84 (95)
T 2dnz_A           82 VTE   84 (95)
T ss_dssp             SSC
T ss_pred             ccc
Confidence            863

>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=99.80  E-value=4.8e-20  Score=129.13  Aligned_cols=81  Identities=11%  Similarity=0.252  Sum_probs=73.6

Q ss_pred             CCCCCcEEEecCCChh-hhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcC--CccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISST-DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG--FPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~-~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng--~~~~g~~l~v~   83 (246)
                      ..+|+++|||+|||.+ +++++|+++|++||.|.+|.+++   +||||||+|.+.++|..|++.||+  ..+.|++|+|.
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~---~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   97 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   97 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec---CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            4678999999999998 99999999999999999999975   689999999999999999998864  66999999999


Q ss_pred             EccCCcc
Q psy4057          84 YSKTDSD   90 (246)
Q Consensus        84 ~a~~~~~   90 (246)
                      ++.....
T Consensus        98 ~a~~~~~  104 (112)
T 1x4f_A           98 LSEKYKK  104 (112)
T ss_dssp             EECSCSS
T ss_pred             ECccccc
Confidence            9976544

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=2.7e-19  Score=125.26  Aligned_cols=84  Identities=19%  Similarity=0.342  Sum_probs=77.5

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC----CCCccEEEEEEcCHHHHHHHHHHh-cCCccCCeeEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT----LKMRGQAFVIFKEIASATNALRSM-QGFPFYDKPMR   81 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~----~~~kg~aFV~f~~~~~A~~Ai~~l-ng~~~~g~~l~   81 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.++++    ++++|||||+|.+.++|.+|++.| |+..+.|++|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            4567899999999999999999999999999999999876    377899999999999999999999 99999999999


Q ss_pred             EEEccCCcc
Q psy4057          82 IQYSKTDSD   90 (246)
Q Consensus        82 v~~a~~~~~   90 (246)
                      |.++..+..
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999976643

>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=2.1e-19  Score=123.42  Aligned_cols=76  Identities=20%  Similarity=0.432  Sum_probs=71.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      |+++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||..++ |+.|+|.||
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~l~V~~a   79 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLG-SRFLKCGYS   79 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEET-TEECEEEEC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeEC-CeEEEEEEc
Confidence            57899999999999999999999999999999999874     589999999999999999999999999 999999998


Q ss_pred             cC
Q psy4057         245 KK  246 (246)
Q Consensus       245 k~  246 (246)
                      +.
T Consensus        80 ~~   81 (96)
T 2x1f_A           80 SN   81 (96)
T ss_dssp             SC
T ss_pred             CC
Confidence            73

>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=2.9e-19  Score=126.82  Aligned_cols=81  Identities=23%  Similarity=0.463  Sum_probs=74.8

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       165 ~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                      ....++.++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|++.|||..|. |++|
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l   97 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIG-MKRL   97 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET-TEEC
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEEC-CEEE
Confidence            3455678999999999999999999999999999999999876     479999999999999999999999999 9999


Q ss_pred             EEEeecC
Q psy4057         240 KISFAKK  246 (246)
Q Consensus       240 ~v~~ak~  246 (246)
                      +|.||+.
T Consensus        98 ~V~~a~~  104 (115)
T 2cpz_A           98 KVQLKRS  104 (115)
T ss_dssp             EEECCCC
T ss_pred             EEEEcCC
Confidence            9999873

>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=99.80  E-value=1.1e-19  Score=128.19  Aligned_cols=75  Identities=21%  Similarity=0.248  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      .+++|||+|||.++++++|+++|++||.|.+|.+++.+ |||||+|.+.++|..|+..|||+.++ |++|+|.||+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~-g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~l~V~~a~~   83 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-ITAIVEFLEPLEARKAFRHLAYSKFH-HVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSS-SCEEEEESCHHHHHHHHHHHTTCBSS-SSBCEEEEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCC-CEEEEEeCCHHHHHHHHHHhCCCEEC-CeEEEEEECCC
Confidence            47899999999999999999999999999999998755 89999999999999999999999999 99999999974

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.2e-19  Score=123.81  Aligned_cols=79  Identities=27%  Similarity=0.418  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ..++.++|||+|||.++++++|+++|++||.|..++++.++     +|||||+|.+.++|..|++.|||..|. |++|+|
T Consensus         8 ~~~~~~~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            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD-GRQIRV   86 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTT-SCCCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC-CeEEEE
Confidence            45578999999999999999999999999999999999864     579999999999999999999999999 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      .||+.
T Consensus        87 ~~a~~   91 (102)
T 1x5s_A           87 DQAGK   91 (102)
T ss_dssp             EEEEC
T ss_pred             EECCC
Confidence            99974

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=5.6e-19  Score=122.82  Aligned_cols=79  Identities=24%  Similarity=0.405  Sum_probs=74.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ....+.++|||+|||.++++++|+++|++||.|.+|+++.+.   +|||||+|.+.++|.+|+..|||..|. |+.|+|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~   88 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVE-GRKIEVN   88 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEET-TEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEE
Confidence            345578999999999999999999999999999999999875   589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus        89 ~a~   91 (103)
T 2cq3_A           89 NAT   91 (103)
T ss_dssp             ECC
T ss_pred             Ecc
Confidence            986

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.80  E-value=2.3e-19  Score=125.22  Aligned_cols=83  Identities=19%  Similarity=0.352  Sum_probs=76.4

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCC---eeEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYD---KPMR   81 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g---~~l~   81 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.++++.  +++|||||+|.+.++|.+|++.|||..+.|   ++|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            34678999999999999999999999999999999998764  678999999999999999999999999988   9999


Q ss_pred             EEEccCCc
Q psy4057          82 IQYSKTDS   89 (246)
Q Consensus        82 v~~a~~~~   89 (246)
                      |.++....
T Consensus        91 V~~a~~~~   98 (105)
T 2dnh_A           91 VKFADTDK   98 (105)
T ss_dssp             EEESCSSC
T ss_pred             EEECccCc
Confidence            99997654

>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=1.3e-19  Score=125.81  Aligned_cols=83  Identities=28%  Similarity=0.367  Sum_probs=77.2

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.++++   ++++|||||+|.+.++|.+|++.|||..+.|++|+|.
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            4568899999999999999999999999999999999876   3689999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++....
T Consensus        88 ~a~~~~   93 (102)
T 2cqb_A           88 LAKPMR   93 (102)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            987654

>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=99.80  E-value=2.7e-19  Score=123.02  Aligned_cols=77  Identities=16%  Similarity=0.207  Sum_probs=71.0

Q ss_pred             CCCCCCcEEEEcCCCC-CCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         166 PEQPPNQILFLTNLPE-ETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~-~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ...+++++|||+|||. ++++++|+++|+.||.|.++++.   +|||||+|.+.++|..|+..|||..++ |+.|+|+||
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~l~V~~a   92 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIEXESQEMNF-GKKLILEVS   92 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC---SSEEEEEESSHHHHHHHHHHHTTSEET-TEECEEEEC
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCEEC-CEEEEEEec
Confidence            4566799999999998 99999999999999999999985   589999999999999999999999999 999999998


Q ss_pred             cC
Q psy4057         245 KK  246 (246)
Q Consensus       245 k~  246 (246)
                      +.
T Consensus        93 ~~   94 (97)
T 2xnq_A           93 SS   94 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            73

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.2e-19  Score=125.95  Aligned_cols=79  Identities=20%  Similarity=0.376  Sum_probs=73.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ...+.++|||+|||.++++++|+++|++||.|.+|.++++.  +++|||||+|.+.++|.+|+. ++|..+.|++|.|.+
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            45667999999999999999999999999999999998764  789999999999999999999 999999999999998


Q ss_pred             cc
Q psy4057          85 SK   86 (246)
Q Consensus        85 a~   86 (246)
                      +.
T Consensus        86 ~~   87 (103)
T 1s79_A           86 KD   87 (103)
T ss_dssp             HH
T ss_pred             ch
Confidence            64

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.80  E-value=1.9e-19  Score=126.28  Aligned_cols=77  Identities=29%  Similarity=0.499  Sum_probs=71.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       165 ~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .....++++|||+|||.++|+++|+++|++||.|..+++.   +|||||+|.+.++|..|+..|||..++ |+.|+|.||
T Consensus        25 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~-g~~l~V~~a  100 (108)
T 2jvo_A           25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFA-NQPLEVVYS  100 (108)
T ss_dssp             ---CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEET-TEECEEESC
T ss_pred             cCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEEC-CeEEEEEEe
Confidence            3456679999999999999999999999999999999998   589999999999999999999999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus       101 ~  101 (108)
T 2jvo_A          101 K  101 (108)
T ss_dssp             S
T ss_pred             c
Confidence            6

>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=5.6e-19  Score=121.92  Aligned_cols=77  Identities=21%  Similarity=0.355  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...+.++|||+|||.++++++|+++|++||.|..++++.++     +|||||+|.+.++|.+|++ |||..+. |++|+|
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~-g~~l~V   83 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIM-GKKVEV   83 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSS-SCBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEEC-CeEEEE
Confidence            45578999999999999999999999999999999999864     5899999999999999999 9999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .||+
T Consensus        84 ~~a~   87 (99)
T 2dgs_A           84 KRAE   87 (99)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9986

>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=99.80  E-value=1.9e-19  Score=123.56  Aligned_cols=78  Identities=24%  Similarity=0.270  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHH----HHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLS----MLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~----~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ....++|||+|||.++++++|+    ++|++||.|.+++++.++  +|||||+|.+.++|.+|++.|||..++ |++|+|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~-gr~l~V   84 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIG-SKKILV   84 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEET-TEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEEC-CeEEEE
Confidence            3457899999999999999999    999999999999999775  689999999999999999999999999 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      +||+.
T Consensus        85 ~~a~~   89 (96)
T 2dgx_A           85 SLATG   89 (96)
T ss_dssp             EECCC
T ss_pred             EEcCC
Confidence            99973

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.7e-19  Score=126.76  Aligned_cols=80  Identities=24%  Similarity=0.400  Sum_probs=74.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ......++|||+|||.++++++|+++|++||.|.+++++.+.   +|||||+|.+.++|.+|+..|||..++ |++|+|+
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~-g~~l~V~  102 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVE-GRKIEVN  102 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEET-TEECEEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEEC-CEEEEEE
Confidence            345578999999999999999999999999999999999864   689999999999999999999999999 9999999


Q ss_pred             eecC
Q psy4057         243 FAKK  246 (246)
Q Consensus       243 ~ak~  246 (246)
                      ||+.
T Consensus       103 ~a~~  106 (109)
T 2err_A          103 NATA  106 (109)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9873

>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=99.80  E-value=2.5e-19  Score=123.23  Aligned_cols=81  Identities=23%  Similarity=0.433  Sum_probs=75.2

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccC--CeeEEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY--DKPMRIQ   83 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~--g~~l~v~   83 (246)
                      ...+++++|||+|||.++++++|+++|++||.|.+|.+.++   +|||||+|.+.++|.+|++.|||..+.  |++|+|.
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS---SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC---CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            45678899999999999999999999999999999988764   899999999999999999999999999  9999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++..+.
T Consensus        89 ~a~~~~   94 (97)
T 1why_A           89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            987653

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=1.3e-19  Score=124.95  Aligned_cols=82  Identities=20%  Similarity=0.323  Sum_probs=75.6

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC------CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL------KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR   81 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (246)
                      .+++++|||+|||.++++++|+++|++||.|..|.+.++.      +++|||||+|.+.++|.+|++.|||..+.|++|+
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            3678999999999999999999999999999999998643      5689999999999999999999999999999999


Q ss_pred             EEEccCCc
Q psy4057          82 IQYSKTDS   89 (246)
Q Consensus        82 v~~a~~~~   89 (246)
                      |.++....
T Consensus        82 V~~a~~~~   89 (98)
T 2cpf_A           82 VRISERAT   89 (98)
T ss_dssp             EECSSCSS
T ss_pred             EEEccCCC
Confidence            99987654

>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=99.80  E-value=5.8e-19  Score=121.39  Aligned_cols=78  Identities=23%  Similarity=0.428  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCC-CCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITP-THAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~-g~~l~v~~ak  245 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.++++..+ +|||||+|.+.++|..|++.|||..+.+ |++|+|.||+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~   91 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECC
Confidence            4567899999999999999999999999999999999988 5899999999999999999999999986 7999999987

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.3e-19  Score=126.03  Aligned_cols=83  Identities=23%  Similarity=0.388  Sum_probs=77.0

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45678999999999999999999999999999999998763   778999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++..+.
T Consensus        91 ~a~~~~   96 (103)
T 2cq0_A           91 WAKPST   96 (103)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            987654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=4.3e-19  Score=120.32  Aligned_cols=76  Identities=25%  Similarity=0.427  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      ..++.++|||+|||.++++++|+++|++||.|.++++.   +|||||+|.+.++|..|+..|||..+. |++|+|.||+.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v~~a~~   79 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLH-GVNINVEASKN   79 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCS-SCBCEEECSSC
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccC-CcEEEEEECCC
Confidence            34578999999999999999999999999999999998   589999999999999999999999999 99999999863

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.80  E-value=2.4e-19  Score=122.82  Aligned_cols=78  Identities=22%  Similarity=0.348  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..++.++|||+|||.++++++|+++|++||.|.+++++.++    +|||||+|.+.++|.+|++.|||..++ |++|+|.
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 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLY-GRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEET-TEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEEC-CCEEEEE
Confidence            44578999999999999999999999999999999999975    589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus        91 ~a~   93 (95)
T 2ywk_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             EcC
Confidence            987

>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=99.80  E-value=3.5e-19  Score=122.93  Aligned_cols=79  Identities=20%  Similarity=0.242  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...++++|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|..|+..|||..+. |++|+|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~V   82 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQ-GRMLHV   82 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESS-SCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEEC-CcEEEE
Confidence            34578999999999999999999999999999999998865     589999999999999999999999999 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      .||+.
T Consensus        83 ~~a~~   87 (99)
T 1whw_A           83 LPSTI   87 (99)
T ss_dssp             EECCC
T ss_pred             EEcCC
Confidence            99873

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.80  E-value=4.2e-19  Score=125.98  Aligned_cols=83  Identities=25%  Similarity=0.372  Sum_probs=77.0

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|++|++.|||..+.|++|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45678999999999999999999999999999999998763   678999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++....
T Consensus        91 ~a~~~~   96 (115)
T 2dgo_A           91 WATRKP   96 (115)
T ss_dssp             ESSCCC
T ss_pred             EccCCC
Confidence            997654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.80  E-value=4.7e-19  Score=125.70  Aligned_cols=80  Identities=18%  Similarity=0.311  Sum_probs=74.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ....+.++|||+|||.++++++|+++|+.||.|..|+++.+.     +|||||+|.+.++|.+|++.|||..|. |+.|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~   88 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG-GRQIR   88 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEET-TEECE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC-CEEEE
Confidence            345579999999999999999999999999999999999875     589999999999999999999999999 99999


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |.||+.
T Consensus        89 V~~a~~   94 (115)
T 2dgo_A           89 TNWATR   94 (115)
T ss_dssp             EEESSC
T ss_pred             EEEccC
Confidence            999873

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=6.4e-19  Score=123.81  Aligned_cols=79  Identities=20%  Similarity=0.445  Sum_probs=73.5

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ....+.++|||+|||.++|+++|+++|++||.|..+++..+.  +|||||+|.+.++|..|++.|||..|. |+.|+|.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~V~~   95 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYD-GYRLRVEF   95 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEET-TEECEEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEEC-CeEEEEEE
Confidence            345578999999999999999999999999999999998765  589999999999999999999999999 99999999


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      |+
T Consensus        96 a~   97 (109)
T 1x4a_A           96 PR   97 (109)
T ss_dssp             CC
T ss_pred             cc
Confidence            86

>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=3.9e-19  Score=123.63  Aligned_cols=78  Identities=21%  Similarity=0.325  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...+.++|||+|||.++++++|+++|++||.|..+.++.++     +|||||+|.+.++|.+|+..|||..+. |+.|+|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~V   87 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELD-GRELRV   87 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBT-TBCCEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEEC-CcEEEE
Confidence            45578999999999999999999999999999999999864     589999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .||+
T Consensus        88 ~~a~   91 (103)
T 2dnm_A           88 QVAR   91 (103)
T ss_dssp             EECS
T ss_pred             EECC
Confidence            9987

>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=1.6e-19  Score=128.20  Aligned_cols=83  Identities=19%  Similarity=0.309  Sum_probs=76.5

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.
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            44677999999999999999999999999999999998754   678999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      +++.+.
T Consensus       101 ~a~~~~  106 (115)
T 2cpz_A          101 LKRSKN  106 (115)
T ss_dssp             CCCCSC
T ss_pred             EcCCCC
Confidence            987654

>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=99.80  E-value=2.9e-19  Score=125.15  Aligned_cols=81  Identities=22%  Similarity=0.336  Sum_probs=75.6

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ....++++|||+|||.++++++|+++|++||.|.+|.++.+.  +++|||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus        24 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            456789999999999999999999999999999999998764  678999999999999999999999999999999999


Q ss_pred             Ecc
Q psy4057          84 YSK   86 (246)
Q Consensus        84 ~a~   86 (246)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            974

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.4e-19  Score=123.92  Aligned_cols=79  Identities=27%  Similarity=0.434  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...++++|||+|||.++++++|+++|++||.|..|+++.++     +|||||+|.+.++|..|+..|||..|. |+.|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v   89 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYD-HLILNV   89 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEET-TEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeC-CcEEEE
Confidence            45579999999999999999999999999999999999875     579999999999999999999999999 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      .||+.
T Consensus        90 ~~a~~   94 (103)
T 2cq0_A           90 EWAKP   94 (103)
T ss_dssp             EESSC
T ss_pred             EECCC
Confidence            99873

>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=99.80  E-value=2.8e-19  Score=125.84  Aligned_cols=82  Identities=16%  Similarity=0.254  Sum_probs=75.8

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.++.+.   +++|||||+|.+.++|.+|+..|||..+.|++|.|.
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            44677899999999999999999999999999999998753   778999999999999999999999999999999999


Q ss_pred             EccCC
Q psy4057          84 YSKTD   88 (246)
Q Consensus        84 ~a~~~   88 (246)
                      ++..+
T Consensus       102 ~a~~~  106 (110)
T 1oo0_B          102 WCFVK  106 (110)
T ss_dssp             ESEES
T ss_pred             EcccC
Confidence            98654

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.80  E-value=3.8e-19  Score=119.97  Aligned_cols=80  Identities=21%  Similarity=0.242  Sum_probs=74.1

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC----CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL----KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~----~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..+++|||+|||.++++++|+++|++||.|.+|.+..+.    +++|||||+|.+.++|.+|++.|||..+.|++|+|.+
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            356899999999999999999999999999999998765    2789999999999999999999999999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      +.+.
T Consensus        82 a~~~   85 (88)
T 4a8x_A           82 VLAP   85 (88)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8654

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=4.2e-19  Score=125.15  Aligned_cols=84  Identities=17%  Similarity=0.329  Sum_probs=77.7

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhc------CCccC
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQ------GFPFY   76 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~ln------g~~~~   76 (246)
                      ....++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.||      +..+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            456778999999999999999999999999999999999764   689999999999999999999999      99999


Q ss_pred             CeeEEEEEccCCc
Q psy4057          77 DKPMRIQYSKTDS   89 (246)
Q Consensus        77 g~~l~v~~a~~~~   89 (246)
                      |++|+|.++..+.
T Consensus        90 g~~l~v~~a~~~~  102 (111)
T 1x4h_A           90 GRQLKVDLAVTRD  102 (111)
T ss_dssp             SCEEEEECCCCCC
T ss_pred             CEEEEEEECCCCc
Confidence            9999999987654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=2.9e-19  Score=124.31  Aligned_cols=83  Identities=23%  Similarity=0.310  Sum_probs=76.6

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC-CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT-LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~-~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.++.+ ++++|||||+|.+.++|.+|++.|||..+.|++|.|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            3457899999999999999999999999999999999876 467899999999999999999999999999999999999


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ..+.
T Consensus        91 ~~~~   94 (103)
T 2d9p_A           91 QRKE   94 (103)
T ss_dssp             SSCC
T ss_pred             cccc
Confidence            7654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=6.3e-19  Score=122.58  Aligned_cols=79  Identities=16%  Similarity=0.309  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC---CccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN---RHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~---~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ...+.++|||+|||.++|+++|+++|++||.|..++++.+   .+|||||+|.+.++|..|+..|||..+. |++|+|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~V~~   89 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVA-TKPLYVAL   89 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSS-SSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeC-CcEEEEEE
Confidence            4457999999999999999999999999999999999986   2589999999999999999999999999 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |+.
T Consensus        90 a~~   92 (103)
T 2d9p_A           90 AQR   92 (103)
T ss_dssp             CSS
T ss_pred             ecc
Confidence            863

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.79  E-value=2.9e-19  Score=128.06  Aligned_cols=74  Identities=20%  Similarity=0.359  Sum_probs=68.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccE-EEEEeCCHHHHHHHHHHhCCCccCCC--CceEEEeec
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI-AFVEFENEMQSAAAKLALHGFKITPT--HAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~-afV~f~~~~~A~~Al~~l~g~~i~~g--~~l~v~~ak  245 (246)
                      -..|||+||++.+|+++|+++|++||.|.+|++..+.+|+ |||+|.+.++|..|++.|||+.|+ |  ++|+|+|||
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~-g~~~~LrI~~ak  104 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIY-NACCTLRIDFSK  104 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEE-TTEEEEEEEECS
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeec-CCCcEEEEEecC
Confidence            3455699999999999999999999999999998877787 999999999999999999999998 5  999999997

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=5.6e-19  Score=119.78  Aligned_cols=78  Identities=14%  Similarity=0.363  Sum_probs=73.3

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ..++.++|||+|||.++++++|+++|++||.|.+|.+.     +|||||+|.+.++|.+|++.|||..+.|++|+|.++.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   78 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASK   78 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-----TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSS
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECC
Confidence            45788999999999999999999999999999999986     6999999999999999999999999999999999987


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      ...
T Consensus        79 ~~~   81 (90)
T 2dnq_A           79 NKS   81 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.79  E-value=6.4e-19  Score=119.93  Aligned_cols=78  Identities=18%  Similarity=0.256  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .++.++|||+|||.++++++|+++|++||.|..+++..+.   +|||||+|.+.++|..|++.|||..+. |+.|+|.||
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~-g~~l~v~~a   83 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLS-GREIDVRID   83 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBT-TBCCCCEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEEC-CcEEEEEEc
Confidence            4578999999999999999999999999999999999853   589999999999999999999999999 999999998


Q ss_pred             cC
Q psy4057         245 KK  246 (246)
Q Consensus       245 k~  246 (246)
                      +.
T Consensus        84 ~~   85 (92)
T 2dgv_A           84 RN   85 (92)
T ss_dssp             SC
T ss_pred             CC
Confidence            73

>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=99.79  E-value=6.8e-19  Score=121.00  Aligned_cols=78  Identities=19%  Similarity=0.333  Sum_probs=72.1

Q ss_pred             cCCCCCcEEEecCCCh-hhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           6 AHICVTNFVYVTHISS-TDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~-~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ...+++++|||+|||. ++++++|+++|++||.|.+|.+     ++|||||+|.+.++|.+|++.|||..+.|++|+|.+
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   91 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-----KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV   91 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE-----eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4567899999999998 9999999999999999999988     489999999999999999999999999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      ++..
T Consensus        92 a~~~   95 (97)
T 2xnq_A           92 SSSN   95 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8654

>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=2e-19  Score=130.16  Aligned_cols=83  Identities=25%  Similarity=0.391  Sum_probs=77.3

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ...+++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            356788999999999999999999999999999999998763   78999999999999999999999999999999999


Q ss_pred             EEccCC
Q psy4057          83 QYSKTD   88 (246)
Q Consensus        83 ~~a~~~   88 (246)
                      .++..+
T Consensus       121 ~~a~~~  126 (129)
T 2kxn_B          121 DFSITK  126 (129)
T ss_dssp             SCCSSS
T ss_pred             EEecCC
Confidence            998654

>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=99.79  E-value=1.5e-19  Score=127.55  Aligned_cols=83  Identities=17%  Similarity=0.306  Sum_probs=75.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHH---HHhhccCCeeEEEEccCC------CCccEEEEEEcCHHHHHHHHHHhcCCccCC
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLY---AIFSQFGQIMDIVALKTL------KMRGQAFVIFKEIASATNALRSMQGFPFYD   77 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~---~~F~~fG~i~~v~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (246)
                      ...+.++|||+|||.++++++|+   ++|++||.|.+|.+.++.      +++|||||+|.+.++|++|++.|||..+.|
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            34567899999999999999999   999999999999998764      456999999999999999999999999999


Q ss_pred             eeEEEEEccCCc
Q psy4057          78 KPMRIQYSKTDS   89 (246)
Q Consensus        78 ~~l~v~~a~~~~   89 (246)
                      ++|+|.++..+.
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            999999997664

>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=2.6e-19  Score=123.63  Aligned_cols=82  Identities=15%  Similarity=0.325  Sum_probs=76.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCee-EEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCee---
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIM-DIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKP---   79 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~-~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~---   79 (246)
                      ...++++|||+|||.++++++|+++|++||.|. +|.++++.   +++|||||+|.+.++|.+|++.|||..+.|+.   
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            456789999999999999999999999999999 99998764   77899999999999999999999999999999   


Q ss_pred             -EEEEEccCC
Q psy4057          80 -MRIQYSKTD   88 (246)
Q Consensus        80 -l~v~~a~~~   88 (246)
                       |+|.++...
T Consensus        85 ~l~v~~a~~~   94 (99)
T 2div_A           85 RFKLNYATYS   94 (99)
T ss_dssp             ECCEEETTCC
T ss_pred             eEEEeecCCC
Confidence             999998654

>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=99.79  E-value=4.9e-19  Score=123.74  Aligned_cols=83  Identities=22%  Similarity=0.353  Sum_probs=76.5

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCcc---CCeeE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPF---YDKPM   80 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~---~g~~l   80 (246)
                      ...+.++|||+|||.++++++|+++|++||.|.+|.++++   ++++|||||+|.+.++|.+|++.|||..+   .|++|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            4567899999999999999999999999999999999886   46899999999999999999999999887   89999


Q ss_pred             EEEEccCCc
Q psy4057          81 RIQYSKTDS   89 (246)
Q Consensus        81 ~v~~a~~~~   89 (246)
                      .|.++....
T Consensus        89 ~v~~a~~~~   97 (106)
T 2dgp_A           89 QVKPADSES   97 (106)
T ss_dssp             EEEECCCCS
T ss_pred             EEEECCccc
Confidence            999987654

>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=99.79  E-value=4.2e-19  Score=123.68  Aligned_cols=81  Identities=14%  Similarity=0.253  Sum_probs=74.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC----CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT----LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~----~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ...+.++|||+|||.++++++|+++|++|| |.+|.++++    ++++|||||+|.+.++|.+|+ .||+..+.|++|+|
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            446789999999999999999999999999 999999976    467899999999999999999 89999999999999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .++..+.
T Consensus        89 ~~a~~~~   95 (104)
T 1wi8_A           89 DVADQAQ   95 (104)
T ss_dssp             EECCCCC
T ss_pred             EEccCCC
Confidence            9987654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.79  E-value=2.6e-19  Score=127.67  Aligned_cols=80  Identities=21%  Similarity=0.303  Sum_probs=73.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567999999999999999999999999999999998763   779999999999999999999999999999999999


Q ss_pred             Ecc
Q psy4057          84 YSK   86 (246)
Q Consensus        84 ~a~   86 (246)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            874

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=5.4e-19  Score=125.18  Aligned_cols=83  Identities=23%  Similarity=0.329  Sum_probs=76.6

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...+++++|||+|||.++++++|+++|++||.|.+|.++++.  +++|||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            456788999999999999999999999999999999998764  678999999999999999999999999999999999


Q ss_pred             EccCC
Q psy4057          84 YSKTD   88 (246)
Q Consensus        84 ~a~~~   88 (246)
                      ++...
T Consensus        90 ~a~~~   94 (114)
T 2do0_A           90 MDERA   94 (114)
T ss_dssp             ECSCC
T ss_pred             EcccC
Confidence            98644

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.8e-19  Score=123.46  Aligned_cols=78  Identities=23%  Similarity=0.399  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ..++.++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||..|. |++|+|
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~V   86 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF-GRTIRV   86 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEET-TEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC-CcEEEE
Confidence            44578999999999999999999999999999999998873     589999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .||+
T Consensus        87 ~~a~   90 (102)
T 2cqb_A           87 NLAK   90 (102)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            9986

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=9.5e-19  Score=122.27  Aligned_cols=77  Identities=23%  Similarity=0.371  Sum_probs=72.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..++++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|..|+..|||..++ |+.|+|.
T Consensus        20 ~~~~~~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           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM-GQPISVD   98 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSS-SSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEEC-CcEEEEE
Confidence            4468999999999999999999999999999999999875     589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus        99 ~a~  101 (106)
T 1p27_B           99 WCF  101 (106)
T ss_dssp             ESE
T ss_pred             eec
Confidence            986

>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=6.2e-20  Score=124.54  Aligned_cols=78  Identities=14%  Similarity=0.146  Sum_probs=68.2

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccC--CeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFG--QIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG--~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      .+|||+|||.++++++|+++|++||  .|.+|.++.+.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.++.
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  99999998753   789999999999999999999999999999999999987


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      ...
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            653

>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=99.79  E-value=5.3e-19  Score=122.04  Aligned_cols=80  Identities=14%  Similarity=0.325  Sum_probs=74.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.+.+   ++|||||+|.+.++|.+|++.|||..+.|++|+|.++.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~---~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   87 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET---TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec---CCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcC
Confidence            457789999999999999999999999999999999875   58999999999999999999999999999999999997


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      ...
T Consensus        88 ~~~   90 (99)
T 2cpj_A           88 HSA   90 (99)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>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=99.79  E-value=4.1e-19  Score=124.79  Aligned_cols=78  Identities=22%  Similarity=0.448  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      ..+..++|||+|||.++++++|+++|++||.|.+|+++.+ +|||||+|.+.++|..|+..|||..++ |++|+|.||+.
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~a~~   98 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIE-GHVVKCYWGKE   98 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEET-TEECEEECCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHcCCCEEC-CcEEEEEecCC
Confidence            3456899999999999999999999999999999999998 489999999999999999999999999 99999999873

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.79  E-value=2.9e-19  Score=122.68  Aligned_cols=80  Identities=20%  Similarity=0.351  Sum_probs=71.3

Q ss_pred             ccCCCCCcEEEecCCCh-hhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           5 LAHICVTNFVYVTHISS-TDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~-~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      +.+.+++++|||+|||. ++++++|+++|++||.|.+|.+     ++|||||+|.+.++|..|++.|||..+.|++|+|.
T Consensus         4 ~~~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i-----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            4 MHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-----KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             -----CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE-----ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             cccCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE-----eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45678999999999998 9999999999999999999988     37999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++....
T Consensus        79 ~a~~~~   84 (96)
T 2kvi_A           79 VSSSNA   84 (96)
T ss_dssp             EEECCC
T ss_pred             EcCcCC
Confidence            987653

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.79  E-value=5.8e-19  Score=121.16  Aligned_cols=75  Identities=19%  Similarity=0.302  Sum_probs=69.3

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPE-ETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~-~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..+++++|||+|||. .+++++|+++|++||.|.++++.   +|||||+|.+.++|..|+..|||..+. |++|+|.||+
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~V~~a~   81 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIECESQEMNF-GKKLILEVSS   81 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE---TTEEEEEESCHHHHHHHHHHHTCSSCB-TTTBCEEEEE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCeeC-CcEEEEEEcC
Confidence            456899999999998 99999999999999999999996   589999999999999999999999999 9999999986

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.79  E-value=2.2e-19  Score=124.21  Aligned_cols=76  Identities=16%  Similarity=0.230  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCC------CCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCC-
Q psy4057         169 PPNQILFLTNLPE------ETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPT-  236 (246)
Q Consensus       169 ~~~~~l~v~nL~~------~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g-  236 (246)
                      ..+++|||+|||.      ++++++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|++.|||+.++ | 
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~-g~   82 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD-LK   82 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSS-SS
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccC-CC
Confidence            3578999999999      99999999999999999999999865     589999999999999999999999999 7 


Q ss_pred             CceEEEeec
Q psy4057         237 HAMKISFAK  245 (246)
Q Consensus       237 ~~l~v~~ak  245 (246)
                      ++|+|.+|+
T Consensus        83 r~l~V~~a~   91 (100)
T 3ns6_A           83 HRLFLYTMK   91 (100)
T ss_dssp             CBCEEEESH
T ss_pred             eEEEEEECc
Confidence            999999985

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=4.1e-19  Score=122.39  Aligned_cols=77  Identities=22%  Similarity=0.389  Sum_probs=71.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--------HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      +++++|||+|||.++++++|+++|++||.|..++++.++        +|||||+|.+.++|..|+..|||..|+ |++|+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~   81 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD-GHKLE   81 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEET-TEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeC-CeEEE
Confidence            468999999999999999999999999999999998743        479999999999999999999999999 99999


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |.||+.
T Consensus        82 V~~a~~   87 (98)
T 2cpf_A           82 VRISER   87 (98)
T ss_dssp             EECSSC
T ss_pred             EEEccC
Confidence            999873

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.79  E-value=9.1e-19  Score=124.37  Aligned_cols=78  Identities=32%  Similarity=0.468  Sum_probs=73.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ..+.++|||+|||.++++++|+++|++||.|..|.+..+.    +|||||+|.+.++|.+|++.|||..|. |+.|+|.|
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 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLH-GKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCS-SSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEE
Confidence            3468899999999999999999999999999999999865    589999999999999999999999999 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |+.
T Consensus        83 a~~   85 (116)
T 2fy1_A           83 AKK   85 (116)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            974

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.79  E-value=3.2e-19  Score=125.22  Aligned_cols=81  Identities=7%  Similarity=0.029  Sum_probs=73.0

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccC-CeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFG-QIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG-~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ..+...+|||+|||+++++++|+++|++|| .|..+.+.. .+++|||||+|.+.++|++|++.|||..+.|++|+|.++
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~-~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT-RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS-CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc-CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            455678999999999999999999999999 899998854 358999999999999999999999999999999999998


Q ss_pred             cCC
Q psy4057          86 KTD   88 (246)
Q Consensus        86 ~~~   88 (246)
                      ...
T Consensus       103 ~~~  105 (111)
T 2jvr_A          103 DNP  105 (111)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            644

>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=99.79  E-value=7e-19  Score=123.62  Aligned_cols=81  Identities=28%  Similarity=0.376  Sum_probs=75.4

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ..++.++|||+|||.++++++|+++|++||.|.+|.+.++   +|||||+|.+.++|.+|++.|||..+.|++|+|.+++
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   97 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   97 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC---CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecC
Confidence            4567899999999999999999999999999999999875   8999999999999999999999999999999999997


Q ss_pred             CCcc
Q psy4057          87 TDSD   90 (246)
Q Consensus        87 ~~~~   90 (246)
                      ....
T Consensus        98 ~~~~  101 (109)
T 1x4g_A           98 ESPD  101 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6643

>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=99.79  E-value=6.1e-19  Score=118.98  Aligned_cols=75  Identities=17%  Similarity=0.271  Sum_probs=70.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR------HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      .+++|||+|||.++|+++|+++|++||.|.+++++.+.      +|||||+|.+.++|..|+..|||..++ |+.|+|++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~   81 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQID-GQEITATA   81 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEET-TEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeEC-CeEEEEEE
Confidence            57899999999999999999999999999999998754      589999999999999999999999999 99999999


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      |+
T Consensus        82 a~   83 (88)
T 4a8x_A           82 VL   83 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            86

>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=5.6e-19  Score=121.91  Aligned_cols=78  Identities=19%  Similarity=0.312  Sum_probs=72.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCce-EEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCc--
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFK-EVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHA--  238 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~-~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~--  238 (246)
                      ...++++|||+|||.++++++|+++|++||.|. +++++.++     +|||||+|.+.++|..|++.|||..+. |+.  
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~~~   83 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLP-GATPA   83 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEES-SCSSC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccC-CCCcc
Confidence            345789999999999999999999999999999 99999875     489999999999999999999999999 888  


Q ss_pred             --eEEEeec
Q psy4057         239 --MKISFAK  245 (246)
Q Consensus       239 --l~v~~ak  245 (246)
                        |+|.||+
T Consensus        84 ~~l~v~~a~   92 (99)
T 2div_A           84 KRFKLNYAT   92 (99)
T ss_dssp             EECCEEETT
T ss_pred             eeEEEeecC
Confidence              9999986

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.79  E-value=4.3e-19  Score=123.84  Aligned_cols=78  Identities=22%  Similarity=0.388  Sum_probs=72.2

Q ss_pred             CcEEEecCCChhh------hHHHHHHHhhccCCeeEEEEcc-CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCe-eEEE
Q psy4057          11 TNFVYVTHISSTD------LKKSLYAIFSQFGQIMDIVALK-TLKMRGQAFVIFKEIASATNALRSMQGFPFYDK-PMRI   82 (246)
Q Consensus        11 ~~~l~V~nl~~~~------~e~~l~~~F~~fG~i~~v~~~~-~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~-~l~v   82 (246)
                      +++|||+|||..+      ++++|+++|++||.|.+|.+.+ +++++|||||+|.+.++|.+|++.|||..+.|+ +|+|
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V   94 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   94 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEE
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEE
Confidence            7899999999999      8999999999999999999884 347899999999999999999999999999998 9999


Q ss_pred             EEccCC
Q psy4057          83 QYSKTD   88 (246)
Q Consensus        83 ~~a~~~   88 (246)
                      .++...
T Consensus        95 ~~a~~~  100 (105)
T 2nlw_A           95 NLFTDF  100 (105)
T ss_dssp             ECSCCC
T ss_pred             EEcchH
Confidence            998643

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=1e-18  Score=118.94  Aligned_cols=75  Identities=17%  Similarity=0.273  Sum_probs=70.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ...+.++|||+|||.++++++|+++|++||.|.+++++++   ||||+|.+.++|.+|+..|||..+. |+.|+|+||+
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~---~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~V~~a~   80 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD---YAFVHMERAEDAVEAIRGLDNTEFQ-GKRMHVQLST   80 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS---EEEEEESCHHHHHHHHHHHTTEEET-TEEEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC---EEEEEECCHHHHHHHHHHhCCCeeC-CcEEEEEEcc
Confidence            4557899999999999999999999999999999999854   9999999999999999999999999 9999999986

>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=99.79  E-value=1e-18  Score=122.18  Aligned_cols=78  Identities=23%  Similarity=0.366  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCcc---CCCCc
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKI---TPTHA  238 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i---~~g~~  238 (246)
                      ..++.++|||+|||.++++++|+++|++||.|.+|+++.++     +|||||+|.+.++|..|++.|||..+   . |++
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~-g~~   87 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGM-NRP   87 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTC-SSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCC-Cce
Confidence            45578999999999999999999999999999999999864     58999999999999999999999987   6 899


Q ss_pred             eEEEeec
Q psy4057         239 MKISFAK  245 (246)
Q Consensus       239 l~v~~ak  245 (246)
                      |+|.||+
T Consensus        88 l~v~~a~   94 (106)
T 2dgp_A           88 IQVKPAD   94 (106)
T ss_dssp             CEEEECC
T ss_pred             EEEEECC
Confidence            9999986

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=7.8e-19  Score=117.17  Aligned_cols=74  Identities=18%  Similarity=0.218  Sum_probs=65.7

Q ss_pred             CCCCCcE-EEEcCCCCCCCHHH----HHHHHccC-CCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         167 EQPPNQI-LFLTNLPEETSEMM----LSMLFNQF-PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       167 ~~~~~~~-l~v~nL~~~~t~e~----l~~~f~~~-G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ..+|+.+ |||+|||.++++++    |+++|++| |.|.+|-    . |+|||.|.+.++|.+|++.|||+.++ |++|+
T Consensus         4 ~~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt----g-G~AfV~F~~~esA~~A~~~l~G~~l~-gr~i~   77 (96)
T 2diu_A            4 GSSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT----G-CSAILRFINQDSAERAQKRMENEDVF-GNRII   77 (96)
T ss_dssp             SCCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC----T-TCEEEEESSHHHHHHHHHHHTTCCSS-SSCCE
T ss_pred             CCCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe----c-CEEEEEECCHHHHHHHHHHhcCCccC-CceEE
Confidence            3456777 88999999999988    55899999 5999881    2 89999999999999999999999999 99999


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |+|||.
T Consensus        78 v~~A~~   83 (96)
T 2diu_A           78 VSFTPK   83 (96)
T ss_dssp             EESSCC
T ss_pred             EEecCC
Confidence            999984

>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=1.7e-18  Score=122.62  Aligned_cols=78  Identities=15%  Similarity=0.236  Sum_probs=73.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+++++.++    +|||||+|.+.++|..|++.|||..|. |+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLF-DRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC-CCEEEEE
Confidence            45578999999999999999999999999999999999875    579999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus        90 ~a~   92 (114)
T 2do0_A           90 MDE   92 (114)
T ss_dssp             ECS
T ss_pred             Ecc
Confidence            986

>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=99.78  E-value=1.1e-18  Score=122.31  Aligned_cols=74  Identities=14%  Similarity=0.109  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCC-----CceEEEe
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPT-----HAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g-----~~l~v~~  243 (246)
                      ...++|||+|||.++|+++|+++|++||.|..++++.+  |||||+|.+.++|..|++.|||..|. |     +.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~-g~~~~~~~i~V~~   89 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFR-SHEGETAYIRVKV   89 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEE-CTTSCEEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCcc-CCcCcceEEEEEe
Confidence            45899999999999999999999999999999999998  89999999999999999999999999 8     9999999


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      |+
T Consensus        90 a~   91 (108)
T 1x4c_A           90 DG   91 (108)
T ss_dssp             SS
T ss_pred             CC
Confidence            86

>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=99.78  E-value=5.9e-19  Score=119.31  Aligned_cols=78  Identities=18%  Similarity=0.303  Sum_probs=72.7

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      .+++|||+|||.++++++|+++|++||.|.++.+.++.   +++|||||+|.+.++|.+|+ .|||..+.|++|+|.+++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            46899999999999999999999999999999998753   77899999999999999999 899999999999999986


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      ..
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=6.3e-19  Score=118.14  Aligned_cols=78  Identities=19%  Similarity=0.279  Sum_probs=72.7

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHh-cCCccCCeeEEEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM-QGFPFYDKPMRIQY   84 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l-ng~~~~g~~l~v~~   84 (246)
                      ...+++++|||+|||.++++++|+++|++||.|.+|.+.+   ++|||||+|.+.++|.+|++.| +|..+.|++|+|.+
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~---~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ---RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG---GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC---CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            3456789999999999999999999999999999999987   5899999999999999999999 99999999999999


Q ss_pred             cc
Q psy4057          85 SK   86 (246)
Q Consensus        85 a~   86 (246)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.78  E-value=1.1e-18  Score=123.70  Aligned_cols=77  Identities=19%  Similarity=0.412  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .+++++|||+|||.++|+++|+++|+.||.|.+++++.+.  +|||||+|.+.++|..|+..|||..++ |+.|+|.||+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v~~a~   83 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVS-NRYLVVLYYN   83 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSS-SCBCEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEEC-CeEEEEEEec
Confidence            3468999999999999999999999999999999998765  589999999999999999999999999 9999999986

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=3.7e-19  Score=122.08  Aligned_cols=77  Identities=25%  Similarity=0.352  Sum_probs=72.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEE-EEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEV-RLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v-~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      +++++|||+|||.++++++|+++|++||.|..+ +++.++     +|||||+|.+.++|..|+..|||..+. |++|+|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v~   81 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLC-NRPITVS   81 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEET-TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEEC-CEEEEEE
Confidence            468999999999999999999999999999999 998873     589999999999999999999999999 9999999


Q ss_pred             eecC
Q psy4057         243 FAKK  246 (246)
Q Consensus       243 ~ak~  246 (246)
                      ||+.
T Consensus        82 ~a~~   85 (96)
T 1x5t_A           82 YAFK   85 (96)
T ss_dssp             ESCC
T ss_pred             Eecc
Confidence            9863

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.78  E-value=4.1e-19  Score=123.06  Aligned_cols=77  Identities=21%  Similarity=0.423  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      .+.+++|||+|||.++++++|+++|++||.|.++++.+.+ |||||+|.+.++|..|+..|||..++ |+.|+|.|||.
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~-g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~l~V~~a~~  100 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK-GCCFIKYDTHEQAAVCIVALANFPFQ-GRNLRTGWGKE  100 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTT-TEEEEECSSHHHHHHHHHHHTTCEET-TEECCCCBCCC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCC-CEEEEEECCHHHHHHHHHHhCCCeEC-CeEEEEEeccC
Confidence            3457999999999999999999999999999999999654 89999999999999999999999999 99999999973

>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=99.78  E-value=3.9e-19  Score=124.61  Aligned_cols=78  Identities=18%  Similarity=0.267  Sum_probs=71.1

Q ss_pred             CCCCCcEEEE--cCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCcc-----CCCCce
Q psy4057         167 EQPPNQILFL--TNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI-----TPTHAM  239 (246)
Q Consensus       167 ~~~~~~~l~v--~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i-----~~g~~l  239 (246)
                      ...++++|||  +||+.++++++|+++|++||.|.+|.++.++ |||||+|.+.++|.+|++.|||+.+     . |++|
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~r-gfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~-g~~l   98 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-PYSFARYRTTEESKRAYVTLNGKEVVDDLGQ-KITL   98 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC-SCEEEEESSHHHHHHHHHHTTTCEEECTTSC-EEEC
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCC-CEEEEEECCHHHHHHHHHHhCCCEEccccCC-CcEE
Confidence            3457899999  6699999999999999999999999988764 8999999999999999999999988     5 8999


Q ss_pred             EEEeecC
Q psy4057         240 KISFAKK  246 (246)
Q Consensus       240 ~v~~ak~  246 (246)
                      .|.|+++
T Consensus        99 ~v~~a~~  105 (114)
T 2cq2_A           99 YLNFVEK  105 (114)
T ss_dssp             EEEEESC
T ss_pred             EEEeccc
Confidence            9999974

