Citrus Sinensis ID: 025973

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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
MEPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK
Secondary Structure (PSIPRED)
ccccccccccccccccEEEEccccccccHHHHHHHHHHHHcccccEEEEEEccccccEEEEEEEEccHHHHHHHHHHHcccccccccEEEccccccHHHHHHccccccHHHHHHHHHHcccccccHHHHHHccccccccccccccccccccccccccccccccccccccccEEEEEccccccccHHHHHHHHcccccEEEEEEEcccccEEEEEEccHHHHHHHHHHHcccEEcccEEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccEEEEEcccccccHHHHHHHHHHHHHccccEEEEEccccccccccEEEEEccHHHHHHHHHHccccEEccEEcEEEEcccccHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHccccEEEEEEcccccEEEEEEccHHHHHHHHHHHcccccccccEEEEEEcc
Coil and Loop (DISEMBL)
mepevanqgneispnntiyINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEkmqgfpfydkpmriQYAKTKsdiiakadgtfvprerrkrheekgkkrkdqhdanqagmglnpayagaygatpplsqipypggaksvipeapappnnilfvqnvphdttpmALQMFfsqfpgfkevrmveakpgiafvEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK
Flexible Loop (DISEMBL)
mepevanqgneispnntIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEkmqgfpfydkPMRIQYAktksdiiakadgtfvprerrkrheekgkkrkdqhdanqAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK
Low Complexity Region (SEG)
MEPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPrerrkrheekgkkrkDQHDANQAGMGLNPayagaygaTPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK
Disordered region (IsUnstruct)
***************NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKA*******************************************************************NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY***
Disordered Region (DISOPRED)
*****************IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKT*********************************************AGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK
Disordered Region (DISEMBL)
*********NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVP*******************ANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK
Disordered Region (DISPRO)
*********NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEE********************************************IPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK
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	245	2.2.26 [Sep-21-2011]
Q39244	250	U1 small nuclear ribonucl	yes	no	1.0	0.98	0.732	1e-102
Q0DKM4	253	U1 small nuclear ribonucl	yes	no	0.967	0.936	0.692	2e-91
A2Y0J7	253	U1 small nuclear ribonucl	N/A	no	0.967	0.936	0.692	2e-91
O22922	232	U2 small nuclear ribonucl	no	no	0.922	0.974	0.518	5e-66
Q8H1S6	229	U2 small nuclear ribonucl	no	no	0.914	0.978	0.491	9e-59
P45429	282	U1 small nuclear ribonucl	N/A	no	0.959	0.833	0.449	4e-57
P09012	282	U1 small nuclear ribonucl	yes	no	0.955	0.829	0.448	8e-57
Q06AA4	282	U1 small nuclear ribonucl	yes	no	0.959	0.833	0.446	1e-56
Q2KIR1	282	U1 small nuclear ribonucl	yes	no	0.951	0.826	0.442	8e-56
B8AM21	232	U2 small nuclear ribonucl	N/A	no	0.885	0.935	0.463	2e-55

>sp|Q39244|RU1A_ARATH U1 small nuclear ribonucleoprotein A OS=Arabidopsis thaliana GN=U1A PE=1 SV=1

 Score =  371 bits (952), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 183/250 (73%), Positives = 209/250 (83%), Gaps = 5/250 (2%)

Query: 1   MEPEVANQG--NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHK 58
           ME + ANQG  +E+SPN TIYINNLNEKVK+D+LK+SL+AVF QFG ILEILAFKT KHK
Sbjct: 1   MEMQEANQGGGSEVSPNQTIYINNLNEKVKLDELKKSLNAVFSQFGKILEILAFKTFKHK 60

Query: 59  GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEE 118
           GQAW+VF +  SA+ A+ KM  FPFYDK MRIQYAKTKSD++AKADGTFVPRE+RKRHEE
Sbjct: 61  GQAWVVFDNTESASTAIAKMNNFPFYDKEMRIQYAKTKSDVVAKADGTFVPREKRKRHEE 120

Query: 119 KGKKRK--DQH-DANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILF 175
           KG  +K  DQH D+ Q GM +N AY G YGA PPLSQ+PYPGG K  +PEAPAPPNNILF
Sbjct: 121 KGGGKKKKDQHHDSTQMGMPMNSAYPGVYGAAPPLSQVPYPGGMKPNMPEAPAPPNNILF 180

Query: 176 VQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQ 235
           VQN+PH+TTPM LQM F Q+ GFKEVRM+EAKPGIAFVE+ DEMQ+TVAMQ LQ  KI Q
Sbjct: 181 VQNLPHETTPMVLQMLFCQYQGFKEVRMIEAKPGIAFVEFADEMQSTVAMQGLQGFKIQQ 240

Query: 236 QQLLITYAKK 245
            Q+LITYAKK
Sbjct: 241 NQMLITYAKK 250

Involved in nuclear pre-mRNA splicing (By similarity). Seems to not be involved in polyadenylation.
Arabidopsis thaliana (taxid: 3702)

>sp|Q0DKM4|RU1A_ORYSJ U1 small nuclear ribonucleoprotein A OS=Oryza sativa subsp. japonica GN=Os05g0154800 PE=3 SV=1

 Score =  335 bits (858), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 169/244 (69%), Positives = 200/244 (81%), Gaps = 7/244 (2%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
           A + N   PN TIYINNLNEK+K+++LK+SL AVF QFG IL++LAFKTLKHKGQAW+VF
Sbjct: 13  APEENGAPPNVTIYINNLNEKIKLEELKKSLRAVFSQFGKILDVLAFKTLKHKGQAWVVF 72

Query: 66  KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHE---EKGKK 122
           +DVASAT A++ MQ FPF++KPMRIQYAKTKSDIIAKADGTFVPRERRKR++   EK +K
Sbjct: 73  EDVASATEALKSMQDFPFHNKPMRIQYAKTKSDIIAKADGTFVPRERRKRNDEKPEKKQK 132

Query: 123 RKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHD 182
           R+  HD +Q G+G+N AY G YGA PPLSQ+P+ G  K ++PE    PNNILFVQN+PH+
Sbjct: 133 REQHHDVSQVGLGVN-AYPGVYGA-PPLSQLPFAGAQKVMMPEIIV-PNNILFVQNLPHE 189

Query: 183 TTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQ-QQLLIT 241
           TTPM LQM F Q+PGFKEVRMVEAKPGIAFVEYGDE QAT AM  LQ  KI +  Q+LI+
Sbjct: 190 TTPMMLQMLFCQYPGFKEVRMVEAKPGIAFVEYGDEGQATAAMNHLQGFKITKDNQMLIS 249

Query: 242 YAKK 245
           YAKK
Sbjct: 250 YAKK 253

Involved in nuclear pre-mRNA splicing.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2Y0J7|RU1A_ORYSI U1 small nuclear ribonucleoprotein A OS=Oryza sativa subsp. indica GN=OsI_18512 PE=3 SV=1

 Score =  335 bits (858), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 169/244 (69%), Positives = 200/244 (81%), Gaps = 7/244 (2%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
           A + N   PN TIYINNLNEK+K+++LK+SL AVF QFG IL++LAFKTLKHKGQAW+VF
Sbjct: 13  APEENGAPPNVTIYINNLNEKIKLEELKKSLRAVFSQFGKILDVLAFKTLKHKGQAWVVF 72

Query: 66  KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHE---EKGKK 122
           +DVASAT A++ MQ FPF++KPMRIQYAKTKSDIIAKADGTFVPRERRKR++   EK +K
Sbjct: 73  EDVASATEALKSMQDFPFHNKPMRIQYAKTKSDIIAKADGTFVPRERRKRNDEKPEKKQK 132

Query: 123 RKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHD 182
           R+  HD +Q G+G+N AY G YGA PPLSQ+P+ G  K ++PE    PNNILFVQN+PH+
Sbjct: 133 REQHHDVSQVGLGVN-AYPGVYGA-PPLSQLPFAGAQKVMMPEIIV-PNNILFVQNLPHE 189

Query: 183 TTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQ-QQLLIT 241
           TTPM LQM F Q+PGFKEVRMVEAKPGIAFVEYGDE QAT AM  LQ  KI +  Q+LI+
Sbjct: 190 TTPMMLQMLFCQYPGFKEVRMVEAKPGIAFVEYGDEGQATAAMNHLQGFKITKDNQMLIS 249

Query: 242 YAKK 245
           YAKK
Sbjct: 250 YAKK 253

Involved in nuclear pre-mRNA splicing.

Oryza sativa subsp. indica (taxid: 39946)

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

 Score =  250 bits (639), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 123/237 (51%), Positives = 171/237 (72%), Gaps = 11/237 (4%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           +I PN +IYI NLNE++K ++LK+SL+ +F QFG IL+++A KT K +GQAW+ F +V +
Sbjct: 5   DIPPNQSIYIQNLNERIKKEELKRSLYCLFSQFGRILDVVALKTPKLRGQAWVTFSEVTA 64

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEK-GKKRKDQHDA 129
           A  AV +MQ FPFYDKPMR+QYAK KSD +AKA+GTFVP++++++ EEK  +KR+D    
Sbjct: 65  AGHAVRQMQNFPFYDKPMRLQYAKAKSDCLAKAEGTFVPKDKKRKQEEKVERKREDSQRP 124

Query: 130 NQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQ 189
           N A        +   G   P  Q   P G +++      PPNNILF+QN+PH+TT M LQ
Sbjct: 125 NTANGPSANGPSANNGVPAPSFQ---PSGQETM------PPNNILFIQNLPHETTSMMLQ 175

Query: 190 MFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITYAKK 245
           + F Q+PGFKE+RM++AKPGIAFVEY D++QA++AMQ LQ  KI  Q  ++I++AKK
Sbjct: 176 LLFEQYPGFKEIRMIDAKPGIAFVEYEDDVQASIAMQPLQGFKITPQNPMVISFAKK 232

Involved in nuclear pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  226 bits (577), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 116/236 (49%), Positives = 169/236 (71%), Gaps = 12/236 (5%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           +I PN +IYI ++NEK+K ++LK+SL+ +F QFG +L+++A KT K +GQAW+VF +V +
Sbjct: 5   DIPPNQSIYIKHINEKIKKEELKRSLYCLFSQFGRLLDVVALKTPKLRGQAWVVFTEVTA 64

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDAN 130
           A+ AV +MQ FPFYDKPMRIQYAK+KSD + KA+G+FVP+E++ + EEK ++++   +  
Sbjct: 65  ASNAVRQMQNFPFYDKPMRIQYAKSKSDYVTKAEGSFVPKEKKMKQEEKVERKRHAEETQ 124

Query: 131 QAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQM 190
           Q  M  N A        PP      P G  ++      PPNNILF+ N+P +T  M LQ+
Sbjct: 125 QPSMP-NGATTQNGMPVPPFQ----PSGQDTM------PPNNILFIHNLPIETNSMMLQL 173

Query: 191 FFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITYAKK 245
            F Q+PGFKE+RM+EAKPGIAFVEY D++Q+++AMQ+LQ  KI  Q  +++++AKK
Sbjct: 174 LFEQYPGFKEIRMIEAKPGIAFVEYEDDVQSSMAMQALQGFKITPQNPMVVSFAKK 229

Involved in nuclear pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  221 bits (563), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 125/278 (44%), Positives = 166/278 (59%), Gaps = 43/278 (15%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E+ PNNTIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  + LK +GQA+++FK+ +S
Sbjct: 5   EVRPNNTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRNLKMRGQAFVIFKETSS 64

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDAN 130
           AT A+  MQGFPFYDKPMRIQY+KT SDIIAK  GTFV R+R+++ + K K  + Q   N
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYSKTDSDIIAKMKGTFVERDRKRQEKRKVKVPEVQGVKN 124

Query: 131 -QAGMGLNPAYAGAYGA---TPPLSQIP-------------------------------- 154
              G  L P   G   A    P ++Q P                                
Sbjct: 125 AMPGAALLPGVPGQMAAMQDMPGMTQAPRMMHMAGQAPYMHHPGMMPPPGMAPGQMPPGG 184

Query: 155 ------YPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP 208
                  PG    + P +  PPN+ILF+ N+P +T  + L M F+QFPGFKEVR+V  + 
Sbjct: 185 MPHGQLMPGQMAPMQPISENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH 244

Query: 209 GIAFVEYGDEMQATVAMQSLQSLKIGQQQLL-ITYAKK 245
            IAFVE+ +E+QA  A +SLQ  KI Q   + I++AKK
Sbjct: 245 DIAFVEFDNEVQAGAARESLQGFKITQSNSMKISFAKK 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|P09012|SNRPA_HUMAN U1 small nuclear ribonucleoprotein A OS=Homo sapiens GN=SNRPA PE=1 SV=3

 Score =  220 bits (560), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 125/279 (44%), Positives = 165/279 (59%), Gaps = 45/279 (16%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRER-RKRHEEKGKKRKDQHDA 129
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GTFV R+R R++ + K ++      A
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKA 124

Query: 130 NQAGMGLNPAYAGAYG---ATPPLSQIP-------------------------------- 154
            Q G G  P      G     PP++Q P                                
Sbjct: 125 VQGG-GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPG 183

Query: 155 -------YPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK 207
                   PG      P +  PPN+ILF+ N+P +T  + L M F+QFPGFKEVR+V  +
Sbjct: 184 AMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR 243

Query: 208 PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLL-ITYAKK 245
             IAFVE+ +E+QA  A  +LQ  KI Q   + I++AKK
Sbjct: 244 HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 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|Q06AA4|SNRPA_PIG U1 small nuclear ribonucleoprotein A OS=Sus scrofa GN=SNRPA PE=2 SV=1

 Score =  219 bits (558), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 124/278 (44%), Positives = 165/278 (59%), Gaps = 43/278 (15%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRER-RKRHEEKGKKRKDQHDA 129
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GTFV R+R R++ + K ++      A
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPASKKA 124

Query: 130 NQAGMG--LNPAYAGAYGATPPLSQIP--------------------------------- 154
            Q G    +  A  G     PP++Q P                                 
Sbjct: 125 VQGGAAAPVVGAVQGPVPGMPPMTQTPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGA 184

Query: 155 ------YPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP 208
                  PG      P +  PPN+ILF+ N+P +T  + L M F+QFPGFKEVR+V  + 
Sbjct: 185 MPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH 244

Query: 209 GIAFVEYGDEMQATVAMQSLQSLKIGQQQLL-ITYAKK 245
            IAFVE+ +E+QA  A  +LQ  KI Q   + I++AKK
Sbjct: 245 DIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 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|Q2KIR1|SNRPA_BOVIN U1 small nuclear ribonucleoprotein A OS=Bos taurus GN=SNRPA PE=2 SV=1

 Score =  217 bits (552), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 124/280 (44%), Positives = 166/280 (59%), Gaps = 47/280 (16%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDAN 130
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GTFV R+R++  E++  K ++   A 
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKR--EKRKPKSQETPAAK 122

Query: 131 QAGMGLNPA-----YAGAYGATPPLSQIP------------------------------- 154
           +A  G   A       G     PP++Q P                               
Sbjct: 123 KAVQGGAAAPVVGTVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQLPP 182

Query: 155 --------YPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA 206
                    PG      P +  PPN+ILF+ N+P +T  + L M F+QFPGFKEVR+V  
Sbjct: 183 GAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG 242

Query: 207 KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLL-ITYAKK 245
           +  IAFVE+ +E+QA  A  +LQ  KI Q   + I++AKK
Sbjct: 243 RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 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|B8AM21|RU2B_ORYSI U2 small nuclear ribonucleoprotein B'' OS=Oryza sativa subsp. indica GN=OsI_11177 PE=3 SV=1

 Score =  215 bits (548), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 114/246 (46%), Positives = 153/246 (62%), Gaps = 29/246 (11%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           +I PN T+Y+ NLNEKVK ++LK+SL+A+  Q+G IL+++A KT K +GQAW+VF ++ +
Sbjct: 5   DIPPNQTVYLRNLNEKVKKEELKRSLYALCSQYGRILDVVALKTPKLRGQAWVVFSEITA 64

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRE----------RRKRHEEKG 120
           AT A   +Q F FY K MR+QYAKTKSD +A  DG+  P+E           +KR  E+ 
Sbjct: 65  ATNAFRGLQEFDFYGKRMRVQYAKTKSDCLATEDGSTAPKEKRKKQEEKAAEKKRRAEEA 124

Query: 121 KKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVP 180
           ++      A   G G   +  G     P                  PAPPNNILF+QN+P
Sbjct: 125 QQSGPNAAAQSNGTGYQASRLGKTSQEP------------------PAPPNNILFIQNLP 166

Query: 181 HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLL 239
            +TT M LQ+ F Q+PGF+EVRM+EAKPGIAFVEY D+ Q+ VAMQ+LQ  KI     + 
Sbjct: 167 AETTSMMLQILFQQYPGFREVRMIEAKPGIAFVEYEDDSQSMVAMQALQGFKITPYNPMA 226

Query: 240 ITYAKK 245
           I+YAKK
Sbjct: 227 ISYAKK 232

Involved in nuclear pre-mRNA splicing.

Oryza sativa subsp. indica (taxid: 39946)

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	245
224068352	251	predicted protein [Populus trichocarpa]	0.979	0.956	0.762	1e-109
118485733	254	unknown [Populus trichocarpa]	0.967	0.933	0.785	1e-109
217072842	245	unknown [Medicago truncatula]	0.942	0.942	0.798	1e-107
255564206	254	small nuclear ribonucleoprotein U)1a,U)2	0.979	0.944	0.795	1e-106
388497184	232	unknown [Medicago truncatula]	0.934	0.987	0.800	1e-106
224128458	231	predicted protein [Populus trichocarpa]	0.934	0.991	0.8	1e-106
449484269	242	PREDICTED: U1 small nuclear ribonucleopr	0.975	0.987	0.757	1e-106
225437410	245	PREDICTED: U1 small nuclear ribonucleopr	0.975	0.975	0.784	1e-104
15226631	250	spliceosomal protein U1A [Arabidopsis th	1.0	0.98	0.732	1e-100
297743906	232	unnamed protein product [Vitis vinifera]	0.934	0.987	0.787	1e-99

>gi|224068352|ref|XP_002302719.1| predicted protein [Populus trichocarpa] gi|222844445|gb|EEE81992.1| predicted protein [Populus trichocarpa]

 Score =  400 bits (1028), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 183/240 (76%), Positives = 211/240 (87%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
           ++ G E+S N TIYINNLNEK+KID+LK++LHAVF QFG ILEILAFKTLKHKGQAW+VF
Sbjct: 12  SSTGTEVSSNMTIYINNLNEKIKIDELKKALHAVFSQFGKILEILAFKTLKHKGQAWVVF 71

Query: 66  KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKD 125
           +DV SA+ A+ +MQ FPFYDKPMRIQYAKTKSDI+AKADGTFVPRE+R+RHEEKGKK+KD
Sbjct: 72  EDVQSASNAMRQMQSFPFYDKPMRIQYAKTKSDIVAKADGTFVPREKRRRHEEKGKKKKD 131

Query: 126 QHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTP 185
           QHD NQ G+GL PAY GAYG TPPLSQIPY GG KS++PEAPAPPNNILF+QN+P++TT 
Sbjct: 132 QHDTNQVGVGLTPAYGGAYGTTPPLSQIPYLGGVKSMVPEAPAPPNNILFIQNLPNETTT 191

Query: 186 MALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
           M LQM F Q+ GFKEVRMVE KPGIAFVEYGDEMQ+TVAM +LQ  K+ Q  +LITYAKK
Sbjct: 192 MMLQMLFQQYAGFKEVRMVETKPGIAFVEYGDEMQSTVAMHALQGFKLQQNSMLITYAKK 251

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118485733|gb|ABK94716.1| unknown [Populus trichocarpa]

 Score =  399 bits (1025), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 187/238 (78%), Positives = 210/238 (88%), Gaps = 1/238 (0%)

Query: 9   GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDV 68
           G ++S N TIYINNLNEK+KID+LK SLHAVF QFG ILEILAFKTLKHKGQAW++F+DV
Sbjct: 17  GTDVSQNMTIYINNLNEKIKIDELKTSLHAVFSQFGKILEILAFKTLKHKGQAWVIFEDV 76

Query: 69  ASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHD 128
            SA+ A+ +MQ FPFYDKPMRIQYAKTKSDIIAKADGTFVPRE+R+RHEEKGKK+KDQHD
Sbjct: 77  QSASNAIRQMQSFPFYDKPMRIQYAKTKSDIIAKADGTFVPREKRRRHEEKGKKKKDQHD 136

Query: 129 ANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMAL 188
           ANQ G+GL PAY GAYG TP L QIPYPGG KS++PEAPAPPNNILF+QN+P++TTPM L
Sbjct: 137 ANQVGVGLTPAYGGAYGTTPSLLQIPYPGGVKSMVPEAPAPPNNILFIQNLPNETTPMML 196

Query: 189 QMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQ-LLITYAKK 245
           QM F Q+PGFKEVRMVEAKPGIAFVEYGDEMQ+T AM  LQ  KI QQ  +LITYAKK
Sbjct: 197 QMLFQQYPGFKEVRMVEAKPGIAFVEYGDEMQSTGAMHGLQGFKILQQNSMLITYAKK 254

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217072842|gb|ACJ84781.1| unknown [Medicago truncatula]

 Score =  393 bits (1009), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 186/233 (79%), Positives = 214/233 (91%), Gaps = 2/233 (0%)

Query: 15  NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAA 74
           N TIYINNLNEK+KID+LK+SLHAVF QFG ILE+LAFKTLKHKGQAW++F+DV SA+ A
Sbjct: 13  NMTIYINNLNEKIKIDELKKSLHAVFSQFGKILEVLAFKTLKHKGQAWVIFEDVTSASNA 72