>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=99.78  E-value=7.5e-19  Score=127.10  Aligned_cols=79  Identities=25%  Similarity=0.373  Sum_probs=73.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ...+++++|||+|||.++++++|+++|++||.|..|+++.++     +|||||+|.+.++|.+|+..|||..|. |++|+
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~-g~~l~  119 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD-GRRIR  119 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSS-SSCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEEC-CEEEE
Confidence            345678999999999999999999999999999999999864     589999999999999999999999999 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.||+
T Consensus       120 V~~a~  124 (129)
T 2kxn_B          120 VDFSI  124 (129)
T ss_dssp             ESCCS
T ss_pred             EEEec
Confidence            99986

>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=99.78  E-value=1.4e-18  Score=121.71  Aligned_cols=78  Identities=22%  Similarity=0.283  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ...++++|||+|||..+++++|+++|+.||.|..++++.+.    +|||||+|.+.++|.+|++.|||..++ |+.|+|+
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLD-GRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeC-CcEEEEE
Confidence            45579999999999999999999999999999999999874    579999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6.6e-19  Score=122.26  Aligned_cols=77  Identities=12%  Similarity=0.166  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .....++|||+|||.++|+++|+++|++||.|.+|+++.++    +|||||+|.+.++|..|+. +||..++ |+.|.|.
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~-gr~l~V~   84 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYK-ETDLLIL   84 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCT-TTTCEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEEC-CEEEEEE
Confidence            34468999999999999999999999999999999999864    5899999999999999999 9999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      +++
T Consensus        85 ~~~   87 (103)
T 1s79_A           85 FKD   87 (103)
T ss_dssp             EHH
T ss_pred             Ech
Confidence            864

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.78  E-value=8.7e-19  Score=123.32  Aligned_cols=78  Identities=29%  Similarity=0.430  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...++++|||+|||.++|+++|+++|+.||.|..++++.++     +|||||+|.+.++|..|+..|||..++ |++|+|
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~l~V  100 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM-GQTIQV  100 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEET-TEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC-CcEEEE
Confidence            34568999999999999999999999999999999999875     589999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .||+
T Consensus       101 ~~a~  104 (110)
T 1oo0_B          101 DWCF  104 (110)
T ss_dssp             EESE
T ss_pred             EEcc
Confidence            9986

>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=99.78  E-value=1.6e-18  Score=122.15  Aligned_cols=78  Identities=24%  Similarity=0.397  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhC------CCccCC
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALH------GFKITP  235 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~------g~~i~~  235 (246)
                      ...+.++|||+|||.++++++|+++|++||.|..|+++.++     +|||||+|.+.++|..|+..||      |..|+ 
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~-   89 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD-   89 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS-
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc-
Confidence            45578999999999999999999999999999999999763     5899999999999999999999      99999 


Q ss_pred             CCceEEEeec
Q psy4057         236 THAMKISFAK  245 (246)
Q Consensus       236 g~~l~v~~ak  245 (246)
                      |++|+|.||+
T Consensus        90 g~~l~v~~a~   99 (111)
T 1x4h_A           90 GRQLKVDLAV   99 (111)
T ss_dssp             SCEEEEECCC
T ss_pred             CEEEEEEECC
Confidence            9999999986

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=1.6e-18  Score=119.15  Aligned_cols=78  Identities=18%  Similarity=0.370  Sum_probs=70.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..+.+++|||+|||.++++++|+++|++||.|. +.++.++ +|||||+|.+.++|..|+..|||..|. |++|+|.||+
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~V~~a~   92 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLG-TDTLRVALAR   92 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSS-SSCCEEEECC
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEEC-CcEEEEEEcC
Confidence            345689999999999999999999999999996 5665544 699999999999999999999999999 9999999986


Q ss_pred             C
Q psy4057         246 K  246 (246)
Q Consensus       246 ~  246 (246)
                      .
T Consensus        93 ~   93 (97)
T 2e5j_A           93 Q   93 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.78  E-value=4e-19  Score=123.10  Aligned_cols=77  Identities=21%  Similarity=0.419  Sum_probs=72.0

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      .+.+++|||+|||.++++++|+++|++||.|.+|.+.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.+++.
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~---~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY---PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe---cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            3457899999999999999999999999999999887   4789999999999999999999999999999999999864

>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=99.78  E-value=9.6e-19  Score=132.04  Aligned_cols=77  Identities=30%  Similarity=0.434  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..++++|||+|||..+++++|+.+|++||.|..|.++.++     +|||||+|.+.++|..|+..|||..|. |++|.|.
T Consensus        69 ~~~~~~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           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM-GQTIQVD  147 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEE
Confidence            4468899999999999999999999999999999999874     589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus       148 ~a~  150 (165)
T 1rk8_A          148 WCF  150 (165)
T ss_dssp             ESE
T ss_pred             Eec
Confidence            986

>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=8.2e-19  Score=124.05  Aligned_cols=83  Identities=18%  Similarity=0.260  Sum_probs=76.4

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCee--------EEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIM--------DIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPF   75 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~--------~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~   75 (246)
                      ...++++|||+|||.++++++|+++|++||.|.        .|.++.+   ++++|||||+|.+.++|.+|++.|||..+
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            456789999999999999999999999999999        6888876   37889999999999999999999999999


Q ss_pred             CCeeEEEEEccCCc
Q psy4057          76 YDKPMRIQYSKTDS   89 (246)
Q Consensus        76 ~g~~l~v~~a~~~~   89 (246)
                      .|++|+|.++....
T Consensus        91 ~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           91 QGSKLKVSLARKKP  104 (113)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCCEEEEEECCCCC
Confidence            99999999987654

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.78  E-value=8e-19  Score=126.54  Aligned_cols=84  Identities=14%  Similarity=0.313  Sum_probs=76.6

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ....++++|||+|||.++++++|+++|++||.|.+|.++.+.   .++|||||+|.+.++|.+|++.|||..+.|++|.|
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   96 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   96 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            345668899999999999999999999999999999998663   67899999999999999999999999999999999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .++....
T Consensus        97 ~~a~~~~  103 (126)
T 3ex7_B           97 DWCFVRG  103 (126)
T ss_dssp             EESEESS
T ss_pred             EEecCCC
Confidence            9986543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=4.8e-19  Score=123.35  Aligned_cols=83  Identities=18%  Similarity=0.231  Sum_probs=76.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhc-cCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCc-cCCeeEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQ-FGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFP-FYDKPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~-fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~-~~g~~l~v   82 (246)
                      ...++++|||+|||.++++++|+++|++ ||.|.+|.++++.  +++|||||+|.+.++|.+|++.|||.. +.|++|+|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            4578899999999999999999999999 9999999998764  778999999999999999999999999 99999999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .++....
T Consensus        85 ~~a~~~~   91 (104)
T 2dhg_A           85 SVAIPKA   91 (104)
T ss_dssp             CBCCCCC
T ss_pred             EEccCCC
Confidence            9986553

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.78  E-value=2.7e-19  Score=118.89  Aligned_cols=72  Identities=24%  Similarity=0.450  Sum_probs=66.8

Q ss_pred             CcEEEecCCChhh------hHHHHHHHhhccCCeeEEEEcc-CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCe-eEEE
Q psy4057          11 TNFVYVTHISSTD------LKKSLYAIFSQFGQIMDIVALK-TLKMRGQAFVIFKEIASATNALRSMQGFPFYDK-PMRI   82 (246)
Q Consensus        11 ~~~l~V~nl~~~~------~e~~l~~~F~~fG~i~~v~~~~-~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~-~l~v   82 (246)
                      +++|||+|||.++      ++++|+++|++||.|.+|.+.+ +++++|||||+|.+.++|.+|++.|||..+.|+ +|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            5799999999999      8899999999999999999875 347899999999999999999999999999999 8876

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.1e-19  Score=121.84  Aligned_cols=78  Identities=15%  Similarity=0.242  Sum_probs=72.7

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      .+++++|||+|||.++++++|+++|++||.|.+|.++.+.   +++|||||+|.+.++|.+|++.|||..+.|+.|++.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            4688999999999999999999999999999999998763   7789999999999999999999999999999998876


Q ss_pred             c
Q psy4057          85 S   85 (246)
Q Consensus        85 a   85 (246)
                      +
T Consensus        82 ~   82 (85)
T 1x4e_A           82 P   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.78  E-value=9.7e-19  Score=117.78  Aligned_cols=78  Identities=22%  Similarity=0.317  Sum_probs=71.8

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...+.++|||+|||.++++++|+++|++||.|.+|.++++   ++++|||||+|.+.++|.+|++ +++..+.|++|+|.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            4567899999999999999999999999999999999876   4778999999999999999996 68889999999998


Q ss_pred             Ec
Q psy4057          84 YS   85 (246)
Q Consensus        84 ~a   85 (246)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.78  E-value=9.4e-19  Score=122.68  Aligned_cols=79  Identities=28%  Similarity=0.461  Sum_probs=73.0

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ....++++|||+|||.++++++|+++|++||.|.+|.+.     +|||||+|.+.++|.+|++.|||..+.|++|+|.++
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-----kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  100 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS  100 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            456788999999999999999999999999999999987     799999999999999999999999999999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ....
T Consensus       101 ~~~~  104 (108)
T 2jvo_A          101 KLPA  104 (108)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            7653

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.78  E-value=5.3e-19  Score=124.11  Aligned_cols=77  Identities=16%  Similarity=0.086  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCC-CceEEEEee-CCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFP-GFKEVRLVP-NRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G-~i~~v~~~~-~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .+...+|||+|||.++++++|+++|++|| .|..+.+.. +.+|||||+|.+.++|..|++.|||..|+ |+.|+|.+|+
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~-Gr~i~V~~a~  103 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFR-GSVITVERDD  103 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEET-TEEEEEEESC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEEC-CeEEEEEECC
Confidence            33578999999999999999999999999 899999964 45799999999999999999999999999 9999999986

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.4e-18  Score=117.76  Aligned_cols=78  Identities=19%  Similarity=0.306  Sum_probs=72.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.+.     ++||||+|.+.++|.+|++.|||..+.|++|+|.++.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   79 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELST   79 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-----SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECC
Confidence            45788999999999999999999999999999999996     4599999999999999999999999999999999987


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      ...
T Consensus        80 ~~~   82 (90)
T 2dnp_A           80 KGQ   82 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=1.4e-18  Score=122.89  Aligned_cols=79  Identities=22%  Similarity=0.287  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCce--------EEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCcc
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFK--------EVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKI  233 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~--------~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i  233 (246)
                      ...+.++|||+|||.++|+++|+++|++||.|.        .++++.++     +|||||+|.+.++|..|+..|||..|
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            455789999999999999999999999999998        69999874     58999999999999999999999999


Q ss_pred             CCCCceEEEeecC
Q psy4057         234 TPTHAMKISFAKK  246 (246)
Q Consensus       234 ~~g~~l~v~~ak~  246 (246)
                      . |+.|+|.||+.
T Consensus        91 ~-g~~l~V~~a~~  102 (113)
T 2cpe_A           91 Q-GSKLKVSLARK  102 (113)
T ss_dssp             T-TEECEEECSSC
T ss_pred             C-CCEEEEEECCC
Confidence            9 99999999873

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.78  E-value=5.3e-19  Score=122.50  Aligned_cols=73  Identities=22%  Similarity=0.336  Sum_probs=70.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ++|||+|||.++|+++|+++|++||.|..++++.+.+|||||+|.+.++|..|++.|||..+. |+.|+|.||+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~V~~a~   73 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVIC-GSRVRVELST   73 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSS-SCCCEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeEC-CcEEEEEEcc
Confidence            479999999999999999999999999999999986799999999999999999999999999 9999999986

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=1.1e-18  Score=121.42  Aligned_cols=82  Identities=21%  Similarity=0.357  Sum_probs=75.2

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ....+.++|||+|||.++++++|+++|++|| |.+|.++++.   +++|||||+|.+.++|.+|+ .|||..+.|++|+|
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 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV   87 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEE
Confidence            3556789999999999999999999999998 9999998764   67899999999999999999 89999999999999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .++....
T Consensus        88 ~~a~~~~   94 (103)
T 2dng_A           88 DIAEGRK   94 (103)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            9987654

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.78  E-value=3.3e-19  Score=120.94  Aligned_cols=73  Identities=18%  Similarity=0.176  Sum_probs=66.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCC--CceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFP--GFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G--~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .+|||+|||.++|+++|+++|++||  .|.+++++.++     +|||||+|.+.++|.+|++.|||..++ |+.|+|.++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~-gr~i~V~~~   80 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELH-GQNPVVTPS   80 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSS-SCCCEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeC-CEEEEEEEC
Confidence            4799999999999999999999999  99999999975     589999999999999999999999999 999999987


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus        81 ~   81 (90)
T 3p5t_L           81 N   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.1e-18  Score=118.28  Aligned_cols=76  Identities=22%  Similarity=0.333  Sum_probs=71.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      ..++.++|||+|||.++|+++|+++|++||.|.+++++++   ||||+|.+.++|..|+..|||..+. |++|+|.||+.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~---~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~a~~   80 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD---YAFVHMEKEADAKAAIAQLNGKEVK-GKRINVELSTK   80 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS---CEEEEESCHHHHHHHHHHHTTCEET-TEECEEEESCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC---EEEEEECCHHHHHHHHHHhCCCEEC-CcEEEEEECCC
Confidence            3457899999999999999999999999999999999854   9999999999999999999999999 99999999863

>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=99.78  E-value=5.8e-19  Score=121.34  Aligned_cols=79  Identities=25%  Similarity=0.460  Sum_probs=71.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLS----MLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~----~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ..+++++|||+|||.++++++|+    ++|++||.|.++++....  +|||||+|.+.++|..|+..|||..++ |++|+
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~   82 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFY-DKPMR   82 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEET-TEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEEC-CcEEE
Confidence            45679999999999999999999    999999999999998532  589999999999999999999999999 99999


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |+||+.
T Consensus        83 v~~a~~   88 (97)
T 1nu4_A           83 IQYAKT   88 (97)
T ss_dssp             EEECSS
T ss_pred             EEEccC
Confidence            999873

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=2.5e-18  Score=118.61  Aligned_cols=77  Identities=30%  Similarity=0.433  Sum_probs=70.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccC--CCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQF--PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~--G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ...+++++|||+|||.++|+++|+++|++|  |.|.++++.   +|||||+|.+.++|..|+..|||..|. |++|+|.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v~~   85 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---RDYAFVHFSNREDAVEAMKALNGKVLD-GSPIEVTL   85 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---SSEEEEEESSHHHHHHHHHHHSSEEET-TEEEEEEC
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe---CCeEEEEeCCHHHHHHHHHHhCCCEeC-CcEEEEEE
Confidence            345578999999999999999999999999  999998876   469999999999999999999999999 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |+.
T Consensus        86 a~~   88 (99)
T 2cpd_A           86 AKP   88 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            873

>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=99.77  E-value=8.4e-19  Score=122.90  Aligned_cols=79  Identities=9%  Similarity=0.169  Sum_probs=72.2

Q ss_pred             CCCCCcEEEe--cCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCcc-----CCee
Q psy4057           7 HICVTNFVYV--THISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF-----YDKP   79 (246)
Q Consensus         7 ~~~~~~~l~V--~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~-----~g~~   79 (246)
                      ...|+++|||  +||+.++++++|+++|++||.|.+|.+..   .||||||+|.+.++|.+|++.|||..+     .|++
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~---~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT---TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            4578899999  77999999999999999999999998865   589999999999999999999999988     6899


Q ss_pred             EEEEEccCC
Q psy4057          80 MRIQYSKTD   88 (246)
Q Consensus        80 l~v~~a~~~   88 (246)
                      |.|.|+...
T Consensus        98 l~v~~a~~~  106 (114)
T 2cq2_A           98 LYLNFVEKV  106 (114)
T ss_dssp             CEEEEESCC
T ss_pred             EEEEecccC
Confidence            999998644

>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=99.77  E-value=6.6e-19  Score=124.12  Aligned_cols=78  Identities=18%  Similarity=0.252  Sum_probs=72.3

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      ..++++|||+|||.++++++|+++|++||.|.+|.+.+   ++|||||+|.+.++|.+|++.|||..+.|++|.|.|+..
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE---GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS---SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC---CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            34578999999999999999999999999999998864   789999999999999999999999999999999999865


Q ss_pred             C
Q psy4057          88 D   88 (246)
Q Consensus        88 ~   88 (246)
                      .
T Consensus        84 ~   84 (111)
T 1whx_A           84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=2.3e-19  Score=124.98  Aligned_cols=81  Identities=21%  Similarity=0.398  Sum_probs=75.2

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            467899999999999999999999999999999998753   67899999999999999999999999999999999999


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ....
T Consensus        86 ~~~~   89 (104)
T 1p1t_A           86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCcc
Confidence            7664

>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=99.77  E-value=1.6e-18  Score=121.51  Aligned_cols=78  Identities=18%  Similarity=0.196  Sum_probs=73.1

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCC-----eeEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD-----KPMRI   82 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g-----~~l~v   82 (246)
                      ..+.++|||+|||.++++++|+++|++||.|..|.++.+    |||||+|.+.++|.+|++.|||..+.|     ++|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V   87 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   87 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT----TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC----CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEE
Confidence            456899999999999999999999999999999999886    999999999999999999999999999     99999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .++....
T Consensus        88 ~~a~~~~   94 (108)
T 1x4c_A           88 KVDGPRS   94 (108)
T ss_dssp             EESSCCS
T ss_pred             EeCCCCC
Confidence            9987654

>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=99.77  E-value=9.9e-19  Score=136.48  Aligned_cols=76  Identities=14%  Similarity=0.212  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCC-CCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         169 PPNQILFLTNLP-EETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       169 ~~~~~l~v~nL~-~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      +++++|||+||| .++|+++|+++|++||.|.+|+++.+++|||||+|.+.++|..|++.|||..+. |++|+|.|||
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~-g~~l~v~~s~   78 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMF-GQKMNVCVSK   78 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEET-TEECEEEECS
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEEC-CceEEEEEcc
Confidence            468999999999 899999999999999999999999988899999999999999999999999999 9999999986

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.77  E-value=2.7e-18  Score=125.92  Aligned_cols=80  Identities=26%  Similarity=0.498  Sum_probs=74.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ....+.++|||+|||.++++++|+++|+.||.|.+|+++.++     +|||||+|.+.++|.+|+..|||..|. |+.|+
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~  115 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL-NKRLK  115 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECS-SCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC-CeEEE
Confidence            345568999999999999999999999999999999999864     589999999999999999999999999 99999


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |.||+.
T Consensus       116 v~~a~~  121 (139)
T 1u6f_A          116 VALAAS  121 (139)
T ss_dssp             EEESSC
T ss_pred             EEECCC
Confidence            999873

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.77  E-value=3.8e-18  Score=121.73  Aligned_cols=77  Identities=26%  Similarity=0.334  Sum_probs=68.7

Q ss_pred             CCCCcEE--EEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccE-EEEEeCCHHHHHHHHHHhCCCccCCC-CceEEEe
Q psy4057         168 QPPNQIL--FLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI-AFVEFENEMQSAAAKLALHGFKITPT-HAMKISF  243 (246)
Q Consensus       168 ~~~~~~l--~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~-afV~f~~~~~A~~Al~~l~g~~i~~g-~~l~v~~  243 (246)
                      .+++.+|  ||+||+..+|+++|+++|++||.|.+|++... .|| |||+|.+.++|..|++.|||+.|+++ ++|+|.|
T Consensus        20 ~~ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           20 SGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             CCCCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             CCCCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            3456664  68999999999999999999999999999875 486 99999999999999999999999832 6999999


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      ||
T Consensus        99 Ak  100 (124)
T 2e5i_A           99 AR  100 (124)
T ss_dssp             CS
T ss_pred             ec
Confidence            97

>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=2.6e-19  Score=122.60  Aligned_cols=79  Identities=19%  Similarity=0.193  Sum_probs=70.4

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      .++.++|||+|||.++++++|+++|++||.|..+.++.+.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            4567999999999999999999999999999877666543   6789999999999999999999999999999999998


Q ss_pred             cc
Q psy4057          85 SK   86 (246)
Q Consensus        85 a~   86 (246)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            74

>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=99.77  E-value=1.6e-18  Score=124.94  Aligned_cols=78  Identities=23%  Similarity=0.368  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...++++|||+|||.++|+++|+++|+.||.|..|.++.+.     +|||||+|.+.++|..|++.|||..|. |+.|+|
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v   96 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM-GQPISV   96 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSS-SSBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeC-CeEEEE
Confidence            34568999999999999999999999999999999999875     689999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      +||+
T Consensus        97 ~~a~  100 (126)
T 3ex7_B           97 DWCF  100 (126)
T ss_dssp             EESE
T ss_pred             EEec
Confidence            9986

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=9.9e-19  Score=120.23  Aligned_cols=80  Identities=18%  Similarity=0.280  Sum_probs=72.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ..+.+++|||+|||.++++++|+++|++||.|. +.++. ++++|||||+|.+.++|.+|++.|||..+.|++|+|.++.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   92 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW-QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR   92 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECC
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc-CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            345589999999999999999999999999996 55544 3789999999999999999999999999999999999987


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      .+
T Consensus        93 ~~   94 (97)
T 2e5j_A           93 QQ   94 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.7e-18  Score=123.07  Aligned_cols=81  Identities=20%  Similarity=0.254  Sum_probs=75.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...+.++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.+|+ .+.|++|+|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            45678999999999999999999999999999999999864   7889999999999999999999998 8999999999


Q ss_pred             EccCC
Q psy4057          84 YSKTD   88 (246)
Q Consensus        84 ~a~~~   88 (246)
                      ++...
T Consensus        92 ~a~~~   96 (116)
T 2cqd_A           92 LAYLG   96 (116)
T ss_dssp             ESTTT
T ss_pred             EcccC
Confidence            98654

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.77  E-value=3.7e-19  Score=123.10  Aligned_cols=80  Identities=13%  Similarity=0.253  Sum_probs=70.8

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC----CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT----LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~----~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ...+.++|||+|||.++++++|+++|++|| |.+|.+.++    ++++|||||+|.+.++|.+|+ .|||..+.|+.|+|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            456789999999999999999999999999 999999865    367899999999999999999 89999999999999


Q ss_pred             EEccCC
Q psy4057          83 QYSKTD   88 (246)
Q Consensus        83 ~~a~~~   88 (246)
                      .++...
T Consensus        93 ~~a~~~   98 (100)
T 2j76_E           93 DVADQA   98 (100)
T ss_dssp             EECCCS
T ss_pred             EeccCC
Confidence            998765

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=2.2e-18  Score=117.27  Aligned_cols=78  Identities=24%  Similarity=0.339  Sum_probs=72.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.+.     ++||||+|.+.++|.+|++.|||..+.|++|+|.++.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   80 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLST   80 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-----SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-----CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            56788999999999999999999999999999999996     4599999999999999999999999999999999997


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      ...
T Consensus        81 ~~~   83 (92)
T 2dgt_A           81 SRL   83 (92)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.77  E-value=1.5e-18  Score=120.62  Aligned_cols=75  Identities=27%  Similarity=0.465  Sum_probs=70.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ...+.++|||+|||.++|+++|+++|++||.|..+++++   +||||+|.+.++|.+|++.|||..|. |+.|+|.||+
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~---~~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~a~   81 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK---DYAFIHFDERDGAVKAMEEMNGKDLE-GENIEIVFAK   81 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS---SCEEEEESSHHHHHHHHHHHTTEEET-TEEEEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC---CEEEEEeCCHHHHHHHHHHHCCCccC-CCEEEEEEcC
Confidence            345789999999999999999999999999999999984   59999999999999999999999999 9999999986

>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=8.8e-19  Score=120.68  Aligned_cols=79  Identities=19%  Similarity=0.227  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ..+..++|||+|||.++++++|+++|++||.|..+.++.++     +|||||+|.+.++|.+|++.|||..|+ |++|+|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~-g~~l~V   89 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG-SRKVKL   89 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEET-TEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeC-CeEEEE
Confidence            44568999999999999999999999999999877766643     589999999999999999999999999 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      .||+.
T Consensus        90 ~~a~~   94 (98)
T 2cqp_A           90 VLGSG   94 (98)
T ss_dssp             EESSC
T ss_pred             EEcCC
Confidence            99863

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=121.60  Aligned_cols=78  Identities=22%  Similarity=0.429  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHcc-CCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCc-cCCCCceE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQ-FPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFK-ITPTHAMK  240 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~-~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~-i~~g~~l~  240 (246)
                      ...++++|||+|||.++|+++|+++|++ ||.|.+++++.++    +|||||+|.+.++|..|+..|||.. ++ |++|+
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 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLG-SKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSS-SSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccC-CEeEE
Confidence            4457899999999999999999999999 9999999999874    5899999999999999999999999 99 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.||+
T Consensus        84 v~~a~   88 (104)
T 2dhg_A           84 LSVAI   88 (104)
T ss_dssp             CCBCC
T ss_pred             EEEcc
Confidence            99986

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.77  E-value=1.1e-18  Score=127.88  Aligned_cols=82  Identities=23%  Similarity=0.364  Sum_probs=75.9

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4557899999999999999999999999999999998764   5789999999999999999999999999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      ++...
T Consensus       119 a~~~~  123 (139)
T 1u6f_A          119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            97654

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.1e-18  Score=123.55  Aligned_cols=75  Identities=20%  Similarity=0.325  Sum_probs=70.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ...++|||+|||.++++++|+++|+.||.|..|+++.++     +|||||+|.+.++|..|+ .|||..|. |+.|+|.|
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~-g~~l~V~~  100 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLL-GVPIIVQA  100 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEET-TEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeC-CeEEEEEe
Confidence            357899999999999999999999999999999999754     589999999999999999 99999999 99999999


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      |+
T Consensus       101 a~  102 (114)
T 2cq4_A          101 SQ  102 (114)
T ss_dssp             HH
T ss_pred             cC
Confidence            86

>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=7e-19  Score=122.76  Aligned_cols=83  Identities=20%  Similarity=0.313  Sum_probs=76.6

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ....+.++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++. |+..+.|++|.|
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            356788999999999999999999999999999999998863   6789999999999999999998 999999999999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .++..+.
T Consensus        90 ~~a~~~~   96 (105)
T 2dh8_A           90 KPCTPRG   96 (105)
T ss_dssp             CCSCCSS
T ss_pred             EEccCCC
Confidence            9987654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.77  E-value=1.3e-18  Score=122.20  Aligned_cols=84  Identities=17%  Similarity=0.248  Sum_probs=71.5

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEE
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR   81 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (246)
                      +....++++|||+|||.++++++|+++|++||.|.+|.++++   ++++|||||+|.+.++|.+|++.+ +..+.|++|+
T Consensus        19 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~   97 (109)
T 2rs2_A           19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTID   97 (109)
T ss_dssp             -------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEE
Confidence            345667899999999999999999999999999999999876   478999999999999999999976 5899999999


Q ss_pred             EEEccCCc
Q psy4057          82 IQYSKTDS   89 (246)
Q Consensus        82 v~~a~~~~   89 (246)
                      |.++..+.
T Consensus        98 V~~a~~~~  105 (109)
T 2rs2_A           98 PKVAFPRR  105 (109)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCCC
Confidence            99987553

>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=1.8e-18  Score=124.39  Aligned_cols=83  Identities=20%  Similarity=0.307  Sum_probs=76.3

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.+..+.  +++|||||+|.+.++|.+|++.|||..+.|++|+|.+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34567899999999999999999999999999999998764  6789999999999999999999999999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      |....
T Consensus       111 a~~~~  115 (124)
T 2kt5_A          111 VASQI  115 (124)
T ss_dssp             ECCTT
T ss_pred             eCCCC
Confidence            87653

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=9.5e-19  Score=123.35  Aligned_cols=77  Identities=13%  Similarity=0.243  Sum_probs=71.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHH---HHHccCCCceEEEEeeCC--------ccEEEEEeCCHHHHHHHHHHhCCCccCCC
Q psy4057         168 QPPNQILFLTNLPEETSEMMLS---MLFNQFPGFKEVRLVPNR--------HDIAFVEFENEMQSAAAKLALHGFKITPT  236 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~---~~f~~~G~i~~v~~~~~~--------~g~afV~f~~~~~A~~Al~~l~g~~i~~g  236 (246)
                      ....++|||+|||.++++++|+   ++|++||.|.+++++.+.        +|||||+|.+.++|.+|++.|||..|+ |
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~-g   90 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD-G   90 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET-T
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC-C
Confidence            3458899999999999999999   999999999999999865        279999999999999999999999999 9


Q ss_pred             CceEEEeec
Q psy4057         237 HAMKISFAK  245 (246)
Q Consensus       237 ~~l~v~~ak  245 (246)
                      ++|+|.||+
T Consensus        91 r~l~V~~a~   99 (111)
T 2cpi_A           91 RTLKASLGT   99 (111)
T ss_dssp             EEEEEESCC
T ss_pred             EEEEEEecc
Confidence            999999986

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.77  E-value=4.9e-19  Score=122.46  Aligned_cols=77  Identities=22%  Similarity=0.373  Sum_probs=68.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR------HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      .....++|||+|||.++++++|+++|+.|| |.+++++.++      +|||||+|.+.++|.+|+ .|||..|. |+.|+
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~-g~~l~   91 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG-NRRIR   91 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBT-TBCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEEC-CeEEE
Confidence            445699999999999999999999999999 9999999875      589999999999999999 89999999 99999


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |.||+.
T Consensus        92 V~~a~~   97 (100)
T 2j76_E           92 VDVADQ   97 (100)
T ss_dssp             CEECCC
T ss_pred             EEeccC
Confidence            999873

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.77  E-value=2.4e-18  Score=119.60  Aligned_cols=78  Identities=24%  Similarity=0.427  Sum_probs=72.6

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.++     ++||||+|.+.++|.+|++.|||..+.|++|.|.++.
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   81 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-----KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK   81 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-----SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-----CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcC
Confidence            45678999999999999999999999999999999885     5799999999999999999999999999999999997


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      ...
T Consensus        82 ~~~   84 (103)
T 2dgu_A           82 PPD   84 (103)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            654

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.3e-18  Score=121.21  Aligned_cols=77  Identities=23%  Similarity=0.391  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      .+.++|||+|||.++++++|+++|+.||.|..++++.++     +|||||+|.+.++|..|++.|||..+. |+.|+|.|
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~   84 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFS-GRALRVDN   84 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCS-SSCBEEEE
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeC-CcEEEEEe
Confidence            357899999999999999999999999999999999875     589999999999999999999999999 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |+.
T Consensus        85 a~~   87 (104)
T 1p1t_A           85 AAS   87 (104)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            863

>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=99.77  E-value=1.4e-18  Score=123.23  Aligned_cols=83  Identities=25%  Similarity=0.460  Sum_probs=74.7

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCe----eEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQI----MDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR   81 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i----~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (246)
                      ...+++++|||+|||.++++++|+++|++||.|    ..+.+. +++++|||||+|.+.++|.+|++.|||..+.|++|+
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~-~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   98 (115)
T 2cpx_A           20 NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM-TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV   98 (115)
T ss_dssp             CCCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE-CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC-CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            345678999999999999999999999999998    555554 668999999999999999999999999999999999


Q ss_pred             EEEccCCc
Q psy4057          82 IQYSKTDS   89 (246)
Q Consensus        82 v~~a~~~~   89 (246)
                      |.++....
T Consensus        99 v~~a~~~~  106 (115)
T 2cpx_A           99 IEFGKNKK  106 (115)
T ss_dssp             EEECCCCS
T ss_pred             EEEccCCC
Confidence            99997654

>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=1.3e-18  Score=129.90  Aligned_cols=79  Identities=15%  Similarity=0.202  Sum_probs=72.5

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccC--CeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFG--QIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG--~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..++|||+|||.++++++|+++|++||  .|.+|.++.+   ++++|||||+|.+.++|.+|++.|||..+.|++|+|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  9999999876   47899999999999999999999999999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      +..+
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8543

>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=5e-19  Score=121.92  Aligned_cols=81  Identities=19%  Similarity=0.189  Sum_probs=72.8

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      .++.++|||+|||.++++++|+++|++||.|..+.++.+   ++++|||||+|.+.++|++|++.|||..+.|++|+|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            456789999999999999999999999999987666554   36789999999999999999999999999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      +...
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8654

>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=1.4e-18  Score=117.50  Aligned_cols=74  Identities=14%  Similarity=0.245  Sum_probs=70.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|+ .|||..+. |+.|+|.+|
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~-g~~l~V~~a   82 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFR-GRQIKVIPK   82 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEET-TEECEEEET
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEEC-CcEEEEEEc
Confidence            36899999999999999999999999999999999875     689999999999999999 99999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus        83 ~   83 (89)
T 3ucg_A           83 R   83 (89)
T ss_dssp             T
T ss_pred             c
Confidence            7

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.77  E-value=3.3e-18  Score=118.90  Aligned_cols=76  Identities=21%  Similarity=0.419  Sum_probs=70.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...+.++|||+|||.++++++|+++|+.|| |.+|+++.++     +|||||+|.+.++|.+|+ .|||..|. |++|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~-g~~l~V   87 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLG-DRSLRV   87 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEET-TEECEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeEC-CeEEEE
Confidence            445689999999999999999999999997 9999999875     589999999999999999 89999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .||+
T Consensus        88 ~~a~   91 (103)
T 2dng_A           88 DIAE   91 (103)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.9e-18  Score=121.37  Aligned_cols=83  Identities=13%  Similarity=0.306  Sum_probs=75.2

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCC-eeEEEEc-cCC---CCccEEEEEEcCHHHHHHHHHHhc--CCccCCee
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQ-IMDIVAL-KTL---KMRGQAFVIFKEIASATNALRSMQ--GFPFYDKP   79 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~-i~~v~~~-~~~---~~kg~aFV~f~~~~~A~~Ai~~ln--g~~~~g~~   79 (246)
                      ..+++++|||+|||.++++++|+++|++||. |.+|.++ .+.   +++|||||+|.+.++|..|++.||  +..+.|++
T Consensus         4 ~s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~   83 (109)
T 2dis_A            4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQ   83 (109)
T ss_dssp             CCCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBC
T ss_pred             cccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCe
Confidence            4567899999999999999999999999998 9999988 443   688999999999999999999996  59999999


Q ss_pred             EEEEEccCCc
Q psy4057          80 MRIQYSKTDS   89 (246)
Q Consensus        80 l~v~~a~~~~   89 (246)
                      |+|.++..+.
T Consensus        84 l~V~~a~~~~   93 (109)
T 2dis_A           84 IAVDWAEPEI   93 (109)
T ss_dssp             CEEEESCSSC
T ss_pred             EEEEEcCCCC
Confidence            9999997654

>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=99.77  E-value=2.4e-18  Score=127.82  Aligned_cols=75  Identities=20%  Similarity=0.309  Sum_probs=68.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-ccEEEEEeCCHHHHHHHHHHhCCCccCC-CCceEEEeec
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFENEMQSAAAKLALHGFKITP-THAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~~~A~~Al~~l~g~~i~~-g~~l~v~~ak  245 (246)
                      ...|||+||++.+|+++|+++|++||.|++|++..++ +|||||+|.+.++|..|++.|||+.|++ +++|+|+|||
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            4557899999999999999999999999999998665 5799999999999999999999999972 4999999997

>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=99.77  E-value=1.6e-18  Score=128.80  Aligned_cols=80  Identities=23%  Similarity=0.366  Sum_probs=75.4

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...+.++|||+|||.++++++|+++|++||.|.+|.++++  ++|||||+|.+.++|.+|++.|||..+.|++|+|.++.
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  146 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN--PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSN  146 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS--SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC--CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcC
Confidence            4567899999999999999999999999999999999887  79999999999999999999999999999999999987


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      ++
T Consensus       147 ~~  148 (150)
T 2i2y_A          147 GE  148 (150)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=2.8e-18  Score=121.88  Aligned_cols=78  Identities=18%  Similarity=0.296  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ....+.++|||+|||.++|+++|+++|++||.|..|+++.++     +|||||+|.+.++|.+|+..||+ .|. |++|+
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~-g~~l~   89 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IID-GRKAN   89 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EET-TEECE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCC-CEEEE
Confidence            455679999999999999999999999999999999999874     58999999999999999999999 898 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.||+
T Consensus        90 V~~a~   94 (116)
T 2cqd_A           90 VNLAY   94 (116)
T ss_dssp             EEEST
T ss_pred             EEEcc
Confidence            99985

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=4.1e-18  Score=117.53  Aligned_cols=78  Identities=18%  Similarity=0.370  Sum_probs=72.4

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhcc--CCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQF--GQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~f--G~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..+++++|||+|||.++++++|+++|++|  |.|.+|.+     .+|||||+|.+.++|.+|++.|||..+.|++|+|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL   85 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE-----eCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            45678999999999999999999999999  99999987     468999999999999999999999999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      ++...
T Consensus        86 a~~~~   90 (99)
T 2cpd_A           86 AKPVD   90 (99)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=5.9e-19  Score=115.46  Aligned_cols=72  Identities=18%  Similarity=0.278  Sum_probs=67.7

Q ss_pred             EEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        13 ~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      +|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|++|++ +||..+.|++|+|.+|
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            58999999999999999999999999999998753   788999999999999999998 9999999999999875

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.76  E-value=2e-18  Score=126.71  Aligned_cols=79  Identities=28%  Similarity=0.390  Sum_probs=73.4

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..+++++|||+|||.++++++|+++|++||.|.+|.++++   ++++|||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4567899999999999999999999999999999999876   4789999999999999999999999999999999998


Q ss_pred             Ec
Q psy4057          84 YS   85 (246)
Q Consensus        84 ~a   85 (246)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.76  E-value=6.1e-19  Score=128.03  Aligned_cols=80  Identities=15%  Similarity=0.316  Sum_probs=74.0

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeE--EEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCC----ccCCe
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTL---KMRGQAFVIFKEIASATNALRSMQGF----PFYDK   78 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~--v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~----~~~g~   78 (246)
                      ..++++|||+|||.++++++|+++|++||.|..  |+++++.   +++|||||+|.+. +|.+|+..|||.    .+.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            457899999999999999999999999999976  8888765   7899999999999 999999999999    99999


Q ss_pred             eEEEEEccCC
Q psy4057          79 PMRIQYSKTD   88 (246)
Q Consensus        79 ~l~v~~a~~~   88 (246)
                      +|+|.++...
T Consensus        99 ~l~V~~a~~~  108 (131)
T 2m2b_A           99 TINVEFAKGS  108 (131)
T ss_dssp             CCCCEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999998765

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.76  E-value=1.4e-17  Score=119.62  Aligned_cols=78  Identities=22%  Similarity=0.273  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ...++++|||+|||.++++++|+++|+.||.|.++++..++    +|||||+|.+.++|..|+..|||..++ |++|+|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLD-GRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESS-SCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEEC-CcEEEEE
Confidence            44568999999999999999999999999999999999874    589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus       110 ~a~  112 (124)
T 2kt5_A          110 LVA  112 (124)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.76  E-value=6.8e-19  Score=120.78  Aligned_cols=82  Identities=18%  Similarity=0.246  Sum_probs=74.6

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ....++++|||+|||.++++++|+++|++||.|..+  ..+++++|||||+|.+.++|.+|++.|||..+.|++|+|.++
T Consensus        11 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~--~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE--EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe--CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            345678999999999999999999999999998877  456688999999999999999999999999999999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ..+.
T Consensus        89 ~~~~   92 (96)
T 1fjc_A           89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            6653

>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=99.76  E-value=1.1e-18  Score=128.57  Aligned_cols=82  Identities=26%  Similarity=0.444  Sum_probs=75.2

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeE--------EEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCe
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK   78 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~--------v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~   78 (246)
                      ...++++|||+|||.++++++|+++|++||.|..        +.+..+++++|||||+|.+.++|.+|++.|||..+.|+
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            4568899999999999999999999999999876        55566789999999999999999999999999999999


Q ss_pred             eEEEEEccCC
Q psy4057          79 PMRIQYSKTD   88 (246)
Q Consensus        79 ~l~v~~a~~~   88 (246)
                      +|.|.+++..
T Consensus       121 ~l~V~~a~~~  130 (143)
T 3egn_A          121 PMVVQFARSA  130 (143)
T ss_dssp             ECEEEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999998654

>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=99.76  E-value=3.6e-18  Score=118.90  Aligned_cols=75  Identities=23%  Similarity=0.379  Sum_probs=70.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR------HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .++.++|||+|||.++++++|+++|+.|| |..|+++.++      +|||||+|.+.++|.+|+ .|||..|. |+.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~-g~~l~V   88 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG-NKRIRV   88 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEET-TEECEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeC-CcEEEE
Confidence            45689999999999999999999999999 9999999864      579999999999999999 99999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .||+
T Consensus        89 ~~a~   92 (104)
T 1wi8_A           89 DVAD   92 (104)
T ss_dssp             EECC
T ss_pred             EEcc
Confidence            9986

>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=3.3e-18  Score=127.90  Aligned_cols=82  Identities=24%  Similarity=0.344  Sum_probs=76.2

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..++++|||+|||.++++++|+++|++||.|.+|.++.+.   .++|||||+|.+.++|.+|++.||+..+.|++|+|.+
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4578999999999999999999999999999999998764   6789999999999999999999999999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      +....
T Consensus       116 a~~~~  120 (156)
T 1h2v_Z          116 DAGFK  120 (156)
T ss_dssp             ESCCC
T ss_pred             CCCCC
Confidence            97643

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2e-18  Score=119.52  Aligned_cols=82  Identities=17%  Similarity=0.215  Sum_probs=71.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...++++|||+|||.++++++|+++|++||.|.-+ ...+++++|||||+|.+.++|++|++.|||..+.|++|+|.++.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~-~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   89 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIKVP-QNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQG   89 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECC-BCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEE-ECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcC
Confidence            45678999999999999999999999999988322 11345789999999999999999999999999999999999987


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      .+.
T Consensus        90 ~~~   92 (101)
T 2fc9_A           90 PRG   92 (101)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            653

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=4.8e-18  Score=116.52  Aligned_cols=78  Identities=17%  Similarity=0.292  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEE-EeeCC-ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVR-LVPNR-HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~-~~~~~-~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ....+++|||+|||.++++++|+++|++||.|..++ ++.++ .+.|||+|.+.++|..|+..|||..+. |++|+|.||
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~-g~~l~V~~a   89 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLE-NFTLKVAYI   89 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCS-SCBCEEEEC
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEEC-CcEEEEEEc
Confidence            344689999999999999999999999999999995 77765 456999999999999999999999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus        90 ~   90 (96)
T 2e44_A           90 P   90 (96)
T ss_dssp             C
T ss_pred             C
Confidence            6

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=5.3e-19  Score=118.56  Aligned_cols=76  Identities=17%  Similarity=0.242  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      +++++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||..+. |+.|++++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~~~~~~   81 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQ-AQMAKQSG   81 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCC-EESCCSSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEe-eEEEeecC
Confidence            468999999999999999999999999999999999874     589999999999999999999999999 99999988


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      ++
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.76  E-value=5.4e-18  Score=114.07  Aligned_cols=76  Identities=13%  Similarity=0.193  Sum_probs=69.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...+.++|||+|||.++++++|+++|++||.|..++++.++     +|||||+|.+.++|.+|++ ++|..++ |+.|+|
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~-g~~i~v   84 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLD-GRVIDP   84 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEET-TEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEEC-CEEEEE
Confidence            45578999999999999999999999999999999999875     5899999999999999995 5888899 999999


Q ss_pred             Eee
Q psy4057         242 SFA  244 (246)
Q Consensus       242 ~~a  244 (246)
                      .+|
T Consensus        85 ~~A   87 (87)
T 3s7r_A           85 KKA   87 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>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=99.76  E-value=2.3e-18  Score=121.94  Aligned_cols=78  Identities=23%  Similarity=0.389  Sum_probs=72.4

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      .+++|||+|||.++++++|+++|++||.|.+|.++.+.   +++|||||+|.+.++|.+|+ .|||..+.|++|+|.++.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            35799999999999999999999999999999998764   67899999999999999999 899999999999999986


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      ..
T Consensus       103 ~~  104 (114)
T 2cq4_A          103 AE  104 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            43

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.5e-18  Score=119.28  Aligned_cols=84  Identities=15%  Similarity=0.183  Sum_probs=72.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...++++|||+|||.++++++|+++|+.|+.|..+....+++++|||||+|.+.++|.+|++.|||..+.|++|+|.+++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   90 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK   90 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            45778999999999999999999999988755444333445788999999999999999999999999999999999997


Q ss_pred             CCcc
Q psy4057          87 TDSD   90 (246)
Q Consensus        87 ~~~~   90 (246)
                      .+..
T Consensus        91 ~~~~   94 (102)
T 2fc8_A           91 PKGE   94 (102)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6643

>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=99.76  E-value=1.1e-18  Score=119.56  Aligned_cols=78  Identities=19%  Similarity=0.213  Sum_probs=69.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ..++.++|||+|||.++++++|+++|++||.|..+.++.++     +|||||+|.+.++|.+|++.|||..|. |++|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~-gr~l~v   89 (95)
T 2ek1_A           11 GKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG-SRKVKL   89 (95)
T ss_dssp             ----CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeEC-CcEEEE
Confidence            34467999999999999999999999999999877777643     589999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .+++
T Consensus        90 ~~a~   93 (95)
T 2ek1_A           90 SGPS   93 (95)
T ss_dssp             ECCC
T ss_pred             Eecc
Confidence            9985

>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=3.3e-18  Score=128.17  Aligned_cols=81  Identities=21%  Similarity=0.379  Sum_probs=75.8

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..+.++|||+|||.++++++|+++|++||.|.+|.++++   ++++|||||+|.+.++|.+|++.|||..+.|++|+|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            456899999999999999999999999999999999876   47899999999999999999999999999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      +...
T Consensus       147 a~~~  150 (158)
T 2kn4_A          147 ARYG  150 (158)
T ss_dssp             ECCS
T ss_pred             CCCC
Confidence            9765

>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=99.75  E-value=4.6e-19  Score=153.00  Aligned_cols=77  Identities=22%  Similarity=0.339  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..+.++|||+|||..+|+++|..+|+.||.|..|.|+.+.     +|||||+|.+.++|..||..|||..|. |+.|.|.
T Consensus        99 ~~~~~~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           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKID-GRRVLVD  177 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEEC-CEEEEEE
Confidence            3467899999999999999999999999999999999863     689999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus       178 ~a~  180 (437)
T 3pgw_S          178 VER  180 (437)
T ss_pred             EeC
Confidence            986

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.75  E-value=3.4e-18  Score=127.54  Aligned_cols=75  Identities=15%  Similarity=0.133  Sum_probs=70.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCC--CceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFP--GFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G--~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..++|||+|||.++|+++|+++|+.||  .|.+|+++.++     +|||||+|.+.++|.+|+..|||..|+ |+.|+|.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~-Gr~l~V~  132 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLN-GEKVDVR  132 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEET-TEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC-CeEeEEE
Confidence            578999999999999999999999999  99999999875     589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      +|+
T Consensus       133 ~a~  135 (156)
T 3n9u_C          133 PAT  135 (156)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            985

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.75  E-value=4e-19  Score=120.47  Aligned_cols=77  Identities=19%  Similarity=0.422  Sum_probs=69.9

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      ++|||+|||.++++++|+++|++||.|.+|.+.++   ++++|||||+|.+.+ |.+|+..|||..+.|++|+|.+|...
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            58999999999999999999999999999999876   477999999999999 99999999999999999999998765


Q ss_pred             c
Q psy4057          89 S   89 (246)
Q Consensus        89 ~   89 (246)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=4e-18  Score=120.71  Aligned_cols=82  Identities=15%  Similarity=0.278  Sum_probs=74.5

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCcc--------C
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPF--------Y   76 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~--------~   76 (246)
                      ...+.++|||+|||.++++++|+++|++||.|.+|.++++.  +++|||||+|.+.++|.+|++.|||..+        .
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            34567999999999999999999999999999999998764  6789999999999999999999999998        6


Q ss_pred             CeeEEEEEccCC
Q psy4057          77 DKPMRIQYSKTD   88 (246)
Q Consensus        77 g~~l~v~~a~~~   88 (246)
                      |++|.|.|+.+.
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            888999998643

>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=99.75  E-value=3e-18  Score=120.59  Aligned_cols=76  Identities=18%  Similarity=0.334  Sum_probs=71.1

Q ss_pred             CCCCcEEEecCCChh-hhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           8 ICVTNFVYVTHISST-DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~-~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ..++++|||+|||.+ +++++|+++|++||.|.+|.+     ++|||||+|.+.++|.+|++.|||..+.|++|+|.++.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   98 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-----HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAG   98 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-----ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-----eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            345689999999999 999999999999999999988     68999999999999999999999999999999999987


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      ..
T Consensus        99 ~~  100 (110)
T 1wf1_A           99 EP  100 (110)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.75  E-value=6.5e-18  Score=123.89  Aligned_cols=79  Identities=22%  Similarity=0.369  Sum_probs=72.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       165 ~~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                      ....++.++|||+|||.++++++|+++|++||.|..++++.++     +|||||+|.+.++|.+|++.|||..|. |++|
T Consensus        57 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l  135 (140)
T 2ku7_A           57 GGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF-GRTI  135 (140)
T ss_dssp             CSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEET-TEEE
T ss_pred             CCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEEC-CEEE
Confidence            3455679999999999999999999999999999999998873     589999999999999999999999999 9999


Q ss_pred             EEEee
Q psy4057         240 KISFA  244 (246)
Q Consensus       240 ~v~~a  244 (246)
                      +|.||
T Consensus       136 ~v~~A  140 (140)
T 2ku7_A          136 RVNLA  140 (140)
T ss_dssp             EEEC-
T ss_pred             EEEeC
Confidence            99987

>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=99.75  E-value=4.3e-18  Score=119.75  Aligned_cols=74  Identities=22%  Similarity=0.372  Sum_probs=69.6

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         168 QPPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~-~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .+++++|||+|||.. +++++|+++|++||.|..+++   .+|||||+|.+.++|..|++.|||..++ |+.|+|.||+
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~V~~a~   98 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLA-GQTLDINMAG   98 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEET-TEECCEEESC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEEC-CeEEEEEECC
Confidence            445789999999999 999999999999999999999   4589999999999999999999999999 9999999987

>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=118.37  Aligned_cols=79  Identities=20%  Similarity=0.353  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccC-------C
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKIT-------P  235 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~-------~  235 (246)
                      ...+.++|||+|||.++++++|+++|++||.|.+++++.++    +|||||+|.+.++|..|+..|||..+.       .
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            44568999999999999999999999999999999999974    579999999999999999999999994       2


Q ss_pred             CCceEEEeec
Q psy4057         236 THAMKISFAK  245 (246)
Q Consensus       236 g~~l~v~~ak  245 (246)
                      +++|.|.||+
T Consensus       101 ~~~l~v~~a~  110 (114)
T 1x5o_A          101 TEPLLCKFSG  110 (114)
T ss_dssp             SSCBEEEECC
T ss_pred             CCceeEEccC
Confidence            7889999986

>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=9e-18  Score=113.99  Aligned_cols=77  Identities=17%  Similarity=0.163  Sum_probs=71.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .....++|||+|||.++++++|+++|+.| .|..++++.+.    +|||||+|.+.++|..|+. |||..|+ |+.|+|.
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-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMG-GRYIEVF   82 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEET-TEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeC-CcEEEEE
Confidence            34568999999999999999999999999 99999999874    5799999999999999999 9999999 9999999


Q ss_pred             eecC
Q psy4057         243 FAKK  246 (246)
Q Consensus       243 ~ak~  246 (246)
                      +|+.
T Consensus        83 ~a~~   86 (91)
T 2dgw_A           83 REKS   86 (91)
T ss_dssp             EESS
T ss_pred             ECCc
Confidence            9863

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.75  E-value=1.5e-18  Score=126.46  Aligned_cols=83  Identities=20%  Similarity=0.371  Sum_probs=76.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.++++++|+++|++||.|..|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  122 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  122 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999998753   788999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      +++...
T Consensus       123 ~a~~~~  128 (135)
T 2lea_A          123 MARYGR  128 (135)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            987653

>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=4.1e-18  Score=115.69  Aligned_cols=80  Identities=13%  Similarity=0.101  Sum_probs=73.8

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC--CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT--LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~--~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      .....++|||+|||.++++++|+++|++| .|.+|.++++  ++++|||||+|.+.++|.+|++ |||..+.|++|.|.+
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            44568999999999999999999999999 8999999876  3678999999999999999999 999999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      +..+
T Consensus        84 a~~~   87 (91)
T 2dgw_A           84 EKSG   87 (91)
T ss_dssp             ESSC
T ss_pred             CCcC
Confidence            8755

>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=99.75  E-value=8.9e-18  Score=119.05  Aligned_cols=79  Identities=29%  Similarity=0.481  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCc----eEEEEeeCC-ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGF----KEVRLVPNR-HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i----~~v~~~~~~-~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ..+++++|||+|||.++|+++|+++|+.||.|    ..+++..+. +|||||+|.+.++|..|+..|||..+. |++|+|
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~-g~~l~v   99 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLY-GKILVI   99 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCS-SCBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeC-CcEEEE
Confidence            44578999999999999999999999999999    667766544 689999999999999999999999999 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      .||+.
T Consensus       100 ~~a~~  104 (115)
T 2cpx_A          100 EFGKN  104 (115)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            99873

>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=99.75  E-value=1.9e-18  Score=117.78  Aligned_cols=79  Identities=22%  Similarity=0.290  Sum_probs=71.3

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCC-eeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcC-CccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQ-IMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG-FPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~-i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng-~~~~g~~l~v~~   84 (246)
                      ..++.++|||+|||.++++++|+++|++||. |..+.+    .++|||||+|.+.++|.+|++.||| ..+.|++|+|.+
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~----~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~   79 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL----LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY   79 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE----EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE----cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEE
Confidence            3567899999999999999999999999999 666655    3689999999999999999999999 999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      +..+.
T Consensus        80 a~~~~   84 (93)
T 2cqh_A           80 SVSKK   84 (93)
T ss_dssp             CCCCC
T ss_pred             ccCcc
Confidence            97654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.75  E-value=1.6e-18  Score=125.88  Aligned_cols=77  Identities=18%  Similarity=0.356  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceE--EEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCC----ccCC
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE--VRLVPNR-----HDIAFVEFENEMQSAAAKLALHGF----KITP  235 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~--v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~----~i~~  235 (246)
                      ...++++|||+|||.++|+++|+++|++||.|..  |+++.++     +|||||+|.+. +|..|+..|||.    .++ 
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~-   96 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTID-   96 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGG-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCC-
Confidence            4467899999999999999999999999999966  9999876     58999999999 999999999999    999 


Q ss_pred             CCceEEEeec
Q psy4057         236 THAMKISFAK  245 (246)
Q Consensus       236 g~~l~v~~ak  245 (246)
                      |++|+|.||+
T Consensus        97 gr~l~V~~a~  106 (131)
T 2m2b_A           97 GKTINVEFAK  106 (131)
T ss_dssp             GCCCCCEECC
T ss_pred             CEEEEEEECC
Confidence            9999999986

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.75  E-value=2.4e-18  Score=112.52  Aligned_cols=70  Identities=21%  Similarity=0.285  Sum_probs=66.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      +|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|++ |||..++ |++|+|.||
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-IHFHEIN-NKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSS-SCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEEC-CEEEEEEeC
Confidence            48999999999999999999999999999999875     5899999999999999998 9999999 999999986

>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=99.75  E-value=4.1e-18  Score=128.56  Aligned_cols=83  Identities=16%  Similarity=0.252  Sum_probs=75.4

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||..+++++|+++|++||.|..|.++.+.   .++|||||+|.+.++|..|++.|||..|.|++|.|.
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            45667889999999999999999999999999999998753   678999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++....
T Consensus       148 ~a~~~~  153 (165)
T 1rk8_A          148 WCFVKG  153 (165)
T ss_dssp             ESEECC
T ss_pred             EecCCC
Confidence            986553

>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=5.6e-18  Score=118.16  Aligned_cols=77  Identities=12%  Similarity=0.317  Sum_probs=70.1

Q ss_pred             CCCCcEEEEcCCCCCC------CHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCC-
Q psy4057         168 QPPNQILFLTNLPEET------SEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTH-  237 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~------t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~-  237 (246)
                      ...+++|||+|||..+      |+++|+++|++||.|.++++++..   +|||||+|.+.++|..|+..|||..++ |+ 
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~-g~~   90 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD-KQH   90 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECS-TTC
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccC-CCc
Confidence            3457899999999999      789999999999999999998522   589999999999999999999999999 87 


Q ss_pred             ceEEEeec
Q psy4057         238 AMKISFAK  245 (246)
Q Consensus       238 ~l~v~~ak  245 (246)
                      +|+|.||+
T Consensus        91 ~l~V~~a~   98 (105)
T 2nlw_A           91 TFRVNLFT   98 (105)
T ss_dssp             EEEEECSC
T ss_pred             eEEEEEcc
Confidence            99999985

>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=99.75  E-value=8.2e-18  Score=125.75  Aligned_cols=78  Identities=17%  Similarity=0.266  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...+.++|||+|||.++|+++|+++|+.||.|..|+++.++     +|||||+|.+.++|.+|+..|||..|+ |++|+|
T Consensus        35 ~~~~~~~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           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLD-DRIIRT  113 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEET-TEECEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEEC-CeEEEE
Confidence            34578999999999999999999999999999999999875     479999999999999999999999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .||+
T Consensus       114 ~~a~  117 (156)
T 1h2v_Z          114 DWDA  117 (156)
T ss_dssp             EEES
T ss_pred             EECC
Confidence            9996

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.3e-17  Score=114.55  Aligned_cols=76  Identities=20%  Similarity=0.378  Sum_probs=69.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      ...++++|||+||  ++|+++|+++|++||.|.+|.+... +|||||+|.+.++|.+|+..|||..|. |++|+|.||+.
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~a~~Ai~~l~g~~~~-g~~l~v~~a~~   86 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP-RNCAFVTYEKMESADQAVAELNGTQVE-SVQLKVNIARK   86 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHTTTEEET-TEEEEEECCSS
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCC-CCEEEEEECCHHHHHHHHHHhCCCeEC-CeEEEEEECCC
Confidence            3456899999996  8999999999999999999999644 489999999999999999999999999 99999999863

>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=99.75  E-value=6e-18  Score=125.71  Aligned_cols=81  Identities=26%  Similarity=0.369  Sum_probs=71.7

Q ss_pred             CCCCc--EEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCC--eeEEEE
Q psy4057           8 ICVTN--FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD--KPMRIQ   83 (246)
Q Consensus         8 ~~~~~--~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g--~~l~v~   83 (246)
                      .+|++  +|||+||++.+++++|+++|++||.|.+|.+... +++|||||+|.+.++|..|++.|||..|.|  ++|+|.
T Consensus        41 ~~ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k-~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           41 AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCCCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES-SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CCCCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            34554  4789999999999999999999999999998643 468999999999999999999999999966  999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      |++.+.
T Consensus       120 ~Ak~~~  125 (164)
T 1sjr_A          120 FSKLTS  125 (164)
T ss_dssp             ECSSSS
T ss_pred             EecCCc
Confidence            998664

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=1.3e-18  Score=114.42  Aligned_cols=73  Identities=19%  Similarity=0.361  Sum_probs=68.7

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ++|||+|||.++++++|+++|++||.|.+|.+.++.   +++|||||+|.+.++|.+|++.++ ..+.|++|+|.+|
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            479999999999999999999999999999998763   678999999999999999999999 9999999999986

>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=2.3e-18  Score=123.78  Aligned_cols=78  Identities=26%  Similarity=0.332  Sum_probs=72.7

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ++++|||+|||.++++++|+++|++||.|.+|.++++   ++++|||||+|.+.++|.+|+ .|||..+.|++|+|.+++
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            3689999999999999999999999999999999875   478999999999999999999 799999999999999987


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      ..
T Consensus       114 ~~  115 (124)
T 2jwn_A          114 TN  115 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.74  E-value=6e-18  Score=117.80  Aligned_cols=80  Identities=19%  Similarity=0.182  Sum_probs=72.5

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeE-EEEccC--CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMD-IVALKT--LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~-v~~~~~--~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..+.++|||+|||+++++++|+++|++||.|.+ |.++.+  ++++|||||+|.+.++|.+|++. |+..+.|++|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            456799999999999999999999999999987 777765  47899999999999999999997 99999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      +...
T Consensus        91 ~~~~   94 (104)
T 1wg5_A           91 SSRA   94 (104)
T ss_dssp             ECTT
T ss_pred             CCHH
Confidence            8544

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=4e-18  Score=118.87  Aligned_cols=78  Identities=13%  Similarity=0.197  Sum_probs=72.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ...++.++|||+|||.++++++|+++|++||.|..|+++.++     +|||||+|.+.++|.+|+.. ||..|. |+.|+
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~-g~~l~   88 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLD-GRNID   88 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEET-TEEEB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeEC-CEEEE
Confidence            355679999999999999999999999999999999999975     48999999999999999999 999999 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.||+
T Consensus        89 V~~a~   93 (105)
T 2dh8_A           89 PKPCT   93 (105)
T ss_dssp             CCCSC
T ss_pred             EEEcc
Confidence            99986

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3e-18  Score=121.71  Aligned_cols=80  Identities=18%  Similarity=0.330  Sum_probs=73.9

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      +.++|||+|||.++++++|+++|++||.|..|.++++.   +++|||||+|.+.++|.+|++. ++..+.|++|+|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            46899999999999999999999999999999998863   7889999999999999999997 9999999999999987


Q ss_pred             CCcc
Q psy4057          87 TDSD   90 (246)
Q Consensus        87 ~~~~   90 (246)
                      .+..
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            6643

>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=99.74  E-value=8.4e-18  Score=116.81  Aligned_cols=82  Identities=17%  Similarity=0.226  Sum_probs=74.0

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...+.++|||+|||.++++++|+++|++||.|..|.++++   ++++|||||+|.+.++|.+|+.  ++..+.|++|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            4467899999999999999999999999999999999876   4778999999999999999999  4778999999999


Q ss_pred             EccCCcc
Q psy4057          84 YSKTDSD   90 (246)
Q Consensus        84 ~a~~~~~   90 (246)
                      ++..+..
T Consensus        89 ~a~~~~~   95 (103)
T 2cqg_A           89 LPNSKQS   95 (103)
T ss_dssp             CCCTTCC
T ss_pred             ecCCCCc
Confidence            9876643

>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=99.74  E-value=2.9e-18  Score=116.91  Aligned_cols=75  Identities=19%  Similarity=0.274  Sum_probs=67.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCC-ceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCC-CccCCCCceEEEeec
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPG-FKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG-FKITPTHAMKISFAK  245 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~-i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g-~~i~~g~~l~v~~ak  245 (246)
                      .++.++|||+|||.++|+++|+++|++||. |..+.+..  +|||||+|.+.++|..|++.||| ..++ |+.|+|.||+
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~~-g~~l~v~~a~   81 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK--SGYAFVDYPDQNWAIRAIETLSGKVELH-GKIMEVDYSV   81 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE--TTEEEECCSCHHHHHHHHHHHTTTCEET-TEECEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEcC--CCEEEEEECCHHHHHHHHHHccCCeeEC-CEEEEEEEcc
Confidence            456899999999999999999999999999 66555543  48999999999999999999999 9999 9999999986

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.74  E-value=9.6e-18  Score=120.17  Aligned_cols=81  Identities=25%  Similarity=0.355  Sum_probs=70.5

Q ss_pred             CCCCCcEEE--ecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccE-EEEEEcCHHHHHHHHHHhcCCccCC--eeEE
Q psy4057           7 HICVTNFVY--VTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ-AFVIFKEIASATNALRSMQGFPFYD--KPMR   81 (246)
Q Consensus         7 ~~~~~~~l~--V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~-aFV~f~~~~~A~~Ai~~lng~~~~g--~~l~   81 (246)
                      ..+|++.|+  |+||++.+++++|+++|++||.|.+|.+.+.  .+|+ |||+|.+.++|..|++.|||..+.|  ++|+
T Consensus        22 ~~~ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~--~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~Lr   99 (130)
T 3zzy_A           22 MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR   99 (130)
T ss_dssp             ---CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE--TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEE
T ss_pred             cCCCCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC--CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEE
Confidence            345566555  7999999999999999999999999988764  4677 9999999999999999999999988  9999


Q ss_pred             EEEccCCc
Q psy4057          82 IQYSKTDS   89 (246)
Q Consensus        82 v~~a~~~~   89 (246)
                      |+||+...
T Consensus       100 I~~ak~~~  107 (130)
T 3zzy_A          100 IDFSKLTS  107 (130)
T ss_dssp             EEECSCSS
T ss_pred             EEecCCCc
Confidence            99997664

>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=8.6e-18  Score=116.33  Aligned_cols=75  Identities=20%  Similarity=0.253  Sum_probs=67.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC----CccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ...+.++|||+|||.++|+++|+++|++||.|   +++.+    .+|||||+|.+.++|.+|+..|||..|. |++|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIE-GRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEET-TEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeC-CeEEEEE
Confidence            45579999999999999999999999999987   44444    2589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus        87 ~a~   89 (101)
T 2fc9_A           87 LQG   89 (101)
T ss_dssp             ECS
T ss_pred             EcC
Confidence            986

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.2e-18  Score=121.20  Aligned_cols=80  Identities=15%  Similarity=0.077  Sum_probs=73.0

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCe-eEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQI-MDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i-~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..+.++|||+|||.++++++|+++|++||.| .+|.++.+.  +++|||||+|.+.++|.+|++. |+..+.|++|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            4567999999999999999999999999999 788888754  7899999999999999999996 99999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      +...
T Consensus        91 a~~~   94 (114)
T 2cpy_A           91 VTLE   94 (114)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8544

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.74  E-value=1.4e-17  Score=115.86  Aligned_cols=81  Identities=17%  Similarity=0.275  Sum_probs=72.2

Q ss_pred             CCCCCcEEEecCCCh-----hhhHHHHHHHhhccCCeeEEEEccC----CCCccEEEEEEcCHHHHHHHHHHhcCCccCC
Q psy4057           7 HICVTNFVYVTHISS-----TDLKKSLYAIFSQFGQIMDIVALKT----LKMRGQAFVIFKEIASATNALRSMQGFPFYD   77 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~-----~~~e~~l~~~F~~fG~i~~v~~~~~----~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (246)
                      ...|+++|+|.||..     +.++++|++.|++||.|.+|.++++    ++++|+|||+|.+.++|.+|++.|||..+.|
T Consensus         4 ~~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~G   83 (105)
T 2pe8_A            4 GKCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGG   83 (105)
T ss_dssp             GGSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            457899999999962     4589999999999999999999876    3679999999999999999999999999999


Q ss_pred             eeEEEEEccC
Q psy4057          78 KPMRIQYSKT   87 (246)
Q Consensus        78 ~~l~v~~a~~   87 (246)
                      |+|.|.++..
T Consensus        84 r~i~v~~a~~   93 (105)
T 2pe8_A           84 RVVKACFYNL   93 (105)
T ss_dssp             EECEEEECCH
T ss_pred             cEEEEEEcCH
Confidence            9999999854

>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=99.74  E-value=4.5e-18  Score=114.77  Aligned_cols=77  Identities=16%  Similarity=0.248  Sum_probs=72.0

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      .++++|||+|||.++++++|+++|++| .|.++.+.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.++..+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~---~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD---RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE---GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe---CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            467899999999999999999999999 89999884   68999999999999999999999999999999999998665


Q ss_pred             c
Q psy4057          89 S   89 (246)
Q Consensus        89 ~   89 (246)
                      .
T Consensus        79 ~   79 (88)
T 1wg1_A           79 A   79 (88)
T ss_dssp             C
T ss_pred             c
Confidence            4

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.6e-18  Score=118.39  Aligned_cols=81  Identities=15%  Similarity=0.170  Sum_probs=72.2

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ...+.++|||+|||+++++++|+++|++|| +.+|.++.+.  +++|||||+|.+.++|++|++ +|+..+.|+.|.|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            456778999999999999999999999999 5599888654  788999999999999999995 899999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      +....
T Consensus        89 ~~~~~   93 (102)
T 1wez_A           89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            86543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.2e-17  Score=114.81  Aligned_cols=78  Identities=23%  Similarity=0.323  Sum_probs=71.6

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...++++|||+|+  ++++++|+++|++||.|.+|.+.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.++.
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~---~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~   85 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD---PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   85 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE---TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCS
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec---CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECC
Confidence            3457899999996  89999999999999999999884   588999999999999999999999999999999999987


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      .+.
T Consensus        86 ~~~   88 (97)
T 1x5p_A           86 KQP   88 (97)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.74  E-value=1.8e-17  Score=118.19  Aligned_cols=80  Identities=20%  Similarity=0.324  Sum_probs=70.8

Q ss_pred             CCCCcEE--EecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccE-EEEEEcCHHHHHHHHHHhcCCccCC--eeEEE
Q psy4057           8 ICVTNFV--YVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ-AFVIFKEIASATNALRSMQGFPFYD--KPMRI   82 (246)
Q Consensus         8 ~~~~~~l--~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~-aFV~f~~~~~A~~Ai~~lng~~~~g--~~l~v   82 (246)
                      .+|+++|  ||+||++.+++++|+++|++||.|.+|.+...   .|+ |||+|.+.++|..|++.|||..|.|  ++|+|
T Consensus        20 ~~ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~---~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V   96 (124)
T 2e5i_A           20 SGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR---NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKI   96 (124)
T ss_dssp             CCCCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES---SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEE
T ss_pred             CCCCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEE
Confidence            4567775  57999999999999999999999999998652   386 9999999999999999999999988  68999


Q ss_pred             EEccCCcc
Q psy4057          83 QYSKTDSD   90 (246)
Q Consensus        83 ~~a~~~~~   90 (246)
                      .+|+....
T Consensus        97 ~~Ak~~~l  104 (124)
T 2e5i_A           97 EYARPTRL  104 (124)
T ss_dssp             ECCSCSCC
T ss_pred             EEecCCcc
Confidence            99987653

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.74  E-value=3.7e-18  Score=121.60  Aligned_cols=79  Identities=13%  Similarity=0.063  Sum_probs=72.4

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCC---eeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQ---IMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~---i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ....++|||+|||+++++++|+++|+.||.   |..|.++.+.  +++|||||+|.+.++|.+|++ +|+..+.|++|+|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            445789999999999999999999999999   8999888654  788999999999999999999 9999999999999


Q ss_pred             EEccC
Q psy4057          83 QYSKT   87 (246)
Q Consensus        83 ~~a~~   87 (246)
                      .++..
T Consensus        93 ~~a~~   97 (118)
T 2db1_A           93 FKSHR   97 (118)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            99843

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.74  E-value=1.4e-18  Score=120.43  Aligned_cols=80  Identities=14%  Similarity=0.214  Sum_probs=71.4

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..+.++|||+|||.++++++|+++|++||.|.. .++.+   ++++|||||+|.+.++|.+|++ |||..+.|++|+|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            346889999999999999999999999999887 34433   4789999999999999999999 999999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      +..+.
T Consensus        92 a~~~~   96 (101)
T 1fj7_A           92 PKGRD   96 (101)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            87653

>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=7.5e-18  Score=119.99  Aligned_cols=77  Identities=18%  Similarity=0.130  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCC---ceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPG---FKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~---i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                      .....++|||+|||.++|+++|+++|+.||.   |..|+++.++    +|||||+|.+.++|.+|++ |||..|+ |+.|
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 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMG-HRYI   90 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEET-TEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeEC-CeEE
Confidence            3446899999999999999999999999999   8999999865    5799999999999999999 9999999 9999


Q ss_pred             EEEeec
Q psy4057         240 KISFAK  245 (246)
Q Consensus       240 ~v~~ak  245 (246)
                      +|.+|+
T Consensus        91 ~V~~a~   96 (118)
T 2db1_A           91 EVFKSH   96 (118)
T ss_dssp             EEEEEC
T ss_pred             EEEECC
Confidence            999985

>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=99.73  E-value=9.5e-18  Score=117.75  Aligned_cols=77  Identities=19%  Similarity=0.305  Sum_probs=70.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCC-ceEEEEe-eC-----CccEEEEEeCCHHHHHHHHHHhC--CCccCCCCc
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPG-FKEVRLV-PN-----RHDIAFVEFENEMQSAAAKLALH--GFKITPTHA  238 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~-i~~v~~~-~~-----~~g~afV~f~~~~~A~~Al~~l~--g~~i~~g~~  238 (246)
                      ..+.++|||+|||.++++++|+++|+.||. |.++.++ .+     .+|||||+|.+.++|..|+..||  +..++ |+.
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~-g~~   83 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLW-GHQ   83 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBT-TBC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceec-CCe
Confidence            446899999999999999999999999998 9999998 33     25899999999999999999996  58999 999


Q ss_pred             eEEEeec
Q psy4057         239 MKISFAK  245 (246)
Q Consensus       239 l~v~~ak  245 (246)
                      |+|.||+
T Consensus        84 l~V~~a~   90 (109)
T 2dis_A           84 IAVDWAE   90 (109)
T ss_dssp             CEEEESC
T ss_pred             EEEEEcC
Confidence            9999986

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.73  E-value=2.8e-18  Score=113.90  Aligned_cols=71  Identities=13%  Similarity=0.360  Sum_probs=64.4

Q ss_pred             CcEEEEcCCCCCC------CHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCC-ceE
Q psy4057         171 NQILFLTNLPEET------SEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTH-AMK  240 (246)
Q Consensus       171 ~~~l~v~nL~~~~------t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~-~l~  240 (246)
                      +++|||+|||..+      ++++|+++|++||.|.++++++..   +|||||+|.+.++|..|+..|||..++ |+ +|+
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~-g~~~l~   79 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD-KQHTFR   79 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCS-SSSCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccC-CceeEE
Confidence            4789999999999      779999999999999999988532   589999999999999999999999999 88 887


Q ss_pred             EE
Q psy4057         241 IS  242 (246)
Q Consensus       241 v~  242 (246)
                      |+
T Consensus        80 V~   81 (81)
T 2krb_A           80 VN   81 (81)
T ss_dssp             CC
T ss_pred             eC
Confidence            63

>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=99.73  E-value=7.7e-18  Score=113.62  Aligned_cols=74  Identities=16%  Similarity=0.276  Sum_probs=69.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      .+++|||+|||.++++++|+++|++| .|.++++. ..+|||||+|.+.++|..|++.|||..++ |++|+|.||+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~-g~~l~V~~a~~   77 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFR-GKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEET-TEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeEC-CcEEEEEEcCC
Confidence            57899999999999999999999999 99999986 44699999999999999999999999999 99999999863

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=5.1e-18  Score=111.47  Aligned_cols=71  Identities=18%  Similarity=0.270  Sum_probs=67.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|+ ..++ |++|+|.+|
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-HELD-SKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCS-SCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccC-CEEEEEEec
Confidence            479999999999999999999999999999999875     5899999999999999999999 8899 999999987

>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=99.73  E-value=3.7e-18  Score=124.15  Aligned_cols=78  Identities=13%  Similarity=0.036  Sum_probs=72.0

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCC---eeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQ---IMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~---i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ....++|||+|||+++++++|+++|++||.   |.+|.++++.  +++|||||+|.+.++|++|++ +|+..+.|++|.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            345789999999999999999999999999   8889888764  788999999999999999999 9999999999999


Q ss_pred             EEcc
Q psy4057          83 QYSK   86 (246)
Q Consensus        83 ~~a~   86 (246)
                      .++.
T Consensus       120 ~~a~  123 (136)
T 2hgl_A          120 FKSH  123 (136)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9974

>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=2.5e-17  Score=114.65  Aligned_cols=78  Identities=18%  Similarity=0.202  Sum_probs=70.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceE-EEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE-VRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~-v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .....++|||+|||.++|+++|+++|+.||.|.+ |+++.+.    +|||||+|.+.++|.+|+.. ||..++ |+.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~-gr~i~v   88 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIG-HRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSS-SSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhC-CcEEEE
Confidence            3456899999999999999999999999999987 8887753    58999999999999999997 999999 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      .++.+
T Consensus        89 ~~~~~   93 (104)
T 1wg5_A           89 FKSSR   93 (104)
T ss_dssp             EEECT
T ss_pred             EECCH
Confidence            98763

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.73  E-value=8.7e-18  Score=117.96  Aligned_cols=78  Identities=17%  Similarity=0.213  Sum_probs=67.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ....+.++|||+|||.++|+++|+++|+.||.|.+|+++.++     +|||||+|.+.++|..|+..+ |..++ |+.|+
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~-g~~l~   97 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELD-SKTID   97 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEET-TEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCC-CEEEE
Confidence            345578999999999999999999999999999999999875     589999999999999999986 58899 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.+|+
T Consensus        98 V~~a~  102 (109)
T 2rs2_A           98 PKVAF  102 (109)
T ss_dssp             EEECC
T ss_pred             EEEcc
Confidence            99985

>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=99.73  E-value=1.7e-17  Score=112.07  Aligned_cols=77  Identities=22%  Similarity=0.335  Sum_probs=63.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCcc--CCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF--YDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~--~g~~l~v~~   84 (246)
                      ..++..+|||+|||.++++++|+++|++||.|.+|.++++  ++|||||+|.+.++|.+    +++..+  .|++|.|.+
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~--srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~   80 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP--FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISN   80 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS--CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC--CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEE
Confidence            4567899999999999999999999999999999999885  89999999999999983    566554  599999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      +.++.
T Consensus        81 a~~k~   85 (89)
T 3d2w_A           81 AEPKH   85 (89)
T ss_dssp             CC---
T ss_pred             cCCCC
Confidence            87553

>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=1e-17  Score=120.36  Aligned_cols=77  Identities=18%  Similarity=0.234  Sum_probs=67.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEee-CC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP-NR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~-~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .....++|||+|||.++|+++|+++|+.||.|..+.++. +.    +|||||+|.+.++|.+||. |||..|+ |+.|+|
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~-gr~i~V   98 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMG-NRFIQV   98 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCST-TSCBEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeEC-CcEEEE
Confidence            344679999999999999999999999999997744443 22    5899999999999999999 9999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .+|+
T Consensus        99 ~~a~  102 (124)
T 1wel_A           99 HPIT  102 (124)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9986

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.73  E-value=7e-18  Score=121.22  Aligned_cols=74  Identities=14%  Similarity=0.255  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..++|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|..|+ .|||..|+ |+.|+|+|+
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~-g~~l~V~~a  112 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFR-GRTIKVLPK  112 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEET-TEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeEC-CeEEEEEEC
Confidence            47899999999999999999999999999999999864     689999999999999999 89999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus       113 ~  113 (124)
T 2jwn_A          113 R  113 (124)
T ss_dssp             S
T ss_pred             C
Confidence            6

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.72  E-value=3.5e-18  Score=111.67  Aligned_cols=72  Identities=19%  Similarity=0.261  Sum_probs=67.1

Q ss_pred             EEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        13 ~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      +|||+|||.++++++|+++|++||.|.+|.+.++   ++++|||||+|.+.++|.+|++ +++..+.|++|.|.+|
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            5899999999999999999999999999999876   3788999999999999999999 5899999999999875

>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=99.72  E-value=2.2e-18  Score=116.75  Aligned_cols=72  Identities=22%  Similarity=0.361  Sum_probs=67.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.+ |..|+..|||..++ |+.|+|+||.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~-g~~l~V~~a~   78 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFM-GRTIRVTEAN   78 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCS-SSSCSEEEC-
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEEC-CeEEEEEEcC
Confidence            579999999999999999999999999999999864     589999999999 99999999999999 9999999986

>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=99.72  E-value=4.7e-17  Score=113.00  Aligned_cols=76  Identities=17%  Similarity=0.180  Sum_probs=69.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...+.++|||+|||.++++++|+++|++||.|..++++.++     +|||||+|.+.++|..|+.  ++..++ |+.|+|
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~-g~~l~v   87 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMID-GRWCDC   87 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEET-TEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeC-CeEEEE
Confidence            45568999999999999999999999999999999999875     5799999999999999999  577899 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .||+
T Consensus        88 ~~a~   91 (103)
T 2cqg_A           88 KLPN   91 (103)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9986

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=1.7e-17  Score=113.74  Aligned_cols=81  Identities=14%  Similarity=0.182  Sum_probs=72.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEE-EEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v-~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+| .++.+. ..+.|||+|.+.++|.+|++.|||..+.|++|+|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~-~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS-ETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS-SSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC-CCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            34457999999999999999999999999999999 476664 3344999999999999999999999999999999998


Q ss_pred             cCC
Q psy4057          86 KTD   88 (246)
Q Consensus        86 ~~~   88 (246)
                      .++
T Consensus        90 ~~~   92 (96)
T 2e44_A           90 PDE   92 (96)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            765

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.72  E-value=6.9e-18  Score=115.70  Aligned_cols=76  Identities=18%  Similarity=0.288  Sum_probs=68.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC--CccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN--RHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~--~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ...+.++|||+|||.++++++|+++|++||.|..+  ...  .+|||||+|.+.++|..|+..|||..++ |++|+|.||
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~--~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~a   88 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID-GRSVSLYYT   88 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE--EETTEEEEEEEEEESSHHHHHHHHHHTTEEEET-TEEEEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe--CCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC-CeEEEEEEc
Confidence            45578999999999999999999999999999877  222  2689999999999999999999999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus        89 ~   89 (96)
T 1fjc_A           89 G   89 (96)
T ss_dssp             S
T ss_pred             C
Confidence            5

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.2e-17  Score=118.61  Aligned_cols=74  Identities=22%  Similarity=0.266  Sum_probs=70.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      +.++|||+|||.++++++|+++|+.||.|..|+++.++     +|||||+|.+.++|..|+.. ||..|+ |+.|+|.||
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~-g~~l~V~~a  103 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSID-GRVVEPKRA  103 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEET-TEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEEC-CEEEEEEEC
Confidence            47999999999999999999999999999999999874     58999999999999999998 999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus       104 ~  104 (116)
T 1x4b_A          104 V  104 (116)
T ss_dssp             S
T ss_pred             C
Confidence            6

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1e-17  Score=117.31  Aligned_cols=75  Identities=13%  Similarity=0.221  Sum_probs=69.2

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      ..+|||+|||+++++++|+++|++| .|.+|.|+.+.  +++|||||+|.+.++|.+|+ .+|+..+.||.|.|..+..
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            5799999999999999999999999 79999998654  78999999999999999999 5999999999999988743

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.5e-17  Score=117.74  Aligned_cols=76  Identities=17%  Similarity=0.244  Sum_probs=70.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCc-eEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGF-KEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i-~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..+.++|||+|||.++|+++|+++|+.||.| ..|+++.++    +|||||+|.+.++|.+|+.. ||..|+ |+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~-gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLN-GREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEET-TEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccC-CeEEEEE
Confidence            4468999999999999999999999999999 889998865    68999999999999999987 999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      +|+
T Consensus        90 ~a~   92 (114)
T 2cpy_A           90 VVT   92 (114)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            986

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.72  E-value=1.8e-17  Score=126.23  Aligned_cols=82  Identities=21%  Similarity=0.310  Sum_probs=76.0

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC--CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT--LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~--~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.+..+  ++++|||||+|.+.++|.+|++.|||..+.|++|.|.+
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999999876  47889999999999999999999999999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      |...
T Consensus       164 a~~~  167 (177)
T 2f3j_A          164 VASQ  167 (177)
T ss_dssp             ESSG
T ss_pred             ecCC
Confidence            8654

>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=99.72  E-value=2e-17  Score=111.19  Aligned_cols=73  Identities=18%  Similarity=0.377  Sum_probs=68.2

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhcc----C-------CeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQF----G-------QIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY   76 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~f----G-------~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~   76 (246)
                      ..+.++|||+|||.++++++|+++|++|    |       .|.++.+.+   ++|||||+|.+.++|.+|+ .|||..+.
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~---~kg~afV~f~~~~~a~~A~-~l~g~~~~   78 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ---DKNFAFLEFRSVDETTQAM-AFDGIIFQ   78 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECS---SSSEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecC---CCcEEEEEcCCHHHHHHHH-hcCCCEEC
Confidence            4678999999999999999999999999    8       899998875   4899999999999999999 99999999


Q ss_pred             CeeEEEEE
Q psy4057          77 DKPMRIQY   84 (246)
Q Consensus        77 g~~l~v~~   84 (246)
                      |++|+|.+
T Consensus        79 g~~l~V~r   86 (87)
T 2hzc_A           79 GQSLKIRR   86 (87)
T ss_dssp             TEECEEEC
T ss_pred             CeEEEEeC
Confidence            99999975

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=3e-17  Score=113.78  Aligned_cols=76  Identities=30%  Similarity=0.493  Sum_probs=67.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ..++.++|||+|||.++++++|+++|+.|+   .++++.++     +|||||+|.+.++|..|+..|||..|. |+.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~V   86 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEID-GNKVTL   86 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET-TEECEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeEC-CeEEEE
Confidence            455789999999999999999999999875   45566554     589999999999999999999999999 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      .||+.
T Consensus        87 ~~a~~   91 (102)
T 2fc8_A           87 DWAKP   91 (102)
T ss_dssp             EECCC
T ss_pred             EEecC
Confidence            99873

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.56  E-value=4.8e-19  Score=125.88  Aligned_cols=84  Identities=24%  Similarity=0.369  Sum_probs=76.8

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeE--------EEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPF   75 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~--------v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~   75 (246)
                      ..+++++|||+|||.++++++|+++|++||.|..        |.++.+   ++++|||||+|.+.++|.+|++.|||..+
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            4578899999999999999999999999999998        888766   37889999999999999999999999999


Q ss_pred             CCeeEEEEEccCCcc
Q psy4057          76 YDKPMRIQYSKTDSD   90 (246)
Q Consensus        76 ~g~~l~v~~a~~~~~   90 (246)
                      .|++|+|.++..+..
T Consensus        83 ~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           83 SGNPIKVSFATRRAD   97 (116)
Confidence            999999999876643

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.71  E-value=2e-17  Score=120.25  Aligned_cols=77  Identities=17%  Similarity=0.103  Sum_probs=71.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCC---ceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPG---FKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~---i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                      .....++|||+|||+++|+++|+++|+.||.   |.+|+++.++    +|||||+|.+.++|.+|++ |||..++ |+.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~-gr~i  117 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMG-HRYI  117 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESS-SSEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEEC-CEEE
Confidence            3446899999999999999999999999999   8899999875    5899999999999999999 9999999 9999


Q ss_pred             EEEeec
Q psy4057         240 KISFAK  245 (246)
Q Consensus       240 ~v~~ak  245 (246)
                      +|.+|+
T Consensus       118 ~V~~a~  123 (136)
T 2hgl_A          118 EVFKSH  123 (136)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            999875

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=2.5e-17  Score=112.50  Aligned_cols=79  Identities=13%  Similarity=0.132  Sum_probs=68.4

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      +....++|||+|||.++++++|+++|++||.|.+| + .+.....||||+|.+.++|.+|++ |||..+.|++|.|.++.
T Consensus         4 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v-~-~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            4 GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-V-MDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             CCTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE-E-ECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE-E-EcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            34567899999999999999999999999999998 2 332221299999999999999999 99999999999999876


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      ..
T Consensus        81 ~~   82 (94)
T 2e5g_A           81 QK   82 (94)
T ss_dssp             CS
T ss_pred             cC
Confidence            54

>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=99.71  E-value=2.1e-17  Score=117.12  Aligned_cols=72  Identities=15%  Similarity=0.163  Sum_probs=65.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCc-----eEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHA-----MKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~-----l~v~~a  244 (246)
                      ..++|||+|||.++++++|+++|++||.|..+.++.+  |||||+|.+.++|..|++.|||..|+ |+.     ++|..+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~-gr~~~~~~i~v~~~   91 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFR-SHEGETAYIRVKVD   91 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCC-CTTSCCCBCEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEEC-CcEeeeEEEEeccC
Confidence            4789999999999999999999999999999999988  89999999999999999999999999 888     666554

>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=99.71  E-value=5e-17  Score=112.60  Aligned_cols=76  Identities=14%  Similarity=0.173  Sum_probs=68.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .....++|||+|||+++|+++|+++|+.||. .+|+++.++    +|||||+|.+.++|.+|++ +|+..|+ |+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~-gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQ-HRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSS-SSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeEC-CcEEEEE
Confidence            3446889999999999999999999999995 499999875    5799999999999999995 8999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ++.
T Consensus        88 ~~~   90 (102)
T 1wez_A           88 LNS   90 (102)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            875

>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=99.71  E-value=2.1e-17  Score=121.68  Aligned_cols=78  Identities=26%  Similarity=0.468  Sum_probs=69.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceE--------EEEeeC--CccEEEEEeCCHHHHHHHHHHhCCCccCCC
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE--------VRLVPN--RHDIAFVEFENEMQSAAAKLALHGFKITPT  236 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~--------v~~~~~--~~g~afV~f~~~~~A~~Al~~l~g~~i~~g  236 (246)
                      ...++++|||+|||.++|+++|+.+|+.||.|..        +++...  .+|||||+|.+.++|..|+..|||..|+ |
T Consensus        41 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~-g  119 (143)
T 3egn_A           41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLF-G  119 (143)
T ss_dssp             CCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEET-T
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeC-C
Confidence            3557899999999999999999999999999865        444442  2689999999999999999999999999 9


Q ss_pred             CceEEEeec
Q psy4057         237 HAMKISFAK  245 (246)
Q Consensus       237 ~~l~v~~ak  245 (246)
                      ++|+|.||+
T Consensus       120 ~~l~V~~a~  128 (143)
T 3egn_A          120 KPMVVQFAR  128 (143)
T ss_dssp             EECEEEECC
T ss_pred             cEEEEEECC
Confidence            999999996

>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=99.71  E-value=1.4e-17  Score=132.10  Aligned_cols=79  Identities=13%  Similarity=0.142  Sum_probs=72.5

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccC--CeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFG--QIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG--~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..++|||+||+.++++++|+++|++||  .|.+|.|+++.   +++|||||+|.+.++|.+||+.||+..|.|+.|+|.+
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            467899999999999999999999999  99999998764   7899999999999999999999999999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      +...
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8543

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.71  E-value=6.3e-18  Score=118.30  Aligned_cols=80  Identities=13%  Similarity=0.085  Sum_probs=73.2

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCC---eeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQ---IMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR   81 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~---i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (246)
                      ......+|||+|||+++++++|+++|+.||.   |.+|.++.+.  +++|||||+|.+.++|.+|++ +|+..+.|++|.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            3456789999999999999999999999998   8999988764  789999999999999999999 999999999999


Q ss_pred             EEEccC
Q psy4057          82 IQYSKT   87 (246)
Q Consensus        82 v~~a~~   87 (246)
                      |.++..
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            999753

>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=99.71  E-value=4.3e-18  Score=122.39  Aligned_cols=80  Identities=16%  Similarity=0.182  Sum_probs=70.3

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEc---cCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~---~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..+.++|||+|||+++++++|+++|++||.|.++.++   .+++++|||||+|.+.++|.+|++ |||..+.|++|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3456899999999999999999999999999773333   344789999999999999999999 999999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      +..+
T Consensus       101 a~~~  104 (124)
T 1wel_A          101 ITKK  104 (124)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.71  E-value=4.1e-17  Score=129.01  Aligned_cols=80  Identities=23%  Similarity=0.305  Sum_probs=71.8

Q ss_pred             CCCCcEEEecCCChhh---------hHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCcc---
Q psy4057           8 ICVTNFVYVTHISSTD---------LKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF---   75 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~---------~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~---   75 (246)
                      ..++++|||+||+.++         ++++|+++|++||+|++|.++.   ++|||||+|.+.++|+.|++.|+|..+   
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~---~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~  207 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE---SKNCGFVKFKYQANAEFAKEAMSNQTLLLP  207 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG---GGTEEEEEESSHHHHHHHHHHHTTCCCCCT
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC---CCCEEEEEeCCHHHHHHHHHHhCCCEEecc
Confidence            4568999999999998         8999999999999999999986   689999999999999999999999999   


Q ss_pred             ---------CCeeEEEEEccCCcc
Q psy4057          76 ---------YDKPMRIQYSKTDSD   90 (246)
Q Consensus        76 ---------~g~~l~v~~a~~~~~   90 (246)
                               .|+.|.|.||..++.
T Consensus       208 ~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          208 SDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             TSTTGGGGGGSCCCEEEECC----
T ss_pred             ccccccccCCCCEEEEEEccCCCC
Confidence                     899999999976643

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.71  E-value=8.4e-18  Score=116.41  Aligned_cols=75  Identities=21%  Similarity=0.286  Sum_probs=67.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC-----CccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..+.++|||+|||.++|+++|+++|+.||.|.. .++.+     .+|||||+|.+.++|.+|++ |||..|. |+.|+|.
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~-g~~l~V~   90 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVF-GNEIKLE   90 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBT-TBCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEEC-CcEEEEE
Confidence            346889999999999999999999999999876 44433     25899999999999999999 9999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus        91 ~a~   93 (101)
T 1fj7_A           91 KPK   93 (101)
T ss_dssp             CCS
T ss_pred             EcC
Confidence            986