Query: 75  VEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEK-GKKRKDQHDANQAG 133
           + +MQGFPFYDKPMRIQYA+TKSD+IAKA+GTFVPRE+RKRH++K GKKRKDQ+DAN AG
Sbjct: 73  LRQMQGFPFYDKPMRIQYARTKSDVIAKAEGTFVPREKRKRHDDKAGKKRKDQNDANLAG 132

Query: 134 MGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFS 193
            GLNPAYAGAYGATP LSQIPYPGGAKS++PEAPAPPNNILF+QN+P++TTPM LQM F 
Sbjct: 133 TGLNPAYAGAYGATPALSQIPYPGGAKSLLPEAPAPPNNILFIQNLPNETTPMMLQMLFL 192

Query: 194 QFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITYAKK 245
           Q+PGFKEVRMVEAKPGIAFVEYGDEMQ+T+AMQ+LQ  KI  Q  +LITYAKK
Sbjct: 193 QYPGFKEVRMVEAKPGIAFVEYGDEMQSTMAMQALQGFKIAPQNPMLITYAKK 245

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564206|ref|XP_002523100.1| small nuclear ribonucleoprotein U)1a,U)2b, putative [Ricinus communis] gi|223537662|gb|EEF39285.1| small nuclear ribonucleoprotein U)1a,U)2b, putative [Ricinus communis]

 Score =  391 bits (1005), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 191/240 (79%), Positives = 217/240 (90%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
            N GNEISPN TIYINNLNEK+K+D+LK+SLHAVF QFG I+EILAFKTLKHKGQAW+VF
Sbjct: 15  VNTGNEISPNMTIYINNLNEKIKLDELKKSLHAVFSQFGKIIEILAFKTLKHKGQAWVVF 74

Query: 66  KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKD 125
           +DV SAT A+ +MQ FPFYDKPMRI +AKTKSD+IAKADGTFVPRE+RKRHEEKGK++K+
Sbjct: 75  EDVQSATNAIRQMQSFPFYDKPMRIHFAKTKSDVIAKADGTFVPREKRKRHEEKGKRKKE 134

Query: 126 QHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTP 185
           QHDANQAG+G+ PAYAGAYGATPPLSQIPYPGGAKS++PEAPAPPNNILF+QN+P+DTT 
Sbjct: 135 QHDANQAGIGMAPAYAGAYGATPPLSQIPYPGGAKSMVPEAPAPPNNILFIQNLPNDTTT 194

Query: 186 MALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
           M LQM F  + GFKEVRMVE+KPGIAFVEY DEMQ+TVAMQ LQ LKI Q  +LITYAKK
Sbjct: 195 MVLQMLFQHYAGFKEVRMVESKPGIAFVEYADEMQSTVAMQGLQGLKIQQNPMLITYAKK 254

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388497184|gb|AFK36658.1| unknown [Medicago truncatula]

 Score =  391 bits (1005), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 185/231 (80%), Positives = 213/231 (92%), Gaps = 2/231 (0%)

Query: 17  TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
           TIYINNLNEK+KID+LK+SLHAVF QFG ILE+LAFKTLKHKGQAW++F+DV SA+ A+ 
Sbjct: 2   TIYINNLNEKIKIDELKKSLHAVFSQFGKILEVLAFKTLKHKGQAWVIFEDVTSASNALR 61

Query: 77  KMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEK-GKKRKDQHDANQAGMG 135
           +MQGFPFYDKPMRIQYA+TKSD+IAKA+GTFVPRE+RKRH++K GKKRKDQ+DAN AG G
Sbjct: 62  QMQGFPFYDKPMRIQYARTKSDVIAKAEGTFVPREKRKRHDDKAGKKRKDQNDANLAGTG 121

Query: 136 LNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQF 195
           LNPAYAGAYGATP LSQIPYPGGAKS++PEAPAPPNNILF+QN+P++TTPM LQM F Q+
Sbjct: 122 LNPAYAGAYGATPALSQIPYPGGAKSLLPEAPAPPNNILFIQNLPNETTPMMLQMLFLQY 181

Query: 196 PGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITYAKK 245
           PGFKEVRMVEAKPGIAFVEYGDEMQ+T+AMQ+LQ  KI  Q  +LITYAKK
Sbjct: 182 PGFKEVRMVEAKPGIAFVEYGDEMQSTMAMQALQGFKIAPQNPMLITYAKK 232

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224128458|ref|XP_002320337.1| predicted protein [Populus trichocarpa] gi|222861110|gb|EEE98652.1| predicted protein [Populus trichocarpa]

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 184/230 (80%), Positives = 205/230 (89%), Gaps = 1/230 (0%)

Query: 17  TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
           TIYINNLNEK+KID+LK SLHAVF QFG ILEILAFKTLKHKGQAW++F+DV SA+ A+ 
Sbjct: 2   TIYINNLNEKIKIDELKTSLHAVFSQFGKILEILAFKTLKHKGQAWVIFEDVQSASNAIR 61

Query: 77  KMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGL 136
           +MQ FPFYDKPMRIQYAKTKSDIIAKADGTFVPRE+R+RHEEKGKK+KDQHDANQ G+GL
Sbjct: 62  QMQSFPFYDKPMRIQYAKTKSDIIAKADGTFVPREKRRRHEEKGKKKKDQHDANQVGVGL 121

Query: 137 NPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFP 196
            PAY GAYG TP L QIPYPGG KS++PEAPAPPNNILF+QN+P++TTPM LQM F Q+P
Sbjct: 122 TPAYGGAYGTTPSLLQIPYPGGVKSMVPEAPAPPNNILFIQNLPNETTPMMLQMLFQQYP 181

Query: 197 GFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQ-QLLITYAKK 245
           GFKEVRMVEAKPGIAFVEYGDEMQ+T AM  LQ  KI QQ  +LITYAKK
Sbjct: 182 GFKEVRMVEAKPGIAFVEYGDEMQSTGAMHGLQGFKILQQNSMLITYAKK 231

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449484269|ref|XP_004156835.1| PREDICTED: U1 small nuclear ribonucleoprotein A-like [Cucumis sativus]

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 184/243 (75%), Positives = 217/243 (89%), Gaps = 4/243 (1%)

Query: 4   EVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWL 63
           EV   GNE+ PN TIYINNLNEK+K+++LK+SL+AVF QFG ILE+LAFKTLKHKGQAW+
Sbjct: 3   EVTTTGNEVPPNMTIYINNLNEKIKLEELKKSLNAVFSQFGKILEVLAFKTLKHKGQAWV 62

Query: 64  VFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKR 123
           VF++V+SAT A+ +MQGFPFYDKPMRIQYAKTKSDIIAK+DG+FVPRE+RKRHEEKG+K+
Sbjct: 63  VFEEVSSATNALRQMQGFPFYDKPMRIQYAKTKSDIIAKSDGSFVPREKRKRHEEKGRKK 122

Query: 124 KDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDT 183
           K+QHDANQAGMGLNPA+AGAYGAT   SQ+PY GG   ++PEAPAPPN+ILFVQN+PH+T
Sbjct: 123 KEQHDANQAGMGLNPAFAGAYGATAH-SQVPYSGGV--MVPEAPAPPNSILFVQNLPHET 179

Query: 184 TPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITY 242
           TPM LQM F Q+PGFKEVRMVEAKPGIAFVEY DE+Q+TVAMQ+LQ  K+  Q  +LITY
Sbjct: 180 TPMMLQMLFCQYPGFKEVRMVEAKPGIAFVEYSDEVQSTVAMQALQGFKMNPQNSMLITY 239

Query: 243 AKK 245
           AKK
Sbjct: 240 AKK 242

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225437410|ref|XP_002270967.1| PREDICTED: U1 small nuclear ribonucleoprotein A [Vitis vinifera]

 Score =  382 bits (981), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 189/241 (78%), Positives = 218/241 (90%), Gaps = 2/241 (0%)

Query: 7   NQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFK 66
           N G EISPN TIYINNLNEK+K+++LK+SL AVF QFG I+E+LAFKTLKHKGQAW+VF+
Sbjct: 5   NTGGEISPNMTIYINNLNEKIKLEELKKSLFAVFSQFGKIMEVLAFKTLKHKGQAWVVFE 64

Query: 67  DVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGK-KRKD 125
           +V+SAT A+ +MQGFPFYDKPMRIQYAKTKSD+IAKADGTFVPRERR+RH+++   KR++
Sbjct: 65  EVSSATNALRQMQGFPFYDKPMRIQYAKTKSDVIAKADGTFVPRERRRRHDDRAGRKRRE 124

Query: 126 QHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTP 185
           QHDANQAG+G+NPAY GAYGA PPLSQIPY GGAKS +PEAPAPPNNILF+QN+PH+ TP
Sbjct: 125 QHDANQAGVGVNPAYGGAYGAAPPLSQIPYLGGAKSAVPEAPAPPNNILFIQNLPHEATP 184

Query: 186 MALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQ-LLITYAK 244
           M LQMFF Q+PGFKEVRMVEAKPGIAFVEYGDEMQ+TVAMQ LQ LKI QQ  +LITYAK
Sbjct: 185 MMLQMFFCQYPGFKEVRMVEAKPGIAFVEYGDEMQSTVAMQGLQGLKINQQNPMLITYAK 244

Query: 245 K 245
           K
Sbjct: 245 K 245

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15226631|ref|NP_182280.1| spliceosomal protein U1A [Arabidopsis thaliana] gi|75319458|sp|Q39244.1|RU1A_ARATH RecName: Full=U1 small nuclear ribonucleoprotein A; Short=U1 snRNP protein A gi|1050430|emb|CAA90283.1| U1snRNP-specific protein [Arabidopsis thaliana] gi|2529669|gb|AAC62852.1| small nuclear ribonucleoprotein U1A [Arabidopsis thaliana] gi|15450591|gb|AAK96567.1| At2g47580/T30B22.12 [Arabidopsis thaliana] gi|16649011|gb|AAL24357.1| small nuclear ribonucleoprotein U1A [Arabidopsis thaliana] gi|20259986|gb|AAM13340.1| small nuclear ribonucleoprotein U1A [Arabidopsis thaliana] gi|22655484|gb|AAM98334.1| At2g47580/T30B22.12 [Arabidopsis thaliana] gi|330255767|gb|AEC10861.1| spliceosomal protein U1A [Arabidopsis thaliana]

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 183/250 (73%), Positives = 209/250 (83%), Gaps = 5/250 (2%)

Query: 1   MEPEVANQG--NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHK 58
           ME + ANQG  +E+SPN TIYINNLNEKVK+D+LK+SL+AVF QFG ILEILAFKT KHK
Sbjct: 1   MEMQEANQGGGSEVSPNQTIYINNLNEKVKLDELKKSLNAVFSQFGKILEILAFKTFKHK 60

Query: 59  GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEE 118
           GQAW+VF +  SA+ A+ KM  FPFYDK MRIQYAKTKSD++AKADGTFVPRE+RKRHEE
Sbjct: 61  GQAWVVFDNTESASTAIAKMNNFPFYDKEMRIQYAKTKSDVVAKADGTFVPREKRKRHEE 120