>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=99.71  E-value=2.1e-17  Score=117.14  Aligned_cols=75  Identities=17%  Similarity=0.222  Sum_probs=66.6

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCee-----EEEE
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKP-----MRIQ   83 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~-----l~v~   83 (246)
                      ...++|||+|||.++++++|+++|++||.|.+|.++.+    |||||+|.+.++|.+|++.|||..+.|++     |+|.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~----g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~   89 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   89 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC----CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEec
Confidence            35689999999999999999999999999999999876    99999999999999999999999999999     6666


Q ss_pred             EccC
Q psy4057          84 YSKT   87 (246)
Q Consensus        84 ~a~~   87 (246)
                      .+..
T Consensus        90 ~~~~   93 (115)
T 3beg_B           90 VDGP   93 (115)
T ss_dssp             ECC-
T ss_pred             cCCC
Confidence            6543

>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=99.70  E-value=5e-17  Score=109.78  Aligned_cols=75  Identities=20%  Similarity=0.278  Sum_probs=64.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccC-CCCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKIT-PTHAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~-~g~~l~v~~ak  245 (246)
                      ..++..+|||+|||.++|+++|+++|++||.|.+++++.+.+|||||+|.+.++|.    .|+|..+. .|+.|.|.+|+
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~----~~~~~~~~~~g~~v~v~~a~   82 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQ----SLCGEDLIIKGISVHISNAE   82 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHH----HHTTCEEEETTEEEEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHH----HHcCCCcccCCEEEEEEEcC
Confidence            45579999999999999999999999999999999999988899999999999997    36776542 28999999986

>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=9.7e-18  Score=116.29  Aligned_cols=81  Identities=15%  Similarity=0.270  Sum_probs=73.5

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.++++.  +++|||||+|.+.++|.+|++  ++..+.|++|.|.+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             CEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEE
Confidence            34567999999999999999999999999999999998864  678999999999999999999  99999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      +....
T Consensus        83 a~~~~   87 (102)
T 2xs2_A           83 AIRKQ   87 (102)
T ss_dssp             EEECC
T ss_pred             CCcCc
Confidence            86543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=4.3e-17  Score=114.07  Aligned_cols=73  Identities=14%  Similarity=0.183  Sum_probs=67.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ...+|||+|||+++|+++|+++|+.| .|.+|+++.++    +|||||+|.+.++|.+|+ .|||..++ |+.|.|..|+
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~-gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMI-QRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEET-TEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeEC-CeEEEEEECC
Confidence            46899999999999999999999999 89999999865    589999999999999999 69999999 9999998874

>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=2.1e-17  Score=115.57  Aligned_cols=77  Identities=16%  Similarity=0.118  Sum_probs=70.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCC---ceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPG---FKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~---i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                      .....++|||+|||.++|+++|+++|+.||.   |..|+++.++    +|||||+|.+.++|.+|+. |||..++ |+.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~-gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMG-QRYV   84 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSS-SSCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeC-CeEE
Confidence            3456899999999999999999999999998   8999999865    5899999999999999999 9999999 9999


Q ss_pred             EEEeec
Q psy4057         240 KISFAK  245 (246)
Q Consensus       240 ~v~~ak  245 (246)
                      +|.+|+
T Consensus        85 ~V~~a~   90 (107)
T 2lmi_A           85 EVYEIN   90 (107)
T ss_dssp             CCEECC
T ss_pred             EEEECC
Confidence            999875

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.70  E-value=9.2e-17  Score=111.64  Aligned_cols=76  Identities=18%  Similarity=0.227  Sum_probs=68.2

Q ss_pred             CCCcEEEEcCCCC-----CCCHHHHHHHHccCCCceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHhCCCccCCCC
Q psy4057         169 PPNQILFLTNLPE-----ETSEMMLSMLFNQFPGFKEVRLVPNR------HDIAFVEFENEMQSAAAKLALHGFKITPTH  237 (246)
Q Consensus       169 ~~~~~l~v~nL~~-----~~t~e~l~~~f~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~  237 (246)
                      .++++|+|+||..     +-++++|+++|++||.|.+++++.++      +|+|||+|.+.++|.+|+..|||+.|+ |+
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~-Gr   84 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFG-GR   84 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEET-TE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEEC-Cc
Confidence            4799999999963     23789999999999999999999753      589999999999999999999999999 99


Q ss_pred             ceEEEeec
Q psy4057         238 AMKISFAK  245 (246)
Q Consensus       238 ~l~v~~ak  245 (246)
                      .|+|.|++
T Consensus        85 ~i~v~~a~   92 (105)
T 2pe8_A           85 VVKACFYN   92 (105)
T ss_dssp             ECEEEECC
T ss_pred             EEEEEEcC
Confidence            99999985

>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=3.4e-17  Score=129.76  Aligned_cols=75  Identities=17%  Similarity=0.166  Sum_probs=70.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCC--CceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFP--GFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G--~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..++|||+|||.++|+++|+++|+.||  .|.+|+|+.++     +|||||+|.+.++|.+||+.|||..|. |+.|+|.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~-Gr~l~V~  145 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELH-GQNPVVT  145 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBT-TBCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeEC-CEEeEEE
Confidence            578999999999999999999999999  99999999975     589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus       146 ~a~  148 (229)
T 3q2s_C          146 PVN  148 (229)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            986

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.70  E-value=8.4e-17  Score=122.53  Aligned_cols=78  Identities=22%  Similarity=0.273  Sum_probs=72.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ...++++|||+|||..+++++|+++|+.||.|..|.++.++    +|||||+|.+.++|..|+..|||..|+ |+.|+|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~-Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLD-GRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCS-SSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEEC-CEEEEEE
Confidence            34568999999999999999999999999999999999864    589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||.
T Consensus       163 ~a~  165 (177)
T 2f3j_A          163 LVA  165 (177)
T ss_dssp             EES
T ss_pred             Eec
Confidence            985

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.69  E-value=5.1e-17  Score=127.59  Aligned_cols=79  Identities=23%  Similarity=0.389  Sum_probs=73.9

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      ..++|||+|||.++++++|+++|++||.|.+|.++++. .++|||||+|.+.++|.+|++.|||..+.|++|.|.++..+
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            45789999999999999999999999999999998865 57899999999999999999999999999999999998654

>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=99.69  E-value=1.1e-17  Score=122.13  Aligned_cols=80  Identities=15%  Similarity=0.173  Sum_probs=71.5

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ..+.++|||+|||+++++++|+++|++|| |.+|.|+.+.  +++|||||+|.+.++|.+|+ .+|+..+.|++|.|.++
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            34678999999999999999999999999 7799998764  78999999999999999999 69999999999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ....
T Consensus       121 ~~~~  124 (139)
T 2hgn_A          121 STTG  124 (139)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            6543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.69  E-value=8.8e-17  Score=120.76  Aligned_cols=80  Identities=25%  Similarity=0.325  Sum_probs=74.6

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.++++++|+++|++||.|.++.+.++   +.++|+|||+|.+.++|.+|++.|||..+.|++|+|.
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            4566889999999999999999999999999999999866   3778999999999999999999999999999999999


Q ss_pred             Ecc
Q psy4057          84 YSK   86 (246)
Q Consensus        84 ~a~   86 (246)
                      ||+
T Consensus       163 ~a~  165 (166)
T 3md3_A          163 WAA  165 (166)
T ss_dssp             ESC
T ss_pred             ecC
Confidence            985

>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=99.69  E-value=1.9e-17  Score=108.15  Aligned_cols=70  Identities=17%  Similarity=0.274  Sum_probs=65.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      +|||+|||.++++++|+++|++||.|.++.++.++     +|||||+|.+.++|.+|++. +|..+. |+.|+|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~-g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVG-LSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBT-TBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeEC-CEEEEEEEC
Confidence            58999999999999999999999999999998764     58999999999999999984 999999 999999986

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=7.8e-17  Score=110.00  Aligned_cols=75  Identities=16%  Similarity=0.200  Sum_probs=65.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ...++|||+|||.++|+++|+++|+.||.|.+|.+.+....||||+|.+.++|.+|+. |||..|+ |+.|+|.+|+
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~-g~~l~V~~a~   80 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLG-GHRLRVRPRE   80 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEET-TEECCCBCSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEEC-CEEEEEEECC
Confidence            3578999999999999999999999999999882222221299999999999999999 9999999 9999999875

>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=99.69  E-value=1.8e-16  Score=111.77  Aligned_cols=83  Identities=18%  Similarity=0.271  Sum_probs=72.8

Q ss_pred             cCCCCCcEEEecCC--Chh---------hhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCc
Q psy4057           6 AHICVTNFVYVTHI--SST---------DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFP   74 (246)
Q Consensus         6 ~~~~~~~~l~V~nl--~~~---------~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~   74 (246)
                      ....|+++|+|.||  +.+         .++++|+++|++||.|.+|.| .+..++|||||+|.+.++|.+|+..|||..
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRHPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETTCTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecCCCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            35678999999999  333         247899999999999999966 566789999999999999999999999999


Q ss_pred             cCCeeEEEEEccCCc
Q psy4057          75 FYDKPMRIQYSKTDS   89 (246)
Q Consensus        75 ~~g~~l~v~~a~~~~   89 (246)
                      +.|++|+|.++....
T Consensus        89 ~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           89 FGGRQITAQAWDGTT  103 (112)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCcEEEEEEeCCCC
Confidence            999999999987654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.52  E-value=1.9e-18  Score=122.81  Aligned_cols=78  Identities=24%  Similarity=0.348  Sum_probs=72.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceE--------EEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE--------VRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKIT  234 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~--------v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~  234 (246)
                      .+++++|||+|||.++++++|+++|++||.|..        ++++.++     +|||||+|.+.++|..|+..|||..+.
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            457899999999999999999999999999998        8888764     589999999999999999999999999


Q ss_pred             CCCceEEEeecC
Q psy4057         235 PTHAMKISFAKK  246 (246)
Q Consensus       235 ~g~~l~v~~ak~  246 (246)
                       |++|+|.||+.
T Consensus        84 -g~~l~V~~a~~   94 (116)
T 2lcw_A           84 -GNPIKVSFATR   94 (116)
Confidence             99999999863

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.69  E-value=6.1e-17  Score=128.02  Aligned_cols=78  Identities=17%  Similarity=0.352  Sum_probs=71.7

Q ss_pred             CCCCCcEEEEcCCCCCC---------CHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCcc----
Q psy4057         167 EQPPNQILFLTNLPEET---------SEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI----  233 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~---------t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i----  233 (246)
                      ....+++|||+||+..+         ++++|+.+|++||.|.+|+++.++ |||||+|.+.++|..|++.|||..+    
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~k-G~AFV~F~~~~~Ae~A~~am~g~~l~~~~  208 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK-NCGFVKFKYQANAEFAKEAMSNQTLLLPS  208 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGG-TEEEEEESSHHHHHHHHHHHTTCCCCCTT
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCC-CEEEEEeCCHHHHHHHHHHhCCCEEeccc
Confidence            35579999999999998         799999999999999999999865 9999999999999999999999999    


Q ss_pred             --------CCCCceEEEeecC
Q psy4057         234 --------TPTHAMKISFAKK  246 (246)
Q Consensus       234 --------~~g~~l~v~~ak~  246 (246)
                              . |+.|.|.||+.
T Consensus       209 ~~e~~~~~~-gr~L~V~wA~~  228 (240)
T 3u1l_A          209 DKEWDDRRE-GTGLLVKWANE  228 (240)
T ss_dssp             STTGGGGGG-SCCCEEEECC-
T ss_pred             cccccccCC-CCEEEEEEccC
Confidence                    6 99999999973

>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=99.69  E-value=5.1e-17  Score=116.36  Aligned_cols=78  Identities=22%  Similarity=0.216  Sum_probs=69.9

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCee--EEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIM--DIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~--~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ...+.++|||+|||+++++++|+++|++|+ |.  +|.++.+.  +++|||||+|.+.++|++|++ +++..+.|++|.|
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~~-i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V  115 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGLE-IVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEV  115 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCC-ceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEE
Confidence            345678999999999999999999999995 77  89888654  789999999999999999999 5789999999999


Q ss_pred             EEcc
Q psy4057          83 QYSK   86 (246)
Q Consensus        83 ~~a~   86 (246)
                      .++.
T Consensus       116 ~~a~  119 (126)
T 2hgm_A          116 FKSS  119 (126)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9874

>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=99.68  E-value=1e-16  Score=127.26  Aligned_cols=78  Identities=23%  Similarity=0.418  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPE-ETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~-~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..+++++|||+|||. ++++++|+++|+.||.|.+|+++.+++|||||+|.+.++|..|++.|||..+. |+.|+|.|++
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~-g~~l~v~~a~  108 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLH-GKPIRITLSK  108 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCS-SSBCEEECCS
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeEC-CeEEEEEEec
Confidence            345799999999999 99999999999999999999999999999999999999999999999999999 9999999986

>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=99.68  E-value=7.4e-17  Score=108.42  Aligned_cols=71  Identities=23%  Similarity=0.371  Sum_probs=67.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccC----C-------CceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCc
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQF----P-------GFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHA  238 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~----G-------~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~  238 (246)
                      +.++|||+|||.++++++|+++|++|    |       .|.++++..++ |||||+|.+.++|.+|+ .|||..+. |+.
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~k-g~afV~f~~~~~a~~A~-~l~g~~~~-g~~   81 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK-NFAFLEFRSVDETTQAM-AFDGIIFQ-GQS   81 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSS-SEEEEEESSHHHHHHHG-GGTTCEET-TEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCC-cEEEEEcCCHHHHHHHH-hcCCCEEC-CeE
Confidence            58999999999999999999999999    8       89999999875 89999999999999999 99999999 999


Q ss_pred             eEEEe
Q psy4057         239 MKISF  243 (246)
Q Consensus       239 l~v~~  243 (246)
                      |+|+.
T Consensus        82 l~V~r   86 (87)
T 2hzc_A           82 LKIRR   86 (87)
T ss_dssp             CEEEC
T ss_pred             EEEeC
Confidence            99873

>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=99.68  E-value=3e-17  Score=110.66  Aligned_cols=77  Identities=22%  Similarity=0.310  Sum_probs=66.7

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      .++++|||+|||.++++++|+++|++||.|.+|.++++  ++|||||+|.+.++|++|...  +..+.|++|.|.++..+
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~   78 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP--FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPK   78 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS--CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC--CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCC
Confidence            56899999999999999999999999999999999875  899999999999999764331  24558999999998765


Q ss_pred             c
Q psy4057          89 S   89 (246)
Q Consensus        89 ~   89 (246)
                      .
T Consensus        79 ~   79 (88)
T 1wf0_A           79 H   79 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=2.7e-17  Score=117.53  Aligned_cols=77  Identities=23%  Similarity=0.197  Sum_probs=69.5

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCe----eEEEEccC--CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQI----MDIVALKT--LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i----~~v~~~~~--~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      ....+|||+|||+++++++|+++|++||.|    ..|.++.+  ++++|||||+|.+.++|.+|++. |+..+.|+.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            567899999999999999999999999975    57877754  47899999999999999999995 999999999999


Q ss_pred             EEcc
Q psy4057          83 QYSK   86 (246)
Q Consensus        83 ~~a~   86 (246)
                      ..+.
T Consensus       100 ~~a~  103 (123)
T 2dha_A          100 FRST  103 (123)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9874

>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=99.68  E-value=1.9e-16  Score=110.06  Aligned_cols=80  Identities=15%  Similarity=0.302  Sum_probs=70.4

Q ss_pred             CCCCcEEEecCC--Ch--------hhhHHHHHHHhhccCCeeEEEEccCC-----CCccEEEEEEcCHHHHHHHHHHhcC
Q psy4057           8 ICVTNFVYVTHI--SS--------TDLKKSLYAIFSQFGQIMDIVALKTL-----KMRGQAFVIFKEIASATNALRSMQG   72 (246)
Q Consensus         8 ~~~~~~l~V~nl--~~--------~~~e~~l~~~F~~fG~i~~v~~~~~~-----~~kg~aFV~f~~~~~A~~Ai~~lng   72 (246)
                      ..|+++|.+.|+  +.        +.++++|++.|++||.|.+|.|+++.     +++|+|||+|.+.++|.+|++.|||
T Consensus         2 g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            2 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             CSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            368999999887  22        23568999999999999999998764     5789999999999999999999999


Q ss_pred             CccCCeeEEEEEccC
Q psy4057          73 FPFYDKPMRIQYSKT   87 (246)
Q Consensus        73 ~~~~g~~l~v~~a~~   87 (246)
                      ..+.||+|+|.++..
T Consensus        82 ~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           82 RKFANRVVVTKYCDP   96 (105)
T ss_dssp             CEETTEECEEEEECH
T ss_pred             CEeCCCEEEEEEeCH
Confidence            999999999999743

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.67  E-value=2.2e-16  Score=123.85  Aligned_cols=81  Identities=21%  Similarity=0.351  Sum_probs=75.6

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .+.++|||+|||.++++++|+++|++||.|..|.+.++.   +++|||||+|.+.++|.+|++.|||..+.|++|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            567899999999999999999999999999999998764   67899999999999999999999999999999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ....
T Consensus       203 ~~~~  206 (216)
T 2qfj_A          203 VTPP  206 (216)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            7654

>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=99.67  E-value=3e-16  Score=117.98  Aligned_cols=75  Identities=21%  Similarity=0.445  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ++++|||+|||.++++++|+++|+.||.|.+++++.++     +|||||+|.+.++|..|++.|||..+. |++|+|.|+
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~-g~~l~v~~~   79 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQ-TKTIKVSYA   79 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEEEEC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccC-CceEEEEec
Confidence            36899999999999999999999999999999999876     489999999999999999999999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus        80 ~   80 (167)
T 1fxl_A           80 R   80 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.2e-16  Score=111.67  Aligned_cols=76  Identities=18%  Similarity=0.193  Sum_probs=64.3

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC------CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT------LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPM   80 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~------~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (246)
                      ...++++|||+|||.++++++|+++|++||.|. +.++.+      ++++|||||+|.+.++|++|++.|++  +.|+.+
T Consensus         4 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G~~~   80 (114)
T 2dnl_A            4 GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDGKLY   80 (114)
T ss_dssp             SSSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETTEEE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCCcEE
Confidence            346789999999999999999999999999999 777765      36799999999999999999998843  566666


Q ss_pred             EEEEc
Q psy4057          81 RIQYS   85 (246)
Q Consensus        81 ~v~~a   85 (246)
                      .+..+
T Consensus        81 ~~~~~   85 (114)
T 2dnl_A           81 LCVSS   85 (114)
T ss_dssp             EEECC
T ss_pred             EeccC
Confidence            66544

>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=99.67  E-value=5e-17  Score=109.58  Aligned_cols=72  Identities=21%  Similarity=0.287  Sum_probs=64.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCcc--CCCCceEEEeec
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI--TPTHAMKISFAK  245 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i--~~g~~l~v~~ak  245 (246)
                      .++++|||+|||.++++++|+++|++||.|.+++++.+.+|||||+|.+.++|++    +++..+  . |++|+|.+|+
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~----~~~~~~~~~-g~~l~v~~a~   76 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQS----LCGEDLIIK-GISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHH----TTTCEEEET-TEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHH----HhcCCceeC-CEEEEEEecC
Confidence            3689999999999999999999999999999999998888999999999999975    455544  6 8999999986

>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=99.66  E-value=2.3e-16  Score=119.33  Aligned_cols=77  Identities=16%  Similarity=0.285  Sum_probs=72.3

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .+.++|||+|||.++++++|+++|++||.|.++.+.++.   +++|||||+|.+.++|.+|++.|||..+.|++|.|.+|
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            446899999999999999999999999999999998763   67899999999999999999999999999999999987

>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=2.7e-16  Score=118.41  Aligned_cols=75  Identities=28%  Similarity=0.492  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ++++|||+|||.++++++|+++|+.||.|.+++++.++     +|||||+|.+.++|..|++.|||..+. |++|+|.|+
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~-g~~l~v~~~   80 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVR-NKRLKVSYA   80 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEET-TEECEEEEC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeC-CcEEEEEec
Confidence            57899999999999999999999999999999999865     479999999999999999999999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus        81 ~   81 (168)
T 1b7f_A           81 R   81 (168)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.66  E-value=8.4e-17  Score=111.52  Aligned_cols=75  Identities=17%  Similarity=0.321  Sum_probs=69.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ...+++|||+|||.++++++|+++|++||.|.+++++.++    +|||||+|.+.++|..|+.  +|..++ |+.|.|.+
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 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFH-GKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEET-TEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeEC-CEEEEEEE
Confidence            3458999999999999999999999999999999999975    5899999999999999999  999999 99999998


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      +.
T Consensus        83 a~   84 (102)
T 2xs2_A           83 AI   84 (102)
T ss_dssp             EE
T ss_pred             CC
Confidence            74

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.66  E-value=2.6e-16  Score=135.81  Aligned_cols=81  Identities=16%  Similarity=0.251  Sum_probs=75.0

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .+.++|||+|||.++++++|.++|++||.|..|.|+.+   +.++|||||+|.+.++|..||+.|||..|.|++|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45689999999999999999999999999999999865   478999999999999999999999999999999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ....
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            7543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.66  E-value=1.9e-16  Score=122.76  Aligned_cols=75  Identities=24%  Similarity=0.438  Sum_probs=72.2

Q ss_pred             CCcEEEEcCCCC-CCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPE-ETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~-~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .+++|||+|||. ++++++|+++|++||.|.+++++.+++|||||+|.+.++|..|+..|||..+. |+.|+|.|++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~-g~~l~v~~a~   77 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLH-GKPIRITLSK   77 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCS-SCCCEEEECC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeec-CeEEEEEEec
Confidence            368999999999 99999999999999999999999998899999999999999999999999999 9999999986

>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=99.66  E-value=2e-16  Score=113.24  Aligned_cols=76  Identities=16%  Similarity=0.200  Sum_probs=67.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCce--EEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFK--EVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~--~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      .....++|||+|||+++|+++|+++|+.| .|.  +|+++.++    +|||||+|.+.++|.+|++ +++..|+ |+.|+
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-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIG-HRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBT-TBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEEC-CEEEE
Confidence            33467899999999999999999999999 676  89999865    5899999999999999998 5789999 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |.+|.
T Consensus       115 V~~a~  119 (126)
T 2hgm_A          115 VFKSS  119 (126)
T ss_dssp             CEEEC
T ss_pred             EEECC
Confidence            98875

>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=99.66  E-value=2.1e-16  Score=120.00  Aligned_cols=79  Identities=19%  Similarity=0.253  Sum_probs=72.8

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      ..++++|||+|||.++++++|+++|++||.|..+  ..+++++|||||+|.+.++|.+|++.|||..+.|++|.|.|+.+
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~--~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  173 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE  173 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE--CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSS
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe--cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCC
Confidence            3467899999999999999999999999999887  55668999999999999999999999999999999999999875


Q ss_pred             C
Q psy4057          88 D   88 (246)
Q Consensus        88 ~   88 (246)
                      +
T Consensus       174 k  174 (175)
T 1fje_B          174 K  174 (175)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.66  E-value=3.6e-16  Score=118.48  Aligned_cols=77  Identities=27%  Similarity=0.419  Sum_probs=71.2

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccC---CeeEEEE
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFY---DKPMRIQ   83 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~---g~~l~v~   83 (246)
                      .++++|||+|||.++++++|+++|++||.|.+|.+.++.  +++|||||+|.+.++|.+|++.|||..+.   |++|+|.
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            367899999999999999999999999999999998764  67899999999999999999999998876   4999999


Q ss_pred             Ec
Q psy4057          84 YS   85 (246)
Q Consensus        84 ~a   85 (246)
                      ||
T Consensus       173 ~a  174 (175)
T 3nmr_A          173 FA  174 (175)
T ss_dssp             EC
T ss_pred             ec
Confidence            97

>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=99.65  E-value=1.4e-16  Score=112.92  Aligned_cols=82  Identities=12%  Similarity=0.219  Sum_probs=72.0

Q ss_pred             cCCCCCcEEEecCCC-----hhhhHHHHHHHhhccCCeeEEEEccCC-------CCccEEEEEEcCHHHHHHHHHHhcCC
Q psy4057           6 AHICVTNFVYVTHIS-----STDLKKSLYAIFSQFGQIMDIVALKTL-------KMRGQAFVIFKEIASATNALRSMQGF   73 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~-----~~~~e~~l~~~F~~fG~i~~v~~~~~~-------~~kg~aFV~f~~~~~A~~Ai~~lng~   73 (246)
                      ...+|+++|++.|+-     .+..+++|++.|++||.|.+|.|+++.       +++|+|||+|.+.++|.+|++.|||.
T Consensus        15 ~~~~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr   94 (118)
T 3ue2_A           15 LRKQESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR   94 (118)
T ss_dssp             HHHHSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             cCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCC
Confidence            345689999999983     245789999999999999999998763       35699999999999999999999999


Q ss_pred             ccCCeeEEEEEccC
Q psy4057          74 PFYDKPMRIQYSKT   87 (246)
Q Consensus        74 ~~~g~~l~v~~a~~   87 (246)
                      .|.||+|+|.++..
T Consensus        95 ~f~GR~i~v~~~~~  108 (118)
T 3ue2_A           95 WFAGRKVVAEVYDQ  108 (118)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EECCcEEEEEEcCh
Confidence            99999999999743

>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=1.4e-16  Score=119.93  Aligned_cols=78  Identities=22%  Similarity=0.327  Sum_probs=72.7

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ++++|||+|||.++++++|+++|++||.|.++.+..+   ++++|||||+|.+.++|.+|++ ++|..+.|++|.|.++.
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            4679999999999999999999999999999999875   4788999999999999999998 89999999999999986


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.65  E-value=4.3e-16  Score=108.29  Aligned_cols=77  Identities=21%  Similarity=0.285  Sum_probs=67.9

Q ss_pred             CCCCcEEEEcCC--CCCCC--------HHHHHHHHccCCCceEEEEeeCC-------ccEEEEEeCCHHHHHHHHHHhCC
Q psy4057         168 QPPNQILFLTNL--PEETS--------EMMLSMLFNQFPGFKEVRLVPNR-------HDIAFVEFENEMQSAAAKLALHG  230 (246)
Q Consensus       168 ~~~~~~l~v~nL--~~~~t--------~e~l~~~f~~~G~i~~v~~~~~~-------~g~afV~f~~~~~A~~Al~~l~g  230 (246)
                      ..|+++|+|.|+  |.++.        +++|+++|++||.|.+|+++.++       +|+|||+|.+.++|.+|+..|||
T Consensus         2 g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            2 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             CSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            358999999998  33443        36999999999999999998753       58999999999999999999999


Q ss_pred             CccCCCCceEEEeec
Q psy4057         231 FKITPTHAMKISFAK  245 (246)
Q Consensus       231 ~~i~~g~~l~v~~ak  245 (246)
                      +.|+ |+.|+|+|+.
T Consensus        82 ~~f~-GR~i~v~~~~   95 (105)
T 3v4m_A           82 RKFA-NRVVVTKYCD   95 (105)
T ss_dssp             CEET-TEECEEEEEC
T ss_pred             CEeC-CCEEEEEEeC
Confidence            9999 9999999973

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.65  E-value=5e-16  Score=120.16  Aligned_cols=81  Identities=15%  Similarity=0.286  Sum_probs=75.4

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .+.++|||+|||.++++++|+++|++||.|.+|.+.++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            577999999999999999999999999999999998753   67899999999999999999999999999999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      .+..
T Consensus       192 ~~~~  195 (198)
T 2yh0_A          192 SVGA  195 (198)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=8.6e-17  Score=117.30  Aligned_cols=74  Identities=15%  Similarity=0.179  Sum_probs=67.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ...++|||+|||+++|+++|+++|++|| |.+|+++.++    +|||||+|.+.++|.+|+ .||+..|+ |+.|+|.++
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~-gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQ-HRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSS-SCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEEC-CEEEEEEEC
Confidence            3578999999999999999999999999 7799999865    589999999999999999 79999999 999999887


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      .
T Consensus       121 ~  121 (139)
T 2hgn_A          121 S  121 (139)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.64  E-value=9.2e-16  Score=125.36  Aligned_cols=79  Identities=27%  Similarity=0.465  Sum_probs=72.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLS----MLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~----~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ...++++|||+|||.++|+++|+    ++|+.||.|.+|++.++.  +|||||+|.+.++|..|+..|||..|. |+.|+
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~   83 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFY-DKPMR   83 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC-CcEEE
Confidence            45679999999999999999976    899999999999998744  589999999999999999999999999 99999


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |.|++.
T Consensus        84 v~~a~~   89 (282)
T 3pgw_A           84 IQYAKT   89 (282)
T ss_pred             EEEecc
Confidence            999863

>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=99.64  E-value=1.3e-15  Score=107.29  Aligned_cols=77  Identities=13%  Similarity=0.169  Sum_probs=67.0

Q ss_pred             CCCCCcEEEEcCCCCCCC-----------HHHHHHHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCcc
Q psy4057         167 EQPPNQILFLTNLPEETS-----------EMMLSMLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKI  233 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t-----------~e~l~~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i  233 (246)
                      ...++++|+|+||.....           +++|+++|++||.|.+|.+ .++  +|||||+|.+.++|.+|+..|||+.|
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   89 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRHPDGVASVSFRDPEEADYCIQTLDGRWF   89 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETTCTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecCCCCEEEEEEECCHHHHHHHHHHcCCCEE
Confidence            445799999999944332           5899999999999999966 433  69999999999999999999999999


Q ss_pred             CCCCceEEEeec
Q psy4057         234 TPTHAMKISFAK  245 (246)
Q Consensus       234 ~~g~~l~v~~ak  245 (246)
                      + |++|+|.||+
T Consensus        90 ~-gr~l~v~~a~  100 (112)
T 2dit_A           90 G-GRQITAQAWD  100 (112)
T ss_dssp             T-TEECEEEECC
T ss_pred             C-CcEEEEEEeC
Confidence            9 9999999985

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=2.9e-16  Score=112.17  Aligned_cols=75  Identities=17%  Similarity=0.142  Sum_probs=67.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCc----eEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGF----KEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i----~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ....+|||+|||+++|+++|+++|+.||.|    ..|+++.+.    +|||||+|.+.++|.+|+.. |+..++ |+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~-gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLG-KRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESS-SCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeC-CeEEE
Confidence            357899999999999999999999999975    689988764    58999999999999999996 999998 99999


Q ss_pred             EEeec
Q psy4057         241 ISFAK  245 (246)
Q Consensus       241 v~~ak  245 (246)
                      |..|.
T Consensus        99 V~~a~  103 (123)
T 2dha_A           99 LFRST  103 (123)
T ss_dssp             CEEEC
T ss_pred             EEECC
Confidence            98774

>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=99.63  E-value=7.7e-16  Score=118.92  Aligned_cols=81  Identities=20%  Similarity=0.272  Sum_probs=71.4

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .+.++|||+|||.++++++|+++|++||.|..|.++++   ++++|||||+|.+.++|.+|++. +|..+.|++|.|.++
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            45689999999999999999999999999999999876   36789999999999999999986 899999999999998


Q ss_pred             cCCcc
Q psy4057          86 KTDSD   90 (246)
Q Consensus        86 ~~~~~   90 (246)
                      .++..
T Consensus       181 ~~k~~  185 (196)
T 1l3k_A          181 LSKQE  185 (196)
T ss_dssp             C----
T ss_pred             CChhH
Confidence            76643

>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=99.63  E-value=5.3e-16  Score=119.76  Aligned_cols=76  Identities=20%  Similarity=0.375  Sum_probs=69.2

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      .++|||+|||.++++++|+++|++||.|.+|.+.++.  +++|||||+|.+.++|.+|++.++ ..+.|++|.|.++..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHH
Confidence            5899999999999999999999999999999998754  788999999999999999998654 599999999998643

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.63  E-value=3e-16  Score=110.60  Aligned_cols=75  Identities=16%  Similarity=0.166  Sum_probs=67.3

Q ss_pred             cEEEecCC----ChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcC----HHH----HHHHHH--HhcCCc
Q psy4057          12 NFVYVTHI----SSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKE----IAS----ATNALR--SMQGFP   74 (246)
Q Consensus        12 ~~l~V~nl----~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~----~~~----A~~Ai~--~lng~~   74 (246)
                      ..|||+||    |+.+++.+|+++|+.||+|.++.++.|+   +++|||||+|.+    +++    |.+|+.  .+||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999876   779999999996    433    888988  789999


Q ss_pred             cCCeeEEEEEcc
Q psy4057          75 FYDKPMRIQYSK   86 (246)
Q Consensus        75 ~~g~~l~v~~a~   86 (246)
                      +.|++|+|.+-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999953

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.62  E-value=4.4e-15  Score=114.60  Aligned_cols=74  Identities=11%  Similarity=0.139  Sum_probs=67.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..++|||+|||.++|+++|+++|++||.|..|+++.+.    +|||||+|.+.++|..|+..++ ..++ |++|+|.+++
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 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYK-ETDLLILFKD  185 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEET-TEECEEEETT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeEC-CEEEEEEEhH
Confidence            36899999999999999999999999999999999854    5899999999999999998665 5899 9999999976

>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=99.61  E-value=2.5e-15  Score=121.57  Aligned_cols=77  Identities=26%  Similarity=0.427  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ....+++|||+|||.++|+++|+++|+.||.|..|++.+++ |||||+|.+.++|..|+..|||..+. |+.|+|.|++
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~k-g~afV~f~~~~~A~~A~~~l~g~~i~-g~~l~v~~a~   94 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR-GFGFIRLESRTLAEIAKAELDGTILK-SRPLRIRFAT   94 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTT-TEEEEECSSHHHHHHHHHHHTTCEET-TEECEEEECC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCC-cEEEEEECCHHHHHHHHHHcCCcEEC-CceeEeeecc
Confidence            44568899999999999999999999999999999998775 89999999999999999999999999 9999999985

>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=99.60  E-value=2e-15  Score=106.86  Aligned_cols=76  Identities=17%  Similarity=0.195  Sum_probs=67.2

Q ss_pred             CCCcEEEEcCCCC--CC---CHHHHHHHHccCCCceEEEEeeCC---------ccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy4057         169 PPNQILFLTNLPE--ET---SEMMLSMLFNQFPGFKEVRLVPNR---------HDIAFVEFENEMQSAAAKLALHGFKIT  234 (246)
Q Consensus       169 ~~~~~l~v~nL~~--~~---t~e~l~~~f~~~G~i~~v~~~~~~---------~g~afV~f~~~~~A~~Al~~l~g~~i~  234 (246)
                      +++++|+|.|+-.  ++   .+++|++.|++||.|.+|+++.++         +|+|||+|.+.++|.+|+..|||+.|+
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            3799999999842  33   368999999999999999999864         289999999999999999999999999


Q ss_pred             CCCceEEEeec
Q psy4057         235 PTHAMKISFAK  245 (246)
Q Consensus       235 ~g~~l~v~~ak  245 (246)
                       |+.|+|.|+.
T Consensus        98 -GR~i~v~~~~  107 (118)
T 3ue2_A           98 -GRKVVAEVYD  107 (118)
T ss_dssp             -TEECEEEEEC
T ss_pred             -CcEEEEEEcC
Confidence             9999999974

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.58  E-value=2.6e-15  Score=105.88  Aligned_cols=73  Identities=7%  Similarity=0.135  Sum_probs=65.0

Q ss_pred             cEEEEcCC----CCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCC----H-HH---HHHHHH--HhCCCc
Q psy4057         172 QILFLTNL----PEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFEN----E-MQ---SAAAKL--ALHGFK  232 (246)
Q Consensus       172 ~~l~v~nL----~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~----~-~~---A~~Al~--~l~g~~  232 (246)
                      +.|||+||    |+.+++++|+++|+.||.|.++.++.|+     +|||||+|.+    . ++   |.+|+.  .|||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999988     6899999996    3 32   788888  789999


Q ss_pred             cCCCCceEEEeec
Q psy4057         233 ITPTHAMKISFAK  245 (246)
Q Consensus       233 i~~g~~l~v~~ak  245 (246)
                      |+ |++|+|.+-+
T Consensus        83 I~-Gr~irV~ln~   94 (136)
T 2j8a_A           83 IM-GFKFEVILNK   94 (136)
T ss_dssp             ET-TEEEEEEECC
T ss_pred             ec-CcEEEEEECc
Confidence            99 9999998743

>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=99.58  E-value=9.9e-15  Score=102.62  Aligned_cols=80  Identities=20%  Similarity=0.299  Sum_probs=70.1

Q ss_pred             CCCCCcEEEecCCC----------hhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccC
Q psy4057           7 HICVTNFVYVTHIS----------STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY   76 (246)
Q Consensus         7 ~~~~~~~l~V~nl~----------~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~   76 (246)
                      ...|+++|.+.||=          ++..+++|++.|++||.|.+|.+.++ .++|+|||+|.+.++|.+|++.|||..|.
T Consensus         3 ~p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~-~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            3 QPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN-SAQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTT-CTTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecC-CCcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            34578999997661          35678899999999999999999776 36899999999999999999999999999


Q ss_pred             CeeEEEEEccC
Q psy4057          77 DKPMRIQYSKT   87 (246)
Q Consensus        77 g~~l~v~~a~~   87 (246)
                      ||.|+|.|+..
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999999853

>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=99.58  E-value=2.6e-15  Score=104.21  Aligned_cols=70  Identities=16%  Similarity=0.335  Sum_probs=61.1

Q ss_pred             ecCCChhhhHHHHHHHh------------hccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEE
Q psy4057          16 VTHISSTDLKKSLYAIF------------SQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR   81 (246)
Q Consensus        16 V~nl~~~~~e~~l~~~F------------~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (246)
                      +.+|+..+++++|++.|            ++||.|.+|.++++.  +++|||||+|.+.++|.+|++.|||..+.||+|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            45666677777666666            999999999999764  6799999999999999999999999999999999


Q ss_pred             EEEc
Q psy4057          82 IQYS   85 (246)
Q Consensus        82 v~~a   85 (246)
                      |.++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=4.8e-15  Score=104.70  Aligned_cols=63  Identities=22%  Similarity=0.290  Sum_probs=56.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--------ccEEEEEeCCHHHHHHHHHHh---CCC
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--------HDIAFVEFENEMQSAAAKLAL---HGF  231 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--------~g~afV~f~~~~~A~~Al~~l---~g~  231 (246)
                      ...+++|||+|||.++|+++|+++|++||.|. +.++.++        +|||||+|.+.++|.+|++.|   ||+
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~   78 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGK   78 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCc
Confidence            34689999999999999999999999999999 7777642        589999999999999999999   555

>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=99.58  E-value=1.1e-14  Score=102.42  Aligned_cols=76  Identities=17%  Similarity=0.145  Sum_probs=66.6

Q ss_pred             CCCcEEEEcCCCCCC----------CHHHHHHHHccCCCceEEEEeeCC-ccEEEEEeCCHHHHHHHHHHhCCCccCCCC
Q psy4057         169 PPNQILFLTNLPEET----------SEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFENEMQSAAAKLALHGFKITPTH  237 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~----------t~e~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~~~A~~Al~~l~g~~i~~g~  237 (246)
                      .++++|.+.|+-..-          .+++|++.|++||.|.+|.+.++. +|+|||+|.+.++|.+|++.|||+.|+ |+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~-GR   83 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFA-GK   83 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEET-TE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEEC-CE
Confidence            378999999974321          135899999999999999998865 699999999999999999999999999 99


Q ss_pred             ceEEEeec
Q psy4057         238 AMKISFAK  245 (246)
Q Consensus       238 ~l~v~~ak  245 (246)
                      .|+|.|+.
T Consensus        84 ~i~v~~~~   91 (114)
T 3s6e_A           84 MITAAYVP   91 (114)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEEc
Confidence            99999974

>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=99.56  E-value=8.8e-15  Score=121.63  Aligned_cols=78  Identities=9%  Similarity=0.224  Sum_probs=69.2

Q ss_pred             cCCCCCcEEEecC--CChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCcc---CCe--
Q psy4057           6 AHICVTNFVYVTH--ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF---YDK--   78 (246)
Q Consensus         6 ~~~~~~~~l~V~n--l~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~---~g~--   78 (246)
                      ...+|+++|||+|  |+..+++++|+++|++||+|.+|.+.+   +||||||+|.+.++|++|++.|||..+   .|+  
T Consensus        13 ~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~---~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             CCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT---TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             ecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            3578899999988  689999999999999999999998754   789999999999999999999999887   355  


Q ss_pred             eEEEEEcc
Q psy4057          79 PMRIQYSK   86 (246)
Q Consensus        79 ~l~v~~a~   86 (246)
                      +|.+.|+.
T Consensus        90 ~ly~~~~~   97 (345)
T 3tht_A           90 TLYLNFVE   97 (345)
T ss_dssp             ECEEEECS
T ss_pred             EEEEEEee
Confidence            68888874

>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=99.56  E-value=7.8e-15  Score=121.94  Aligned_cols=79  Identities=19%  Similarity=0.276  Sum_probs=69.3

Q ss_pred             CCCCCcEEEEcC--CCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccC--CCC--ceE
Q psy4057         167 EQPPNQILFLTN--LPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKIT--PTH--AMK  240 (246)
Q Consensus       167 ~~~~~~~l~v~n--L~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~--~g~--~l~  240 (246)
                      ..+|+.+|||+|  |+.++|+++|+++|++||.|.+|.+.++ +|||||+|.+.++|++|++.|||+.+.  .|+  +|.
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~-kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly   92 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   92 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTT-CSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEE
Confidence            466899999999  5789999999999999999999998875 499999999999999999999999883  144  688


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |.|+++
T Consensus        93 ~~~~~~   98 (345)
T 3tht_A           93 LNFVEK   98 (345)
T ss_dssp             EEECSS
T ss_pred             EEEeec
Confidence            898753

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=3.7e-14  Score=97.32  Aligned_cols=75  Identities=20%  Similarity=0.175  Sum_probs=64.0

Q ss_pred             CCCcEEEEcCCC-------CCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         169 PPNQILFLTNLP-------EETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       169 ~~~~~l~v~nL~-------~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ....+|.|.-..       .++++++|+++|++||.|.+|+++...+|||||+|.+.++|..|++.+++  +. |++|+|
T Consensus         8 ~~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~-g~~l~V   84 (100)
T 2d9o_A            8 QGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LV-DNPLKI   84 (100)
T ss_dssp             CSSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CS-SSBCEE
T ss_pred             CccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CC-CCeEEE
Confidence            346677776543       46899999999999999999999977789999999999999999998665  56 899999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      .||+.
T Consensus        85 ~~a~~   89 (100)
T 2d9o_A           85 SWLEG   89 (100)
T ss_dssp             ECSSC
T ss_pred             EEccC
Confidence            99873

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.53  E-value=4e-15  Score=103.23  Aligned_cols=68  Identities=13%  Similarity=0.254  Sum_probs=58.3

Q ss_pred             EcCCCCCCCHHHHHHHH------------ccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCce
Q psy4057         176 LTNLPEETSEMMLSMLF------------NQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAM  239 (246)
Q Consensus       176 v~nL~~~~t~e~l~~~f------------~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l  239 (246)
                      +.|||..+++++|++.|            ++||.|.+|+++.+.    +|||||+|.+.++|.+|+..|||+.++ |++|
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 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFN-GQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEET-TEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEEC-CEEE
Confidence            34455556666666555            999999999999875    699999999999999999999999999 9999


Q ss_pred             EEEee
Q psy4057         240 KISFA  244 (246)
Q Consensus       240 ~v~~a  244 (246)
                      +|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99997

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=4.8e-14  Score=96.74  Aligned_cols=75  Identities=21%  Similarity=0.372  Sum_probs=63.1

Q ss_pred             CcEEEecCC-------ChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057          11 TNFVYVTHI-------SSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus        11 ~~~l~V~nl-------~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      .++|-|.-.       +.++++++|+++|++||.|.+|.++  ++++|||||+|.+.++|..|++.+++  +.|++|+|.
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~--~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~   85 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS--SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKIS   85 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE--SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEE
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc--cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEE
Confidence            456666322       3568999999999999999999997  37899999999999999999998554  679999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++....
T Consensus        86 ~a~~~~   91 (100)
T 2d9o_A           86 WLEGQP   91 (100)
T ss_dssp             CSSCCC
T ss_pred             EccCCC
Confidence            987654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=3.3e-13  Score=89.17  Aligned_cols=74  Identities=14%  Similarity=0.212  Sum_probs=65.3

Q ss_pred             CCCCCcEEEEcCCC----CCCCH----HHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCc
Q psy4057         167 EQPPNQILFLTNLP----EETSE----MMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHA  238 (246)
Q Consensus       167 ~~~~~~~l~v~nL~----~~~t~----e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~  238 (246)
                      ..||.-+|+|.-.+    .++-+    .+|.+.|++||.|..++++.++   +||+|.+.++|.+|++ |||..++ |+.
T Consensus         3 ~GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~---~fVtF~d~~sAlaAi~-mnG~~v~-Gr~   77 (91)
T 2dnr_A            3 SGSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK---MWVTFLEGSSALNVLS-LNGKELL-NRT   77 (91)
T ss_dssp             CCCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS---EEEEESSHHHHHHGGG-GTTCEET-TEE
T ss_pred             CCCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC---EEEEECChHHHHHHHh-cCCeEeC-CeE
Confidence            56788899998765    23444    5899999999999999999987   9999999999999999 9999999 999


Q ss_pred             eEEEeec
Q psy4057         239 MKISFAK  245 (246)
Q Consensus       239 l~v~~ak  245 (246)
                      |+|.+++
T Consensus        78 LkV~lkt   84 (91)
T 2dnr_A           78 ITIALKS   84 (91)
T ss_dssp             EEEEECC
T ss_pred             EEEEeCC
Confidence            9999986

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.39  E-value=1.6e-12  Score=85.94  Aligned_cols=76  Identities=24%  Similarity=0.309  Sum_probs=65.1

Q ss_pred             CCCCCcEEEecCCC--------hhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCe
Q psy4057           7 HICVTNFVYVTHIS--------STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK   78 (246)
Q Consensus         7 ~~~~~~~l~V~nl~--------~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~   78 (246)
                      ..||..||+|.-.+        ++....+|.+.|++||.|..+++..+.     +||+|.+.++|.+|++ |||..+.||
T Consensus         3 ~GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-----~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            3 SGSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-----MWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             CCCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-----EEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-----EEEEECChHHHHHHHh-cCCeEeCCe
Confidence            36899999994433        344557899999999999999997753     9999999999999999 999999999


Q ss_pred             eEEEEEccCC
Q psy4057          79 PMRIQYSKTD   88 (246)
Q Consensus        79 ~l~v~~a~~~   88 (246)
                      .|+|.++.++
T Consensus        77 ~LkV~lkt~d   86 (91)
T 2dnr_A           77 TITIALKSPS   86 (91)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEEEeCCCC
Confidence            9999997543

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.38  E-value=4.1e-12  Score=89.41  Aligned_cols=78  Identities=13%  Similarity=0.196  Sum_probs=70.0

Q ss_pred             CCCCCCCCcEEEEcCCCCC-CCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCC-HHHHHHHHHHhC--CCccCCCCce
Q psy4057         164 GVPEQPPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFEN-EMQSAAAKLALH--GFKITPTHAM  239 (246)
Q Consensus       164 ~~~~~~~~~~l~v~nL~~~-~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~-~~~A~~Al~~l~--g~~i~~g~~l  239 (246)
                      ..-..+++++|+|+||+.+ ++.++|+++|+.||.|..|.+..++. .|||.|.+ .++|..|+..||  |..|. |..+
T Consensus        11 ~~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~-tgfVrf~~~~~~A~~av~~ln~~~~~i~-g~~~   88 (121)
T 1owx_A           11 GSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK-EGIILFKEKAKEALGKAKDANNGNLQLR-NKEV   88 (121)
T ss_dssp             CCCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS-EEEEEESSCHHHHHHHHHHTTTSCBCTT-SSSE
T ss_pred             CcccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC-EEEEEECCChHHHHHHHHHhhcCCcEEe-CcEE
Confidence            3446778999999999999 99999999999999999999999985 79999999 899999999994  78888 7888


Q ss_pred             EEEe
Q psy4057         240 KISF  243 (246)
Q Consensus       240 ~v~~  243 (246)
                      ++..
T Consensus        89 ~~ev   92 (121)
T 1owx_A           89 TWEV   92 (121)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8764

>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=99.29  E-value=3.4e-12  Score=84.71  Aligned_cols=73  Identities=16%  Similarity=0.192  Sum_probs=64.6

Q ss_pred             CCCCCCcEEEEcCCCCC-----CCH----HHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCC
Q psy4057         166 PEQPPNQILFLTNLPEE-----TSE----MMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPT  236 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~-----~t~----e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g  236 (246)
                      ...||.-+++|.-++.+     +.+    .+|.+.|++||.|..++++.++   +||+|.+.++|.+|++ |||..++ |
T Consensus        10 ~~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~---~fVtF~d~~sAl~AI~-ldG~~v~-G   84 (95)
T 1ufw_A           10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---MLVTFADSHSALSVLD-VDGMKVK-G   84 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---EEEECSCSHHHHHHHH-GGGSEET-T
T ss_pred             ecCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc---EEEEEcChHHHHHHHh-cCCeeeC-C
Confidence            46789999999977632     333    5789999999999999999997   9999999999999998 9999999 9


Q ss_pred             CceEEEe
Q psy4057         237 HAMKISF  243 (246)
Q Consensus       237 ~~l~v~~  243 (246)
                      +.|+|.+
T Consensus        85 r~L~V~~   91 (95)
T 1ufw_A           85 RAVKISG   91 (95)
T ss_dssp             EEEEEEC
T ss_pred             eEEEEec
Confidence            9999986

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.26  E-value=2.1e-11  Score=85.79  Aligned_cols=77  Identities=16%  Similarity=0.217  Sum_probs=69.1

Q ss_pred             CCCCCcEEEecCCChh-hhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcC-HHHHHHHHHHhc--CCccCCeeEEE
Q psy4057           7 HICVTNFVYVTHISST-DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKE-IASATNALRSMQ--GFPFYDKPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~-~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~-~~~A~~Ai~~ln--g~~~~g~~l~v   82 (246)
                      ..+++..|||+||+.+ +++++|+++|++||+|..|.+.++..   .|||.|.+ ..+|..|++.+|  +..+.|..+++
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~---tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~   90 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK---EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   90 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS---EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC---EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEE
Confidence            5688999999999999 99999999999999999999877544   59999999 899999999995  68899999888


Q ss_pred             EEcc
Q psy4057          83 QYSK   86 (246)
Q Consensus        83 ~~a~   86 (246)
                      ....
T Consensus        91 evL~   94 (121)
T 1owx_A           91 EVLE   94 (121)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            8753

>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=99.26  E-value=1.2e-11  Score=82.04  Aligned_cols=72  Identities=21%  Similarity=0.275  Sum_probs=62.7

Q ss_pred             CCCCCcEEEecCCC---------hhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCC
Q psy4057           7 HICVTNFVYVTHIS---------STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD   77 (246)
Q Consensus         7 ~~~~~~~l~V~nl~---------~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (246)
                      ..||..||+|.-++         ++....+|.+.|++||.|..+++..+.     +||+|.+.++|.+|++ |||..+.|
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-----~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-----MLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-----EEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-----EEEEEcChHHHHHHHh-cCCeeeCC
Confidence            46899999997654         222346799999999999999998764     9999999999999999 99999999


Q ss_pred             eeEEEEE
Q psy4057          78 KPMRIQY   84 (246)
Q Consensus        78 ~~l~v~~   84 (246)
                      |.|+|.+
T Consensus        85 r~L~V~~   91 (95)
T 1ufw_A           85 RAVKISG   91 (95)
T ss_dssp             EEEEEEC
T ss_pred             eEEEEec
Confidence            9999987

>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=99.05  E-value=7.7e-10  Score=86.99  Aligned_cols=74  Identities=18%  Similarity=0.202  Sum_probs=62.2

Q ss_pred             CCcEEEEcCCCC-----CCCHHHHHHHHccCCCceEEEEeeCC---------ccEEEEEeCCHHHHHHHHHHhCCCccCC
Q psy4057         170 PNQILFLTNLPE-----ETSEMMLSMLFNQFPGFKEVRLVPNR---------HDIAFVEFENEMQSAAAKLALHGFKITP  235 (246)
Q Consensus       170 ~~~~l~v~nL~~-----~~t~e~l~~~f~~~G~i~~v~~~~~~---------~g~afV~f~~~~~A~~Al~~l~g~~i~~  235 (246)
                      .+.++.+.|+..     +-.+++|+..|++||.|.++.+..+.         +|++||+|.+.++|.+|++.|||+.+. 
T Consensus       123 ~s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~-  201 (222)
T 3dxb_A          123 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA-  201 (222)
T ss_dssp             BCSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSS-
T ss_pred             ccccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceEC-
Confidence            456666666522     33567999999999999999998531         489999999999999999999999999 


Q ss_pred             CCceEEEee
Q psy4057         236 THAMKISFA  244 (246)
Q Consensus       236 g~~l~v~~a  244 (246)
                      |+.|++.|+
T Consensus       202 gr~i~~~~~  210 (222)
T 3dxb_A          202 GRKVVAEVY  210 (222)
T ss_dssp             SSBCEEEEC
T ss_pred             CeEEEEEEc
Confidence            999999996

>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=99.05  E-value=5.6e-10  Score=87.78  Aligned_cols=66  Identities=15%  Similarity=0.272  Sum_probs=59.6

Q ss_pred             hhhhHHHHHHHhhccCCeeEEEEccCC-------CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          21 STDLKKSLYAIFSQFGQIMDIVALKTL-------KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        21 ~~~~e~~l~~~F~~fG~i~~v~~~~~~-------~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      .+..+++|++.|++||.|.++.++++.       +++|++||+|.+.++|.+|+..|||..+.||+|.+.|+.
T Consensus       139 ~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          139 DDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             CTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            456778999999999999999998532       678999999999999999999999999999999999974

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.93  E-value=6.5e-09  Score=70.34  Aligned_cols=71  Identities=14%  Similarity=0.285  Sum_probs=67.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccC-----CCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQF-----PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~-----G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..++|-+-|||..+++..|+.+.+.+     |.++.|.+.++-.| |+|+|.+...|.+|.-.|+|.+|. |++|++.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~G-Aivef~d~~~AgKasLaL~G~ef~-gr~Lr~g   95 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNG-AIIIFRDSKFAAKMLMILNGSQFQ-GKVIRSG   95 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTE-EEEECSCHHHHHHHHHHHSSEEET-TEEEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCc-eEEEEccchhhHHHHhhcCCeeec-CeEEEec
Confidence            47889999999999999999999999     99999999999866 999999999999999999999999 9999986

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.76  E-value=2e-08  Score=67.95  Aligned_cols=81  Identities=19%  Similarity=0.252  Sum_probs=71.4

Q ss_pred             cccccCCCC---CcEEEecCCChhhhHHHHHHHhhcc-----CCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCC
Q psy4057           2 NIILAHICV---TNFVYVTHISSTDLKKSLYAIFSQF-----GQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF   73 (246)
Q Consensus         2 ~~~~~~~~~---~~~l~V~nl~~~~~e~~l~~~F~~f-----G~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~   73 (246)
                      +++|++-.+   .++|-+-+||..++...++.+..++     |.|..|.+..|.  .| |+|+|.+...|-+|.=.|+|.
T Consensus         9 k~il~s~~~~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH--~G-Aivef~d~~~AgKasLaL~G~   85 (117)
T 2l9w_A            9 KRLLASRNSKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF--NG-AIIIFRDSKFAAKMLMILNGS   85 (117)
T ss_dssp             HHHHHCCCTTTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT--TE-EEEECSCHHHHHHHHHHHSSE
T ss_pred             HHHHhccCCccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC--Cc-eEEEEccchhhHHHHhhcCCe
Confidence            345666655   7899999999999999999999999     999999997763  33 999999999999999889999


Q ss_pred             ccCCeeEEEEEc
Q psy4057          74 PFYDKPMRIQYS   85 (246)
Q Consensus        74 ~~~g~~l~v~~a   85 (246)
                      .|.|++|+|.-.
T Consensus        86 ef~gr~Lr~gTv   97 (117)
T 2l9w_A           86 QFQGKVIRSGTI   97 (117)
T ss_dssp             EETTEEEEEECH
T ss_pred             eecCeEEEecCH
Confidence            999999999865

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.46  E-value=3.2e-07  Score=61.89  Aligned_cols=73  Identities=21%  Similarity=0.284  Sum_probs=63.2

Q ss_pred             CcEEEEcCCCCCC-C----HHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         171 NQILFLTNLPEET-S----EMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~-t----~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..+|+++||+.++ +    .+.++++|..|+++....+.+.=+ -..|.|.+.++|.+|...|||+.|. |+.|+|.||.
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR-Rirv~F~~~~~A~~AR~~Lh~~~f~-g~~~r~YFgq   82 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK-RVRINFSNPLSAADARLRLHKTEFL-GKEMKLYFAQ   82 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT-EEEEECSSTTHHHHHHHTSTTSEET-TEECEEECCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce-EEEEEeCChHHHHHHHHHhccceec-CceeEEEecC
Confidence            5679999998866 2    257899999999998888777653 3899999999999999999999999 9999999974

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.33  E-value=5.3e-06  Score=55.68  Aligned_cols=71  Identities=15%  Similarity=0.143  Sum_probs=60.0

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhcc-----CCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQF-----GQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~f-----G~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++|.|.|||.++.++.|.-+|+.-     |+|+++....     +-|+|+|.+.+.|++.+. -....|.|.+|.|.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-----~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV~   79 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-----CGGVLTFREPADAERVLA-QADHELHGAQLSLR   79 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-----TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEEE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-----CcEEEEEcChHHHHHHhc-CCcceecCeEEEEE
Confidence            456899999999999999999999872     6899886633     779999999999999988 33578888999998


Q ss_pred             Ec
Q psy4057          84 YS   85 (246)
Q Consensus        84 ~a   85 (246)
                      ..
T Consensus        80 P~   81 (104)
T 2dhx_A           80 PA   81 (104)
T ss_dssp             EC
T ss_pred             cC
Confidence            74

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.30  E-value=2.3e-06  Score=57.69  Aligned_cols=72  Identities=14%  Similarity=0.242  Sum_probs=63.3

Q ss_pred             cEEEecCCChhhh-----HHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          12 NFVYVTHISSTDL-----KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        12 ~~l~V~nl~~~~~-----e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ++|+|.||+.++-     .+.++++|..|+++.....+++.+   -..|.|.++++|.+|-..|++..+.|+.|+|-++.
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR---Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq   82 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK---RVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT---EEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce---EEEEEeCChHHHHHHHHHhccceecCceeEEEecC
Confidence            6899999988763     367899999999999987777543   47999999999999999999999999999999986

>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=98.01  E-value=4.2e-05  Score=50.64  Aligned_cols=63  Identities=14%  Similarity=0.271  Sum_probs=57.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-------ccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-------HDIAFVEFENEMQSAAAKLALHGFKIT  234 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-------~g~afV~f~~~~~A~~Al~~l~g~~i~  234 (246)
                      +.|.|++||+.+|++++.+.++..+.+....++++.       ..-|+|.|.+.+++..-.+.++|+.|.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            468999999999999999999999999888888866       246999999999999999999999885

>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=97.99  E-value=3.5e-05  Score=51.10  Aligned_cols=58  Identities=21%  Similarity=0.297  Sum_probs=49.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhC
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH  229 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~  229 (246)
                      ....++++| ++|.++...||.++|+.||. ..|+.+.|-  .|||.|.+++.|..|+..+.
T Consensus        13 p~r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT--sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           13 PKRDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT--SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT--EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC--eEEEEecCHHHHHHHHHhcc
Confidence            335778888 99999999999999999995 557777775  59999999999999999774

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.81  E-value=3.6e-05  Score=51.19  Aligned_cols=56  Identities=21%  Similarity=0.298  Sum_probs=49.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhC
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH  229 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~  229 (246)
                      ..++++| ++|.++...||.++|+.|| -..|+.+.|-  .|||.|.+++.|..|+..+.
T Consensus         5 R~HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT--sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            5 SDHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT--SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT--EEEEEEEEECHHHHHHHHHT
T ss_pred             CCeEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC--eEEEEecCHHHHHHHHHhcc
Confidence            3567788 9999999999999999999 4678888885  59999999999999999875

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.66  E-value=0.0008  Score=45.13  Aligned_cols=69  Identities=7%  Similarity=0.106  Sum_probs=55.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHcc-----CCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQ-----FPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~-----~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ...++|.|.|||..+.++.|.-.|+.     -|.|.++....   +-|+|+|.+...|++.|.. .-+.++ +.+|.|.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k-~~H~L~-~~~LsV~   79 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ-ADHELH-GAQLSLR   79 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC-SCCBSS-SSBCEEE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC-Ccceec-CeEEEEE
Confidence            35789999999999999999999976     36778887776   3599999999999998763 245566 6777664

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.48  E-value=0.00055  Score=47.39  Aligned_cols=69  Identities=9%  Similarity=0.190  Sum_probs=54.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ..+-|.|-++|... -..+.+.|++||.|.+..... ...+-.|.|.+..+|++||. .||..|.++.-|=|
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~-~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV   91 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN-TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGV   91 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS-SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEE
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC-CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEE
Confidence            47788888898875 566788899999999888743 34799999999999999988 59999883333333

>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=97.44  E-value=0.00045  Score=45.76  Aligned_cols=55  Identities=24%  Similarity=0.346  Sum_probs=44.9

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhc
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ   71 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~ln   71 (246)
                      .+.++| +.|.++...||..+|++||.|. |..+.    ...|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~Wid----DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWID----DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEE----TTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEc----CCeEEEEecCHHHHHHHHHhcc
Confidence            456667 9999999999999999999543 33333    3679999999999999998653

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.42  E-value=0.0011  Score=45.89  Aligned_cols=69  Identities=17%  Similarity=0.247  Sum_probs=56.3

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCee-EEEEE
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKP-MRIQY   84 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~-l~v~~   84 (246)
                      .+.|-|.+.|... -..+...|++||.|.+...   ....++-.|.|.+..+|++|+. .||..+.|.. |=|.+
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~---~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM---SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   93 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE---CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc---CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEE
Confidence            5678888999886 4578889999999999865   3466999999999999999999 6999887644 34554

>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=97.33  E-value=0.00093  Score=44.14  Aligned_cols=65  Identities=15%  Similarity=0.169  Sum_probs=54.0

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-----CCccEEEEEEcCHHHHHHHHHHhcCCccC
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-----KMRGQAFVIFKEIASATNALRSMQGFPFY   76 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-----~~kg~aFV~f~~~~~A~~Ai~~lng~~~~   76 (246)
                      .+|-|++||+.++|+++.+.++....+.-.......     ..-..|+|.|.+.+++....+.++|..|.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            468899999999999999999999877665554432     22267999999999999999999998884

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.24  E-value=0.00037  Score=46.40  Aligned_cols=75  Identities=13%  Similarity=0.261  Sum_probs=58.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-------ccEEEEEeCCHHHHHHHHHHhCCCccCCC----Cc
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-------HDIAFVEFENEMQSAAAKLALHGFKITPT----HA  238 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-------~g~afV~f~~~~~A~~Al~~l~g~~i~~g----~~  238 (246)
                      .+..|.|+.||+.+|++++.+.++..-.+....++++.       ..-|+|.|.+.++...-.+..+|+.|.+.    .+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            36779999999999999999888877666666666654       13599999999999999999999887422    33


Q ss_pred             eEEEee
Q psy4057         239 MKISFA  244 (246)
Q Consensus       239 l~v~~a  244 (246)
                      -.|+||
T Consensus        88 a~VE~A   93 (97)
T 2l08_A           88 AVVEFA   93 (97)
T ss_dssp             EEEEEC
T ss_pred             eEEEec
Confidence            446665

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.11  E-value=0.00068  Score=45.05  Aligned_cols=55  Identities=22%  Similarity=0.350  Sum_probs=45.5

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhc
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ   71 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~ln   71 (246)
                      .+.++| +.|.++...||..+|++||. ..|..+.|    ..|||.|.+++.|..|+..+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidD----TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD----TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEET----TEEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcC----CeEEEEecCHHHHHHHHHhcc
Confidence            456777 99999999999999999993 44444443    679999999999999999764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.84  E-value=0.00052  Score=59.01  Aligned_cols=57  Identities=18%  Similarity=0.128  Sum_probs=43.8

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHH
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALR   68 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~   68 (246)
                      +..++|+|. .+.+.++.+|.++|++||+|.++.+.++  ..-||.|+|.+.+++..++.
T Consensus        51 qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~--~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           51 QAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES--FGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS--SSEEEEEECC---CCHHHHS
T ss_pred             HhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc--CCeEEEEEeCCHHHHHHHHh
Confidence            345899997 7999999999999999999999988764  34799999999999998765

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.76  E-value=0.00078  Score=57.95  Aligned_cols=56  Identities=18%  Similarity=0.173  Sum_probs=43.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHH
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL  226 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~  226 (246)
                      ..+.|+|. .|...++.+|.+.|++||.|.++.+-.+..-||+|+|.+.++++.++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            36789997 789999999999999999999999998876799999999998886643

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.53  E-value=0.0087  Score=41.99  Aligned_cols=73  Identities=21%  Similarity=0.210  Sum_probs=54.1

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEE-EccC-----------C-----CCccEEEEEEcCHHHHHHHHHHhcCC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIV-ALKT-----------L-----KMRGQAFVIFKEIASATNALRSMQGF   73 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~-~~~~-----------~-----~~kg~aFV~f~~~~~A~~Ai~~lng~   73 (246)
                      ...|.|-+-|++... .+.+.|++||.|.+-. ..++           .     ...++-.|+|.+..+|++|+. .||.
T Consensus         7 e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            456777888766554 7778999999987722 1110           0     135788999999999999999 7999


Q ss_pred             ccCCeeEEEEEc
Q psy4057          74 PFYDKPMRIQYS   85 (246)
Q Consensus        74 ~~~g~~l~v~~a   85 (246)
                      .+.|.-|=|.+.
T Consensus        85 ii~G~mIGV~Py   96 (132)
T 3p3d_A           85 VFNGVLLGVIPY   96 (132)
T ss_dssp             EETTEECEEEEC
T ss_pred             EeCcEEEEEEEC
Confidence            999986667664

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.00  E-value=0.0054  Score=43.04  Aligned_cols=69  Identities=13%  Similarity=0.246  Sum_probs=48.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceE-EEEee------------------CCccEEEEEeCCHHHHHHHHHHhCCC
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKE-VRLVP------------------NRHDIAFVEFENEMQSAAAKLALHGF  231 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~-v~~~~------------------~~~g~afV~f~~~~~A~~Al~~l~g~  231 (246)
                      ..-|.|-+.|.+.+. .+-+.|++||.|.+ +...+                  ...+|.-|.|.+..+|.+||+ .||.
T Consensus         7 e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            455677778876555 46677899999955 22211                  013589999999999999987 7999


Q ss_pred             ccCCCCceEEE
Q psy4057         232 KITPTHAMKIS  242 (246)
Q Consensus       232 ~i~~g~~l~v~  242 (246)
                      .|. |.-|=|.
T Consensus        85 ii~-G~mIGV~   94 (132)
T 3p3d_A           85 VFN-GVLLGVI   94 (132)
T ss_dssp             EET-TEECEEE
T ss_pred             EeC-cEEEEEE
Confidence            998 7644443

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.87  E-value=0.0093  Score=39.62  Aligned_cols=69  Identities=10%  Similarity=0.084  Sum_probs=51.9

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC----CCc-cEEEEEEcCHHHHHHHHHHhcCCccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL----KMR-GQAFVIFKEIASATNALRSMQGFPFY   76 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~----~~k-g~aFV~f~~~~~A~~Ai~~lng~~~~   76 (246)
                      ...+-+|.|+.||+.+||+++.+.++..-++.........    .+. ..|+|.|.+.++.....+..+|..|.
T Consensus         6 ~~~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            6 HHHSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             cccceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            3456789999999999999988888876554332221211    111 56999999999999999999998874

>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=93.53  E-value=0.28  Score=42.86  Aligned_cols=57  Identities=23%  Similarity=0.295  Sum_probs=48.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCC
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG  230 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g  230 (246)
                      ...+++|+ +|..+...+|.++|+.||. .+|+.+.+.  .|||.|.+.+.|..++..+..
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widdt--~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDDT--SAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSSS--EEEEECSCHHHHHHHHHHHTT
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcCC--eEEEEECCHHHHHHHHHHHHh
Confidence            46788887 9999999999999999996 466666664  699999999999999998854

>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=92.07  E-value=0.38  Score=42.04  Aligned_cols=56  Identities=25%  Similarity=0.323  Sum_probs=44.4

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG   72 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng   72 (246)
                      ...++|+ .|..+...+|.++|+.||.+ +|..+    +...|||.|.+.+.|..++..++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~wi----ddt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWI----DDTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEEC----SSSEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEE----cCCeEEEEECCHHHHHHHHHHHHh
Confidence            4566666 88888899999999999954 44332    446799999999999999998753

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=89.34  E-value=0.8  Score=28.57  Aligned_cols=69  Identities=12%  Similarity=0.211  Sum_probs=42.0

Q ss_pred             EEEEc-CCCCCCCHHHHHHHHccCCCc-----eEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         173 ILFLT-NLPEETSEMMLSMLFNQFPGF-----KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       173 ~l~v~-nL~~~~t~e~l~~~f~~~G~i-----~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      +|++. +=-..++.-+|..++..-+.+     -.|.+..   .|.||+-.. +.|..+++.|++..+. |+.++|+.++|
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d---~~s~v~v~~-~~~~~~~~~l~~~~i~-g~~~~v~~~~~   76 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMD---NASYVEILN-GKGPHVLKVMKNTTVK-GKQLKVNKANK   76 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEECS---SCEEEEECT-TCHHHHHHHHTTCCC----CCCEEECC-
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEeC---CcEEEEECH-HHHHHHHHHhccccCc-CceEEEEECCC
Confidence            35553 223356666777777666655     3344432   378998874 5577889999999999 99999998875

---

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	246
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-15
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-06
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-08
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	5e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	5e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	4e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	6e-10
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-09
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-08
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-06
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-07
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-08
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-07
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	9e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	9e-05
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	7e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-08
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 8e-08
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 7e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	4e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	9e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-06
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	5e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	5e-04
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	5e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	6e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	5e-04
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	9e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-05
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	3e-05
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-05
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-06
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-06
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-04
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	6e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	7e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-05
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	7e-05
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-04
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-04
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-04
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	0.001
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	3e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.001
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-04
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	0.002
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	0.003

>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 = 67.4 bits (164), Expect = 2e-15
 Identities = 59/86 (68%), Positives = 77/86 (89%), Gaps = 4/86 (4%)

Query: 14 VYVTHISST----DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
          +Y+ +++      +LKKSL+AIFS+FGQI+DI+  ++LKMRGQAFVIFKE++SATNALRS
Sbjct: 6  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 65

Query: 70 MQGFPFYDKPMRIQYSKTDSDVISKI 95
          MQGFPFYDKPMRIQY+KTDSD+I+K+
Sbjct: 66 MQGFPFYDKPMRIQYAKTDSDIIAKM 91

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 7/83 (8%)

Query: 170 PNQILFLTNLPEETSEMML----SMLFNQFPGFKEVRLVPNRHD--IAFVEFENEMQSAA 223
           PN  +++ NL E+  +  L      +F++F    ++ +  +      AFV F+    +  
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 224 AKLALHGFKITPTHAMKISFAKK 246
           A  ++ GF       M+I +AK 
Sbjct: 62  ALRSMQGFPF-YDKPMRIQYAKT 83

>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 = 63.9 bits (155), Expect = 7e-14
 Identities = 23/103 (22%), Positives = 48/103 (46%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
           +Y+ ++      + +Y IF ++G I  I    T + RG A+V++++I  A NA   + GF
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 69

Query: 74  PFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDP 116
              ++ + + Y   +            E+ K ++++     DP
Sbjct: 70  NVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDP 112

>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 = 48.5 bits (115), Expect = 4e-08
 Identities = 15/79 (18%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD--IAFVEFENEMQSAAAKL 226
             N+IL++ NLP + +   +  +F ++   +++R+         A+V +E+   +  A  
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 227 ALHGFKITPTHAMKISFAK 245
            L GF +     + + +  
Sbjct: 65  HLSGFNVC-NRYLVVLYYN 82

>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 = 57.9 bits (139), Expect = 5e-12
 Identities = 72/80 (90%), Positives = 75/80 (93%)

Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
           EQPPNQILFLTNLPEET+EMMLSMLFNQFPGFKEVRLVPNRHDIAFVEF  E+QS AAK 
Sbjct: 4   EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKE 63

Query: 227 ALHGFKITPTHAMKISFAKK 246
           AL GFKITPTHAMKI+FAKK
Sbjct: 64  ALQGFKITPTHAMKITFAKK 83

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.2 bits (138), Expect = 8e-12
 Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          +YV  +     +  LY  FS  G I+ I   +   T +  G A+V F++ A A  AL +M
Sbjct: 3  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 71 QGFPFYDKPMRIQYSKTD 88
                 KP+RI +S+ D
Sbjct: 63 NFDVIKGKPVRIMWSQRD 80

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (119), Expect = 4e-09
 Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
           L++ +L  + +E ML   F+       +R+  +         A+V F+    +  A   +
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 229 HGFKITPTHAMKISFAKK 246
           +   I     ++I ++++
Sbjct: 63  NFDVI-KGKPVRIMWSQR 79

>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 = 56.4 bits (136), Expect = 3e-11
 Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 14 VYVTHISSTDLKKS-LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
          V++ ++++  +KKS + AIFS++G+I+          +G AFV +    +A  A+    G
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCS-----VHKGFAFVQYVNERNARAAVAGEDG 72

Query: 73 FPFYDKPMRIQYSKTDSD 90
               + + I  +     
Sbjct: 73 RMIAGQVLDINLAAEPKV 90

>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 = 46.0 bits (109), Expect = 1e-07
 Identities = 16/87 (18%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 161 ATAGVPEQPPNQILFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEM 219
           ++     +  N  +F+ NL      +  +  +F+++       +       AFV++ NE 
Sbjct: 5   SSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNER 61

Query: 220 QSAAAKLALHGFKITPTHAMKISFAKK 246
            + AA     G  I     + I+ A +
Sbjct: 62  NARAAVAGEDGRMI-AGQVLDINLAAE 87

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 6e-11
 Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
           P N  ++   +    ++ ++   F+ F    E+R V      +FV F     +A A +++
Sbjct: 16  PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIR-VFPEKGYSFVRFSTHESAAHAIVSV 74

Query: 229 HGFKITPTHAMKISFAK 245
           +G  I   H +K  + K
Sbjct: 75  NGTTI-EGHVVKCYWGK 90

>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 = 53.8 bits (129), Expect = 2e-10
 Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          VY   I+S    + +   FS FGQIM+I   +    +G +FV F    SA +A+ S+ G 
Sbjct: 21 VYCGGIASGLTDQLMRQTFSPFGQIMEI---RVFPEKGYSFVRFSTHESAAHAIVSVNGT 77

Query: 74 PFYDKPMRIQYSKTDSD 90
                ++  + K   D
Sbjct: 78 TIEGHVVKCYWGKESPD 94

>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 = 53.3 bits (127), Expect = 5e-10
 Identities = 14/102 (13%), Positives = 35/102 (34%), Gaps = 9/102 (8%)

Query: 10  VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
                     S ++ +    ++F  + +       +  K   +  + F    SA +A   
Sbjct: 10  ACV-ANDDVFSESETRAKFESLFRTYDKDTTF---QYFKSFKRVRINFSNPLSAADARLR 65

Query: 70  MQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPA 111
           +    F  K M++ +++T       I  + +  P   +  P+
Sbjct: 66  LHKTEFLGKEMKLYFAQT-----LHIGSSHLAPPNPDKSGPS 102

>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 = 36.7 bits (84), Expect = 4e-04
 Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 7/83 (8%)

Query: 169 PPNQILFLTNLPEE-----TSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAA 223
             +  L      ++      +      LF  +      +   +      + F N + +A 
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK-RVRINFSNPLSAAD 61

Query: 224 AKLALHGFKITPTHAMKISFAKK 246
           A+L LH         MK+ FA+ 
Sbjct: 62  ARLRLH-KTEFLGKEMKLYFAQT 83

>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 = 52.5 bits (125), Expect = 6e-10
 Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE-VRLVPNRHDIAFVEFENEMQSAAAKL 226
            PP+  L L+N+P   SE  L +LF+   G  +  +       +A ++  +  ++  A +
Sbjct: 7   FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALI 66

Query: 227 ALHGFKITPTHAMKISFAK 245
            LH   +   H +++SF+K
Sbjct: 67  DLHNHDLGENHHLRVSFSK 85

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.9 bits (124), Expect = 1e-09
 Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 5/86 (5%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK----TLKMRGQAFVIFKEIASATNA 66
          T+ + V +I     ++ +  +FS FG++  +   K    T   RG  FV F     A  A
Sbjct: 8  TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 67

Query: 67 LRSM-QGFPFYDKPMRIQYSKTDSDV 91
            ++      Y + + ++++ ++  V
Sbjct: 68 FNALCHSTHLYGRRLVLEWADSEVTV 93

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.7 bits (121), Expect = 3e-09
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENE 218
           VP++     + + N+P + ++  +  LF+ F   K VRL              FV+F  +
Sbjct: 2   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 61

Query: 219 MQSAAAKLALHGFKITPTHAMKISFAKK 246
             +  A  AL          + + +A  
Sbjct: 62  QDAKKAFNALCHSTHLYGRRLVLEWADS 89

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.3 bits (120), Expect = 3e-09
 Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
          + V+++        +  +F++FG +    +   ++ +  G A V F+  A A  A++   
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 72 GFPFYDKPMRIQYSKT 87
          G P   +PM IQ   +
Sbjct: 63 GVPLDGRPMNIQLVTS 78

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.8 bits (116), Expect = 1e-08
 Identities = 16/75 (21%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLV----PNRHDIAFVEFENEMQSAAAKLALH 229
           L ++NL    S+  +  LF +F   K+  +           A V FE +  +  A    +
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 230 GFKITPTHAMKISFA 244
           G  +     M I   
Sbjct: 63  GVPL-DGRPMNIQLV 76

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 50.4 bits (120), Expect = 3e-09
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 4/79 (5%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKM---RGQAFVIFKEIASATNAL 67
          TN + V ++      + LYA+F   G I     ++  K     G AFV F     +  A+
Sbjct: 3  TN-LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 68 RSMQGFPFYDKPMRIQYSK 86
          + + G    +K +++ Y++
Sbjct: 62 KVLNGITVRNKRLKVSYAR 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 43.4 bits (102), Expect = 1e-06
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
           L +  LP++ ++  L  LF         R++ +      +  AFV+F +EM S  A   L
Sbjct: 5   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 64

Query: 229 HGFKITPTHAMKISFAK 245
           +G  +     +K+S+A+
Sbjct: 65  NGITV-RNKRLKVSYAR 80

>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 = 50.5 bits (120), Expect = 4e-09
 Identities = 15/84 (17%), Positives = 29/84 (34%), Gaps = 7/84 (8%)

Query: 169 PPNQILFLT--NLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
              Q L +    L    S   L  +  +      +  +P     +F  +    +S  A +
Sbjct: 16  YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL-MPPNKPYSFARYRTTEESKRAYV 74

Query: 227 ALHGFKITPTHAMKI----SFAKK 246
            L+G ++      KI    +F +K
Sbjct: 75  TLNGKEVVDDLGQKITLYLNFVEK 98

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 6e-09
 Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 4/81 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL----KTLKMRGQAFVIFKEIASATNALRS 69
          +++ ++     +K LY  FS FG I+    +     T   +G AF+ F    ++  A+ +
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 70 MQGFPFYDKPMRIQYSKTDSD 90
          M G    ++P+ + Y+     
Sbjct: 61 MNGQYLCNRPITVSYAFKKDS 81

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 1e-05
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENEMQSAAAKLA 227
           +F+ NL  E  E +L   F+ F    +   +    D       AF+ F +   S AA  A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 228 LHGFKITPTHAMKISFAKK 246
           ++G  +     + +S+A K
Sbjct: 61  MNGQYL-CNRPITVSYAFK 78

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.5 bits (115), Expect = 2e-08
 Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 15 YVTHISSTDLKKSLYAIFSQFGQIMDIVAL------KTLKMRGQAFVIFKEIASATNALR 68
          ++ +++ +  +++L  +FS+ G I              L   G  FV +K+   A  AL+
Sbjct: 2  FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 69 SMQGFPFYDKPMRIQYSK 86
           +QG       + ++ S+
Sbjct: 62 QLQGHTVDGHKLEVRISE 79

>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 = 41.9 bits (98), Expect = 3e-06
 Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 9/81 (11%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI--------AFVEFENEMQSAAAK 225
           LF+ NL   T+E  L  +F++    K   +   ++           FVE++   Q+  A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 226 LALHGFKITPTHAMKISFAKK 246
             L G  +   H +++  +++
Sbjct: 61  KQLQGHTV-DGHKLEVRISER 80

>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 = 48.4 bits (115), Expect = 2e-08
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 3/80 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          +YV ++S    ++ +Y +FS+ G I  I+           G  FV +   A A NA+R +
Sbjct: 10 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 71 QGFPFYDKPMRIQYSKTDSD 90
           G    D+ +R  +     +
Sbjct: 70 NGTRLDDRIIRTDWDAGFKE 89

>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 = 45.3 bits (107), Expect = 3e-07
 Identities = 13/77 (16%), Positives = 34/77 (44%), Gaps = 6/77 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI-----AFVEFENEMQSAAAKLAL 228
           L++ NL   T+E  +  LF++    K++ +  ++         FVE+ +   +  A   +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 229 HGFKITPTHAMKISFAK 245
           +G ++     ++  +  
Sbjct: 70  NGTRL-DDRIIRTDWDA 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 = 48.0 bits (114), Expect = 2e-08
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQI---MDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
          +YVT++  T     L  IF ++G I     +    T + RG AFV + +   A  A+ ++
Sbjct: 9  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 68

Query: 71 QGFPF--YDKPMRIQY 84
                   +P+ ++ 
Sbjct: 69 NNVIPEGGSQPLSVRL 84

>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 = 48.0 bits (114), Expect = 2e-08
 Identities = 15/84 (17%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQS 221
           E   +  L++TNLP   ++  L  +F ++    +  ++ ++       +AFV +    ++
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 222 AAAKLALHGFKIT-PTHAMKISFA 244
             A  AL+       +  + +  A
Sbjct: 62  QEAISALNNVIPEGGSQPLSVRLA 85

>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 = 48.1 bits (114), Expect = 2e-08
 Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          +   ++S    +  L  +F    +I  +   +  K +G A++ FK  A A   L   QG 
Sbjct: 19 LLAKNLSFNITEDELKEVFEDALEIRLVS--QDGKSKGIAYIEFKSEADAEKNLEEKQGA 76

Query: 74 PFYDKPMRIQYSK 86
              + + + Y+ 
Sbjct: 77 EIDGRSVSLYYTG 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 = 45.4 bits (107), Expect = 2e-07
 Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 1/81 (1%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
            +    + L   NL    +E  L  +F      + V        IA++EF++E  +    
Sbjct: 11  KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNL 70

Query: 226 LALHGFKITPTHAMKISFAKK 246
               G +I    ++ + +  +
Sbjct: 71  EEKQGAEI-DGRSVSLYYTGE 90

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 3e-08
 Identities = 13/79 (16%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          +++  + +      +  + + FG +     +K   T   +G AF  + +I     A+  +
Sbjct: 4  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 71 QGFPFYDKPMRIQYSKTDS 89
           G    DK + +Q +   +
Sbjct: 64 NGMQLGDKKLLVQRASVGA 82

>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 = 43.5 bits (102), Expect = 9e-07
 Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 6/77 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAAKLAL 228
           LF+  LP   ++  +  L   F   K   LV +         AF E+ +   +  A   L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 229 HGFKITPTHAMKISFAK 245
           +G ++     + +  A 
Sbjct: 64  NGMQL-GDKKLLVQRAS 79

>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 = 48.2 bits (114), Expect = 4e-08
 Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 171 NQILFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH 229
           N +L ++NL PE  +   L +LF  +   + V+++ N+ + A V+  +  Q+  A   L+
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 230 GFKITPTHAMKISFAKK 246
           G K+     ++I+ +K 
Sbjct: 62  GHKLH-GKPIRITLSKH 77

>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 = 38.6 bits (89), Expect = 9e-05
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 14 VYVTHISSTDL-KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
          + V++++   +  +SL+ +F  +G +  +  L     +  A V   +   A  A+  + G
Sbjct: 5  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF--NKKENALVQMADGNQAQLAMSHLNG 62

Query: 73 FPFYDKPMRIQYSKTDS 89
             + KP+RI  SK  +
Sbjct: 63 HKLHGKPIRITLSKHQN 79

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 4e-08
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 3/79 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
          VYV  +     +  L+ +F Q G +++        T + +G  FV F     A  A++ M
Sbjct: 12 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 71

Query: 71 QGFPFYDKPMRIQYSKTDS 89
               Y KP+R+  +   +
Sbjct: 72 DMIKLYGKPIRVNKASAHN 90

>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 = 46.9 bits (111), Expect = 7e-08
 Identities = 18/87 (20%), Positives = 36/87 (41%), Gaps = 6/87 (6%)

Query: 165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEM 219
           + E+  +  +++  L E+ SE +L  LF Q        +  +R         FVEF +E 
Sbjct: 3   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 62

Query: 220 QSAAAKLALHGFKITPTHAMKISFAKK 246
            +  A   +   K+     ++++ A  
Sbjct: 63  DADYAIKIMDMIKL-YGKPIRVNKASA 88

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.3 bits (112), Expect = 5e-08
 Identities = 11/78 (14%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          ++V ++     ++ +  +F ++G+  ++      K +G  F+  +    A  A   +   
Sbjct: 11 LFVGNLPPDITEEEMRKLFEKYGKAGEV---FIHKDKGFGFIRLETRTLAEIAKVELDNM 67

Query: 74 PFYDKPMRIQYSKTDSDV 91
          P   K +R++++   + +
Sbjct: 68 PLRGKQLRVRFACHSASL 85

>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 = 45.7 bits (108), Expect = 2e-07
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           LF+ NLP + +E  +  LF ++    EV  +       F+  E    +  AK+ L    +
Sbjct: 11  LFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEIAKVELDNMPL 69

Query: 234 TPTHAMKISFAKK 246
                +++ FA  
Sbjct: 70  -RGKQLRVRFACH 81

>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 = 47.0 bits (111), Expect = 7e-08
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAA 223
           G  +  P   L++  L   TS   L+  F++F   + +         A++++E+   + A
Sbjct: 10  GYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTID-HVKGDSFAYIQYESLDAAQA 68

Query: 224 AKLALHGFKIT-PTHAMKISFAK 245
           A   + GF +  P   +++ FAK
Sbjct: 69  ACAKMRGFPLGGPDRRLRVDFAK 91

>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 = 47.0 bits (111), Expect = 8e-08
 Identities = 10/74 (13%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQ 71
           V +        ++    +  ++G++ ++         + G  +V F+    A  A+  + 
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 72  GFPFYDKPMRIQYS 85
              F  +P+  + S
Sbjct: 90  NRWFNGQPIHAELS 103

>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 = 38.9 bits (90), Expect = 7e-05
 Identities = 11/81 (13%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 159 PMATAGVPEQPPNQI--LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAF 212
           P  ++   +   + +  + +    +E  E + + +  ++   +E+ +  N  D      +
Sbjct: 13  PQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVY 72

Query: 213 VEFENEMQSAAAKLALHGFKI 233
           V+F  E  +  A + L+    
Sbjct: 73  VKFRREEDAEKAVIDLNNRWF 93

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 1e-07
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 1/78 (1%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL-KTLKMRGQAFVIFKEIASATNALRSMQG 72
          +YV ++S    +  +  +FSQ G       + +        FV F E   A  AL +M G
Sbjct: 11 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 70

Query: 73 FPFYDKPMRIQYSKTDSD 90
               K +++ ++ T S 
Sbjct: 71 RKILGKEVKVNWATTPSS 88

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 1e-07
 Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 4/83 (4%)

Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAA 223
           +    + L++ NL  + +E+++  LF+Q    K  +++          FVEF     +AA
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query: 224 AKLALHGFKITPTHAMKISFAKK 246
           A  A++G KI     +K+++A  
Sbjct: 64  ALAAMNGRKI-LGKEVKVNWATT 85

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 1e-07
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 3/83 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          + V ++        L+ IFS+FG ++ I+   T   + QA + + +  SA +A  S+ G 
Sbjct: 10 IIVENLFYPVTLDVLHQIFSKFGTVLKII-TFTKNNQFQALLQYADPVSAQHAKLSLDGQ 68

Query: 74 PFYD--KPMRIQYSKTDSDVISK 94
            Y+    +RI +SK  S  +  
Sbjct: 69 NIYNACCTLRIDFSKLTSLNVKY 91

>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 = 45.4 bits (107), Expect = 4e-07
 Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 2/84 (2%)

Query: 165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-DIAFVEFENEMQSAA 223
           +  Q P   + + NL    +  +L  +F++F    ++      +   A +++ + + +  
Sbjct: 1   MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQH 60

Query: 224 AKLALHGFKI-TPTHAMKISFAKK 246
           AKL+L G  I      ++I F+K 
Sbjct: 61  AKLSLDGQNIYNACCTLRIDFSKL 84

>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 = 45.8 bits (108), Expect = 2e-07
 Identities = 17/77 (22%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           L+++ LP+  ++  L  LF+Q+      R++ ++       + F+ F+  +++  A   L
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 68

Query: 229 HGFKIT-PTHAMKISFA 244
           +G K +  T  + + FA
Sbjct: 69  NGQKPSGATEPITVKFA 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 = 40.8 bits (95), Expect = 9e-06
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKM---RGQAFVIFKEIASATNALRSM 70
          +YV+ +  T  +K L  +FSQ+G+I+    L        RG  F+ F +   A  A++ +
Sbjct: 9  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 68

Query: 71 QGFPFY--DKPMRIQYS 85
           G       +P+ ++++
Sbjct: 69 NGQKPSGATEPITVKFA 85

>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 = 45.5 bits (107), Expect = 2e-07
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 5/70 (7%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAA 223
            PN  L +  L   T+E  L  +F+++    +V +V ++        AFV FEN   +  
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 224 AKLALHGFKI 233
           AK   +G ++
Sbjct: 67  AKERANGMEL 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 = 42.8 bits (100), Expect = 2e-06
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNAL 67
             + V  +S    ++ L  +FS++G I D+  +   ++ + RG AFV F+ +  A  A 
Sbjct: 9  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 68 RSMQGFPFYDKPMRI 82
              G     + +R+
Sbjct: 69 ERANGMELDGRRIRV 83

>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 = 45.8 bits (108), Expect = 2e-07
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          +YV ++  +  ++ +   F+           +  K+R  AFV F     A  A++++ G 
Sbjct: 11 LYVRNLMLSTSEEMIEKEFNNIKPGAVE---RVKKIRDYAFVHFSNREDAVEAMKALNGK 67

Query: 74 PFYDKPMRIQYSK 86
               P+ +  +K
Sbjct: 68 VLDGSPIEVTLAK 80

>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 = 45.0 bits (106), Expect = 3e-07
 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK 232
           IL++ NL   TSE M+   FN        R+   R   AFV F N   +  A  AL+G  
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-YAFVHFSNREDAVEAMKALNGKV 68

Query: 233 ITPTHAMKISFAK 245
           +     ++++ AK
Sbjct: 69  L-DGSPIEVTLAK 80

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 2e-07
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
          +++ ++  +   K+LY  FS FG I+   V       +G  FV F+   +A  A+  M G
Sbjct: 11 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 70

Query: 73 FPFYDKPMRIQYSKTDSD 90
              D+ + +   K+  +
Sbjct: 71 MLLNDRKVFVGRFKSRKE 88

>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 = 41.9 bits (98), Expect = 3e-06
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 4/76 (5%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHG 230
           +F+ NL +      L   F+ F      ++V +        FV FE +  +  A   ++G
Sbjct: 11  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 70

Query: 231 FKITPTHAMKISFAKK 246
             +     + +   K 
Sbjct: 71  MLL-NDRKVFVGRFKS 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 = 45.0 bits (106), Expect = 3e-07
 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 3/80 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          + VT++S    +  L  +F  FG I  I   K   T + +G AF+ F     A  A+  +
Sbjct: 11 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 70