Query: 119 KGKKRK--DQH-DANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILF 175
           KG  +K  DQH D+ Q GM +N AY G YGA PPLSQ+PYPGG K  +PEAPAPPNNILF
Sbjct: 121 KGGGKKKKDQHHDSTQMGMPMNSAYPGVYGAAPPLSQVPYPGGMKPNMPEAPAPPNNILF 180

Query: 176 VQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQ 235
           VQN+PH+TTPM LQM F Q+ GFKEVRM+EAKPGIAFVE+ DEMQ+TVAMQ LQ  KI Q
Sbjct: 181 VQNLPHETTPMVLQMLFCQYQGFKEVRMIEAKPGIAFVEFADEMQSTVAMQGLQGFKIQQ 240

Query: 236 QQLLITYAKK 245
            Q+LITYAKK
Sbjct: 241 NQMLITYAKK 250

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743906|emb|CBI36876.3| unnamed protein product [Vitis vinifera]

 Score =  368 bits (945), Expect = e-99,   Method: Compositional matrix adjust.
 Identities = 182/231 (78%), Positives = 211/231 (91%), Gaps = 2/231 (0%)

Query: 17  TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
           TIYINNLNEK+K+++LK+SL AVF QFG I+E+LAFKTLKHKGQAW+VF++V+SAT A+ 
Sbjct: 2   TIYINNLNEKIKLEELKKSLFAVFSQFGKIMEVLAFKTLKHKGQAWVVFEEVSSATNALR 61

Query: 77  KMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGK-KRKDQHDANQAGMG 135
           +MQGFPFYDKPMRIQYAKTKSD+IAKADGTFVPRERR+RH+++   KR++QHDANQAG+G
Sbjct: 62  QMQGFPFYDKPMRIQYAKTKSDVIAKADGTFVPRERRRRHDDRAGRKRREQHDANQAGVG 121

Query: 136 LNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQF 195
           +NPAY GAYGA PPLSQIPY GGAKS +PEAPAPPNNILF+QN+PH+ TPM LQMFF Q+
Sbjct: 122 VNPAYGGAYGAAPPLSQIPYLGGAKSAVPEAPAPPNNILFIQNLPHEATPMMLQMFFCQY 181

Query: 196 PGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQ-LLITYAKK 245
           PGFKEVRMVEAKPGIAFVEYGDEMQ+TVAMQ LQ LKI QQ  +LITYAKK
Sbjct: 182 PGFKEVRMVEAKPGIAFVEYGDEMQSTVAMQGLQGLKINQQNPMLITYAKK 232

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

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	245
TAIR|locus:2061976	250	U1A "spliceosomal protein U1A"	1.0	0.98	0.664	3.4e-84
UNIPROTKB|A2Y0J7	253	OsI_18512 "U1 small nuclear ri	0.967	0.936	0.627	1.9e-74
UNIPROTKB|Q0DKM4	253	LOC_Os05g06280 "U1 small nucle	0.967	0.936	0.627	1.9e-74
TAIR|locus:2065742	232	U2B'' "U2 small nuclear ribonu	0.922	0.974	0.489	5.3e-56
TAIR|locus:2007417	229	AT1G06960 [Arabidopsis thalian	0.914	0.978	0.470	4.3e-54
UNIPROTKB|Q06AA4	282	SNRPA "U1 small nuclear ribonu	0.4	0.347	0.693	2e-53
RGD|1307416	281	Snrpa "small nuclear ribonucle	0.4	0.348	0.693	2e-53
UNIPROTKB|F1M6Z8	285	Snrpa "Protein Snrpa" [Rattus	0.4	0.343	0.693	2e-53
UNIPROTKB|Q2KIR1	282	SNRPA "U1 small nuclear ribonu	0.4	0.347	0.693	2e-53
MGI|MGI:1855690	287	Snrpa "small nuclear ribonucle	0.4	0.341	0.663	9.9e-52

TAIR|locus:2061976 U1A "spliceosomal protein U1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 843 (301.8 bits), Expect = 3.4e-84, P = 3.4e-84
 Identities = 166/250 (66%), Positives = 190/250 (76%)

Query:     1 MEPEVANQG--NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHK 58
             ME + ANQG  +E+SPN TIYINNLNEKVK+D+LK+SL+AVF QFG ILEILAFKT KHK
Sbjct:     1 MEMQEANQGGGSEVSPNQTIYINNLNEKVKLDELKKSLNAVFSQFGKILEILAFKTFKHK 60

Query:    59 GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPXXXXXXXXX 118
             GQAW+VF +  SA+ A+ KM  FPFYDK MRIQYAKTKSD++AKADGTFVP         
Sbjct:    61 GQAWVVFDNTESASTAIAKMNNFPFYDKEMRIQYAKTKSDVVAKADGTFVPREKRKRHEE 120

Query:   119 XXXXXX--DQH-DANQAGMGLNPXXXXXXXXTPPLSQIPYPGGAKSVIPEAPAPPNNILF 175
                     DQH D+ Q GM +N          PPLSQ+PYPGG K  +PEAPAPPNNILF
Sbjct:   121 KGGGKKKKDQHHDSTQMGMPMNSAYPGVYGAAPPLSQVPYPGGMKPNMPEAPAPPNNILF 180

Query:   176 VQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQ 235
             VQN+PH+TTPM LQM F Q+ GFKEVRM+EAKPGIAFVE+ DEMQ+TVAMQ LQ  KI Q
Sbjct:   181 VQNLPHETTPMVLQMLFCQYQGFKEVRMIEAKPGIAFVEFADEMQSTVAMQGLQGFKIQQ 240

Query:   236 QQLLITYAKK 245
              Q+LITYAKK
Sbjct:   241 NQMLITYAKK 250

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0009651 "response to salt stress" evidence=IGI

GO:0005730 "nucleolus" evidence=IDA

GO:0005685 "U1 snRNP" evidence=ISS;IDA

GO:0005829 "cytosol" evidence=IDA

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

UNIPROTKB|A2Y0J7 OsI_18512 "U1 small nuclear ribonucleoprotein A" [Oryza sativa Indica Group (taxid:39946)]

 Score = 751 (269.4 bits), Expect = 1.9e-74, P = 1.9e-74
 Identities = 153/244 (62%), Positives = 180/244 (73%)

Query:     6 ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
             A + N   PN TIYINNLNEK+K+++LK+SL AVF QFG IL++LAFKTLKHKGQAW+VF
Sbjct:    13 APEENGAPPNVTIYINNLNEKIKLEELKKSLRAVFSQFGKILDVLAFKTLKHKGQAWVVF 72

Query:    66 KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPXXXXXXXXXX---XXX 122
             +DVASAT A++ MQ FPF++KPMRIQYAKTKSDIIAKADGTFVP                
Sbjct:    73 EDVASATEALKSMQDFPFHNKPMRIQYAKTKSDIIAKADGTFVPRERRKRNDEKPEKKQK 132

Query:   123 XXDQHDANQAGMGLNPXXXXXXXXTPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHD 182
                 HD +Q G+G+N          PPLSQ+P+ G  K ++PE   P NNILFVQN+PH+
Sbjct:   133 REQHHDVSQVGLGVN--AYPGVYGAPPLSQLPFAGAQKVMMPEIIVP-NNILFVQNLPHE 189

Query:   183 TTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQ-QLLIT 241
             TTPM LQM F Q+PGFKEVRMVEAKPGIAFVEYGDE QAT AM  LQ  KI +  Q+LI+
Sbjct:   190 TTPMMLQMLFCQYPGFKEVRMVEAKPGIAFVEYGDEGQATAAMNHLQGFKITKDNQMLIS 249

Query:   242 YAKK 245
             YAKK
Sbjct:   250 YAKK 253

GO:0005685 "U1 snRNP" evidence=ISS

UNIPROTKB|Q0DKM4 LOC_Os05g06280 "U1 small nuclear ribonucleoprotein A" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 751 (269.4 bits), Expect = 1.9e-74, P = 1.9e-74
 Identities = 153/244 (62%), Positives = 180/244 (73%)

Query:     6 ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
             A + N   PN TIYINNLNEK+K+++LK+SL AVF QFG IL++LAFKTLKHKGQAW+VF
Sbjct:    13 APEENGAPPNVTIYINNLNEKIKLEELKKSLRAVFSQFGKILDVLAFKTLKHKGQAWVVF 72

Query:    66 KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPXXXXXXXXXX---XXX 122
             +DVASAT A++ MQ FPF++KPMRIQYAKTKSDIIAKADGTFVP                
Sbjct:    73 EDVASATEALKSMQDFPFHNKPMRIQYAKTKSDIIAKADGTFVPRERRKRNDEKPEKKQK 132

Query:   123 XXDQHDANQAGMGLNPXXXXXXXXTPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHD 182
                 HD +Q G+G+N          PPLSQ+P+ G  K ++PE   P NNILFVQN+PH+
Sbjct:   133 REQHHDVSQVGLGVN--AYPGVYGAPPLSQLPFAGAQKVMMPEIIVP-NNILFVQNLPHE 189

Query:   183 TTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQ-QLLIT 241
             TTPM LQM F Q+PGFKEVRMVEAKPGIAFVEYGDE QAT AM  LQ  KI +  Q+LI+
Sbjct:   190 TTPMMLQMLFCQYPGFKEVRMVEAKPGIAFVEYGDEGQATAAMNHLQGFKITKDNQMLIS 249

Query:   242 YAKK 245
             YAKK
Sbjct:   250 YAKK 253

GO:0005685 "U1 snRNP" evidence=ISS

TAIR|locus:2065742 U2B'' "U2 small nuclear ribonucleoprotein B" [Arabidopsis thaliana (taxid:3702)]

 Score = 577 (208.2 bits), Expect = 5.3e-56, P = 5.3e-56
 Identities = 116/237 (48%), Positives = 157/237 (66%)

Query:    11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
             +I PN +IYI NLNE++K ++LK+SL+ +F QFG IL+++A KT K +GQAW+ F +V +
Sbjct:     5 DIPPNQSIYIQNLNERIKKEELKRSLYCLFSQFGRILDVVALKTPKLRGQAWVTFSEVTA 64

Query:    71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPXXXXXXXXXXXXXXXDQHDAN 130
             A  AV +MQ FPFYDKPMR+QYAK KSD +AKA+GTFVP               +     
Sbjct:    65 AGHAVRQMQNFPFYDKPMRLQYAKAKSDCLAKAEGTFVPKDKKRKQEEKVERKREDSQRP 124

Query:   131 QAGMGLNPXXXXXXXXTP-PLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQ 189
                 G +          P P  Q   P G +++      PPNNILF+QN+PH+TT M LQ
Sbjct:   125 NTANGPSANGPSANNGVPAPSFQ---PSGQETM------PPNNILFIQNLPHETTSMMLQ 175

Query:   190 MFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQ-LLITYAKK 245
             + F Q+PGFKE+RM++AKPGIAFVEY D++QA++AMQ LQ  KI  Q  ++I++AKK
Sbjct:   176 LLFEQYPGFKEIRMIDAKPGIAFVEYEDDVQASIAMQPLQGFKITPQNPMVISFAKK 232