Query: 71 QGFPFYDKPMRIQYSKTDSD 90
           GF +    + ++++K  ++
Sbjct: 71 SGFGYDHLILNVEWAKPSTN 90

>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 = 41.2 bits (96), Expect = 7e-06
 Identities = 21/84 (25%), Positives = 33/84 (39%), Gaps = 6/84 (7%)

Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQS 221
               N  + +TNL E+T E  L  LF  F     + L  ++        AF+ F     +
Sbjct: 4   RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 63

Query: 222 AAAKLALHGFKITPTHAMKISFAK 245
           A A   + GF       + + +AK
Sbjct: 64  ARAIAGVSGFGY-DHLILNVEWAK 86

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.6 bits (107), Expect = 3e-07
 Identities = 12/81 (14%), Positives = 24/81 (29%), Gaps = 2/81 (2%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
            +   + ++ +  L E   E  L     +F     V  +      A VEFEN   +    
Sbjct: 10  HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVM-MMPFKRQALVEFENIDSAKECV 68

Query: 226 LALHGFKITP-THAMKISFAK 245
                  +         +++ 
Sbjct: 69  TFAADVPVYIAGQQAFFNYST 89

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 4e-07
 Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQI---MDIVALKTLKMRGQAFVIFKEIASATNAL 67
          TN + V ++     ++   ++F   G+I     +    T +  G  FV + +   A  A+
Sbjct: 3  TN-LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 68 RSMQGFPFYDKPMRIQYSK 86
           ++ G     K +++ Y++
Sbjct: 62 NTLNGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 1e-05
 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFENEMQSAAAKLAL 228
           L +  LP+  ++     LF      +  +LV +          FV + +   +  A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 229 HGFKITPTHAMKISFAK 245
           +G ++  T  +K+S+A+
Sbjct: 65  NGLRL-QTKTIKVSYAR 80

>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 = 44.7 bits (105), Expect = 5e-07
 Identities = 15/93 (16%), Positives = 38/93 (40%), Gaps = 11/93 (11%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIV-----ALKTLKMRGQAFVIFKEIASATNALR 68
          +++  I     ++ +    ++  + +  V     A   +K RG AFV ++   +A  A R
Sbjct: 4  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 69 SMQG--FPFYDKPMRIQYSKT----DSDVISKI 95
           +       +   + + +++     D DV+  +
Sbjct: 64 KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV 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 = 36.2 bits (83), Expect = 5e-04
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 171 NQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHD------IAFVEFENEMQSAA 223
           N  LF+  +P+      +     +   G  +V +  +  D       AFVE+E+   +A 
Sbjct: 1   NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 60

Query: 224 AKLALHGFKITP-THAMKISFAK 245
           A+  L   +I    H + + +A+
Sbjct: 61  ARRKLMPGRIQLWGHQIAVDWAE 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 = 44.2 bits (104), Expect = 5e-07
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
           N +YV     T     L   FS FG I+D+        R  AFV ++++ SA  A+  +
Sbjct: 5  GNTLYVYGEDMTP--TLLRGAFSPFGNIIDL---SMDPPRNCAFVTYEKMESADQAVAEL 59

Query: 71 QGFPFYDKPMRIQYSK 86
           G       +++  ++
Sbjct: 60 NGTQVESVQLKVNIAR 75

>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 = 44.3 bits (104), Expect = 6e-07
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSA 222
           +P   I+ + N+P   S   +   F  +        +           A V FE+  ++ 
Sbjct: 6   KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 65

Query: 223 AAKLALHGFKITPTHAMKISFA 244
           AA + L+   I  +  +K+   
Sbjct: 66  AAVIDLNDRPIG-SRKVKLVLG 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 = 35.8 bits (82), Expect = 5e-04
 Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 3/73 (4%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
          + V ++  T     +   F  +  I   V L   +     G+A V F+    AT A+  +
Sbjct: 12 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 71

Query: 71 QGFPFYDKPMRIQ 83
             P   + +++ 
Sbjct: 72 NDRPIGSRKVKLV 84

>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 = 43.9 bits (103), Expect = 9e-07
 Identities = 21/103 (20%), Positives = 41/103 (39%), Gaps = 13/103 (12%)

Query: 148 QPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR 207
           + PV +P           PE+   + +F   L        L   F+     ++VR++ +R
Sbjct: 1   KSPVREPVDNLS------PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 54

Query: 208 HD-----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK 245
           +      IA+VEF    QS    + L G ++     + +  ++
Sbjct: 55  NSRRSKGIAYVEFCEI-QSVPLAIGLTGQRL-LGVPIIVQASQ 95

>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 = 38.9 bits (90), Expect = 6e-05
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 4/76 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          V+   +++    + L   FS  G++ D+  +    + + +G A+V F EI S   A+  +
Sbjct: 21 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 79

Query: 71 QGFPFYDKPMRIQYSK 86
           G      P+ +Q S+
Sbjct: 80 TGQRLLGVPIIVQASQ 95

>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 = 43.5 bits (102), Expect = 1e-06
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          +YV  ++     K L+A F  FG I DI       T K RG AFV F+    A  A+ +M
Sbjct: 8  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 71 QGFPFYDKPMRIQYSK 86
               + + +R+  +K
Sbjct: 68 NESELFGRTIRVNLAK 83

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.7 bits (87), Expect = 1e-04
 Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAA 223
              ++L++  L EE  + +L   F  F    ++++  +         AFVEFE    +AA
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 224 AKLALHGFKITPTHAMKISFAK 245
           A   ++  ++     ++++ AK
Sbjct: 63  AIDNMNESEL-FGRTIRVNLAK 83

>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 = 43.8 bits (103), Expect = 1e-06
 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 3/68 (4%)

Query: 23 DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
          ++++ L    S+FGQI  ++        G A V F++   A   ++++ G  F  + +  
Sbjct: 31 EIREDLRVECSKFGQIRKLLLFDR-HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

Query: 83 QYS--KTD 88
          Q     TD
Sbjct: 90 QAWDGTTD 97

>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 = 43.1 bits (101), Expect = 1e-06
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 3/73 (4%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           +F+     + +E  L   F+Q+    +V +       AFV F ++  + +        K 
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIK- 66

Query: 234 TPTHAMKISFAKK 246
               ++ IS A+ 
Sbjct: 67  --GISVHISNAEP 77

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 1e-06
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
          N +Y+ ++S       L  +F      +     + L   G AFV + +   A  A+ ++ 
Sbjct: 2  NKLYIGNLSPAVTADDLRQLFGDRKLPLAG---QVLLKSGYAFVDYPDQNWAIRAIETLS 58

Query: 72 G-FPFYDKPMRIQYSK 86
          G    + K M + YS 
Sbjct: 59 GKVELHGKIMEVDYSV 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 = 39.3 bits (91), Expect = 3e-05
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 1/72 (1%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           L++ NL    +   L  LF           V  +   AFV++ ++  +  A   L G   
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDR-KLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 62

Query: 234 TPTHAMKISFAK 245
                M++ ++ 
Sbjct: 63  LHGKIMEVDYSV 74

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 2e-06
 Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 4/80 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          + V ++      + ++ +   +            + +  AFV       A NA++    +
Sbjct: 8  ILVKNLPQDSNCQEVHDLLKDYDLKY----CYVDRNKRTAFVTLLNGEQAQNAIQMFHQY 63

Query: 74 PFYDKPMRIQYSKTDSDVIS 93
           F  K + +Q   TD+ + S
Sbjct: 64 SFRGKDLIVQLQPTDALLCS 83

>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 = 39.7 bits (92), Expect = 3e-05
 Identities = 12/73 (16%), Positives = 26/73 (35%), Gaps = 3/73 (4%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           + + NLP++++   +  L   +   K   +  N+    FV   N  Q+  A    H +  
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRTA-FVTLLNGEQAQNAIQMFHQYSF 65

Query: 234 TPTHAMKISFAKK 246
                + +     
Sbjct: 66  R-GKDLIVQLQPT 77

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.9 bits (98), Expect = 3e-06
 Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
           +F+  L  +T++  L   F QF   KE  ++ +          FV F ++       LA 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ-AGVDKVLAQ 61

Query: 229 HGFKI 233
              ++
Sbjct: 62  SRHEL 66

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.8 bits (90), Expect = 4e-05
 Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 4/74 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          +++  +S    ++ L   F QFG++ + + ++   T + RG  FV F + A     L + 
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 71 QGFPFYDKPMRIQY 84
                 K +  + 
Sbjct: 62 SRHELDSKTIDPKV 75

>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 = 42.0 bits (98), Expect = 4e-06
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD-IVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
          ++V++I        L  +F QFG+I+D  +       +G  FV F+  A A  A   + G
Sbjct: 14 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 73

Query: 73 FPFYDKPMRIQYSK 86
               + + +  + 
Sbjct: 74 TVVEGRKIEVNNAT 87

>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 = 40.0 bits (93), Expect = 2e-05
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 4/76 (5%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH---DIAFVEFENEMQSAAAKLALHG 230
           L ++N+P    +  L  +F QF    +V ++ N        FV FEN   +  A+  LHG
Sbjct: 14  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 73

Query: 231 FKITPTHAMKISFAKK 246
             +     ++++ A  
Sbjct: 74  TVV-EGRKIEVNNATA 88

>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 = 42.0 bits (98), Expect = 5e-06
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMR---GQAFVIFKEIASATNAL 67
          +  ++V ++S T  ++ L  +FS +G + ++        +   G AFV F     A  A 
Sbjct: 8  SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67

Query: 68 RSMQGFPFYDKPMRIQYSKTDSD 90
            + G  F  + + +  S    +
Sbjct: 68 AEVDGQVFQGRMLHVLPSTIKKE 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 = 40.1 bits (93), Expect = 2e-05
 Identities = 16/78 (20%), Positives = 27/78 (34%), Gaps = 6/78 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
           LF+ NL   +SE  L  LF+ +    E+    +         AFV F     +  A   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 229 HGFKITPTHAMKISFAKK 246
            G        + +  +  
Sbjct: 71  DGQVF-QGRMLHVLPSTI 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 = 41.7 bits (97), Expect = 5e-06
 Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 3/80 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
          ++V  +S    ++SL  +FS++GQI ++V +K   T + RG  FV F+ I  A +A+ +M
Sbjct: 8  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 71 QGFPFYDKPMRIQYSKTDSD 90
           G     + +R+  +   SD
Sbjct: 68 NGKSVDGRQIRVDQAGKSSD 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 = 36.3 bits (83), Expect = 4e-04
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 6/78 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI-----AFVEFENEMQSAAAKLAL 228
           LF+  L  +T+E  L  +F+++    EV +V +R         FV FEN   +  A +A+
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 229 HGFKITPTHAMKISFAKK 246
           +G  +     +++  A K
Sbjct: 68  NGKSV-DGRQIRVDQAGK 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 = 41.6 bits (97), Expect = 6e-06
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKM---RGQAFVIFKEIASATNALRSM 70
          ++VT I     +  +   F  +G+I +I      +    +G A V ++    A  A  ++
Sbjct: 10 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 69

Query: 71 QGFPFYDKPMRIQYSKT 87
           G     + +++ +   
Sbjct: 70 NGAEIMGQTIQVDWCFV 86

>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 = 40.5 bits (94), Expect = 1e-05
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 6/79 (7%)

Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLA 227
           ILF+T++ EE  E  +   F  +   K + L  +R        A VE+E   Q+ AAK A
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 228 LHGFKITPTHAMKISFAKK 246
           L+G +I     +++ +   
Sbjct: 69  LNGAEI-MGQTIQVDWCFV 86

>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 = 41.7 bits (97), Expect = 6e-06
 Identities = 15/85 (17%), Positives = 32/85 (37%), Gaps = 11/85 (12%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL-----------KTLKMRGQAFVIFKEIAS 62
          +YV  ++ +     L   F Q G +                 +T K +G A V +++  +
Sbjct: 11 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 70

Query: 63 ATNALRSMQGFPFYDKPMRIQYSKT 87
          A  A+    G  F    +++  ++ 
Sbjct: 71 AKAAVEWFDGKDFQGSKLKVSLARK 95

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 7e-06
 Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 6/91 (6%)

Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEF 215
           A     E P    LF+ +LP+E  +  L  +F  F      ++  ++         FV +
Sbjct: 8   AAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 67

Query: 216 ENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
           +N + + AA  +++GF+I     +K+   + 
Sbjct: 68  DNPVSAQAAIQSMNGFQI-GMKRLKVQLKRS 97

>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 = 41.0 bits (95), Expect = 2e-05
 Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 13/115 (11%)

Query: 137 QQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFP 196
           Q  Q+Q L  QQ    Q  PP  M     PE    + L +  +P    E+ L  LF ++ 
Sbjct: 15  QTAQLQQLQQQQQ---QHIPPTQM----NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYG 67

Query: 197 GFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
             + V++V +R         FV+F++   +  A   L+GF I     +K++ A  
Sbjct: 68  PIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI-LNKRLKVALAAS 121

>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 = 39.2 bits (91), Expect = 3e-05
 Identities = 13/63 (20%), Positives = 20/63 (31%), Gaps = 5/63 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI-----AFVEFENEMQSAAAKLAL 228
           L +  LP +T+E  L   F+ F     V++  +          FV F             
Sbjct: 11  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 70

Query: 229 HGF 231
           H  
Sbjct: 71  HMI 73

>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 = 39.4 bits (91), Expect = 5e-05
 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 6/82 (7%)

Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAA 223
            PN++L+L NL    +E  L  LF +F   K   +            AF+ F N+  +  
Sbjct: 16  EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 75

Query: 224 AKLALHGFKITPTHAMKISFAK 245
           A   ++G+K+     + I F K
Sbjct: 76  ALHLVNGYKL-YGKILVIEFGK 96

>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 = 37.5 bits (86), Expect = 2e-04
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 11  TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNAL 67
              +Y+ ++S    ++ L ++F++F +           T +MRGQAF+ F     A  AL
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 68  RSMQGFPFYDKPMRIQYSKTDSD 90
             + G+  Y K + I++ K    
Sbjct: 78  HLVNGYKLYGKILVIEFGKNKKQ 100

>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 = 38.2 bits (88), Expect = 6e-05
 Identities = 7/76 (9%), Positives = 28/76 (36%), Gaps = 3/76 (3%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQI---MDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
          +++T+   +  ++++  +      +   + + +L+    R  A++       A   +  +
Sbjct: 4  LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 71 QGFPFYDKPMRIQYSK 86
           G       +  + S 
Sbjct: 64 NGLKIEGYTLVTKVSN 79

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.5 bits (89), Expect = 7e-05
 Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 6/78 (7%)

Query: 14 VYVTHI-SSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALR--SM 70
          V++       +L+  L  +   FG I +      L    +AF+       A  A+   + 
Sbjct: 11 VHIMDFQRGKNLRYQLLQLVEPFGVISNH---LILNKINEAFIEMATTEDAQAAVDYYTT 67

Query: 71 QGFPFYDKPMRIQYSKTD 88
               + KP+R+  S+  
Sbjct: 68 TPALVFGKPVRVHLSQKY 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 = 37.7 bits (87), Expect = 1e-04
 Identities = 12/65 (18%), Positives = 25/65 (38%), Gaps = 6/65 (9%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
           +F+  L  +T++  L   F++F    +  L  +          FV F+   +S    +  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKES-ESVDKVMDQ 60

Query: 229 HGFKI 233
              K+
Sbjct: 61  KEHKL 65

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 1e-04
 Identities = 13/81 (16%), Positives = 36/81 (44%), Gaps = 9/81 (11%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKTLKMRGQAFVIFKEIASATN 65
          +YV +I     ++++   F+   ++          ++A++  + +  AF+ F+ +   T 
Sbjct: 4  LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 66 ALRSMQGFPFYDKPMRIQYSK 86
          A+    G  F  + ++I+   
Sbjct: 64 AMA-FDGIIFQGQSLKIRRPH 83

>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 = 37.3 bits (86), Expect = 2e-04
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 8/73 (10%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQ 220
           PEQ   + LF+  L  ET++  L   F Q+    +  ++ + +        FV +    +
Sbjct: 3   PEQL--RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 221 SAAAKLALHGFKI 233
             AA +     K+
Sbjct: 61  VDAA-MNARPHKV 72

>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 = 37.6 bits (86), Expect = 2e-04
 Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 2/80 (2%)

Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
                 ++   NLP  T    +   F++F     V  +P     A VEF   +++  A  
Sbjct: 6   SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVL-LPEGGITAIVEFLEPLEARKAFR 64

Query: 227 ALHGFKITPTHAMKISFAKK 246
            L          + + +A  
Sbjct: 65  HLAY-SKFHHVPLYLEWAPI 83

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.6 bits (84), Expect = 2e-04
 Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 6/65 (9%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
           +F+  L   T+   +   F QF    +  L+ ++         FV FE+E         +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE-DIVEKVCEI 60

Query: 229 HGFKI 233
           H  +I
Sbjct: 61  HFHEI 65

>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 = 37.5 bits (86), Expect = 2e-04
 Identities = 11/71 (15%), Positives = 25/71 (35%), Gaps = 1/71 (1%)

Query: 164 GVPEQPPN-QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSA 222
           G  E+     + F  +L ++T    L +LF+     K +  V    +   +  E   ++ 
Sbjct: 3   GSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEAL 62

Query: 223 AAKLALHGFKI 233
                 +   +
Sbjct: 63  GKAKDANNGNL 73

>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 = 37.0 bits (85), Expect = 3e-04
 Identities = 14/80 (17%), Positives = 36/80 (45%), Gaps = 4/80 (5%)

Query: 14  VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
           +++  +S    ++SL   + Q+G++ D V ++   + + RG  FV F  +A    A+   
Sbjct: 23  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-A 81

Query: 71  QGFPFYDKPMRIQYSKTDSD 90
           +      + +  + +    +
Sbjct: 82  RPHSIDGRVVEPKRAVAREE 101

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 6/73 (8%)

Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
            E+   + LF+  L  ET+E  L   + Q+    +  ++ +          FV F +  +
Sbjct: 15  REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 74

Query: 221 SAAAKLALHGFKI 233
             AA +A     I
Sbjct: 75  VDAA-MAARPHSI 86

>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 = 36.4 bits (83), Expect = 3e-04
 Identities = 12/73 (16%), Positives = 22/73 (30%), Gaps = 3/73 (4%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
           + +  LP + +   +  L + +        V      AFV   N  Q+ AA    H    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKY--CFVDKYKGTAFVTLLNGEQAEAAINTFHQ-SR 57

Query: 234 TPTHAMKISFAKK 246
                + +     
Sbjct: 58  LRERELSVQLQPT 70

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.5 bits (78), Expect = 0.001
 Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 4/76 (5%)

Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
          + +  +      + ++ + S +            K +G AFV       A  A+ +    
Sbjct: 1  ILIRGLPGDVTNQEVHDLLSDYELKYCF----VDKYKGTAFVTLLNGEQAEAAINTFHQS 56

Query: 74 PFYDKPMRIQYSKTDS 89
             ++ + +Q   TD+
Sbjct: 57 RLRERELSVQLQPTDA 72

>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 = 36.1 bits (83), Expect = 3e-04
 Identities = 10/65 (15%), Positives = 22/65 (33%), Gaps = 6/65 (9%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
           +F+  L  +T E  +   F  F   + + L  +          F+ F+ E +     +  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE-EPVKKIMEK 60

Query: 229 HGFKI 233
               +
Sbjct: 61  KYHNV 65

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 7e-04
 Identities = 12/65 (18%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
           +F+  + E+T E  L   F Q+   + + ++ +R        AFV F++        +  
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI-VIQ 63

Query: 229 HGFKI 233
               +
Sbjct: 64  KYHTV 68

>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 = 34.4 bits (78), Expect = 0.002
 Identities = 11/65 (16%), Positives = 25/65 (38%), Gaps = 5/65 (7%)

Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI-----AFVEFENEMQSAAAKLAL 228
           L++  L   T++  L  L   +      + + ++         FV+F++   +  A  AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 229 HGFKI 233
               +
Sbjct: 61  KASGV 65

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.0 bits (77), Expect = 0.003
 Identities = 13/84 (15%), Positives = 29/84 (34%), Gaps = 9/84 (10%)

Query: 8  ICVTNFVYVTHIS---STDLKKSLYAIFSQFGQIMDIVALK------TLKMRGQAFVIFK 58
          +   N V+V  +S   +          F +FG+I  +V         +      A+V + 
Sbjct: 5  VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYI 64

Query: 59 EIASATNALRSMQGFPFYDKPMRI 82
              A  A++ +       + ++ 
Sbjct: 65 RSEDALRAIQCVNNVVVDGRTLKA 88

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	246
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.92
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.87
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.87
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.86
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.86
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.86
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.86
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.86
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.86
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.86
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.86
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.86
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.86
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.85
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.85
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.85
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.85
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.85
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.85
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.85
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.85
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.85
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.84
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.84
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.84
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.84
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.84
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.84
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.84
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.84
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.84
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.84
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.83
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.83
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.83
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.83
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.83
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.83
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.83
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.82
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.82
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.82
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.82
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.82
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.82
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.82
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.82
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.82
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.82
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.82
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.82
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.81
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.81
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.81
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.81
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.81
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.81
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.81
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.81
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.81
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.81
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.81
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.81
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.8
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.8
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.8
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.8
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.8
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.8
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.8
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.8
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.8
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.8
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.8
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.8
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.8
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.8
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.8
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.79
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.79
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.79
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.79
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.79
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.79
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.79
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.79
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.79
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.79
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.79
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.78
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.78
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.78
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.78
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.78
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.78
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.78
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.78
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.78
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.78
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.78
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.77
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.77
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.77
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.77
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.77
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.77
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.76
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.76
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.76
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.75
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.75
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.75
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.75
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.74
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.74
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.74
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.7
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.7
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.68
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.67
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.67
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	99.66
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.66
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.65
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.64
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.63
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.63
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.6
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
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	99.6
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.58
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.51
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.5
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.32
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.17
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.16
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.14
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.82
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.32
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.83
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.55

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5.5e-32  Score=206.65  Aligned_cols=162  Identities=17%  Similarity=0.293  Sum_probs=139.4

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ..++|||+|||+++++++|+++|++||.|.++.++++.   .++|||||+|.+.++|..|+. +++..+.++.+.+....
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            34899999999999999999999999999999998754   788999999999999999998 66777888888887754


Q ss_pred             CCccccccccCccccccccccCCCCCCCChhHHhhhhhhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCCCCC
Q psy4057          87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP  166 (246)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (246)
                      ......                                                                       ...
T Consensus        84 ~~~~~~-----------------------------------------------------------------------~~~   92 (183)
T d1u1qa_          84 SREDSQ-----------------------------------------------------------------------RPG   92 (183)
T ss_dssp             CTTGGG-----------------------------------------------------------------------STT
T ss_pred             hccccc-----------------------------------------------------------------------ccc
Confidence            332100                                                                       011


Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .....++|||+|||..+|+++|+++|+.||.|..+.++.++     +|||||+|.+.++|.+|++ ++|..+. |+.|+|
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~-G~~i~V  170 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVN-GHNCEV  170 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEET-TEEEEE
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeEC-CEEEEE
Confidence            33467899999999999999999999999999999999865     4799999999999999997 7999998 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .+|.
T Consensus       171 ~~A~  174 (183)
T d1u1qa_         171 RKAL  174 (183)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9984

>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=99.92  E-value=1e-24  Score=144.26  Aligned_cols=81  Identities=89%  Similarity=1.296  Sum_probs=76.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ...||+++|||+|||.++|+++|+++|++||.|.+++++++++|||||+|.+.++|..|++.|||+.|.+|++|+|+|||
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            35678999999999999999999999999999999999998889999999999999999999999999757999999999


Q ss_pred             C
Q psy4057         246 K  246 (246)
Q Consensus       246 ~  246 (246)
                      |
T Consensus        83 k   83 (83)
T d2b0ga1          83 K   83 (83)
T ss_dssp             C
T ss_pred             C
Confidence            7

>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=99.87  E-value=3.2e-22  Score=134.08  Aligned_cols=85  Identities=22%  Similarity=0.286  Sum_probs=78.6

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      |....+.++|||+|||.++++++|+++|++||.|.+|.+.++. ..+|||||+|.+.++|..|+..|||..+.|++|+|.
T Consensus         2 m~d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           2 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            5667788999999999999999999999999999999998876 568999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ||....
T Consensus        82 ~a~~~~   87 (90)
T d2cqia1          82 WATTPS   87 (90)
T ss_dssp             ECCCTT
T ss_pred             EcCCCC
Confidence            987543

>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=99.87  E-value=2.7e-22  Score=140.55  Aligned_cols=80  Identities=25%  Similarity=0.491  Sum_probs=76.1

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      .+++++|||+|||.++++++|+++|++||.|.+|++..+++++|||||+|.+.++|..|++.|||..+.|++|+|.++..
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999753

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.87  E-value=2.2e-22  Score=132.64  Aligned_cols=78  Identities=21%  Similarity=0.396  Sum_probs=72.8

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ++++|||+|||.++++++|+++|++||.|.++.++++.   +++|||||+|.+.++|++|++.|||..+.|++|+|.+|+
T Consensus         1 s~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~   80 (82)
T d1b7fa1           1 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   80 (82)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            36789999999999999999999999999999998754   678999999999999999999999999999999999985


Q ss_pred             C
Q psy4057          87 T   87 (246)
Q Consensus        87 ~   87 (246)
                      +
T Consensus        81 p   81 (82)
T d1b7fa1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=5.3e-22  Score=133.75  Aligned_cols=83  Identities=23%  Similarity=0.346  Sum_probs=76.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|++|++.|||..+.|++|+|.
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   84 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   84 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45567899999999999999999999999999999998754   788999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      +|.+..
T Consensus        85 ~A~~~~   90 (93)
T d1x5ua1          85 KASAHN   90 (93)
T ss_dssp             ETTTTS
T ss_pred             EcCCCC
Confidence            997653

>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=99.86  E-value=4.2e-22  Score=132.86  Aligned_cols=83  Identities=16%  Similarity=0.250  Sum_probs=75.2

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      .....+.+|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|++|++.|||..+.|++|+|
T Consensus         2 ~~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V   81 (88)
T d1rk8a_           2 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV   81 (88)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345567899999999999999999999999999999998764   67899999999999999999999999999999999


Q ss_pred             EEccCC
Q psy4057          83 QYSKTD   88 (246)
Q Consensus        83 ~~a~~~   88 (246)
                      .||.++
T Consensus        82 ~~a~~k   87 (88)
T d1rk8a_          82 DWCFVK   87 (88)
T ss_dssp             EESEEC
T ss_pred             EEecCC
Confidence            998643

>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=99.86  E-value=9.8e-22  Score=131.18  Aligned_cols=79  Identities=25%  Similarity=0.425  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..||+++|||+|||.++|+++|+++|+.||.|.++.+..++ +|+|||+|.+.++|.+|+..|||..+..|++|+|+|||
T Consensus         6 ~~pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2           6 IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             CCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            35789999999999999999999999999999887766643 68999999999999999999999999558999999998

>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=99.86  E-value=4e-22  Score=135.02  Aligned_cols=77  Identities=22%  Similarity=0.462  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      .+.+++|||+|||.++++++|+++|++||.|.+|++++++ |||||+|.+.++|..|+..|||..|+ |+.|+|+|||.
T Consensus        15 ~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~k-g~afV~f~~~~~A~~Ai~~l~~~~i~-g~~l~v~~ak~   91 (96)
T d1x4ga1          15 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-GYSFVRFSTHESAAHAIVSVNGTTIE-GHVVKCYWGKE   91 (96)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHTTCEET-TEECEEECCCC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecc-eEEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEEcCC
Confidence            3457899999999999999999999999999999999986 89999999999999999999999999 99999999984

>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=4.2e-22  Score=131.25  Aligned_cols=74  Identities=28%  Similarity=0.497  Sum_probs=70.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      +++|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|++|++.|||..+. |++|+|+||+
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~-g~~l~v~~a~   80 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVR-NKRLKVSYAR   80 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEET-TEECEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEEC-CEEEEEEEcC
Confidence            5789999999999999999999999999999998854     579999999999999999999999999 9999999997

>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=99.86  E-value=9e-22  Score=132.87  Aligned_cols=84  Identities=19%  Similarity=0.343  Sum_probs=76.7

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC----CCCccEEEEEEcCHHHHHHHHHHh-cCCccCCeeE
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT----LKMRGQAFVIFKEIASATNALRSM-QGFPFYDKPM   80 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~----~~~kg~aFV~f~~~~~A~~Ai~~l-ng~~~~g~~l   80 (246)
                      ....++++|||+|||.++++++|+++|++||.|.+|.++++    ++++|||||+|.+.++|.+|+..| ||..+.|++|
T Consensus         3 p~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l   82 (94)
T d2cpha1           3 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   82 (94)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEE
Confidence            34567899999999999999999999999999999999765    368999999999999999999998 8999999999


Q ss_pred             EEEEccCCc
Q psy4057          81 RIQYSKTDS   89 (246)
Q Consensus        81 ~v~~a~~~~   89 (246)
                      .|.||+.+.
T Consensus        83 ~V~~A~~~~   91 (94)
T d2cpha1          83 VLEWADSEV   91 (94)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEcCCCC
Confidence            999997654

>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=99.86  E-value=4.9e-22  Score=130.18  Aligned_cols=73  Identities=18%  Similarity=0.278  Sum_probs=70.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      .|||+|||+++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||..++ |++|+|+||++
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 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK-GKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEET-TEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEEC-CEEEEEEEeCC
Confidence            59999999999999999999999999999999865     489999999999999999999999999 99999999986

>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=99.86  E-value=2.5e-22  Score=134.86  Aligned_cols=84  Identities=65%  Similarity=1.031  Sum_probs=77.0

Q ss_pred             CCCcEEEecCCChhhhHHHHH----HHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           9 CVTNFVYVTHISSTDLKKSLY----AIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~----~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      .|+++|||+|||.++++++|+    ++|++||+|.+|.+.++++++|||||+|.+.++|..|+..|||..+.|++|+|.|
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            489999999999999998875    5689999999999988878899999999999999999999999999999999999


Q ss_pred             ccCCcccc
Q psy4057          85 SKTDSDVI   92 (246)
Q Consensus        85 a~~~~~~~   92 (246)
                      |+.+++..
T Consensus        81 ak~~~~~~   88 (91)
T d1nu4a_          81 AKTDSDII   88 (91)
T ss_dssp             CSSCCTHH
T ss_pred             eCCCchhh
Confidence            98776543

>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=99.86  E-value=9e-22  Score=131.86  Aligned_cols=79  Identities=27%  Similarity=0.468  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      +..+.++|||+|||.++|+++|+++|++||.|.+++++.++   +|||||+|.+.++|..|++.|||..+. |+.|+|.|
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~-g~~i~v~~   82 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKIL-GKEVKVNW   82 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEET-TEEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEEC-CEEEEEEE
Confidence            45568899999999999999999999999999999998865   579999999999999999999999999 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |+.
T Consensus        83 a~~   85 (90)
T d2cqia1          83 ATT   85 (90)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            974

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=3.7e-22  Score=133.50  Aligned_cols=80  Identities=29%  Similarity=0.402  Sum_probs=74.9

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ..+++|||+|||.++++++|+++|++||+|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.+|
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            467899999999999999999999999999999998754   78999999999999999999999999999999999998


Q ss_pred             cCC
Q psy4057          86 KTD   88 (246)
Q Consensus        86 ~~~   88 (246)
                      +++
T Consensus        83 ~p~   85 (89)
T d2cqba1          83 KPM   85 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.86  E-value=9.8e-22  Score=132.40  Aligned_cols=81  Identities=25%  Similarity=0.348  Sum_probs=75.2

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..++++|||+|||.++++++|+++|++||+|.+|.++++.   +++|||||+|.+.++|..|++.|||..+.|++|+|.|
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4678999999999999999999999999999999998764   6789999999999999999999999999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      +...
T Consensus        84 a~~~   87 (93)
T d1h2vz_          84 DAGF   87 (93)
T ss_dssp             ESCC
T ss_pred             cCCC
Confidence            8543

>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=99.86  E-value=6.3e-22  Score=129.63  Aligned_cols=76  Identities=30%  Similarity=0.425  Sum_probs=71.3

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      .+|||+|||.++++++|+++|++||+|.+|+++++.   +++|||||+|.+.++|..|++.|||..+.|++|+|.||+.
T Consensus         1 aslfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            379999999999999999999999999999999764   6789999999999999999999999999999999999853

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.1e-21  Score=129.32  Aligned_cols=77  Identities=16%  Similarity=0.364  Sum_probs=72.0

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      ..+|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|+.|++.|||..+.|++|+|.+|++
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            4579999999999999999999999999999998753   7789999999999999999999999999999999999864

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.6e-21  Score=128.46  Aligned_cols=74  Identities=22%  Similarity=0.449  Sum_probs=70.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .++|||+|||.++++++|+++|++||.|.+++++.+.     +|||||+|.+.++|..|++.|||..++ |++|+|.|||
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~-g~~l~v~~Ak   80 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQ-TKTIKVSYAR   80 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEEee
Confidence            3579999999999999999999999999999999864     579999999999999999999999999 9999999997

>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=2e-21  Score=133.19  Aligned_cols=80  Identities=24%  Similarity=0.475  Sum_probs=74.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      ...|++++|||+|||.++++++|+++|+.||.|.+++++.+.     +|||||+|.+.++|..|++.|||+.|+ |++|+
T Consensus        13 ~~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~-g~~i~   91 (102)
T d2cpza1          13 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIG-MKRLK   91 (102)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET-TEECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEEC-CEEEE
Confidence            355678899999999999999999999999999999999865     579999999999999999999999999 99999


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |+||+.
T Consensus        92 V~~a~~   97 (102)
T d2cpza1          92 VQLKRS   97 (102)
T ss_dssp             EECCCC
T ss_pred             EEEeCC
Confidence            999873

>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=99.85  E-value=9e-22  Score=131.86  Aligned_cols=82  Identities=23%  Similarity=0.391  Sum_probs=76.0

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..++++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            4567899999999999999999999999999999998764   6889999999999999999999999999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      |++.+
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            97653

>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=9e-22  Score=129.90  Aligned_cols=76  Identities=24%  Similarity=0.377  Sum_probs=71.4

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI   82 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v   82 (246)
                      +..|+++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|..|+..|||..+.|++|+|
T Consensus         5 ~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           5 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            56789999999999999999999999999999999998754   67899999999999999999999999999999987

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.9e-21  Score=130.07  Aligned_cols=77  Identities=17%  Similarity=0.281  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ...+++|||+|||.++|+++|+++|++||.|.+|+++.++     +|||||+|.+.++|..|++.|||..++ |++|+|+
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~-gr~i~V~   82 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLD-DRIIRTD   82 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEET-TEECEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEE
Confidence            3468999999999999999999999999999999999865     479999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus        83 ~a~   85 (93)
T d1h2vz_          83 WDA   85 (93)
T ss_dssp             EES
T ss_pred             EcC
Confidence            985

>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=99.85  E-value=1.8e-21  Score=126.72  Aligned_cols=74  Identities=23%  Similarity=0.366  Sum_probs=70.4

Q ss_pred             EEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        13 ~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      +|||+|||.++++++|+++|++||.|.++.+..+.  +++|||||+|.+.++|+.|++.|||..+.|++|+|.++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999998754  788999999999999999999999999999999999975

>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=9.4e-22  Score=134.79  Aligned_cols=83  Identities=19%  Similarity=0.309  Sum_probs=76.6

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..+|+++|||+|||.++++++|+++|++||.|.++.++.+.   +++|||||+|.+.++|..|++.|||..+.|++|+|.
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45778999999999999999999999999999999888653   788999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++..+.
T Consensus        94 ~a~~k~   99 (102)
T d2cpza1          94 LKRSKN   99 (102)
T ss_dssp             CCCCSC
T ss_pred             EeCCCC
Confidence            987664

>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=99.85  E-value=2.9e-21  Score=130.31  Aligned_cols=78  Identities=22%  Similarity=0.378  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHh-CCCccCCCCceE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR------HDIAFVEFENEMQSAAAKLAL-HGFKITPTHAMK  240 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l-~g~~i~~g~~l~  240 (246)
                      ...+++|||+|||.++++++|+++|++||.|.+++++.+.      +|||||+|.+.++|..|++.| ||..++ |++|+
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~-Gr~l~   83 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY-GRRLV   83 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS-SCBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEEC-CEEEE
Confidence            4467889999999999999999999999999999998753      589999999999999999998 899999 99999


Q ss_pred             EEeecC
Q psy4057         241 ISFAKK  246 (246)
Q Consensus       241 v~~ak~  246 (246)
                      |.||+.
T Consensus        84 V~~A~~   89 (94)
T d2cpha1          84 LEWADS   89 (94)
T ss_dssp             EEECCC
T ss_pred             EEEcCC
Confidence            999974

>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=2.8e-21  Score=128.82  Aligned_cols=75  Identities=31%  Similarity=0.453  Sum_probs=70.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .+.+|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|..|+..|||..++ |++|+|+||
T Consensus         6 ~~~~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_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM-GQTIQVDWC   84 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEET-TEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEEC-CEEEEEEEe
Confidence            57899999999999999999999999999999999865     579999999999999999999999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus        85 ~   85 (88)
T d1rk8a_          85 F   85 (88)
T ss_dssp             E
T ss_pred             c
Confidence            6

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=3.1e-21  Score=129.89  Aligned_cols=77  Identities=22%  Similarity=0.291  Sum_probs=72.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .+..++|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||+.++ |+.|+|+
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~-g~~l~V~   84 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY-GKPIRVN   84 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCS-SCBCEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEEC-CEEEEEE
Confidence            3457899999999999999999999999999999998865     579999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus        85 ~A~   87 (93)
T d1x5ua1          85 KAS   87 (93)
T ss_dssp             ETT
T ss_pred             EcC
Confidence            986

>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=99.85  E-value=4.9e-21  Score=128.98  Aligned_cols=82  Identities=21%  Similarity=0.308  Sum_probs=75.8

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ....++|||+|||.++++++|+++|++||+|.+|.++.+. .++|||||+|.+.++|.+|+..|||..+.|++|+|.+|+
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            4456789999999999999999999999999999998876 578999999999999999999999999999999999997


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      ++.
T Consensus        88 ~r~   90 (93)
T d2cq3a1          88 ARV   90 (93)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            653

>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=99.85  E-value=2.6e-21  Score=130.96  Aligned_cols=80  Identities=29%  Similarity=0.374  Sum_probs=74.1

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      .+++++|||+|||.++++++|+++|++||.|.+|++.+   .+|||||+|.+.++|..|+..|||..+.|++|+|.|+++
T Consensus        15 ~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~---~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          15 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP---EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEe---cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45567999999999999999999999999999999987   489999999999999999999999999999999999976


Q ss_pred             Ccc
Q psy4057          88 DSD   90 (246)
Q Consensus        88 ~~~   90 (246)
                      +++
T Consensus        92 ~p~   94 (96)
T d1x4ga1          92 SPD   94 (96)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            643

>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=99.85  E-value=4.3e-21  Score=128.00  Aligned_cols=80  Identities=18%  Similarity=0.263  Sum_probs=72.7

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCcc-CCeeEEEEEc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF-YDKPMRIQYS   85 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~-~g~~l~v~~a   85 (246)
                      -.||+++|||+|||.++++++|+++|++||.|.++.+.. ++++|||||+|.+.++|.+|+..|||..+ .|++|+|.|+
T Consensus         6 ~~pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~-~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           6 IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF-QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             CCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC-SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee-ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            358999999999999999999999999999998886643 46789999999999999999999999988 5899999998


Q ss_pred             cC
Q psy4057          86 KT   87 (246)
Q Consensus        86 ~~   87 (246)
                      +.
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=99.85  E-value=1.8e-21  Score=135.21  Aligned_cols=74  Identities=24%  Similarity=0.451  Sum_probs=70.9

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         171 NQILFLTNLPE-ETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~-~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      +++|||+|||+ .+|+++|+++|+.||.|.+++++++++|||||+|.+.++|.+|++.|||..|+ |++|+|+|||
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~-g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLH-GKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCS-SSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEECC
Confidence            68999999965 69999999999999999999999999999999999999999999999999999 9999999986

>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=99.84  E-value=4.6e-21  Score=129.66  Aligned_cols=81  Identities=20%  Similarity=0.306  Sum_probs=76.2

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      ..++++|||+|||.++++++|+++|++||.|..+.+.++..+++||||+|.+.++|..|++.|||..+.|++|+|.+++.
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            35678999999999999999999999999999999988888999999999999999999999999999999999999865


Q ss_pred             C
Q psy4057          88 D   88 (246)
Q Consensus        88 ~   88 (246)
                      .
T Consensus        91 ~   91 (95)
T d1x4aa1          91 G   91 (95)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=9.9e-21  Score=127.45  Aligned_cols=79  Identities=24%  Similarity=0.405  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      .....++|||+|||.++++++|+++|++||.|.+++++.+.   +|||||+|.+.++|..|+..|||..++ |+.|+|.|
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~-g~~l~V~~   85 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVE-GRKIEVNN   85 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEET-TEECEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEEC-CEEEEEEe
Confidence            34457789999999999999999999999999999999875   589999999999999999999999999 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |+.
T Consensus        86 A~~   88 (93)
T d2cq3a1          86 ATA   88 (93)
T ss_dssp             CCS
T ss_pred             cCc
Confidence            974

>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=4.5e-21  Score=130.74  Aligned_cols=82  Identities=22%  Similarity=0.288  Sum_probs=75.6

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ...+++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|+.|++.|||..+.|++|+|.+
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            3456789999999999999999999999999999998754   7889999999999999999999999999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      +..+.
T Consensus        85 a~~~~   89 (99)
T d1whwa_          85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87654

>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=99.84  E-value=5.6e-21  Score=126.69  Aligned_cols=74  Identities=23%  Similarity=0.438  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..++|||+|||.++++++|+++|++||.|.++++.+++ +||||+|.+.++|..|++.|||..|+ |++|+|+||.
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 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-GFGFIRLETRTLAEIAKVELDNMPLR-GKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT-TEEEEECSSSHHHHHHHHHHTTCCBT-TBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeeccc-ceEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEECC
Confidence            45679999999999999999999999999999999886 89999999999999999999999999 9999999986

>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=99.84  E-value=5.8e-21  Score=125.87  Aligned_cols=78  Identities=21%  Similarity=0.349  Sum_probs=72.6

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCcc-CCeeEEEEEc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF-YDKPMRIQYS   85 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~-~g~~l~v~~a   85 (246)
                      ..||+++|||+|||.++++++|+++|++||.|.+|++.++  .+|||||+|.+.++|..|++.|||..+ .|++|+|.||
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN--RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT--TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc--cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            5689999999999999999999999999999999999775  578999999999999999999999988 5689999998


Q ss_pred             c
Q psy4057          86 K   86 (246)
Q Consensus        86 ~   86 (246)
                      +
T Consensus        82 k   82 (83)
T d2b0ga1          82 K   82 (83)
T ss_dssp             C
T ss_pred             c
Confidence            5

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=6.2e-21  Score=133.55  Aligned_cols=75  Identities=20%  Similarity=0.412  Sum_probs=71.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .+++|||+|||.++|+++|+++|++||.|.+|++..+.  +|||||+|.+.++|..|++.|||+.|+ |++|+|.||+
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~-gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVC-NRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEET-TEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEEcC
Confidence            58899999999999999999999999999999998865  689999999999999999999999999 9999999985

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=2.5e-21  Score=128.14  Aligned_cols=77  Identities=16%  Similarity=0.301  Sum_probs=72.6

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      .+|||+|||.++++++|+++|++||+|.+|+++++   ++++|||||+|.++++|..|++.|||..+.|++|.|.+|...
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            47999999999999999999999999999999876   478999999999999999999999999999999999998654

>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=99.84  E-value=2.1e-21  Score=129.77  Aligned_cols=79  Identities=23%  Similarity=0.403  Sum_probs=73.7

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCc
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDS   89 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~   89 (246)
                      ..+|||+|||.++++++|+++|++||.|.++.++.+. .++|||||+|.+.++|++|++.|||..+.|++|+|.++.++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            4679999999999999999999999999999998876 678999999999999999999999999999999999987653

>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=99.84  E-value=9.4e-21  Score=125.38  Aligned_cols=75  Identities=23%  Similarity=0.490  Sum_probs=68.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCC-CCceEEEe
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITP-THAMKISF  243 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~-g~~l~v~~  243 (246)
                      .+++|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||..+.| .++|+|.|
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            46789999999999999999999999999999999864     5799999999999999999999999983 26799999


Q ss_pred             e
Q psy4057         244 A  244 (246)
Q Consensus       244 a  244 (246)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            7

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=4.2e-21  Score=128.52  Aligned_cols=75  Identities=28%  Similarity=0.462  Sum_probs=71.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      +.++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|++.|||..++ |++|+|+||
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~-g~~i~v~~a   85 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYD-HLILNVEWA   85 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEET-TEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEEC-CEEEEEEee
Confidence            57899999999999999999999999999999999865     579999999999999999999999999 999999999


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      |
T Consensus        86 k   86 (90)
T d2cq0a1          86 K   86 (90)
T ss_dssp             S
T ss_pred             e
Confidence            7

>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=99.84  E-value=1.3e-20  Score=124.78  Aligned_cols=75  Identities=19%  Similarity=0.415  Sum_probs=69.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCC-CCceEEEe
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITP-THAMKISF  243 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~-g~~l~v~~  243 (246)
                      .+++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||..+.+ +++|+|.|
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            56789999999999999999999999999999999865     5799999999999999999999999973 38899999


Q ss_pred             e
Q psy4057         244 A  244 (246)
Q Consensus       244 a  244 (246)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            7

>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=99.84  E-value=3e-21  Score=129.02  Aligned_cols=75  Identities=24%  Similarity=0.424  Sum_probs=71.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..++|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|..|+..|||..++ |++|+|.||
T Consensus         4 ~~~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           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF-GRTIRVNLA   82 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEET-TEEEEEEEC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEEC-CEEEEEEEe
Confidence            57899999999999999999999999999999999865     589999999999999999999999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus        83 ~   83 (89)
T d2cqba1          83 K   83 (89)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.84  E-value=5.5e-21  Score=126.54  Aligned_cols=75  Identities=25%  Similarity=0.459  Sum_probs=69.4