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0000354 "cis assembly of pre-catalytic spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0015030 "Cajal body" evidence=IDA

GO:0005686 "U2 snRNP" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

TAIR|locus:2007417 AT1G06960 [Arabidopsis thaliana (taxid:3702)]

 Score = 559 (201.8 bits), Expect = 4.3e-54, P = 4.3e-54
 Identities = 111/236 (47%), Positives = 156/236 (66%)

Query:    11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
             +I PN +IYI ++NEK+K ++LK+SL+ +F QFG +L+++A KT K +GQAW+VF +V +
Sbjct:     5 DIPPNQSIYIKHINEKIKKEELKRSLYCLFSQFGRLLDVVALKTPKLRGQAWVVFTEVTA 64

Query:    71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPXXXXXXXXXXXXXXXDQHDAN 130
             A+ AV +MQ FPFYDKPMRIQYAK+KSD + KA+G+FVP                  +  
Sbjct:    65 ASNAVRQMQNFPFYDKPMRIQYAKSKSDYVTKAEGSFVPKEKKMKQEEKVERKRHAEETQ 124

Query:   131 QAGMGLNPXXXXXXXXTPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQM 190
             Q  M  N          PP      P G  ++      PPNNILF+ N+P +T  M LQ+
Sbjct:   125 QPSMP-NGATTQNGMPVPPFQ----PSGQDTM------PPNNILFIHNLPIETNSMMLQL 173

Query:   191 FFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQ-LLITYAKK 245
              F Q+PGFKE+RM+EAKPGIAFVEY D++Q+++AMQ+LQ  KI  Q  +++++AKK
Sbjct:   174 LFEQYPGFKEIRMIEAKPGIAFVEYEDDVQSSMAMQALQGFKITPQNPMVVSFAKK 229

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005686 "U2 snRNP" evidence=IDA

GO:0015030 "Cajal body" evidence=IDA

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

 Score = 358 (131.1 bits), Expect = 2.0e-53, Sum P(2) = 2.0e-53
 Identities = 68/98 (69%), Positives = 84/98 (85%)

Query:    11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
             E  PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  ++LK +GQA+++FK+V+S
Sbjct:     5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64

Query:    71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFV 108
             AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GTFV
Sbjct:    65 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 102

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 = 358 (131.1 bits), Expect = 2.0e-53, Sum P(2) = 2.0e-53
 Identities = 68/98 (69%), Positives = 84/98 (85%)

Query:    11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
             E  PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  ++LK +GQA+++FK+V+S
Sbjct:     5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64

Query:    71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFV 108
             AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GTFV
Sbjct:    65 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 102

GO:0003723 "RNA binding" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=ISO

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

 Score = 358 (131.1 bits), Expect = 2.0e-53, Sum P(2) = 2.0e-53
 Identities = 68/98 (69%), Positives = 84/98 (85%)

Query:    11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
             E  PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  ++LK +GQA+++FK+V+S
Sbjct:     9 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 68

Query:    71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFV 108
             AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GTFV
Sbjct:    69 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 106

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

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

 Score = 358 (131.1 bits), Expect = 2.0e-53, Sum P(2) = 2.0e-53
 Identities = 68/98 (69%), Positives = 84/98 (85%)

Query:    11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
             E  PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  ++LK +GQA+++FK+V+S
Sbjct:     5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64

Query:    71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFV 108
             AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GTFV
Sbjct:    65 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 102

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

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

 Score = 342 (125.4 bits), Expect = 9.9e-52, Sum P(2) = 9.9e-52
 Identities = 65/98 (66%), Positives = 81/98 (82%)

Query:    11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
             E   N+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  + +K +GQA+++FK+V S
Sbjct:    11 ETRANHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTS 70

Query:    71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFV 108
             AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GT+V
Sbjct:    71 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTYV 108

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

---

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)
Q39244	RU1A_ARATH	No assigned EC number	0.732	1.0	0.98	yes	no
O74968	RU1A_SCHPO	No assigned EC number	0.3823	0.8979	0.8835	yes	no
Q0DKM4	RU1A_ORYSJ	No assigned EC number	0.6926	0.9673	0.9367	yes	no
P43332	SNRPA_DROME	No assigned EC number	0.4537	0.8653	0.9814	yes	no
Q62189	SNRPA_MOUSE	No assigned EC number	0.4377	0.9428	0.8048	yes	no
P09012	SNRPA_HUMAN	No assigned EC number	0.4480	0.9551	0.8297	yes	no
Q06AA4	SNRPA_PIG	No assigned EC number	0.4460	0.9591	0.8333	yes	no
A2Y0J7	RU1A_ORYSI	No assigned EC number	0.6926	0.9673	0.9367	N/A	no
Q2KIR1	SNRPA_BOVIN	No assigned EC number	0.4428	0.9510	0.8262	yes	no
Q54J05	RU2B_DICDI	No assigned EC number	0.4098	0.9714	0.9875	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	245
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-44
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	2e-39
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	9e-37
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	2e-36
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	1e-30
cd12481	80	cd12481, RRM2_U2B, RNA recognition motif 2 found i	2e-20
cd12480	80	cd12480, RRM2_U1A, RNA recognition motif 2 found i	2e-19
cd12479	80	cd12479, RRM2_SNF, RNA recognition motif 2 found i	3e-19
smart00360	73	smart00360, RRM, RNA recognition motif	7e-14
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-11
smart00360	73	smart00360, RRM, RNA recognition motif	4e-11
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	4e-11
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	8e-11
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	2e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-09
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	2e-09
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	2e-09
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-09
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	7e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-08
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	1e-07
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-07
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	4e-07
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	5e-07
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	5e-07
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	7e-07
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	8e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-06
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-06
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	8e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	8e-06
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-06
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	9e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-05
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-05
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	2e-05
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	2e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	3e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-05
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	5e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	5e-05
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	5e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-05
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-05
cd12690	97	cd12690, RRM3_PTBPH1_PTBPH2, RNA recognition motif	6e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-05
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	7e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	9e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-04
cd12693	96	cd12693, RRM2_PTBP1_like, RNA recognition motif 2	1e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-04
cd12782	100	cd12782, RRM2_PTBP1, RNA recognition motif 2 in ve	1e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-04
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-04
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	3e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	3e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	4e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	4e-04
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	4e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-04
cd12784	103	cd12784, RRM2_ROD1, RNA recognition motif 2 in ver	7e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	9e-04
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.001
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	0.001
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	0.001
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	0.001
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	0.001
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	0.002
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.002
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	0.002
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	0.002
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.002
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	0.002
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.002
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	0.002
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.002
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.003
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.003
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.003
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	0.004
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	0.004
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.004

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

 Score =  143 bits (362), Expect = 3e-44
 Identities = 55/78 (70%), Positives = 69/78 (88%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
          T+YINNLNEK+K D+LK+SL+A+F QFG +L+I+A KTLK +GQA++VFKDV SAT A+ 
Sbjct: 1  TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 77 KMQGFPFYDKPMRIQYAK 94
           +QGFPFYDKPMRIQYAK
Sbjct: 61 ALQGFPFYDKPMRIQYAK 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|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score =  131 bits (330), Expect = 2e-39
 Identities = 62/88 (70%), Positives = 78/88 (88%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
           PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+SAT 
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 74  AVEKMQGFPFYDKPMRIQYAKTKSDIIA 101
           A+  MQGFPFYDKPMRIQYAKT SDIIA
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSDIIA 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|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score =  124 bits (313), Expect = 9e-37
 Identities = 55/91 (60%), Positives = 80/91 (87%)

Query: 15  NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAA 74
           N+TIYINNLN+K+K ++LK+SL+A+F QFG +++I+A KT+K +GQA+++FK+++SAT A
Sbjct: 1   NHTIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNA 60

Query: 75  VEKMQGFPFYDKPMRIQYAKTKSDIIAKADG 105
           + ++QGFPFY KPMRIQYAKT SDI++K  G
Sbjct: 61  LRQLQGFPFYGKPMRIQYAKTDSDIVSKMRG 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|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score =  123 bits (309), Expect = 2e-36
 Identities = 55/78 (70%), Positives = 69/78 (88%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
          TIYINNLNEKVK ++LK+SL+A+F QFG IL+I+A KTLK +GQA++VFKD++SAT A+ 
Sbjct: 1  TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALR 60

Query: 77 KMQGFPFYDKPMRIQYAK 94
           MQGFPFYDKPMRI Y+K
Sbjct: 61 SMQGFPFYDKPMRIAYSK 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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score =  108 bits (271), Expect = 1e-30
 Identities = 41/73 (56%), Positives = 53/73 (72%), Gaps = 2/73 (2%)

Query: 170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQ 229
           PN ILF+QN+P +TT   L+M F+QFPGFKEVR+V  + GIAFVE+  E QATVA+Q+LQ
Sbjct: 1   PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVP-RRGIAFVEFETEEQATVALQALQ 59

Query: 230 SLKI-GQQQLLIT 241
             KI     + I+
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|240925 cd12481, RRM2_U2B, RNA recognition motif 2 found in vertebrate U2 small nuclear ribonucleoprotein B" (U2B")

 Score = 82.0 bits (202), Expect = 2e-20
 Identities = 42/78 (53%), Positives = 52/78 (66%), Gaps = 1/78 (1%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL 228
           PPN ILF+ N+P +T  M L M F+QFPGFKEVR+V  +  IAFVE+ +E QA  A  +L
Sbjct: 3   PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENEAQAGAARDAL 62

Query: 229 QSLKIGQQQLL-ITYAKK 245
           Q  KI     + ITYAKK
Sbjct: 63  QGFKITPSHAMKITYAKK 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|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 = 79.4 bits (195), Expect = 2e-19
 Identities = 40/78 (51%), Positives = 56/78 (71%), Gaps = 1/78 (1%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL 228
           PPN+ILF+ N+P +T  + L M F+QFPGFKEVR+V  +  IAFVE+ +E+QA  A ++L
Sbjct: 3   PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAREAL 62

Query: 229 QSLKIGQQQLL-ITYAKK 245
           Q  KI Q   + I++AKK
Sbjct: 63  QGFKITQSNAMKISFAKK 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|240923 cd12479, RRM2_SNF, RNA recognition motif 2 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 79.0 bits (194), Expect = 3e-19
 Identities = 40/78 (51%), Positives = 54/78 (69%), Gaps = 1/78 (1%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL 228
           PPN ILF+ N+P +T  M L M F+QFPGFKEVR+V  +  IAFVE+ +E+Q+  A ++L
Sbjct: 3   PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENEVQSAAAKEAL 62

Query: 229 QSLKIG-QQQLLITYAKK 245
           Q  KI     + IT+AKK
Sbjct: 63  QGFKITPTHAMKITFAKK 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|214636 smart00360, RRM, RNA recognition motif

 Score = 64.5 bits (158), Expect = 7e-14
 Identities = 18/77 (23%), Positives = 39/77 (50%), Gaps = 7/77 (9%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATA 73
          T+++ NL      ++L++    +F +FG +  +   +   T K KG A++ F+    A  
Sbjct: 1  TLFVGNLPPDTTEEELRE----LFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEK 56

Query: 74 AVEKMQGFPFYDKPMRI 90
          A+E + G     +P+++
Sbjct: 57 ALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 60.4 bits (147), Expect = 2e-12
 Identities = 16/76 (21%), Positives = 35/76 (46%), Gaps = 6/76 (7%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAV 75
          +++ NL      + L++    +F +FG I  +   +    K KG A++ F+    A  A+
Sbjct: 1  LFVGNLPPDTTEEDLRE----LFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKAL 56

Query: 76 EKMQGFPFYDKPMRIQ 91
          E + G     + +++ 
Sbjct: 57 EALNGKELDGRKLKVS 72

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

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

 Score = 58.0 bits (141), Expect = 1e-11
 Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 4/69 (5%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV----EAKPGIAFVEYGDEMQATVAMQSLQ 229
           LFV N+P DTT   L+  FS+F   + +R+V        G AFVE+ DE  A  A+++L 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 230 SLKIGQQQL 238
             ++G ++L
Sbjct: 61  GKELGGREL 69

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

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

 Score = 62.3 bits (150), Expect = 2e-11
 Identities = 29/138 (21%), Positives = 55/138 (39%), Gaps = 17/138 (12%)

Query: 1   MEPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKH 57
                 ++      NNT+++ NL   V  + L+     +FK+FG +  +      +T K 
Sbjct: 101 SSESPKSRQKSKEENNTLFVGNLPYDVTEEDLR----ELFKKFGPVKRVRLVRDRETGKS 156

Query: 58  KGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHE 117
           +G A++ F+   SA  A+E++ G     +P+R+Q A+  S           PR     + 
Sbjct: 157 RGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQ----------PRSELSNNL 206

Query: 118 EKGKKRKDQHDANQAGMG 135
           +    +K           
Sbjct: 207 DASFAKKLSRGKALLLEK 224

Length = 306

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

 Score = 56.8 bits (138), Expect = 4e-11
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           LFV N+P DTT   L+  FS+F   + VR+V  K      G AFVE+  E  A  A+++L
Sbjct: 2   LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61

Query: 229 QSLKIGQQQLLI 240
              ++  + L +
Sbjct: 62  NGKELDGRPLKV 73

Length = 73

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

 Score = 57.2 bits (139), Expect = 4e-11
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTI----LEILAFKTLKHKGQAWLVFKDVAS 70
          +  +Y+ NL+++V  + L   +   F    +      +I      + KGQA++ F     
Sbjct: 1  SKRLYVKNLSKRVTEEDLV-YIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEI 59

Query: 71 ATAAVEKMQGFPFYDKPMRIQYA 93
          AT A+  + G+    KPM IQ+ 
Sbjct: 60 ATKALNLVNGYVLKGKPMVIQFG 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 55.6 bits (135), Expect = 8e-11
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 2/58 (3%)

Query: 36 LHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA 93
          L+ +F  FG + +I   K  K  G A++ F    +A  AV+ + G  F  +P+R+ Y+
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|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 59.8 bits (145), Expect = 2e-10
 Identities = 48/239 (20%), Positives = 89/239 (37%), Gaps = 32/239 (13%)

Query: 36  LHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK--PMRIQYA 93
           L+ +F  +G +L I+ F    +  QA + F+ V SA  A   + G   Y+    ++I+YA
Sbjct: 113 LYQIFNPYGKVLRIVTFTK-NNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYA 171

Query: 94  K-TKSDIIAKADGTF---VPRERRKRHEEKGKKRKDQHDANQ---AGMGLNPAYAGAYGA 146
           K T+ ++    D +     P    +R     +  + +  A          +  Y+   G 
Sbjct: 172 KPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGP 231

Query: 147 TPPLSQIPYPGGAKSVIPEAPAP--------------------PNNILFVQNVPHD-TTP 185
             PL+      G     P    P                    P ++L V  +  +    
Sbjct: 232 LAPLA-GGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNC 290

Query: 186 MALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
             L   F  +   + V+ ++ K   A +E  D  QA +A+  L  +K+  + L +  +K
Sbjct: 291 DRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSK 349

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067). Length = 481

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

 Score = 53.0 bits (128), Expect = 1e-09
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAV 75
          +++ NL      + LK     +F +FG I  I   +  T + KG A++ F+D   A  A+
Sbjct: 1  LFVGNLPPDTTEEDLKD----LFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKAL 56

Query: 76 EKMQGFPFYDKPMR 89
          E + G     + +R
Sbjct: 57 EALNGKELGGRELR 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|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 52.6 bits (127), Expect = 2e-09
 Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 3/62 (4%)

Query: 170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPG--IAFVEYGDEMQATVAMQS 227
           P N LFV N+  +TT   L+  FS+ PGF+ ++M   K G  + FVE+ D   AT A+ S
Sbjct: 1   PCNTLFVANLGPNTTEEELRQLFSRQPGFRRLKMH-NKGGGPVCFVEFEDVSFATQALNS 59

Query: 228 LQ 229
           LQ
Sbjct: 60  LQ 61

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|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 = 2e-09
 Identities = 22/67 (32%), Positives = 31/67 (46%), Gaps = 6/67 (8%)

Query: 172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV--EAKPG----IAFVEYGDEMQATVAM 225
             LFV  +P D     L   F  FPG++  R+V  E K G    + FV++     A  AM
Sbjct: 1   RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAM 60

Query: 226 QSLQSLK 232
            +LQ  +
Sbjct: 61  DALQGYR 67

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

 Score = 51.5 bits (124), Expect = 3e-09
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP----GIAFVEYGDEMQATVAMQSLQ 229
           LFV N+P DTT   L+  FS+F   + VR+V  K     G AFVE+     A  A+++L 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 230 SLKIGQQQLLI 240
             ++  ++L +
Sbjct: 61  GKELDGRKLKV 71

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|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 = 51.4 bits (124), Expect = 7e-09
 Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 9/69 (13%)

Query: 34 QSLHAVFKQFGTILEILAFKTLKHKGQAW--LV-FKDVASATAAVEKMQGFPFYDK--PM 88
            LH VF  +G + +IL F     K      LV F  V SA  A + + G   YD    +
Sbjct: 16 DVLHQVFSPYGAVEKILIF----EKNTGVQALVQFDSVESAENAKKALNGRNIYDGCCTL 71

Query: 89 RIQYAKTKS 97
           IQ+++ K 
Sbjct: 72 DIQFSRLKE 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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 50.1 bits (120), Expect = 2e-08
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV---EAKP-GIAFVEYGDEMQATVAMQSLQ 229
           LFV  +P   T   L+  F +    K VR+V     KP G+A+VEY +E  A+ A+  + 
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64

Query: 230 SLKIGQQQL 238
             +I ++ +
Sbjct: 65  GTEIKEKTI 73

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|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 7/81 (8%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVAS 70
          P   +  +NLN+ +     +  L  + K++G + E+  +   KT KH G A +VF  V S
Sbjct: 1  PPREVTFSNLNDNI----DEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKS 56

Query: 71 ATAAVEKMQGFPFYDKPMRIQ 91
          A   VEK+       K +++ 
Sbjct: 57 AKRCVEKLNQTSVMGKIIKVF 77

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 7/76 (9%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAA 74
          +Y+  L E+V      + LHA F  FG I +I   L ++T KH+G A++ F++   A AA
Sbjct: 1  LYVGGLAEEVDE----KVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAA 56

Query: 75 VEKMQGFPFYDKPMRI 90
          ++ M     + + +R+
Sbjct: 57 IDNMNESELFGRTIRV 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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 46.0 bits (110), Expect = 4e-07
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 5/64 (7%)

Query: 33 KQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPF--YDKPMRI 90
             L   F +FG I  I        +  A++ ++ + +A AA E ++GFP     + +R+
Sbjct: 12 LAELEREFDRFGAIRRI---DYDPGRNYAYIEYESIEAAQAAKEALRGFPLGGPGRRLRV 68

Query: 91 QYAK 94
           +A 
Sbjct: 69 DFAD 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|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 = 24/89 (26%), Positives = 42/89 (47%), Gaps = 18/89 (20%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQ-----AWLVFKDV 68
          P NT+++ NL      ++L+Q    +F +         F+ LK   +      ++ F+DV
Sbjct: 1  PCNTLFVANLGPNTTEEELRQ----LFSRQ------PGFRRLKMHNKGGGPVCFVEFEDV 50

Query: 69 ASATAAVEKMQGFPFYDK---PMRIQYAK 94
          + AT A+  +QG          +RI+YAK
Sbjct: 51 SFATQALNSLQGAVLSSSDRGGIRIEYAK 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|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 45.9 bits (109), Expect = 5e-07
 Identities = 20/78 (25%), Positives = 43/78 (55%), Gaps = 8/78 (10%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
           +YI N+++ +  ++L+      F Q+G   EI +   L+ K  A++ F ++++A  A++
Sbjct: 5  NVYIGNIDDSLTEEKLRN----DFSQYG---EIESVNYLREKNCAFVNFTNISNAIKAID 57

Query: 77 KMQGFPFYDKPMRIQYAK 94
           ++  P + K  +I Y K
Sbjct: 58 GVKSHPLFKK-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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 45.3 bits (108), Expect = 7e-07
 Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 4/78 (5%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAA 74
          N  +Y+ NL  K+  +     L+ +F ++G I +I    T + +G A++V++D+  A  A
Sbjct: 2  NRILYVRNLPFKISSE----ELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNA 57

Query: 75 VEKMQGFPFYDKPMRIQY 92
           + + GF   ++ + + Y
Sbjct: 58 CDHLSGFNVANRYLVVLY 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|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 = 45.3 bits (108), Expect = 8e-07
 Identities = 20/83 (24%), Positives = 44/83 (53%), Gaps = 7/83 (8%)

Query: 16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASAT 72
          N ++++ L+ +    +L+    A+F +FG + E+L  K   T + +G  ++ F+ V  A 
Sbjct: 2  NKLFVSGLSTRTTEKELE----ALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDAD 57

Query: 73 AAVEKMQGFPFYDKPMRIQYAKT 95
          AA+  + G     + ++++ AK 
Sbjct: 58 AAIRDLNGKELEGRVIKVEKAKR 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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 10/84 (11%)

Query: 170 PNNILFVQNVPHDTTPMALQMFFSQFPGF--KEVRMVEAKP-----GIAFVEYGDEMQAT 222
           P N L ++ +   TT   +    S       K+VR++  K      G AFVE+     AT
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 223 VAMQSLQS---LKIGQQQLLITYA 243
             M +L +     I  + + ++YA
Sbjct: 61  QWMDALNNLDPFVIDGRVVRVSYA 84

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

>gnl|CDD|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 = 22/77 (28%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQ-AWLVFKDVASATAAV 75
          +I++  L+  V     K+ L+  F + G ILE+   K   H    A++ F+   +A  AV
Sbjct: 5  SIFVGQLSPDV----TKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAV 60