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCC--eeEEEEEc
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYD--KPMRIQYS   85 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g--~~l~v~~a   85 (246)
                      +++|||+|||.++++++|+++|++||+|.++.++++.   +++|||||+|.+.++|.+|++.|||..+.|  ++|+|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            5789999999999999999999999999999998754   788999999999999999999999999987  55899885

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5.8e-21  Score=127.95  Aligned_cols=80  Identities=29%  Similarity=0.475  Sum_probs=73.8

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      -.++|||+|||.++++++|+++|++||.|..+.++++.   .++|||||+|.+.++|+.|++.|||..+.|++|+|.++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            46789999999999999999999999999999887643   788999999999999999999999999999999999987


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      ...
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.84  E-value=4.6e-21  Score=125.88  Aligned_cols=77  Identities=9%  Similarity=0.173  Sum_probs=68.6

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      .++|||+|||.++++++|+++|++||.|..+.++.+   ++++|||||+|.+.++|++|++.|||..+.|++|+|.+|++
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            369999999999999999999999999988877654   37889999999999999999999999999999999999864

>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=8.5e-21  Score=125.67  Aligned_cols=77  Identities=23%  Similarity=0.402  Sum_probs=71.1

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCC--eeEEEE
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYD--KPMRIQ   83 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g--~~l~v~   83 (246)
                      ..+++|||+|||.++++++|+++|++||.|.+++++++.   +++|||||+|.+.++|.+|++.|||..+.|  ++|+|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            356789999999999999999999999999999998754   788999999999999999999999999876  889999


Q ss_pred             Ec
Q psy4057          84 YS   85 (246)
Q Consensus        84 ~a   85 (246)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.83  E-value=9.5e-21  Score=123.60  Aligned_cols=73  Identities=22%  Similarity=0.402  Sum_probs=69.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      .+++|||+|++  +|+++|+++|++||.|.++++.+++ |||||+|.+.++|..|++.|||..++ |+.|+|+|||+
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~-~~afV~f~~~~~A~~Ai~~lng~~~~-g~~l~V~~a~~   76 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-NCAFVTYEKMESADQAVAELNGTQVE-SVQLKVNIARK   76 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTT-TEEEEECSSHHHHHHHHHHHTTCBCS-SCBCEEEECCS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCC-CEEEEEEcccHHHHHHHHHhCCCEEC-CEEEEEEEecC
Confidence            47899999996  8999999999999999999998876 89999999999999999999999999 99999999985

>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=99.83  E-value=1.2e-20  Score=127.52  Aligned_cols=78  Identities=19%  Similarity=0.419  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ...++++|||+|||.++|+++|+++|++||.|..+.+..+.  ++||||+|.+.++|..|++.|||+.|. |++|+|+||
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~-g~~l~V~~a   88 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYD-GYRLRVEFP   88 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEET-TEECEEECC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEec
Confidence            34567899999999999999999999999999999987754  689999999999999999999999999 999999999


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      |
T Consensus        89 ~   89 (95)
T d1x4aa1          89 R   89 (95)
T ss_dssp             C
T ss_pred             c
Confidence            7

>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=99.83  E-value=5.7e-21  Score=133.14  Aligned_cols=75  Identities=21%  Similarity=0.248  Sum_probs=70.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      .+++|||+|||.++++++|+++|++||.|.+|.+.+.+ |||||+|.+.++|.+|++.|||..|. |++|.|+||++
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~k-g~afV~f~~~~~A~~A~~~lng~~~~-gr~l~v~~a~~   83 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-ITAIVEFLEPLEARKAFRHLAYSKFH-HVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSS-SCEEEEESCHHHHHHHHHHHTTCBSS-SSBCEEEEEET
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccC-ceEEEEEcCHHHHHHHHHHHcCCccC-CCeEEEEECCC
Confidence            57899999999999999999999999999999987665 89999999999999999999999999 99999999864

>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=1e-20  Score=124.80  Aligned_cols=77  Identities=17%  Similarity=0.287  Sum_probs=71.0

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ...++|||+|||.++++++|+++|++||.|.++.++++.   +++|||||+|.+.++|++|++ +++..+.|++|+|..|
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            345899999999999999999999999999999998764   788999999999999999998 7999999999999987


Q ss_pred             c
Q psy4057          86 K   86 (246)
Q Consensus        86 ~   86 (246)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            4

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=2.8e-20  Score=126.19  Aligned_cols=79  Identities=23%  Similarity=0.420  Sum_probs=72.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCC-CCceEEEeec
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITP-THAMKISFAK  245 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~-g~~l~v~~ak  245 (246)
                      ..+|+++|||+|||.++++++|+++|++||.|..+++.+++ +||||+|.+.++|..|++.|||..|.+ +++|+|+|||
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak   91 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD-SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSS-CCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccc-cEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCC
Confidence            45678999999999999999999999999999999999876 799999999999999999999999983 3689999997


Q ss_pred             C
Q psy4057         246 K  246 (246)
Q Consensus       246 ~  246 (246)
                      .
T Consensus        92 ~   92 (97)
T d1whya_          92 S   92 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=1.8e-20  Score=127.77  Aligned_cols=77  Identities=21%  Similarity=0.251  Sum_probs=71.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ..+++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||+.|+ |++|+|.+
T Consensus         6 ~~~~~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_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQ-GRMLHVLP   84 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESS-SCEEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEEC-CEEEEEEE
Confidence            357789999999999999999999999999999998865     579999999999999999999999999 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |+.
T Consensus        85 a~~   87 (99)
T d1whwa_          85 STI   87 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            873

>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=99.83  E-value=7e-21  Score=126.15  Aligned_cols=72  Identities=24%  Similarity=0.437  Sum_probs=67.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC--------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR--------HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       174 l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~--------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      |||+|||.++|+++|+++|++||.|.++.++.++        +|||||+|.+.++|..|++.|||..++ |++|+|.||+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~-g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD-GHKLEVRISE   79 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEET-TEECEEECSS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEECC
Confidence            7999999999999999999999999999998743        479999999999999999999999999 9999999986


Q ss_pred             C
Q psy4057         246 K  246 (246)
Q Consensus       246 ~  246 (246)
                      +
T Consensus        80 ~   80 (85)
T d2cpfa1          80 R   80 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.83  E-value=1.1e-20  Score=123.00  Aligned_cols=72  Identities=24%  Similarity=0.322  Sum_probs=68.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .|||+|||.++++++|+++|++||.|.++++..++    +|||||+|.+.++|+.|++.|||+.++ |++|+|+||.
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLD-GRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEET-TEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEEee
Confidence            59999999999999999999999999999999865    579999999999999999999999999 9999999985

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.5e-20  Score=123.89  Aligned_cols=73  Identities=26%  Similarity=0.368  Sum_probs=68.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      .+++++|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|..|++.|||..|+ |++|+|
T Consensus         6 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           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD-GRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEET-TEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEEC-CEEeEC
Confidence            3468899999999999999999999999999999999865     579999999999999999999999999 999987

>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=9.9e-21  Score=125.22  Aligned_cols=73  Identities=22%  Similarity=0.357  Sum_probs=69.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..|||+|||.++|+++|+++|++||.|.++++++++     +|||||+|.+.++|..|++.|||..++ |++|+|.||+
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~-g~~l~V~~A~   79 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG-DKKLLVQRAS   79 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCS-SSCCEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEECC
Confidence            469999999999999999999999999999999865     589999999999999999999999999 9999999986

>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=99.83  E-value=2e-20  Score=127.41  Aligned_cols=85  Identities=16%  Similarity=0.316  Sum_probs=76.5

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhc------CCcc
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQ------GFPF   75 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~ln------g~~~   75 (246)
                      +.....+++|||+|||.++++++|+++|++||.|.++.+..+.   +++|||||+|.+.++|..|++.||      |..+
T Consensus         2 P~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~   81 (98)
T d1x4ha1           2 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL   81 (98)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES
T ss_pred             ccCCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEE
Confidence            4567788999999999999999999999999999999988754   688999999999999999999987      5678


Q ss_pred             CCeeEEEEEccCCc
Q psy4057          76 YDKPMRIQYSKTDS   89 (246)
Q Consensus        76 ~g~~l~v~~a~~~~   89 (246)
                      .|++|+|.++.++.
T Consensus        82 ~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          82 DGRQLKVDLAVTRD   95 (98)
T ss_dssp             SSCEEEEECCCCCC
T ss_pred             CCEEEEEEECCCCC
Confidence            99999999987654

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=6.7e-21  Score=126.23  Aligned_cols=75  Identities=21%  Similarity=0.381  Sum_probs=69.5

Q ss_pred             EEecCCChhhhHHHHHHHhhccCCeeEEEEccCC------CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL------KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        14 l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      |||+|||.++++++|+++|++||.|.++.++++.      +++|||||+|.+.++|..|++.|||..+.|++|.|.++..
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            7999999999999999999999999999998653      3579999999999999999999999999999999999854


Q ss_pred             C
Q psy4057          88 D   88 (246)
Q Consensus        88 ~   88 (246)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.82  E-value=3.7e-20  Score=134.04  Aligned_cols=77  Identities=25%  Similarity=0.468  Sum_probs=71.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ....++|||+|||.++|+++|+++|++||.|.+|+++.++     +|||||+|.+.++|..|++.|||+.|+ |++|+|.
T Consensus        39 ~~~~~~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          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL-NKRLKVA  117 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECS-SCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEEC-CEEEEEE
Confidence            3346789999999999999999999999999999999864     589999999999999999999999999 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      ||+
T Consensus       118 ~a~  120 (139)
T d1u6fa1         118 LAA  120 (139)
T ss_dssp             ESS
T ss_pred             EcC
Confidence            986

>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=123.91  Aligned_cols=74  Identities=15%  Similarity=0.249  Sum_probs=67.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .++|||+|||.++|+++|+++|++||.|..+.++.+.     +|||||+|.+.++|++|++.|||..++ |++|+|+||+
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~-g~~i~V~~a~   79 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIE-GYTLVTKVSN   79 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEET-TEECEEEECC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEEcc
Confidence            3689999999999999999999999999887776543     589999999999999999999999999 9999999986

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.3e-20  Score=125.73  Aligned_cols=81  Identities=16%  Similarity=0.214  Sum_probs=72.6

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ..+.+++|||+|||.++++++|+++|++||.|.+|.++.+   ++++|||||+|.+.++|.+|++.+  ..+.|+.|.|.
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 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEE
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEE
Confidence            3567899999999999999999999999999999999875   478999999999999999999854  47899999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++.++.
T Consensus        82 ~a~~k~   87 (90)
T d2cqga1          82 LPNSKQ   87 (90)
T ss_dssp             CCCTTC
T ss_pred             eCCCCC
Confidence            987653

>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=99.82  E-value=1.9e-20  Score=124.13  Aligned_cols=78  Identities=14%  Similarity=0.330  Sum_probs=72.3

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      ...++|||+|||.++++++|+++|++||.|.+|.+.+   .+|||||+|.+.++|..|++.|||..+.|++|+|.+|...
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~---~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1           6 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET---TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeec---ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            3457899999999999999999999999999999876   5799999999999999999999999999999999998765


Q ss_pred             c
Q psy4057          89 S   89 (246)
Q Consensus        89 ~   89 (246)
                      .
T Consensus        83 ~   83 (86)
T d2cpja1          83 A   83 (86)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=7.6e-21  Score=127.00  Aligned_cols=75  Identities=19%  Similarity=0.288  Sum_probs=70.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      ..+|||+|||.++|+++|+++|++||.|..++++.++   +|||||+|.+.++|..|++.|||+.++ |++|+|+||+.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~-g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN-DRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEET-TEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEEC-CEEEEEEECCC
Confidence            4579999999999999999999999999999999865   589999999999999999999999999 99999999974

>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=99.82  E-value=3.8e-20  Score=123.33  Aligned_cols=78  Identities=17%  Similarity=0.302  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHh--CCCccCCCCceEEEee
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL--HGFKITPTHAMKISFA  244 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l--~g~~i~~g~~l~v~~a  244 (246)
                      ..+|+++|||+|||.++++++|+++|++||.|.++++.+++ ++|||+|.+.++|.+|++.|  ++..++ |++|+|.||
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~-~~afV~f~~~e~A~~a~~~~~~~~~~~~-g~~l~v~~s   81 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-NQAFLELATEEAAITMVNYYSAVTPHLR-NQPIYIQYS   81 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHHHSCCEET-TEECEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc-eEEEEEeCCHHHHHHHHHHHccCCCccC-CCEEEEEEC
Confidence            56799999999999999999999999999999999999876 79999999999999999976  567888 999999999


Q ss_pred             cC
Q psy4057         245 KK  246 (246)
Q Consensus       245 k~  246 (246)
                      |.
T Consensus        82 k~   83 (88)
T d2cq1a1          82 NH   83 (88)
T ss_dssp             SC
T ss_pred             CC
Confidence            74

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.82  E-value=1.1e-20  Score=125.38  Aligned_cols=78  Identities=21%  Similarity=0.248  Sum_probs=69.8

Q ss_pred             CCcEEEecCCChhhh-HHHHHHHhhccCCeeEEEEccC----CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057          10 VTNFVYVTHISSTDL-KKSLYAIFSQFGQIMDIVALKT----LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~-e~~l~~~F~~fG~i~~v~~~~~----~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      .+++|||+|||.+++ +++|+++|++||.|++|.+..+    ++++|||||+|.+.++|.+|++ |||..+.|++|+|.+
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            468999999999986 5669999999999999998653    3788999999999999999996 999999999999999


Q ss_pred             ccCC
Q psy4057          85 SKTD   88 (246)
Q Consensus        85 a~~~   88 (246)
                      |+.+
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8754

>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=2.9e-20  Score=124.43  Aligned_cols=76  Identities=28%  Similarity=0.443  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ...+|||+|||.++++++|+++|++||.|..+.++.+.     +|||||+|.+.++|..|++.|||+.|+ |++|+|.||
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~-g~~l~V~~a   82 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD-GRQIRVDQA   82 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTT-SCCCEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEEC-CEEEEEEEc
Confidence            46779999999999999999999999999999988754     589999999999999999999999999 999999998


Q ss_pred             cC
Q psy4057         245 KK  246 (246)
Q Consensus       245 k~  246 (246)
                      ++
T Consensus        83 ~~   84 (90)
T d1x5sa1          83 GK   84 (90)
T ss_dssp             EC
T ss_pred             CC
Confidence            64

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=8.3e-21  Score=130.62  Aligned_cols=79  Identities=22%  Similarity=0.417  Sum_probs=73.3

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      +.++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|..|++.|||..+.|++|+|.++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45789999999999999999999999999999998754   678999999999999999999999999999999999986


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      ..
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            54

>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=99.82  E-value=4.5e-20  Score=122.43  Aligned_cols=75  Identities=32%  Similarity=0.394  Sum_probs=70.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ...++|||+|||.++|+++|+++|++||.|..+.+...+ |||||+|.+.++|..|+..|||..|. |+.|+|+|||
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~r-g~afV~f~~~~~A~~Ai~~l~~~~i~-g~~i~V~~ak   80 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR-DYAFVHFSNREDAVEAMKALNGKVLD-GSPIEVTLAK   80 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECS-SEEEEEESSHHHHHHHHHHHSSEEET-TEEEEEECCC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcccc-EEEEEEeCCHHHHHHHHHHcCCCEEC-CEEEEEEecc
Confidence            356899999999999999999999999999988887765 89999999999999999999999999 9999999986

>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=99.82  E-value=1.7e-20  Score=135.94  Aligned_cols=81  Identities=23%  Similarity=0.379  Sum_probs=74.3

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ...++|||+|||.++++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|..|++.|||..|.|++|+|.++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            345789999999999999999999999999999998754   67899999999999999999999999999999999998


Q ss_pred             cCCc
Q psy4057          86 KTDS   89 (246)
Q Consensus        86 ~~~~   89 (246)
                      ....
T Consensus       120 ~~~~  123 (139)
T d1u6fa1         120 ASGH  123 (139)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6543

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=3.7e-20  Score=126.96  Aligned_cols=79  Identities=20%  Similarity=0.274  Sum_probs=72.0

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      +..++|||+|||..+++++|+++|++||.|.+|.++++.   +++|||||+|.+.++|.+|++.+|+ .+.|++|+|.++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            445779999999999999999999999999999998764   7899999999999999999998876 799999999998


Q ss_pred             cCC
Q psy4057          86 KTD   88 (246)
Q Consensus        86 ~~~   88 (246)
                      ...
T Consensus        87 ~~~   89 (103)
T d2cqda1          87 YLG   89 (103)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            654

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4.3e-20  Score=123.05  Aligned_cols=80  Identities=19%  Similarity=0.277  Sum_probs=73.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHh--cCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM--QGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l--ng~~~~g~~l~v~~   84 (246)
                      +.+|+++|||+|||.++++++|+++|++||.|.++.+.+   ++++|||+|.+.++|..|++.+  ++..+.|++|+|.|
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~---~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~   80 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK---GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQY   80 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccc---cceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEE
Confidence            678999999999999999999999999999999998875   5799999999999999999865  57889999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      ++.+.
T Consensus        81 sk~~~   85 (88)
T d2cq1a1          81 SNHKE   85 (88)
T ss_dssp             CSCSS
T ss_pred             CCCCC
Confidence            97553

>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=99.82  E-value=2.8e-20  Score=121.31  Aligned_cols=76  Identities=24%  Similarity=0.336  Sum_probs=70.1

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      ++.+++|||+|++  +++++|+++|++||.|.+|.+.+   .+|||||+|.+.++|..|++.|||..+.|++|+|.|+++
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~---~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP---PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET---TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc---CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            4568999999985  89999999999999999998865   679999999999999999999999999999999999975


Q ss_pred             C
Q psy4057          88 D   88 (246)
Q Consensus        88 ~   88 (246)
                      +
T Consensus        77 ~   77 (79)
T d2bz2a1          77 Q   77 (79)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.82  E-value=2.5e-20  Score=127.09  Aligned_cols=77  Identities=23%  Similarity=0.376  Sum_probs=71.7

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ..++|||+|||.++++++|+++|+.||.|.+|.++++   ++++|||||+|.+.++|.+|++ |||..|.|++|+|.++.
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            3578999999999999999999999999999999986   4789999999999999999995 99999999999999975


Q ss_pred             C
Q psy4057          87 T   87 (246)
Q Consensus        87 ~   87 (246)
                      .
T Consensus        96 ~   96 (101)
T d2cq4a1          96 A   96 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=6.8e-21  Score=123.46  Aligned_cols=73  Identities=19%  Similarity=0.351  Sum_probs=68.6

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ++|||+|||.++++++|+++|++||.|.++.++++.   +++|||||+|.+.++|++|++ +|+..+.|++|.|..|
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            579999999999999999999999999999998764   789999999999999999997 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=1.7e-20  Score=123.67  Aligned_cols=75  Identities=23%  Similarity=0.507  Sum_probs=68.6

Q ss_pred             EEecCCChhhhHHHHHHHhhccCCeeEE-EEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        14 l~V~nl~~~~~e~~l~~~F~~fG~i~~v-~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      |||+|||.++++++|+++|++||.|.++ +++++.   +++|||||+|.+.++|.+|++.|||..+.|++|+|.+|.++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            7999999999999999999999998764 666553   78899999999999999999999999999999999998754

>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=99.81  E-value=1.9e-20  Score=130.44  Aligned_cols=78  Identities=18%  Similarity=0.252  Sum_probs=71.9

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      ..++++|||+|||.++++++|+++|++||+|..|.+.   +++|||||+|.+.++|.+|++.|||..|.|++|.|.|+..
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~---~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP---EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC---SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee---ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            4567899999999999999999999999999999874   4789999999999999999999999999999999999854


Q ss_pred             C
Q psy4057          88 D   88 (246)
Q Consensus        88 ~   88 (246)
                      .
T Consensus        84 ~   84 (111)
T d1whxa_          84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=2.2e-20  Score=120.54  Aligned_cols=72  Identities=25%  Similarity=0.379  Sum_probs=67.1

Q ss_pred             EEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        13 ~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      +|||+|||.++++++|+++|++||+|.++.++++.   +++|||||+|.+.++|++|++ +++..+.|++|.|..|
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            58999999999999999999999999999998764   788999999999999999997 8999999999998754

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=2.1e-20  Score=127.49  Aligned_cols=74  Identities=20%  Similarity=0.311  Sum_probs=69.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..++|||+|||.++|+++|+++|+.||.|.+++++.+.     +|||||+|.+.++|.+|+. |||..|+ |+.|+|.+|
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   94 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLL-GVPIIVQAS   94 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEET-TEEEEEEEH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEEC-CEEEEEEEC
Confidence            36799999999999999999999999999999999864     5799999999999999995 9999999 999999997


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus        95 ~   95 (101)
T d2cq4a1          95 Q   95 (101)
T ss_dssp             H
T ss_pred             C
Confidence            5

>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=99.81  E-value=7e-20  Score=124.54  Aligned_cols=78  Identities=21%  Similarity=0.302  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEcCCCCC-CCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHH--HhCCCccCCCCceEEEe
Q psy4057         167 EQPPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL--ALHGFKITPTHAMKISF  243 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~-~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~--~l~g~~i~~g~~l~v~~  243 (246)
                      ...++++|||+|||.+ +|+++|.++|++||.|.++++++++ |+|||+|.+.++|..|++  .+++..|+ |++|+|+|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k-~~afV~f~~~~~A~~Ai~~~~~~~~~~~-gr~l~V~~   91 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK-SQAFIEMETREDAMAMVDHCLKKALWFQ-GRCVKVDL   91 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT-TEEEEECSSHHHHHHHHHHHHHSCCCSS-SSCCEEEE
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC-CcEEEEecchHHHHHHHHHHhcCCceEC-CEEEEEEE
Confidence            4456899999999985 8999999999999999999999876 899999999999999998  57888999 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |++
T Consensus        92 s~~   94 (99)
T d1x4fa1          92 SEK   94 (99)
T ss_dssp             ECS
T ss_pred             cCC
Confidence            975

>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=99.81  E-value=5.5e-21  Score=131.16  Aligned_cols=83  Identities=25%  Similarity=0.398  Sum_probs=76.1

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEcc---CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~---~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...|+++|||+|||.++++++|+++|++||.|..+.+..   +++++|||||+|.+.++|..|++.|||..+.|++|+|.
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   93 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE   93 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEE
Confidence            456889999999999999999999999999999887765   35789999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ||+.+.
T Consensus        94 ~ak~k~   99 (102)
T d2cpxa1          94 FGKNKK   99 (102)
T ss_dssp             ECCCCS
T ss_pred             eCCCcc
Confidence            997654

>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=99.81  E-value=3.7e-20  Score=128.51  Aligned_cols=76  Identities=22%  Similarity=0.410  Sum_probs=70.6

Q ss_pred             CcEEEecCCCh-hhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057          11 TNFVYVTHISS-TDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus        11 ~~~l~V~nl~~-~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      +++|||+||++ .+++++|+++|++||.|.+|.++++  .+|||||+|.+.++|..|++.|||..+.|++|+|.+++..
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~--~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN--KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT--TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec--ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            68999999965 5899999999999999999999886  5799999999999999999999999999999999998644

>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=99.81  E-value=6.3e-20  Score=124.43  Aligned_cols=82  Identities=22%  Similarity=0.399  Sum_probs=74.5

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCC--eeEEE
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD--KPMRI   82 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g--~~l~v   82 (246)
                      ....+|+++|||+|||.++++++|+++|++||.|..+.+.+   .++||||+|.+.++|..|++.||+..+.|  ++|+|
T Consensus        11 ~g~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~---~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          11 YGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK---GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS---SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec---cccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            35678999999999999999999999999999999998865   57899999999999999999999999976  57999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .|++..+
T Consensus        88 ~~ak~~~   94 (97)
T d1whya_          88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
Confidence            9987653

>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=99.81  E-value=2e-19  Score=123.47  Aligned_cols=79  Identities=18%  Similarity=0.182  Sum_probs=71.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhC--CCccCCCCceEEEe
Q psy4057         166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH--GFKITPTHAMKISF  243 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~--g~~i~~g~~l~v~~  243 (246)
                      ...+++++|||+|||.++|+++|+++|++||.|.++++.+++ ++|||+|.+.++|..|+..|+  +..+. |++|+|+|
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k-~~AfV~f~~~e~A~~ai~~~~~~~~~~~-g~~l~v~~   87 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK-RQALVEFENIDSAKECVTFAADVPVYIA-GQQAFFNY   87 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHHHSCCBSS-SSBCEEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecc-eeEEEEeCCHHHHHHHHHHHcCCCcEEe-eEEEEEEE
Confidence            356689999999999999999999999999999999998876 899999999999999999884  56677 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      |+.
T Consensus        88 s~~   90 (104)
T d1wexa_          88 STS   90 (104)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            873

>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=3.3e-20  Score=126.93  Aligned_cols=78  Identities=18%  Similarity=0.326  Sum_probs=72.2

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      .++|||+|||+++++++|+++|++||.|.++.|.++.   .++|||||+|.+.++|.+|++ ++|..|.|++|.|.+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            4799999999999999999999999999999998764   789999999999999999997 899999999999999876


Q ss_pred             Cc
Q psy4057          88 DS   89 (246)
Q Consensus        88 ~~   89 (246)
                      +.
T Consensus        99 ke  100 (103)
T d1x4ba1          99 RE  100 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            53

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.5e-20  Score=122.94  Aligned_cols=75  Identities=23%  Similarity=0.301  Sum_probs=67.8

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCC-ccCCeeEEEEEccCCc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF-PFYDKPMRIQYSKTDS   89 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~-~~~g~~l~v~~a~~~~   89 (246)
                      ++|||+|||.++++++|+++|++||.|.++.+.+   ++|||||+|.+.++|..|++.|||. .+.|++|+|.++.++.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~---~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL---KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE---ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec---ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            4799999999999999999999999988765544   6899999999999999999999995 6999999999987653

>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=99.81  E-value=3.3e-20  Score=124.34  Aligned_cols=76  Identities=25%  Similarity=0.467  Sum_probs=69.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHH----HHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         170 PNQILFLTNLPEETSEMMLS----MLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~----~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      |+++|||+|||.++++++|+    ++|++||.|.+|++..+.  +|||||+|.+.++|..|++.|||..++ |++|+|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~-g~~l~v~~   80 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFY-DKPMRIQY   80 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEET-TEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEE
Confidence            68999999999999999886    468999999999987743  589999999999999999999999999 99999999


Q ss_pred             ecC
Q psy4057         244 AKK  246 (246)
Q Consensus       244 ak~  246 (246)
                      ||.
T Consensus        81 ak~   83 (91)
T d1nu4a_          81 AKT   83 (91)
T ss_dssp             CSS
T ss_pred             eCC
Confidence            973

>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=99.81  E-value=7e-20  Score=126.73  Aligned_cols=84  Identities=25%  Similarity=0.299  Sum_probs=75.6

Q ss_pred             ccCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCcc--CCeeEEE
Q psy4057           5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF--YDKPMRI   82 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~--~g~~l~v   82 (246)
                      |+...|..+|||+|||+++++++|+++|++||.|.+|.+.++ +++|+|||+|.+.++|..|+..|||..+  .|++|+|
T Consensus         1 ~~~~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~-~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           1 MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             SCCCCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE-TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCCCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee-CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            456778899999999999999999999999999999999765 4689999999999999999999999988  5788999


Q ss_pred             EEccCCc
Q psy4057          83 QYSKTDS   89 (246)
Q Consensus        83 ~~a~~~~   89 (246)
                      .+++...
T Consensus        80 ~~s~~~~   86 (108)
T d2adba1          80 DFSKLTS   86 (108)
T ss_dssp             EECSSCS
T ss_pred             EecCCcc
Confidence            9986543

>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=99.80  E-value=5.6e-20  Score=126.41  Aligned_cols=75  Identities=24%  Similarity=0.405  Sum_probs=70.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..++|||+|||.++|+++|+++|++||.|.+|+++.++     +|||||+|.+.++|..|++.|||..|. |++|+|.||
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~-g~~i~V~~a   85 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFS-GRALRVDNA   85 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCS-SSCBEEEET
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEEC-CEEEEEEEC
Confidence            35789999999999999999999999999999999865     479999999999999999999999999 999999998


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus        86 ~   86 (104)
T d1p1ta_          86 A   86 (104)
T ss_dssp             T
T ss_pred             C
Confidence            5

>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=99.80  E-value=2.5e-20  Score=123.58  Aligned_cols=75  Identities=21%  Similarity=0.337  Sum_probs=67.5

Q ss_pred             CCcEEEEcCCCCCCC-HHHHHHHHccCCCceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         170 PNQILFLTNLPEETS-EMMLSMLFNQFPGFKEVRLVPNR------HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t-~e~l~~~f~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..++|||+|||.++| +++|+++|++||.|.+++++.+.      +|||||+|.+.++|..|++ |||+.++ |+.|+|+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~-gr~l~V~   80 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLG-NREISVS   80 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEET-TEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEEC-CEEEEEE
Confidence            478999999999987 45699999999999999987642      5799999999999999996 9999999 9999999


Q ss_pred             eecC
Q psy4057         243 FAKK  246 (246)
Q Consensus       243 ~ak~  246 (246)
                      ||++
T Consensus        81 ~a~~   84 (86)
T d2ghpa3          81 LADK   84 (86)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9974

>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=8.1e-20  Score=119.23  Aligned_cols=74  Identities=22%  Similarity=0.296  Sum_probs=68.8

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      -++|||+|||.++++++|+++|++||.|..+.+..+.   +++|||||+|.+.++|.+|++ +||..|.|++|.|..|
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            4799999999999999999999999999999988754   678999999999999999996 8999999999999876

>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=99.80  E-value=1.3e-19  Score=120.20  Aligned_cols=77  Identities=18%  Similarity=0.272  Sum_probs=70.9

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      ...++|||+|||.++++++|+++|++||.|..+.+.   +++|||||+|.+.++|..|+..|||..+.|++|+|.||++.
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~---~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE---ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc---cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCC
Confidence            456899999999999999999999999999887664   47899999999999999999999999999999999998755

>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=99.80  E-value=7.7e-20  Score=126.50  Aligned_cols=78  Identities=22%  Similarity=0.348  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-ccEEEEEeCCHHHHHHHHHHhCCCccC-CCCceEEEeec
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFENEMQSAAAKLALHGFKIT-PTHAMKISFAK  245 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~~~A~~Al~~l~g~~i~-~g~~l~v~~ak  245 (246)
                      ..+..+|||+|||.++|+++|+++|++||.|.++.+..++ +|+|||+|.+.++|..|+..|||..|. .|+.|+|.|+|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            4468889999999999999999999999999999998865 689999999999999999999999985 37999999986

>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=99.80  E-value=8.9e-21  Score=127.00  Aligned_cols=79  Identities=14%  Similarity=0.231  Sum_probs=71.5

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEcc--CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~--~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ..++.+|||+|||.++++++|+++|++||.|.++.++.  +++++|||||+|.+.++|++|++ |||..+.|++|+|.+|
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            34566999999999999999999999999998887764  35899999999999999999996 9999999999999998


Q ss_pred             cC
Q psy4057          86 KT   87 (246)
Q Consensus        86 ~~   87 (246)
                      +.
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.80  E-value=1.1e-19  Score=124.35  Aligned_cols=84  Identities=18%  Similarity=0.256  Sum_probs=73.4

Q ss_pred             cCCCCCcEEEecCCChhhhHHHHHHHhhccCCeeE--------EEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCc
Q psy4057           6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKT---LKMRGQAFVIFKEIASATNALRSMQGFP   74 (246)
Q Consensus         6 ~~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~--------v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~   74 (246)
                      ...+.+++|||+|||.++++++|+++|+.||.|..        +.+.++   ++++|||||+|.+.++|.+|++.|||..
T Consensus         3 ~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~   82 (101)
T d2cpea1           3 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   82 (101)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCE
Confidence            34567899999999999999999999999998853        444443   3678999999999999999999999999


Q ss_pred             cCCeeEEEEEccCCc
Q psy4057          75 FYDKPMRIQYSKTDS   89 (246)
Q Consensus        75 ~~g~~l~v~~a~~~~   89 (246)
                      |.|++|+|.+++.+.
T Consensus        83 ~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          83 FQGSKLKVSLARKKP   97 (101)
T ss_dssp             ETTEECEEECSSCCC
T ss_pred             ECCEEEEEEEcCCCC
Confidence            999999999997653

>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=99.80  E-value=1.5e-19  Score=116.52  Aligned_cols=69  Identities=17%  Similarity=0.303  Sum_probs=63.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       174 l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      |||+|||+++++++|+++|++|| +..+++... +|||||+|.+.++|.+|++.|||+.++ |++|+|+||+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~~-~g~afv~f~~~~~A~~Ai~~ln~~~~~-g~~l~V~~a~   69 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKY-KGTAFVTLLNGEQAEAAINTFHQSRLR-ERELSVQLQP   69 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTEESS-SCEEEEEECC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeeccc-ceeEEEEECCHHHHHHHHHHhCCccCC-CCEEEEEEeC
Confidence            79999999999999999999999 666666555 489999999999999999999999999 9999999986

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=3.4e-20  Score=126.72  Aligned_cols=78  Identities=14%  Similarity=0.228  Sum_probs=71.3

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...++|||+|||.++++++|+++|++||.|..+.+..+.  +++|||||+|.+.++|++|++.|||..+.|+++.|.+++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            345789999999999999999999999999999888654  778999999999999999999999999999999887764

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=5.3e-20  Score=119.20  Aligned_cols=71  Identities=18%  Similarity=0.265  Sum_probs=66.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      |.|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|++ +|++.++ |+.|.|..|
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-QSRHELD-SKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCS-SCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEEC-CeEEEEEEC
Confidence            579999999999999999999999999999998865     5899999999999999997 7999999 999999886

>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=99.80  E-value=3e-20  Score=121.46  Aligned_cols=71  Identities=18%  Similarity=0.248  Sum_probs=66.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCC-ccCCCCceEEEeec
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF-KITPTHAMKISFAK  245 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~-~i~~g~~l~v~~ak  245 (246)
                      +|||+|||.++|+++|+++|++||.|..+++...+ |||||+|.+.++|..|++.|||. .++ |++|+|.||+
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~r-g~aFV~f~~~~~A~~Ai~~lng~~~~~-G~~i~V~~a~   74 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-GYAFVDYPDQNWAIRAIETLSGKVELH-GKIMEVDYSV   74 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEET-TEEEECCSCHHHHHHHHHHHTTTCEET-TEECEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEeccc-ceEEEEECCHHHHHHHHHHhCCCeEEC-CEEEEEEEcC
Confidence            69999999999999999999999999888888765 89999999999999999999996 588 9999999986

>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=99.80  E-value=2.8e-20  Score=127.59  Aligned_cols=79  Identities=28%  Similarity=0.405  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC-----CccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ...|+++|||+|||.++++++|+++|++||.|..+.+..+     .+|||||+|.+.++|..|++.|||..|+ |++|+|
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~-g~~l~V   92 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLY-GKILVI   92 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCS-SCBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEEC-CEEEEE
Confidence            3457899999999999999999999999999988877753     2589999999999999999999999999 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      +|||.
T Consensus        93 ~~ak~   97 (102)
T d2cpxa1          93 EFGKN   97 (102)
T ss_dssp             EECCC
T ss_pred             EeCCC
Confidence            99974

>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=99.80  E-value=6.8e-20  Score=121.90  Aligned_cols=73  Identities=18%  Similarity=0.286  Sum_probs=65.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .+++|||+|||.++++++|+++|++|| +..+.+... ++||||+|.+.++|..|++.|||+.++ |++|+|+|++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~~-kg~afV~f~~~~~A~~Ai~~ln~~~~~-G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRN-KRTAFVTLLNGEQAQNAIQMFHQYSFR-GKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEGG-GTEEEECCSCHHHHHHHHHHHTTEEET-TEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeecc-CCceEEEECCHHHHHHHHHHhCCCEEC-CEEEEEEEcC
Confidence            467899999999999999999999999 344444443 489999999999999999999999999 9999999987

>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=99.80  E-value=5.9e-20  Score=118.68  Aligned_cols=72  Identities=18%  Similarity=0.278  Sum_probs=67.2

Q ss_pred             EEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        13 ~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      +|||+|||.++++++|+++|++||.|..+.+..+.   .+++||||+|.+.++|++|++ +||..+.|++|+|++|
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            59999999999999999999999999999887654   678999999999999999997 9999999999999875

>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=99.80  E-value=7.5e-20  Score=124.08  Aligned_cols=75  Identities=21%  Similarity=0.318  Sum_probs=68.0

Q ss_pred             CCCCcEEEEcCCC-CCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         168 QPPNQILFLTNLP-EETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       168 ~~~~~~l~v~nL~-~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      ...+++|||+||| ..+++++|+++|++||.|.++++.   +|||||+|.+.++|.+|++.|||+.|+ |++|+|.||+.
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~---rg~aFV~f~~~~~A~~Ai~~lng~~~~-g~~l~V~~a~~   87 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH---KGFAFVQYVNERNARAAVAGEDGRMIA-GQVLDINLAAE   87 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE---TEEEEEEESSHHHHHHHHHTTTTCEET-TEECEEEETTS
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe---CCeEEEEECCHHHHHHHHHHcCCCEEC-CEEEEEEECCC
Confidence            3456789999997 578899999999999999999984   489999999999999999999999999 99999999863

>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=99.80  E-value=4.2e-20  Score=125.12  Aligned_cols=79  Identities=18%  Similarity=0.255  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      ...++++|||+|||.++|+++|+++|+.||.|..++.....++||||+|.+.++|..|++.|||..++ |++|+|.||+.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~-gr~i~V~~a~~   90 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID-GRSVSLYYTGE   90 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEET-TEEEEEEECSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEEC-CEEEEEEEeCC
Confidence            44568999999999999999999999999999877654444689999999999999999999999999 99999999863

>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=99.80  E-value=1.1e-19  Score=120.00  Aligned_cols=75  Identities=21%  Similarity=0.405  Sum_probs=70.0

Q ss_pred             CCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ..++|||+|||.++++++|.++|+.||.|..|.+.++.  +++|||||+|.+.++|.+|++ ++|..+.|++|.|.+.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEc
Confidence            46899999999999999999999999999999998654  778999999999999999996 7999999999999985

>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=99.79  E-value=5.9e-20  Score=121.03  Aligned_cols=72  Identities=26%  Similarity=0.389  Sum_probs=65.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHccCCCceE-EEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeecC
Q psy4057         174 LFLTNLPEETSEMMLSMLFNQFPGFKE-VRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK  246 (246)
Q Consensus       174 l~v~nL~~~~t~e~l~~~f~~~G~i~~-v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak~  246 (246)
                      |||+|||.++|+++|+++|++||.|.+ ++++.++     +|||||+|.+.++|..|++.|||..++ |++|+|+||+.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~-gr~l~v~~a~~   78 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLC-NRPITVSYAFK   78 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEET-TEECEEEESCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEEC-CEEEEEEEecC
Confidence            799999999999999999999999965 4677654     589999999999999999999999999 99999999863

>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=99.79  E-value=3e-19  Score=122.62  Aligned_cols=80  Identities=20%  Similarity=0.308  Sum_probs=73.0

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHh--cCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM--QGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l--ng~~~~g~~l~v~~   84 (246)
                      ..+|+++|||+|||.++++++|+++|++||.|.++.+.+   .+++|||+|.+.++|..|++.|  ++..+.|++|+|.|
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~---~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~   87 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP---FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe---cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEE
Confidence            568999999999999999999999999999999998865   6899999999999999999987  56778999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      ++.+.
T Consensus        88 s~~~~   92 (104)
T d1wexa_          88 STSKR   92 (104)
T ss_dssp             CSSSS
T ss_pred             cCCCc
Confidence            97653

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.8e-19  Score=123.44  Aligned_cols=76  Identities=18%  Similarity=0.299  Sum_probs=69.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .+..++|||+|||..+++++|+++|+.||.|.+++++.++     +|||||+|.+.++|.+|++.+|+ .|+ |++|+|.
T Consensus         7 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           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IID-GRKANVN   84 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EET-TEECEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCC-CEEEEEE
Confidence            3356789999999999999999999999999999999864     58999999999999999999987 688 9999999


Q ss_pred             eec
Q psy4057         243 FAK  245 (246)
Q Consensus       243 ~ak  245 (246)
                      +|.
T Consensus        85 ~a~   87 (103)
T d2cqda1          85 LAY   87 (103)
T ss_dssp             EST
T ss_pred             EcC
Confidence            985

>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=99.79  E-value=4.3e-20  Score=122.71  Aligned_cols=70  Identities=16%  Similarity=0.144  Sum_probs=66.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      +|||+|||.++++++|+++|++||.|.++++..+  |||||+|.+.++|..|+..|||..|. |+.|+|.|++
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~-g~~i~v~~~~   71 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFR-SHEGETAYIR   71 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCC-CTTSCCCBCE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc--ceeeEEeCCHHHHHHHHHHhCCCEEC-CcEeEEeEEe
Confidence            5999999999999999999999999999998776  79999999999999999999999999 9999998865

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=5.2e-20  Score=118.50  Aligned_cols=72  Identities=19%  Similarity=0.261  Sum_probs=66.6

Q ss_pred             EEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        13 ~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      +|||+|||.++++++|+++|++||+|.+|.++.+.   +++|||||+|.+.++|++|++ +++..+.|+.|.|..|
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            59999999999999999999999999999998764   789999999999999999997 5778899999998764

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.7e-19  Score=123.18  Aligned_cols=76  Identities=18%  Similarity=0.248  Sum_probs=68.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ...++|||+|||.++++++|+++|++||.|..+++..+.    +|||||+|.+.++|.+|++.|||..|. |+++.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~-gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIK-TPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCC-CCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEEC-CcCCccCCC
Confidence            346899999999999999999999999999999988865    479999999999999999999999999 888777665


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      +
T Consensus        95 ~   95 (101)
T d1x5oa1          95 E   95 (101)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.79  E-value=6.1e-20  Score=124.28  Aligned_cols=81  Identities=19%  Similarity=0.256  Sum_probs=73.3

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...++++|||+|||.++++++|+++|++||.|..+.  .+++++|||||+|.+.++|..|++.|||..+.|++|+|.|+.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~--~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~   89 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS--QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE--ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee--ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            345689999999999999999999999999987764  355789999999999999999999999999999999999987


Q ss_pred             CCc
Q psy4057          87 TDS   89 (246)
Q Consensus        87 ~~~   89 (246)
                      ++.
T Consensus        90 ~k~   92 (96)
T d1fjca_          90 EKG   92 (96)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>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=99.79  E-value=5.3e-20  Score=122.45  Aligned_cols=77  Identities=16%  Similarity=0.244  Sum_probs=68.2

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      ..+++|||+|||.++++++|+++|++|| +..+.+   .+++|||||+|.+.++|++|++.|||..+.|++|+|++++.+
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~---~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV---DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE---EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee---eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            4578999999999999999999999999 333333   357899999999999999999999999999999999998665


Q ss_pred             c
Q psy4057          89 S   89 (246)
Q Consensus        89 ~   89 (246)
                      .
T Consensus        79 ~   79 (88)
T d1wg1a_          79 A   79 (88)
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=99.79  E-value=3.2e-19  Score=117.50  Aligned_cols=74  Identities=19%  Similarity=0.235  Sum_probs=68.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..++|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|++ ++|..|. |+.|+|..|
T Consensus         5 ~~~~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           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVD-GRVVEPKRA   82 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEET-TEECEEEEC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEEC-CEEEEEEee
Confidence            35789999999999999999999999999999999865     5899999999999999997 6999999 999999987


Q ss_pred             c
Q psy4057         245 K  245 (246)
Q Consensus       245 k  245 (246)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=99.79  E-value=4.2e-19  Score=120.35  Aligned_cols=73  Identities=15%  Similarity=0.153  Sum_probs=69.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ...+|||+|||.++++++|+++|++||.|.++.+..+  |||||+|.+.++|.+|++.|||..|. |+.|+|.|++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~lng~~~~-g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD--GMGMVEYLRKEDMEYALRKLDDTKFR-SHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT--TEEEEEESSHHHHHHHHHHHSSEEEE-CTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc--ceEEEEECCHHHHHHHHHHhCCCEeC-CeEEEEEEEe
Confidence            4678999999999999999999999999999998754  79999999999999999999999999 9999999976

>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=99.79  E-value=3.4e-19  Score=121.17  Aligned_cols=77  Identities=25%  Similarity=0.391  Sum_probs=69.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhC------CCccCCC
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALH------GFKITPT  236 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~------g~~i~~g  236 (246)
                      ...+++|||+|||.++|+++|+++|++||.|..++++.+.     +|||||+|.+.++|..|++.||      |..+. |
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~-g   83 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD-G   83 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS-S
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEEC-C
Confidence            3457899999999999999999999999999999998865     5899999999999999999997      56677 8


Q ss_pred             CceEEEeec
Q psy4057         237 HAMKISFAK  245 (246)
Q Consensus       237 ~~l~v~~ak  245 (246)
                      ++|+|+||+
T Consensus        84 r~l~v~~a~   92 (98)
T d1x4ha1          84 RQLKVDLAV   92 (98)
T ss_dssp             CEEEEECCC
T ss_pred             EEEEEEECC
Confidence            999999986

>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=99.79  E-value=1.9e-19  Score=121.89  Aligned_cols=79  Identities=14%  Similarity=0.364  Sum_probs=70.5

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCC-eeEEEEccC----CCCccEEEEEEcCHHHHHHHHHHhcC--CccCCeeEEEE
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQ-IMDIVALKT----LKMRGQAFVIFKEIASATNALRSMQG--FPFYDKPMRIQ   83 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~-i~~v~~~~~----~~~kg~aFV~f~~~~~A~~Ai~~lng--~~~~g~~l~v~   83 (246)
                      +++|||+|||.++++++|+++|+.||+ |.++.++++    ++++|||||+|.+.++|..|++.|++  ..+.|++|+|.
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            468999999999999999999999996 999999875    37889999999999999999999865  56689999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ||++..
T Consensus        81 ~A~p~~   86 (96)
T d2disa1          81 WAEPEI   86 (96)
T ss_dssp             ESCSSC
T ss_pred             EcCCCC
Confidence            997654

>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=99.79  E-value=5.8e-20  Score=122.48  Aligned_cols=74  Identities=18%  Similarity=0.305  Sum_probs=67.2