Query: 76 EKMQGFPFYDKPMRIQY 92
          E        +K M +QY
Sbjct: 61 ESENHSMLKNKTMHVQY 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 43.7 bits (104), Expect = 2e-06
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV---EAKPGIAFVEYGDEMQATVAMQSLQS 230
           L+V+N+P   T   L+ FFS +   + VR+V   +   G AFVE+     A  A++ L  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 231 LKIGQQQL 238
           L +  + L
Sbjct: 61  LVLDGRTL 68

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

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

 Score = 46.5 bits (109), Expect = 4e-06
 Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 5/81 (6%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATV 223
             NN LFV N+P+D T   L+  F +F   K VR+V  +      G AFVE+  E  A  
Sbjct: 113 EENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEK 172

Query: 224 AMQSLQSLKIGQQQLLITYAK 244
           A++ L   ++  + L +  A+
Sbjct: 173 AIEELNGKELEGRPLRVQKAQ 193

Length = 306

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

 Score = 43.6 bits (103), Expect = 4e-06
 Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 6/73 (8%)

Query: 16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTI--LEILAFKTLKHKGQAWLVFKDVASATA 73
          + ++++ L   V     K+ L  +FK+ G +  + ++  ++ K KG A++ +++ +SA+ 
Sbjct: 3  HKLFVSGLPFSVT----KEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQ 58

Query: 74 AVEKMQGFPFYDK 86
          AV KM G    +K
Sbjct: 59 AVLKMDGTEIKEK 71

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 43.3 bits (103), Expect = 4e-06
 Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 5/67 (7%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVE 76
          +Y+ NL   V  + L+      F  +G +  +   +   + +G A++ F     A AA++
Sbjct: 1  LYVRNLPPSVTEEDLR----EFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALK 56

Query: 77 KMQGFPF 83
          K+ G   
Sbjct: 57 KLNGLVL 63

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

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

 Score = 42.5 bits (101), Expect = 5e-06
 Identities = 19/56 (33%), Positives = 32/56 (57%)

Query: 188 LQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA 243
           L   FS F   +++++++ KPG AFVE+  E  A  A+Q L  +  G + L + Y+
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|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 = 42.6 bits (101), Expect = 8e-06
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 7/73 (9%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
          T+Y+ NL   +     ++ L   F  FG I E+   +  K KG A++ F    +A  A+ 
Sbjct: 2  TVYVGNLPHGLT----EEELQRTFSPFGAIEEV---RVFKDKGYAFVRFDTHEAAATAIV 54

Query: 77 KMQGFPFYDKPMR 89
           + G     + ++
Sbjct: 55 AVNGTSINGQTVK 67

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

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

 Score = 43.0 bits (102), Expect = 8e-06
 Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE-----AKPGIAFVEYGDEMQATVA 224
           P   LFV  +   TT   L+  FS++   + +R+V         G AFVEY  E  A  A
Sbjct: 2   PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 61

Query: 225 MQSLQSLKIGQQQLLITY 242
            +    L I   ++ + +
Sbjct: 62  YRDAHKLVIDGSEIFVDF 79

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

>gnl|CDD|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 = 42.6 bits (101), Expect = 8e-06
 Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 5/74 (6%)

Query: 175 FVQNVPHDTTPMALQMFFSQFPGFKEVRMVE----AKP-GIAFVEYGDEMQATVAMQSLQ 229
           FV N+P+D T   L   FS+       R+V      KP G  F E+ D   A  A+++L 
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 230 SLKIGQQQLLITYA 243
             +   + L + +A
Sbjct: 62  GYEFNGRALRVDFA 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|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 42.2 bits (99), Expect = 9e-06
 Identities = 21/67 (31%), Positives = 29/67 (43%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
           LFV NVP D T   L+  F  +   + V+      GI  V + D   A  A++ L    +
Sbjct: 4   LFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCGRHM 63

Query: 234 GQQQLLI 240
            QQ L  
Sbjct: 64  QQQALGG 70

This subfamily corresponds to the RRM1 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 protein 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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 7/76 (9%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAA 74
          +Y+ NL+  +  D L+     +F+ FG I  +   +   T + KG  ++ F D   A  A
Sbjct: 1  LYVGNLHFNITEDDLRG----IFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKA 56

Query: 75 VEKMQGFPFYDKPMRI 90
          +E++ GF    +P+++
Sbjct: 57 LEQLNGFELAGRPIKV 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|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 19/71 (26%), Positives = 33/71 (46%)

Query: 173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLK 232
            LFV+N+  +     L+  F QF   + +       G   V Y D   A  A ++LQ  +
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTE 62

Query: 233 IGQQQLLITYA 243
           +G ++L I ++
Sbjct: 63  LGGRKLDIHFS 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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 9/81 (11%)

Query: 18 IYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATA 73
          IYI  L  E  + D L      VF Q+G I++I      KT K KG A+L ++D  S   
Sbjct: 12 IYIGGLPYELTEGDIL-----CVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTIL 66

Query: 74 AVEKMQGFPFYDKPMRIQYAK 94
          AV+ + G     + +R+ + +
Sbjct: 67 AVDNLNGIKLLGRTIRVDHVR 87

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

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 5/77 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           LFV+N+P+DTT   L+ FFS+    K   +V+ K      G  +V +  E  A  A++  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 229 QSLKIGQQQLLITYAKK 245
           +  K G +++ + +AKK
Sbjct: 62  KKTKFGGRKIHVEFAKK 78

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

>gnl|CDD|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 = 19/75 (25%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
          T+ + NL+  +   +L+     +F QFG + +I   +T     Q ++ F D+ +A AA++
Sbjct: 3  TLLVFNLDSPISDQELRS----LFSQFGEVKDIR--ETPLRPSQKFVEFYDIRAAEAALD 56

Query: 77 KMQGFPFYDKPMRIQ 91
           + G PF    ++++
Sbjct: 57 ALNGRPFLGGRLKVK 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|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 4/78 (5%)

Query: 18 IYINNLNEKVKIDQLKQS-LHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
          +YI N+++      L +  L    +++G   EI + + L+ K  A++ F ++ +A AA++
Sbjct: 5  VYIGNVSDVGDERNLPEKELRKECEKYG---EIESIRILREKACAFINFMNIPNAIAALQ 61

Query: 77 KMQGFPFYDKPMRIQYAK 94
           + G   YD  +RI Y K
Sbjct: 62 TLNGKKPYDTIVRINYGK 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|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 = 40.7 bits (96), Expect = 3e-05
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 7/78 (8%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAA 74
          N T+++  L+  V  D+L+    ++F  FG   EI+  K    KG  ++ F   A+A AA
Sbjct: 1  NTTVFVGGLDPAVTEDELR----SLFGPFG---EIVYVKIPPGKGCGFVQFVHRAAAEAA 53

Query: 75 VEKMQGFPFYDKPMRIQY 92
          ++++QG       +R+ +
Sbjct: 54 IQQLQGTIIGGSRIRLSW 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 10/81 (12%)

Query: 173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQS 227
            +F++N+P D T   L+  FSQF   K  R+V+ K      G AFV++  +  A   +++
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 228 LQS-----LKIGQQQLLITYA 243
             +     L +  ++L++T A
Sbjct: 62  ADNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 21/63 (33%), Positives = 28/63 (44%), Gaps = 7/63 (11%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASATA 73
           I++  L      D    SL   F QFG I E   I   +T K +G  ++ FKD  SA  
Sbjct: 2  KIFVGGLPYHTTDD----SLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAER 57

Query: 74 AVE 76
          A +
Sbjct: 58 ACK 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSL 228
           L+V N+P++ T   L+  F QF      R++  +      G  FVE     +A  A++ L
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 229 QSLKIGQQQLLITYAKK 245
                G + L +  A+ 
Sbjct: 62  NGTDFGGRTLTVNEARP 78

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

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 40.6 bits (95), Expect = 4e-05
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV----EAKP-GIAFVEYGDEMQATVAMQSL 228
           +FV N+P++ T   L+  FS+       R+V      KP G  F EY D+  A  AM++L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 229 QSLKIGQQQLLITYA 243
              ++  +QL +  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

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

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 6/77 (7%)

Query: 172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQ 226
             L V+NVP + T   L+  FS F   K VR+ + K      G AFVE+  + +A  AM+
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 227 SLQSLKIGQQQLLITYA 243
           +L+S  +  + L++ YA
Sbjct: 60  ALKSTHLYGRHLVLEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 39.9 bits (94), Expect = 5e-05
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 10/74 (13%)

Query: 18 IYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
          +++ NLN +KV     K+ L  +F ++G IL I    +L HKG  ++ F +   A AAV 
Sbjct: 3  VFVGNLNTDKVS----KEDLEEIFSKYGKILGI----SL-HKGYGFVQFDNEEDARAAVA 53

Query: 77 KMQGFPFYDKPMRI 90
             G     + + I
Sbjct: 54 GENGREIAGQKLDI 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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 40.0 bits (94), Expect = 5e-05
 Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTL--KHKGQAWLVFKDVASAT 72
          + T+++ NL+ +V     ++ L+ +F Q G +  +   K    K K  A++ FK   S  
Sbjct: 1  DRTLFVGNLDARVT----EEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVP 56

Query: 73 AAVEKMQGFPFYDKPMRIQ 91
           A++ + G   + + +RI+
Sbjct: 57 YAIQLLNGIRLFGRELRIK 75

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

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

 Score = 40.0 bits (94), Expect = 5e-05
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           L V  +P D T   L+  F      +  ++V  +      G  FV+Y DE  A  A+ +L
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 229 QSLKIGQQQLLITYA 243
              +I  ++L ++YA
Sbjct: 63  NGFEIRNKRLKVSYA 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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 39.9 bits (94), Expect = 6e-05
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 11/80 (13%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEI------LAFKTLKHKGQAWLVFKDVASA 71
          IY+ NL+ K+  D     L  +F +FG +  I         +   + G A++ FKD +SA
Sbjct: 3  IYVRNLDFKLDEDD----LRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSA 58

Query: 72 TAAVEKMQGFPFYDKPMRIQ 91
            A++ + G     + + + 
Sbjct: 59 ENALQ-LNGTELGGRKISVS 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|241134 cd12690, RRM3_PTBPH1_PTBPH2, RNA recognition motif 3 in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2)

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 7/67 (10%)

Query: 20 INNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKG-QAWLVFKDVASATAAVEKM 78
          I N+   V +D     LH VF  FG + +I  F+  K+ G QA + + DV +A  A E +
Sbjct: 8  IENMQYAVTVD----VLHTVFSAFGFVQKIAIFE--KNGGFQALIQYPDVPTAVNAKEAL 61

Query: 79 QGFPFYD 85
          +G   YD
Sbjct: 62 EGHCIYD 68

This subfamily corresponds to the RRM3 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 97

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

 Score = 43.3 bits (102), Expect = 7e-05
 Identities = 45/237 (18%), Positives = 83/237 (35%), Gaps = 10/237 (4%)