Q ss_pred             CCcEEEecCCChhhhHHHH---HHHhhccCCeeEEEEccCC------CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeE
Q psy4057          10 VTNFVYVTHISSTDLKKSL---YAIFSQFGQIMDIVALKTL------KMRGQAFVIFKEIASATNALRSMQGFPFYDKPM   80 (246)
Q Consensus        10 ~~~~l~V~nl~~~~~e~~l---~~~F~~fG~i~~v~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (246)
                      ..++|||+|||+++++++|   +++|++||+|.+|.+.++.      ..+|||||+|.+.++|.+|++.|||..+.|++|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3578999999999999999   7789999999999998764      234899999999999999999999999999999


Q ss_pred             EEE
Q psy4057          81 RIQ   83 (246)
Q Consensus        81 ~v~   83 (246)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            984

>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=99.78  E-value=1.2e-19  Score=123.14  Aligned_cols=76  Identities=21%  Similarity=0.319  Sum_probs=69.3

Q ss_pred             CCCCcEEEecCCC-hhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           8 ICVTNFVYVTHIS-STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         8 ~~~~~~l~V~nl~-~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      ...+++|||+||+ ..+++++|+++|++||.|.+|.+     ++|||||+|.+.++|.+|++.|||..+.|++|+|.++.
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i-----~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   86 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-----HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAA   86 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE-----ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETT
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE-----eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            4456789999996 57888899999999999999988     57999999999999999999999999999999999986


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      ..
T Consensus        87 ~~   88 (98)
T d1wf2a_          87 EP   88 (98)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.78  E-value=2.1e-19  Score=119.68  Aligned_cols=77  Identities=12%  Similarity=0.173  Sum_probs=70.7

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHh--CCCccCCCCceEEEee
Q psy4057         168 QPPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL--HGFKITPTHAMKISFA  244 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~-~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l--~g~~i~~g~~l~v~~a  244 (246)
                      ..++++|||+|||.. +|+++|.++|++||.|.++++.+++ ++|||+|.+.++|..|+..|  ++..+. |++|+|+||
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k-~~afV~f~~~~~A~~A~~~l~~~~~~~~-gr~l~V~~s   82 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI-NEAFIEMATTEDAQAAVDYYTTTPALVF-GKPVRVHLS   82 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS-SCEEEEESSHHHHHHHHHHHHHSCCEET-TEECEEEEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc-eEEEEEEcchhhHHHHHHHHhhCCCccC-CceEEEEEC
Confidence            457999999999985 7899999999999999999999887 69999999999999999976  677899 999999999


Q ss_pred             cC
Q psy4057         245 KK  246 (246)
Q Consensus       245 k~  246 (246)
                      ++
T Consensus        83 ~~   84 (89)
T d1x4da1          83 QK   84 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>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=99.78  E-value=2.5e-19  Score=115.40  Aligned_cols=72  Identities=15%  Similarity=0.285  Sum_probs=65.5

Q ss_pred             EEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCCc
Q psy4057          14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDS   89 (246)
Q Consensus        14 l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~   89 (246)
                      |||+|||+++++++|+++|++|| +..+.+   .+++|||||+|.+.++|.+|++.|||..+.|++|+|+++..++
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~---~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV---DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE---ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee---cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 555544   4689999999999999999999999999999999999986654

>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=99.78  E-value=5.4e-19  Score=117.82  Aligned_cols=74  Identities=18%  Similarity=0.185  Sum_probs=67.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ..+++|||+|||.++|+++|+++|+.||.|.+++++.++     +|||||+|.+.++|.+|++.  +..++ |+.|.|.+
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~-Gr~i~v~~   82 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMID-GRWCDCKL   82 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEET-TEEEEEEC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccC-CEEeEEEe
Confidence            357889999999999999999999999999999999976     58999999999999999984  44788 99999999


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      |+
T Consensus        83 a~   84 (90)
T d2cqga1          83 PN   84 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            86

>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=3.8e-19  Score=121.60  Aligned_cols=79  Identities=22%  Similarity=0.287  Sum_probs=69.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCce--------EEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCcc
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFK--------EVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKI  233 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~--------~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i  233 (246)
                      ..+.+++|||+|||..+|+++|+++|+.||.|.        .+.+..++     +|||||+|.+.++|..|++.|||+.|
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            345688999999999999999999999999984        44444443     48999999999999999999999999


Q ss_pred             CCCCceEEEeecC
Q psy4057         234 TPTHAMKISFAKK  246 (246)
Q Consensus       234 ~~g~~l~v~~ak~  246 (246)
                      . |++|+|+|||.
T Consensus        84 ~-gr~i~V~~a~~   95 (101)
T d2cpea1          84 Q-GSKLKVSLARK   95 (101)
T ss_dssp             T-TEECEEECSSC
T ss_pred             C-CEEEEEEEcCC
Confidence            9 99999999974

>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=99.78  E-value=2e-19  Score=122.22  Aligned_cols=80  Identities=11%  Similarity=0.263  Sum_probs=72.2

Q ss_pred             CCCCCcEEEecCCChh-hhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHH--HhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISST-DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALR--SMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~-~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~--~lng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.+ +++++|.++|++||.|.+|.+.+   ++|+|||+|.+.++|..|++  .+++..+.|++|+|.
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~---~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~   90 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   90 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEee---cCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEE
Confidence            4567899999999986 89999999999999999998875   57999999999999999997  578899999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      +|+...
T Consensus        91 ~s~~~~   96 (99)
T d1x4fa1          91 LSEKYK   96 (99)
T ss_dssp             EECSCS
T ss_pred             EcCCcc
Confidence            997554

>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=99.78  E-value=9.7e-20  Score=121.22  Aligned_cols=77  Identities=22%  Similarity=0.313  Sum_probs=70.0

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      .++++|||+|||.++++++|+++|++||.|.+|++..  .+++||||+|.+.++|++|+.  ++..+.|++|+|.++.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~--~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k   78 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK--PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPK   78 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS--SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee--ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCC
Confidence            5689999999999999999999999999999997754  478999999999999999986  788999999999998765


Q ss_pred             c
Q psy4057          89 S   89 (246)
Q Consensus        89 ~   89 (246)
                      .
T Consensus        79 ~   79 (88)
T d1wf0a_          79 H   79 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.8e-19  Score=121.68  Aligned_cols=79  Identities=14%  Similarity=0.275  Sum_probs=69.8

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC----CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL----KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~----~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      .|.++|||+|||.++++++|+++|++|| +.++.++.+.    +++|||||+|.+.++|++|+ .||+..|.|++|+|.+
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-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            4668999999999999999999999999 7777776543    67899999999999998777 4999999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      |..+.
T Consensus        91 a~~~~   95 (104)
T d1wi8a_          91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=3.4e-19  Score=115.05  Aligned_cols=70  Identities=21%  Similarity=0.285  Sum_probs=65.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .|||+|||.++|+++|+++|++||.|..+.++.++     ++||||+|.+.++|.+|++ |||+.|+ |+.|+|.+|
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-IHFHEIN-NKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBT-TBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEEC-CeEEEEEEC
Confidence            48999999999999999999999999999988855     5799999999999999996 9999999 999999987

>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=99.78  E-value=3.4e-19  Score=114.74  Aligned_cols=73  Identities=16%  Similarity=0.169  Sum_probs=67.7

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC-CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .+|||+|||+++++++|+++|+.||.|.+|.+.++. ..++||||+|.++++|++|+. +|+..|.|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            489999999999999999999999999999998776 556899999999999999996 8999999999999864

>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=99.78  E-value=5.1e-20  Score=123.23  Aligned_cols=75  Identities=23%  Similarity=0.313  Sum_probs=68.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ...+|||+|||.++|+++|+++|+.||.|..++++.++    +|||||+|.+.++|.+||+ |||..++ |+.|+|.+||
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~-g~~i~V~~ak   89 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVF-GNEIKLEKPK   89 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEET-TEEEEEECCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEEC-CEEEEEEecC
Confidence            56799999999999999999999999999888776533    5899999999999999996 9999999 9999999998


Q ss_pred             C
Q psy4057         246 K  246 (246)
Q Consensus       246 ~  246 (246)
                      .
T Consensus        90 ~   90 (91)
T d1fjeb1          90 G   90 (91)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=7e-19  Score=114.67  Aligned_cols=72  Identities=19%  Similarity=0.359  Sum_probs=66.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .++|||+|||.++|+++|+++|++||.|..+.+..++     +|||||+|.+.++|.+|+. |||+.|+ |+.|+|..|
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-QKYHTVN-GHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEET-TEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEEC-CEEEEEEEC
Confidence            4789999999999999999999999999999999865     5899999999999999985 8999999 999999876

>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=99.78  E-value=9.7e-20  Score=121.23  Aligned_cols=74  Identities=19%  Similarity=0.222  Sum_probs=69.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..+++|||+|||.++|+++|+++|++||.|.++++..+.++||||+|.+.++|+.|+.  +++.|+ |++|+|.||+
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~-g~~l~v~~a~   76 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIK-GISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEET-TEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEEC-CEEeEEEeCC
Confidence            3588999999999999999999999999999999998888999999999999999985  888999 9999999985

>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=99.77  E-value=6.4e-19  Score=117.25  Aligned_cols=79  Identities=19%  Similarity=0.312  Sum_probs=71.4

Q ss_pred             CCCCCcEEEecCCChh-hhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHh--cCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISST-DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM--QGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~-~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l--ng~~~~g~~l~v~   83 (246)
                      ...++++|||+|||.. ++++||.++|++||.|.+|.+.+   .+++|||+|.+.++|..|++.|  ++..+.|++|+|.
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~---~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~   80 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN---KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   80 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS---SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeec---cceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEE
Confidence            4678999999999986 89999999999999999998876   5689999999999999999965  6788999999999


Q ss_pred             EccCC
Q psy4057          84 YSKTD   88 (246)
Q Consensus        84 ~a~~~   88 (246)
                      ||+..
T Consensus        81 ~s~~~   85 (89)
T d1x4da1          81 LSQKY   85 (89)
T ss_dssp             EECCC
T ss_pred             ECCCc
Confidence            98654

>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=99.77  E-value=8.2e-20  Score=121.32  Aligned_cols=72  Identities=18%  Similarity=0.222  Sum_probs=67.2

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccC
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKT   87 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   87 (246)
                      ++|||+|||.++++++|+++|++||.|.++.+.++    |||||+|.+.++|++|++.|||..|.|+.|+|.++..
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc----ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            57999999999999999999999999999988654    8999999999999999999999999999999988643

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=3.5e-19  Score=121.75  Aligned_cols=73  Identities=21%  Similarity=0.254  Sum_probs=68.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      .++|||+|||.++|+++|+++|++||.|..+.++.++     +|||||+|.+.++|.+|+. ++|..|. |+.|.|.+|+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~-G~~i~V~~a~   97 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSID-GRVVEPKRAV   97 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEET-TEEEEEECCS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeEC-CEEEEEEECc
Confidence            5799999999999999999999999999999998864     5899999999999999986 8999998 9999999986

>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=99.77  E-value=4.6e-19  Score=114.20  Aligned_cols=70  Identities=17%  Similarity=0.216  Sum_probs=64.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .|||+|||.++|+++|+++|++||.|.++.++.++     +|||||+|.+.++|.+|++ +++..|. |+.|.|..|
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-QKEHKLN-GKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBT-TBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEEC-CCEEEeeEC
Confidence            48999999999999999999999999999999865     5899999999999999997 8999999 999999754

>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=99.77  E-value=5.5e-19  Score=113.74  Aligned_cols=71  Identities=15%  Similarity=0.152  Sum_probs=65.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC---ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ++|||+|||.++++++|+++|+.||.|..+++..++   +++|||+|.+.++|.+|+. |||+.|+ |++|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~-g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVG-QNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEET-TEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEEC-CEEEEEEEC
Confidence            479999999999999999999999999999999876   4799999999999999985 8999999 999999754

>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=99.77  E-value=1.6e-19  Score=120.27  Aligned_cols=72  Identities=14%  Similarity=0.274  Sum_probs=66.3

Q ss_pred             CCcEEEEcCCCCCCCHHHH---HHHHccCCCceEEEEeeCC--------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCc
Q psy4057         170 PNQILFLTNLPEETSEMML---SMLFNQFPGFKEVRLVPNR--------HDIAFVEFENEMQSAAAKLALHGFKITPTHA  238 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l---~~~f~~~G~i~~v~~~~~~--------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~  238 (246)
                      ..++|||+|||+++++++|   +++|++||.|.++.+++++        .|||||+|.+.++|..|++.|||+.++ |++
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~-gr~   85 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD-GRT   85 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET-TEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEEC-CEE
Confidence            3567999999999999999   6789999999999999864        279999999999999999999999999 999


Q ss_pred             eEEE
Q psy4057         239 MKIS  242 (246)
Q Consensus       239 l~v~  242 (246)
                      |+|+
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9986

>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=99.77  E-value=9.9e-19  Score=120.06  Aligned_cols=75  Identities=23%  Similarity=0.379  Sum_probs=66.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR------HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .|.++|||+|||.++|+++|+++|+.|| +..++++.+.      +|||||+|.+.++|++|+ .|||..|. |+.|+|.
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~-gr~l~V~   89 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG-NKRIRVD   89 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEET-TEECEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEEC-CEEEEEE
Confidence            3568999999999999999999999999 7778877643      479999999999998776 59999999 9999999


Q ss_pred             eecC
Q psy4057         243 FAKK  246 (246)
Q Consensus       243 ~ak~  246 (246)
                      ||+.
T Consensus        90 ~a~~   93 (104)
T d1wi8a_          90 VADQ   93 (104)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9873

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=9.4e-19  Score=115.49  Aligned_cols=74  Identities=12%  Similarity=0.172  Sum_probs=68.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEeec
Q psy4057         170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK  245 (246)
Q Consensus       170 ~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~ak  245 (246)
                      ..++|||+|||.++|+++|+++|+.||.|..+++..++    +|||||+|.+.++|.+|++ ++|..+. |+.|+|.|++
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 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYK-ETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEET-TEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEEC-CEEEEEEEcC
Confidence            36789999999999999999999999999999998865    5799999999999999996 7999999 9999999875

>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=99.76  E-value=1.7e-19  Score=115.47  Aligned_cols=68  Identities=18%  Similarity=0.341  Sum_probs=63.9

Q ss_pred             EEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEE
Q psy4057          14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR   81 (246)
Q Consensus        14 l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (246)
                      |||+|||.++++++|+++|++||.|..+.+.++.   .++|+|||+|.+.++|++|++.|||..+.|+.|+
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            7999999999999999999999999999888754   7889999999999999999999999999999864

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=7.3e-19  Score=118.92  Aligned_cols=74  Identities=20%  Similarity=0.293  Sum_probs=66.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCC-ceEEEEeeCC------ccEEEEEeCCHHHHHHHHHHhCCC--ccCCCCceEE
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPG-FKEVRLVPNR------HDIAFVEFENEMQSAAAKLALHGF--KITPTHAMKI  241 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~-i~~v~~~~~~------~g~afV~f~~~~~A~~Al~~l~g~--~i~~g~~l~v  241 (246)
                      ++.|||+|||.++++++|+++|+.||+ |..++++++.      +|||||+|.+.++|..|++.|++.  .++ |++|+|
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~-g~~i~V   79 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLW-GHQIAV   79 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBT-TBCCEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEEC-CEEEEE
Confidence            578999999999999999999999996 8999998753      479999999999999999999754  456 899999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      .||+
T Consensus        80 ~~A~   83 (96)
T d2disa1          80 DWAE   83 (96)
T ss_dssp             EESC
T ss_pred             EEcC
Confidence            9996

>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=99.76  E-value=7.1e-19  Score=119.17  Aligned_cols=76  Identities=14%  Similarity=0.123  Sum_probs=70.2

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEccCC
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTD   88 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   88 (246)
                      .+.++|||+|||.++++++|+++|++||.|.++.+.    ++|||||+|.+.++|++|++.|||..|.|+.|+|.++..+
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~----~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~   88 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ----KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVY   88 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE----TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhccccccccc----ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecC
Confidence            456789999999999999999999999999999885    4599999999999999999999999999999999997544

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.5e-18  Score=117.47  Aligned_cols=77  Identities=14%  Similarity=0.171  Sum_probs=68.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      ..+...+|||+|||+++|+++|+++|+.||. ..++++.+.    +|||||+|.+.++|+.|++ |||+.|+ |+.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~-gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQ-HRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSS-SSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEEC-CEEEEEE
Confidence            4556789999999999999999999999985 567777765    5799999999999999986 8999999 9999999


Q ss_pred             eecC
Q psy4057         243 FAKK  246 (246)
Q Consensus       243 ~ak~  246 (246)
                      +++.
T Consensus        88 ~s~~   91 (102)
T d1weza_          88 LNST   91 (102)
T ss_dssp             EECC
T ss_pred             EcCC
Confidence            9863

>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=99.75  E-value=5.9e-19  Score=113.45  Aligned_cols=70  Identities=17%  Similarity=0.266  Sum_probs=64.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       173 ~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .|||+|||.++|+++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|++ +++..++ |+.|.|..|
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-KKYHNVG-LSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBT-TBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEEC-CEEeEEEEC
Confidence            48999999999999999999999999999999875     5899999999999999997 4778899 999999876

>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=1.9e-18  Score=114.46  Aligned_cols=76  Identities=24%  Similarity=0.284  Sum_probs=67.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceE-EEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE-VRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~-v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .|...+|+|+|||.++++++|+++|+.||.+.. +.+..+.    +|+|||+|.+.++|.+|++.|||+.+. |++|+|+
T Consensus         6 ~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~-gr~i~v~   84 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG-SRKVKLV   84 (86)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEET-TEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEEC-CEEEEEE
Confidence            445778999999999999999999999999954 4555533    589999999999999999999999999 9999999


Q ss_pred             ee
Q psy4057         243 FA  244 (246)
Q Consensus       243 ~a  244 (246)
                      +|
T Consensus        85 l~   86 (86)
T d2cqpa1          85 LG   86 (86)
T ss_dssp             ES
T ss_pred             EC
Confidence            86

>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=1.1e-18  Score=115.58  Aligned_cols=77  Identities=16%  Similarity=0.173  Sum_probs=67.9

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeE-EEEcc--CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMD-IVALK--TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~-v~~~~--~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      |+..+|||+|||+++++++|+++|+.||.+.. +.+..  +++++|+|||+|.+.++|++|++.||+..+.|++|+|.++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45567999999999999999999999999865 34443  3478899999999999999999999999999999999874

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=5.8e-19  Score=112.95  Aligned_cols=66  Identities=18%  Similarity=0.325  Sum_probs=61.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceE
Q psy4057         174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMK  240 (246)
Q Consensus       174 l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~  240 (246)
                      |||+|||.++|+++|+++|++||.|..+++..++     +|+|||+|.+.++|.+|++.|||+.|. |+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~-Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQ-AQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCC-EESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEEC-CEECc
Confidence            7999999999999999999999999999998865     589999999999999999999999999 88764

>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=99.74  E-value=7.9e-19  Score=120.08  Aligned_cols=75  Identities=21%  Similarity=0.285  Sum_probs=68.7

Q ss_pred             CCCcEEEEcCCCCCC-CH----HHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         169 PPNQILFLTNLPEET-SE----MMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~-t~----e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      +.+.+|||+||+.++ ++    ++|+++|++||.|.++++.+++ ++|||+|.+.++|.+|++.|||+.|+ |++|+|.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~-~~afV~f~~~~~A~~Ai~~lng~~~~-g~~l~v~~   80 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-KRVRINFSNPLSAADARLRLHKTEFL-GKEMKLYF   80 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT-TEEEEECSSTTHHHHHHHTSTTSEET-TEECEEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCC-CEEEEEECCHHHHHHHHHHhcccccC-CCEeEEee
Confidence            357899999999976 33    5799999999999999999876 79999999999999999999999999 99999999


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      |+
T Consensus        81 a~   82 (104)
T d1weya_          81 AQ   82 (104)
T ss_dssp             CC
T ss_pred             cc
Confidence            96

>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=99.74  E-value=2.9e-18  Score=117.26  Aligned_cols=78  Identities=13%  Similarity=0.156  Sum_probs=70.4

Q ss_pred             CCCcEEEecCCChhhh-----HHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           9 CVTNFVYVTHISSTDL-----KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~-----e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      +.+++|||+||+.++.     +++|.++|++||.|.++.+++   +++||||+|.+.++|.+|++.|||..+.|++|+|.
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k---~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   79 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK---SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET---TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec---CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEe
Confidence            5678999999999874     356999999999999998875   78999999999999999999999999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      |++...
T Consensus        80 ~a~~~~   85 (104)
T d1weya_          80 FAQTLH   85 (104)
T ss_dssp             CCCCSS
T ss_pred             ecccCC
Confidence            996554

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1.4e-17  Score=114.19  Aligned_cols=78  Identities=18%  Similarity=0.200  Sum_probs=67.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEee-CC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP-NR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~-~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ....+.+|||+|||+++|+++|+++|+.||.+....++. +.    +|+|||+|.+.++|++|++ +|+..|. |+.|+|
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~-gR~i~V   88 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIG-HRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSS-SSCCEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEc-ceEEEE
Confidence            344577899999999999999999999999997654444 33    5899999999999999986 9999999 999999


Q ss_pred             EeecC
Q psy4057         242 SFAKK  246 (246)
Q Consensus       242 ~~ak~  246 (246)
                      .++++
T Consensus        89 ~~~~~   93 (104)
T d1wg5a_          89 FKSSR   93 (104)
T ss_dssp             EEECT
T ss_pred             EECCH
Confidence            99864

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=3e-18  Score=117.07  Aligned_cols=81  Identities=15%  Similarity=0.170  Sum_probs=71.2

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ....+.+|||+|||+++++++|+++|+.|| +..|.++.+.  +.+|||||+|.+.++|++|++ +|+..|.||.|+|.+
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            456678999999999999999999999999 5566666544  778999999999999999986 999999999999999


Q ss_pred             ccCCc
Q psy4057          85 SKTDS   89 (246)
Q Consensus        85 a~~~~   89 (246)
                      +....
T Consensus        89 s~~~~   93 (102)
T d1weza_          89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             cCCCC
Confidence            87654

>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=1.2e-17  Score=114.43  Aligned_cols=82  Identities=20%  Similarity=0.190  Sum_probs=70.8

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccC---CCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT---LKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~---~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ....+.+|||+|||+++++++|+++|+.+|.|..+.++.+   ++++|+|||+|.+.++|++|++ +|+..|.||.|.|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            3455678999999999999999999999998877544432   3788999999999999999996 99999999999999


Q ss_pred             EccCCc
Q psy4057          84 YSKTDS   89 (246)
Q Consensus        84 ~a~~~~   89 (246)
                      ++....
T Consensus        90 ~~~~~~   95 (104)
T d1wg5a_          90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            986553

>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=99.70  E-value=1.7e-17  Score=112.84  Aligned_cols=77  Identities=18%  Similarity=0.284  Sum_probs=66.2

Q ss_pred             CCCCcEEEEcC--CCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCCc----eEE
Q psy4057         168 QPPNQILFLTN--LPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHA----MKI  241 (246)
Q Consensus       168 ~~~~~~l~v~n--L~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~----l~v  241 (246)
                      ..|+++|+|.|  ||.++|+++|+++|++||.|..+++.+++ +||||+|.+.++|..|+..|||+.+..++.    +.+
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k-~~aFV~f~~~e~A~~A~~~lng~~i~~~~~~~i~~~~   93 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-PYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL   93 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC-SCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCc-cEEEEEECCHHHHHHHHHHhCCCCCCCCCCcEEEEEE
Confidence            45788899965  99999999999999999999999999886 799999999999999999999998853543    344


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      +|.+
T Consensus        94 ~~~~   97 (101)
T d2cq2a1          94 NFVE   97 (101)
T ss_dssp             EEES
T ss_pred             Eeee
Confidence            5554

>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=99.70  E-value=7.1e-18  Score=115.47  Aligned_cols=77  Identities=16%  Similarity=0.115  Sum_probs=67.9

Q ss_pred             CCCcEEEecCCChhhhHHHHHHHhhccCCeeE-EEEcc--CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057           9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMD-IVALK--TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus         9 ~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~-v~~~~--~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      ....||||+|||+++++++|.++|+.||.|.. +.+..  .++++|+|||+|.+.++|++|++ +||..|.|++|.|.++
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            34578999999999999999999999998876 44433  34789999999999999999996 9999999999999987


Q ss_pred             c
Q psy4057          86 K   86 (246)
Q Consensus        86 ~   86 (246)
                      .
T Consensus        85 ~   85 (103)
T d2cpya1          85 T   85 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.68  E-value=6.9e-19  Score=117.62  Aligned_cols=74  Identities=16%  Similarity=0.298  Sum_probs=65.8

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEcc--------CCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--------TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~--------~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ++|||+|||.++++++|+++|++||.|..+.+..        ..+++|||||+|.+.++|+.|++ |||..+.|++|+|.
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            7899999999999999999999999987765542        23789999999999999999995 99999999999997


Q ss_pred             Ecc
Q psy4057          84 YSK   86 (246)
Q Consensus        84 ~a~   86 (246)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=3.2e-17  Score=112.14  Aligned_cols=75  Identities=19%  Similarity=0.273  Sum_probs=65.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHccCCCceE-EEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEe
Q psy4057         169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKE-VRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISF  243 (246)
Q Consensus       169 ~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~-v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~  243 (246)
                      ....+|||+|||+++|+++|+++|+.||.+.. +.+..+.    +|+|||+|.+.++|..|++ |||..|. |+.|.|.+
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~-gr~i~V~~   83 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLN-GREAFVHV   83 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEET-TEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeEC-CcEEEEEE
Confidence            34678999999999999999999999999965 4454433    6899999999999999996 9999999 99999998


Q ss_pred             ec
Q psy4057         244 AK  245 (246)
Q Consensus       244 ak  245 (246)
                      +.
T Consensus        84 ~~   85 (103)
T d2cpya1          84 VT   85 (103)
T ss_dssp             EC
T ss_pred             CC
Confidence            74

>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=99.67  E-value=1.8e-16  Score=110.04  Aligned_cols=76  Identities=14%  Similarity=0.244  Sum_probs=65.9

Q ss_pred             CCCCCcEE-EEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCH-HHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         167 EQPPNQIL-FLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENE-MQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       167 ~~~~~~~l-~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~-~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..+..++| ||+|||.++|+++|+++|++||.|.+|.+++++ |||||.|.+. ++|..|+..|||..+. ++.+.|.|+
T Consensus         6 ~~~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~k-g~gfV~F~~~~~~A~~a~~~~~~~~l~-~~~~~v~~~   83 (113)
T d1owxa_           6 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-KEGIILFKEKAKEALGKAKDANNGNLQ-LRNKEVTWE   83 (113)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-SEEEEEESSCHHHHHHHHHHTTTSCBC-TTSSSEEEE
T ss_pred             CCCCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCC-ceEEEEecCcHHHHHHHHHHhcCCcee-cCceEEEEe
Confidence            44555666 889999999999999999999999999999886 8999999986 6899999999999988 666666654

>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=99.66  E-value=1.5e-17  Score=113.59  Aligned_cols=73  Identities=15%  Similarity=0.276  Sum_probs=67.7

Q ss_pred             EEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC--CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEc
Q psy4057          13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS   85 (246)
Q Consensus        13 ~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   85 (246)
                      .++|.++..+++|++|.++|++||+|.+|.|+++.  +++|+|||+|.+.++|.+|++.|||..+.|++|.|.|+
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            46678888999999999999999999999998764  78899999999999999999999999999999999986

>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=8.5e-17  Score=111.59  Aligned_cols=75  Identities=19%  Similarity=0.226  Sum_probs=64.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEE-EeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEE
Q psy4057         168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVR-LVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKIS  242 (246)
Q Consensus       168 ~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~-~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~  242 (246)
                      .....+|||+|||+++|+++|+++|+.||.+..+. +..+.    +|+|||+|.+.++|.+|+. |||..|+ |+.|.|.
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~-gR~i~V~   92 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMG-NRFIQVH   92 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCST-TSCBEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCC-CEEEEEE
Confidence            33577999999999999999999999999985533 33332    5899999999999999996 9999999 9999998


Q ss_pred             ee
Q psy4057         243 FA  244 (246)
Q Consensus       243 ~a  244 (246)
                      .+
T Consensus        93 ~~   94 (112)
T d1wela1          93 PI   94 (112)
T ss_dssp             EE
T ss_pred             Ec
Confidence            76

>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=99.66  E-value=4e-16  Score=105.56  Aligned_cols=84  Identities=18%  Similarity=0.290  Sum_probs=73.4

Q ss_pred             ccCCCCCcEEEecCC--Chh---------hhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCC
Q psy4057           5 LAHICVTNFVYVTHI--SST---------DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF   73 (246)
Q Consensus         5 ~~~~~~~~~l~V~nl--~~~---------~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~   73 (246)
                      ++...++++|+|.||  |.+         .++++|++.|++||.|..|.+.++ ..+|+|||+|.++++|.+|+..|||.
T Consensus         2 p~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~-~~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           2 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR-HPDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT-CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC-CCccEEEEEECCHHHHHHHHHHhCCc
Confidence            356789999999999  544         355789999999999999988654 67899999999999999999999999


Q ss_pred             ccCCeeEEEEEccCCc
Q psy4057          74 PFYDKPMRIQYSKTDS   89 (246)
Q Consensus        74 ~~~g~~l~v~~a~~~~   89 (246)
                      .|.||+|.|.++..+.
T Consensus        81 ~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          81 WFGGRQITAQAWDGTT   96 (99)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCEEEEEEEeCCcC
Confidence            9999999999976553

>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=99.65  E-value=2.2e-16  Score=107.19  Aligned_cols=66  Identities=11%  Similarity=0.182  Sum_probs=60.6

Q ss_pred             CCCCCcEEEe--cCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCcc
Q psy4057           7 HICVTNFVYV--THISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF   75 (246)
Q Consensus         7 ~~~~~~~l~V--~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~   75 (246)
                      ...|+++|||  +|||.++++++|+++|++||.|.+|.+.+   .++||||+|.+.++|.+|++.|||..+
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~---~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT---TCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeecc---CccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            4678899999  55999999999999999999999998765   578999999999999999999999887

>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=99.64  E-value=3.8e-17  Score=113.37  Aligned_cols=78  Identities=17%  Similarity=0.184  Sum_probs=68.0

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEc---cCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEE
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY   84 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~---~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   84 (246)
                      ..+..+|||+|||+++++++|.++|+.||.+..+.++   .+++++|+|||+|.+.++|++|++ |||..|.|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            3456799999999999999999999999988653222   345888999999999999999996 999999999999998


Q ss_pred             cc
Q psy4057          85 SK   86 (246)
Q Consensus        85 a~   86 (246)
                      +.
T Consensus        94 ~~   95 (112)
T d1wela1          94 IT   95 (112)
T ss_dssp             EC
T ss_pred             cC
Confidence            74

>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=99.63  E-value=7e-16  Score=105.38  Aligned_cols=79  Identities=15%  Similarity=0.296  Sum_probs=70.5

Q ss_pred             CCCCcEEEecCC----------ChhhhHHHHHHHhhccCCeeEEEEccCC-----CCccEEEEEEcCHHHHHHHHHHhcC
Q psy4057           8 ICVTNFVYVTHI----------SSTDLKKSLYAIFSQFGQIMDIVALKTL-----KMRGQAFVIFKEIASATNALRSMQG   72 (246)
Q Consensus         8 ~~~~~~l~V~nl----------~~~~~e~~l~~~F~~fG~i~~v~~~~~~-----~~kg~aFV~f~~~~~A~~Ai~~lng   72 (246)
                      .+|+++|+|.||          .++.+.++|++.|++||.|++|.|.++.     ...|++||.|.+.++|.+|+..|||
T Consensus         1 g~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~G   80 (104)
T d1o0pa_           1 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   80 (104)
T ss_dssp             CCCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSS
T ss_pred             CCCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCC
Confidence            379999999998          4456778899999999999999998743     3458999999999999999999999


Q ss_pred             CccCCeeEEEEEcc
Q psy4057          73 FPFYDKPMRIQYSK   86 (246)
Q Consensus        73 ~~~~g~~l~v~~a~   86 (246)
                      ..+.||+|.|.|+.
T Consensus        81 r~f~gR~v~v~f~~   94 (104)
T d1o0pa_          81 RKFANRVVVTKYCD   94 (104)
T ss_dssp             CCSSSSCCEEEEEC
T ss_pred             CEECCeEEEEEEcC
Confidence            99999999999975

>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=99.63  E-value=4.8e-18  Score=113.43  Aligned_cols=72  Identities=21%  Similarity=0.354  Sum_probs=63.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeC----------CccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEE
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN----------RHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKI  241 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~----------~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v  241 (246)
                      ++|||+|||.++|+++|+++|+.||.+..+.+...          .+|||||+|.+.++|..|+. |||+.+. |+.|+|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~-Gr~l~V   79 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQ-GQSLKI   79 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSS-SSCCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEEC-CEEEEE
Confidence            68999999999999999999999999876665431          25899999999999999985 9999999 999999


Q ss_pred             Eeec
Q psy4057         242 SFAK  245 (246)
Q Consensus       242 ~~ak  245 (246)
                      +.+|
T Consensus        80 ~r~k   83 (90)
T d1u2fa_          80 RRPH   83 (90)
T ss_dssp             BCTT
T ss_pred             CCCC
Confidence            7655

>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=99.60  E-value=1.4e-15  Score=102.74  Aligned_cols=76  Identities=13%  Similarity=0.191  Sum_probs=67.1

Q ss_pred             CCCCcEEEEcCC--CCCC---------CHHHHHHHHccCCCceEEEEeeCC-ccEEEEEeCCHHHHHHHHHHhCCCccCC
Q psy4057         168 QPPNQILFLTNL--PEET---------SEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFENEMQSAAAKLALHGFKITP  235 (246)
Q Consensus       168 ~~~~~~l~v~nL--~~~~---------t~e~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~~~A~~Al~~l~g~~i~~  235 (246)
                      ...+++|+|+||  |.++         .+++|++.|++||.|..+.+..+. +|+|||+|.+.++|..|+..|||+.|+ 
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~-   83 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG-   83 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET-
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEEC-
Confidence            447999999998  5432         136899999999999999988865 699999999999999999999999999 


Q ss_pred             CCceEEEee
Q psy4057         236 THAMKISFA  244 (246)
Q Consensus       236 g~~l~v~~a  244 (246)
                      |++|+|+|+
T Consensus        84 gr~i~v~~~   92 (99)
T d2dita1          84 GRQITAQAW   92 (99)
T ss_dssp             TEECEEEEC
T ss_pred             CEEEEEEEe
Confidence            999999986

>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=99.60  E-value=1.1e-15  Score=115.24  Aligned_cols=81  Identities=20%  Similarity=0.251  Sum_probs=73.6

Q ss_pred             CCCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC---CCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEE
Q psy4057           7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ   83 (246)
Q Consensus         7 ~~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   83 (246)
                      ...+.++|||+|||..+++++|+++|+.||.|..+.+..+.   +++|||||+|.+.++|.+|++ +++..+.|++|.|.
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            35567899999999999999999999999999999988753   778999999999999999997 79999999999999


Q ss_pred             EccCC
Q psy4057          84 YSKTD   88 (246)
Q Consensus        84 ~a~~~   88 (246)
                      +|.++
T Consensus       172 ~A~~k  176 (183)
T d1u1qa_         172 KALSK  176 (183)
T ss_dssp             ECCCH
T ss_pred             ecCCc
Confidence            98654

>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=99.60  E-value=1e-15  Score=104.53  Aligned_cols=77  Identities=21%  Similarity=0.285  Sum_probs=67.1

Q ss_pred             CCCCcEEEEcCC--CCCCC--------HHHHHHHHccCCCceEEEEeeCC-------ccEEEEEeCCHHHHHHHHHHhCC
Q psy4057         168 QPPNQILFLTNL--PEETS--------EMMLSMLFNQFPGFKEVRLVPNR-------HDIAFVEFENEMQSAAAKLALHG  230 (246)
Q Consensus       168 ~~~~~~l~v~nL--~~~~t--------~e~l~~~f~~~G~i~~v~~~~~~-------~g~afV~f~~~~~A~~Al~~l~g  230 (246)
                      ++|+++|+|.|+  |.++.        .++|++.|++||.|.+|.++++.       .|++||+|.+.++|.+|+..|||
T Consensus         1 g~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~G   80 (104)
T d1o0pa_           1 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   80 (104)
T ss_dssp             CCCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSS
T ss_pred             CCCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCC
Confidence            368999999999  44432        35799999999999999998743       37999999999999999999999


Q ss_pred             CccCCCCceEEEeec
Q psy4057         231 FKITPTHAMKISFAK  245 (246)
Q Consensus       231 ~~i~~g~~l~v~~ak  245 (246)
                      +.|+ |+.|.+.|+.
T Consensus        81 r~f~-gR~v~v~f~~   94 (104)
T d1o0pa_          81 RKFA-NRVVVTKYCD   94 (104)
T ss_dssp             CCSS-SSCCEEEEEC
T ss_pred             CEEC-CeEEEEEEcC
Confidence            9999 9999999974

>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=99.60  E-value=5.3e-17  Score=110.83  Aligned_cols=72  Identities=13%  Similarity=0.178  Sum_probs=66.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC----ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      ..++|++++.++++++|+++|++||.|.+|+|+++.    +|+|||+|.+.++|.+|++.|||+.++ |++|+|+|+
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFN-GQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEET-TEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEEC-CEEEEEEEC
Confidence            457788888899999999999999999999998754    589999999999999999999999999 999999985

>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=99.58  E-value=1.9e-15  Score=104.70  Aligned_cols=77  Identities=13%  Similarity=0.222  Sum_probs=66.2

Q ss_pred             CCCcEE-EecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCH-HHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057           9 CVTNFV-YVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEI-ASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus         9 ~~~~~l-~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~-~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      +.+..| ||+|||+++++++|+++|++||+|.+|.+++   .+|||||.|.++ ++|..|+..+|+..+.++.+.|.++.
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~---~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR---GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT---TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEec---CCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            444444 9999999999999999999999999999976   589999999996 67999999999999888887777754


Q ss_pred             CC
Q psy4057          87 TD   88 (246)
Q Consensus        87 ~~   88 (246)
                      ..
T Consensus        85 ~~   86 (113)
T d1owxa_          85 LE   86 (113)
T ss_dssp             CC
T ss_pred             cc
Confidence            33

>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=99.51  E-value=3.5e-14  Score=91.89  Aligned_cols=72  Identities=18%  Similarity=0.220  Sum_probs=61.5

Q ss_pred             CcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCee-EEEEEccC
Q psy4057          11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKP-MRIQYSKT   87 (246)
Q Consensus        11 ~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~-l~v~~a~~   87 (246)
                      ++.|+|+++|++.+++.| +.|++||.|.++.+.   ++++||||+|.+.++|++|+. +||..+.|+. |.|.+...
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~---~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS---NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC---SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec---CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            467999999999996555 579999999999764   478999999999999999996 9999999986 46877643

>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=99.50  E-value=2.9e-14  Score=92.25  Aligned_cols=70  Identities=10%  Similarity=0.226  Sum_probs=60.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCCC-ceEEEee
Q psy4057         171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTH-AMKISFA  244 (246)
Q Consensus       171 ~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g~-~l~v~~a  244 (246)
                      .+-|+|.|+|++.+++.| +.|++||.|.++++.+++ +||||+|.+.++|.+||+ |||..|. |+ .|.|..+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~-~~~fV~f~~~~~A~~Al~-~nG~~~~-g~~~vgV~~~   74 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTG-NWMHIRYQSKLQARKALS-KDGRIFG-ESIMIGVKPC   74 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSS-SEEEEEESSHHHHHHHHT-TTTCEET-TTEECEEEEC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCC-CEEEEEEcccHHHHHHHh-cCCCeEC-CcEEEEEEeC
Confidence            567999999999987655 579999999999987765 899999999999999996 9999999 66 4567654

>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=98.32  E-value=9.5e-07  Score=53.04  Aligned_cols=59  Identities=29%  Similarity=0.392  Sum_probs=52.8

Q ss_pred             HHHHHHHHccCCCceEEEEeeCC--ccEEEEEeCCHHHHHHHHHHhCCCccCCCCceEEEee
Q psy4057         185 EMMLSMLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA  244 (246)
Q Consensus       185 ~e~l~~~f~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~Al~~l~g~~i~~g~~l~v~~a  244 (246)
                      .+.|.+.|.+||.|.++.+.+-.  .-.|-|...+..+|+.|+..|+-++|+ +++|.|+|+
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG-~KRI~Vs~~   70 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIG-SKKILVSLA   70 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEET-TEEEEEEEC
T ss_pred             HHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcC-CeEEEEEEe
Confidence            45677889999999999998754  347999999999999999999999999 999999997

>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=98.17  E-value=1.1e-05  Score=48.37  Aligned_cols=69  Identities=16%  Similarity=0.297  Sum_probs=61.2

Q ss_pred             CCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCCeeEEEEEcc
Q psy4057          18 HISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK   86 (246)
Q Consensus        18 nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   86 (246)
                      +|+.....+-|.+.|.++|.|.++.+.......-.|-|...+..+|..|+..|+...+.+++|.|.++.
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            466777788899999999999999887654556779999999999999999999999999999999974

>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=98.16  E-value=4.4e-06  Score=52.74  Aligned_cols=72  Identities=22%  Similarity=0.318  Sum_probs=60.4

Q ss_pred             CCCCCcEEEec---------CCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhcCCccCC
Q psy4057           7 HICVTNFVYVT---------HISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD   77 (246)
Q Consensus         7 ~~~~~~~l~V~---------nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (246)
                      ..||..+|.|.         +.=.+....+|.+.|..||+|.-|+...     +...|+|.+-++|.+|+. ++|..+.|
T Consensus        11 qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~-----d~mwVTF~dG~SAL~al~-l~g~~v~G   84 (95)
T d1ufwa_          11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ-----GQMLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET-----TEEEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             cCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeC-----CeEEEEECCcHHHHHHhc-cCCeEEcc
Confidence            56899999992         1223334678999999999999998865     579999999999999999 99999999


Q ss_pred             eeEEEEE
Q psy4057          78 KPMRIQY   84 (246)
Q Consensus        78 ~~l~v~~   84 (246)
                      +.|.|..
T Consensus        85 ~~l~It~   91 (95)
T d1ufwa_          85 RAVKISG   91 (95)
T ss_dssp             EEEEEEC
T ss_pred             eEEEEec
Confidence            9999975

>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=98.14  E-value=2.6e-06  Score=53.81  Aligned_cols=73  Identities=16%  Similarity=0.204  Sum_probs=59.3

Q ss_pred             CCCCCCcEEEEcCCCCCCC---------HHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhCCCccCCC
Q psy4057         166 PEQPPNQILFLTNLPEETS---------EMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPT  236 (246)
Q Consensus       166 ~~~~~~~~l~v~nL~~~~t---------~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~g~~i~~g  236 (246)
                      -..||.-++.|.=...+..         ..+|.+.|..||+|.-+|++.+.   ..|+|.+-++|.+|++ |+|.++. |
T Consensus        10 ~qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~---mwVTF~dG~SAL~al~-l~g~~v~-G   84 (95)
T d1ufwa_          10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---MLVTFADSHSALSVLD-VDGMKVK-G   84 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---EEEECSCSHHHHHHHH-GGGSEET-T
T ss_pred             ccCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCe---EEEEECCcHHHHHHhc-cCCeEEc-c
Confidence            3677888888853332221         23788889999999999999885   9999999999999976 9999999 9


Q ss_pred             CceEEEe
Q psy4057         237 HAMKISF  243 (246)
Q Consensus       237 ~~l~v~~  243 (246)
                      +.|+|+-
T Consensus        85 ~~l~It~   91 (95)
T d1ufwa_          85 RAVKISG   91 (95)
T ss_dssp             EEEEEEC
T ss_pred             eEEEEec
Confidence            9999874

>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=97.82  E-value=5.1e-05  Score=48.48  Aligned_cols=63  Identities=14%  Similarity=0.271  Sum_probs=57.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCC-------ccEEEEEeCCHHHHHHHHHHhCCCccC
Q psy4057         172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-------HDIAFVEFENEMQSAAAKLALHGFKIT  234 (246)
Q Consensus       172 ~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~-------~g~afV~f~~~~~A~~Al~~l~g~~i~  234 (246)
                      +.|.|+.||+.+|++++.+.++..|.+....+.++.       ..-|+|.|.+.++...-.+..+|+.|.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            578999999999999999999999999999998865       146999999999999999999999885

>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=97.32  E-value=0.00046  Score=43.89  Aligned_cols=66  Identities=15%  Similarity=0.156  Sum_probs=55.6

Q ss_pred             cEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCC----CCc-cEEEEEEcCHHHHHHHHHHhcCCccCC
Q psy4057          12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL----KMR-GQAFVIFKEIASATNALRSMQGFPFYD   77 (246)
Q Consensus        12 ~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~----~~k-g~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (246)
                      .+|.|+.||+.++|+++.+.++..|++....-....    .+. ..|+|.|.+.++.....+..+|..+.+
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            468899999999999999999999998877665533    222 569999999999999999999988843

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.83  E-value=0.0037  Score=39.72  Aligned_cols=60  Identities=22%  Similarity=0.245  Sum_probs=48.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHccCCCceEEEEeeCCccEEEEEeCCHHHHHHHHHHhC
Q psy4057         167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH  229 (246)
Q Consensus       167 ~~~~~~~l~v~nL~~~~t~e~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~Al~~l~  229 (246)
                      ..|....+|.-.+|..+...+|.++|+.||.|.--.| .+-  -|||.-.+.++|..++..+.
T Consensus        11 ~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-ddT--Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          11 LQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DDT--SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ETT--EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cCc--eEEEEecCHHHHHHHHHHhc
Confidence            3455666777779999999999999999999754343 443  59999999999999987754

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.55  E-value=0.018  Score=36.49  Aligned_cols=59  Identities=20%  Similarity=0.196  Sum_probs=48.1

Q ss_pred             CCCCcEEEecCCChhhhHHHHHHHhhccCCeeEEEEccCCCCccEEEEEEcCHHHHHHHHHHhc
Q psy4057           8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ   71 (246)
Q Consensus         8 ~~~~~~l~V~nl~~~~~e~~l~~~F~~fG~i~~v~~~~~~~~kg~aFV~f~~~~~A~~Ai~~ln   71 (246)
                      .++-.-||.-..|......||.++|++||.|.--.|     ..-.|||...+.++|+.++..+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-----ddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-----DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-----ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-----cCceEEEEecCHHHHHHHHHHhc
Confidence            344556888899999999999999999998776555     22479999999999999987543