Query: 8   QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAFKTLKHKGQAWLVF 65
           +    +    +Y+ NL++ V  ++L++    +F + G I   +++  +    +G  ++ F
Sbjct: 278 ERKMKAQGVNLYVKNLDDTVTDEKLRE----LFSECGEITSAKVMLDEKGVSRGFGFVCF 333

Query: 66  KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKD 125
            +   A  AV +M G     KP+ +  A+ K    A     F+  + R R    G     
Sbjct: 334 SNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGG 393

Query: 126 QHDANQ-AGMGLNPAYAGAYGATPPLSQIPYPGG-AKSVIPEAPAPPNNILFVQNVPHDT 183
                   G G    + G     P +S +P P G    + P   AP N +        + 
Sbjct: 394 AMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNA 453

Query: 184 TPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQ-QLL 239
                       P ++ + + +  P           Q     Q L S     Q Q+L
Sbjct: 454 AQKPPMQPVMYPPNYQSLPLSQDLP-QPQSTASQGGQNKKLAQVLASATPQMQKQVL 509

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|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 17/81 (20%), Positives = 41/81 (50%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
          P+  +++ +L      D+L+ ++   F ++GT++ +   +  + +  A++ F +   A  
Sbjct: 1  PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKN 60

Query: 74 AVEKMQGFPFYDKPMRIQYAK 94
          A+ K QG     + +R + AK
Sbjct: 61 ALAKGQGTILDGRHIRCERAK 81

This subfamily corresponds to the RRM1 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 = 86

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

 Score = 39.5 bits (93), Expect = 9e-05
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP--GIAFVEYGDEMQATVAMQSL 228
           N IL+V+N+P   +   L   F ++   +++R+   K   G AFV Y D   A  A   L
Sbjct: 2   NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 229 QSLKIGQQQLLITY 242
               +  + L++ Y
Sbjct: 62  SGFNVANRYLVVLY 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|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 = 38.8 bits (91), Expect = 1e-04
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
           ++V N+PH  T   LQ  FS F   +EVR+ + K G AFV +     A  A+ ++    I
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK-GYAFVRFDTHEAAATAIVAVNGTSI 61

Query: 234 GQQQL 238
             Q +
Sbjct: 62  NGQTV 66

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

 Score = 42.6 bits (100), Expect = 1e-04
 Identities = 25/90 (27%), Positives = 46/90 (51%), Gaps = 7/90 (7%)

Query: 7   NQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWL 63
           +Q  +I     +Y+ NL+  +   +L+Q    +F+ FG I ++   +   T + KG  ++
Sbjct: 178 HQPGDIPNFLKLYVGNLHFNITEQELRQ----IFEPFGDIEDVQLHRDPETGRSKGFGFI 233

Query: 64  VFKDVASATAAVEKMQGFPFYDKPMRIQYA 93
            F D   A  A+E M GF    +P+++ YA
Sbjct: 234 QFHDAEEAKEALEVMNGFELAGRPIKVGYA 263

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 28/82 (34%), Positives = 44/82 (53%), Gaps = 7/82 (8%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEK 77
          + + N+   V +D     LH +F +FGT+L+I+ F T  ++ QA + F D  SA AA   
Sbjct: 6  VIVENMTYPVTLD----VLHQIFSKFGTVLKIITF-TKNNQFQALIQFADAVSAQAAKLS 60

Query: 78 MQGFPFYDK--PMRIQYAKTKS 97
          + G   Y+    +RI Y+K  S
Sbjct: 61 LDGQNIYNGCCTLRIDYSKLTS 82

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

 Score = 39.4 bits (93), Expect = 1e-04
 Identities = 25/81 (30%), Positives = 44/81 (54%), Gaps = 7/81 (8%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAF--KTLKHKGQAWLVFKDVASATA 73
          TI + NL+E    D L+     +F+ FG I  + LA   +T + +G A++ F     A  
Sbjct: 1  TIRVTNLSEDADEDDLR----ELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAER 56

Query: 74 AVEKMQGFPFYDKPMRIQYAK 94
          A+EK+ GF + +  + +++AK
Sbjct: 57 AIEKLNGFGYDNLILSVEWAK 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|241226 cd12782, RRM2_PTBP1, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein 1 (PTB)

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 7/87 (8%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          SP   I + NL   V +D     LH +F +FGT+L+I+ F T  ++ QA L + D  SA 
Sbjct: 2  SPVLRIIVENLFYPVTLD----VLHQIFSKFGTVLKIITF-TKNNQFQALLQYADPVSAQ 56

Query: 73 AAVEKMQGFPFYDK--PMRIQYAKTKS 97
           A   + G   Y+    +RI ++K  S
Sbjct: 57 HAKLSLDGQNIYNACCTLRIDFSKLTS 83

This subgroup corresponds to the RRM2 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence shows that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution. . Length = 100

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 5/58 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQ 226
           +FV  +P+ TT  +L+ +FSQF   +E  ++  +      G  FV + D+  A  A +
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 41.3 bits (97), Expect = 2e-04
 Identities = 47/238 (19%), Positives = 91/238 (38%), Gaps = 65/238 (27%)

Query: 18  IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAV 75
           +Y+ NL+  V  D+L++    +F +FG I      K  + + +G A++ F+    A  AV
Sbjct: 181 LYVKNLDPSVNEDKLRE----LFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAV 236

Query: 76  EKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRK--RHEEKGKKRKD--QHDANQ 131
           E+M G               K  +  +    +V R +++  R  E  +K ++  Q    +
Sbjct: 237 EEMNG--------------KKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMK 282

Query: 132 AGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMF 191
           A  G+N                                    L+V+N+    T   L+  
Sbjct: 283 A-QGVN------------------------------------LYVKNLDDTVTDEKLREL 305

Query: 192 FSQFPGFKEVR-MVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
           FS+       + M++ K    G  FV + +  +A  A+  +    +G + L +  A++
Sbjct: 306 FSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQR 363

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 7/65 (10%)

Query: 170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIA----FVEYGDEMQAT--V 223
           PN I FV  +P DTT   L+ FFS+F   K+V+++  + G++    FV +  +  A   +
Sbjct: 2   PNRI-FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKIL 60

Query: 224 AMQSL 228
           AM +L
Sbjct: 61  AMGNL 65

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|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 = 38.4 bits (90), Expect = 3e-04
 Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 3/67 (4%)

Query: 30 DQLKQSLHAVFKQFGTILEI-LAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK 86
          D  ++ L  +F + G ++   L     T K KG  +  F+D+ +A +A+  + G+ F  +
Sbjct: 9  DATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGR 68

Query: 87 PMRIQYA 93
           +R+ +A
Sbjct: 69 ALRVDFA 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|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
          T+++ N+N  V+     + L A+F+QFG I  +  +   KH+G   + + D+ +A  A  
Sbjct: 3  TLFVRNINSNVE----DEELRALFEQFGDIRTL--YTACKHRGFIMVSYYDIRAARRAKR 56

Query: 77 KMQGFPFYDKPMRIQYAKTK 96
           +QG     + + I ++  K
Sbjct: 57 ALQGTELGGRKLDIHFSIPK 76

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

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 7/75 (9%)

Query: 19 YINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAAV 75
          Y+ +L+  V    L +    +F   G +L I       T +  G A++ F++ A A  A+
Sbjct: 3  YVGDLHPDVTEAMLYE----IFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERAL 58

Query: 76 EKMQGFPFYDKPMRI 90
          + +       KP+RI
Sbjct: 59 DTLNFDVIKGKPIRI 73

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

>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 27/89 (30%), Positives = 42/89 (47%), Gaps = 15/89 (16%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTI----------LEILAFK-TLKHKGQAWL 63
          NNTI++  L E V I+ +       FKQ G I          + +   + T K KG+A +
Sbjct: 2  NNTIFVQGLGEDVTIESVAD----YFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 57

Query: 64 VFKDVASATAAVEKMQGFPFYDKPMRIQY 92
           F D  SA AA++   G  F   P+++ +
Sbjct: 58 SFDDPPSAKAAIDWFDGKEFSGNPIKVSF 86

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 14/83 (16%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTI----------LEILAFKTLKHKGQAWLVFKD 67
          IYI+ L + V  D L      +F   G I          ++I   K  + KG+A + + D
Sbjct: 1  IYISGLPDDVTEDSLA----ELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDD 56

Query: 68 VASATAAVEKMQGFPFYDKPMRI 90
           ++A AA+E   G+ F    +++
Sbjct: 57 PSAAQAAIEWFNGYEFRGNKIKV 79

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 7/69 (10%)

Query: 16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASAT 72
          N IY+ +++  +  D +K    +VF+ FG I         +T KHKG  ++ +++  SA 
Sbjct: 1  NRIYVASVHPDLSEDDIK----SVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQ 56

Query: 73 AAVEKMQGF 81
           A+  M  F
Sbjct: 57 DAIASMNLF 65

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

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 12/72 (16%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQA--------WLVFKDV 68
          T+++ NLN K   + LK+     F++ G +  +   K    KG          ++ FK  
Sbjct: 2  TLFVKNLNFKTTEETLKK----HFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSK 57

Query: 69 ASATAAVEKMQG 80
           +A  A++++QG
Sbjct: 58 EAAQKALKRLQG 69

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

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

 Score = 37.5 bits (88), Expect = 4e-04
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 7/68 (10%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
          PN  +++ NL E+      K+ L  +F QF    E+   + +  +G A++ F+    AT 
Sbjct: 1  PNKILFLQNLPEETT----KEMLEMLFNQFPGFKEV---RLVPRRGIAFVEFETEEQATV 53

Query: 74 AVEKMQGF 81
          A++ +QGF
Sbjct: 54 ALQALQGF 61

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

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGI---AFVEYGDEMQATVAMQSLQS 230
           L+V N+    T   L   FSQ    K  +++  + G    AFVEY D   A  A+Q++  
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLI-REHGNDPYAFVEYYDHRSAAAALQTMNG 59

Query: 231 LKIGQQQLLITYA 243
             I  Q++ + +A
Sbjct: 60  RLILGQEIKVNWA 72

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

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 4/61 (6%)

Query: 33 KQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY 92
          +  L  +F ++G + +++     K KG A + F    +A AAVE   G P    P+ + +
Sbjct: 18 EDELRKIFSKYGDVSDVVVSS--KKKGSAIVEFASKKAAEAAVENECGLP--SNPLLVSW 73

Query: 93 A 93
           
Sbjct: 74 L 74

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFKDVASATAAV 75
          + + NL  K     LK+    +F  FG + E  I      K KG A++ F   A A  A+
Sbjct: 2  LIVRNLPFKCTEADLKK----LFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAI 57

Query: 76 EKMQGFPFYDKPMRIQYA 93
          + + G     +P+ + +A
Sbjct: 58 KGVNGKKIKGRPVAVDWA 75

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

>gnl|CDD|241228 cd12784, RRM2_ROD1, RNA recognition motif 2 in vertebrate regulator of differentiation 1 (Rod1)

 Score = 37.7 bits (87), Expect = 7e-04
 Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 7/87 (8%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          SP   I + NL   V +    + LH +F +FGT+L+I+ F T  ++ QA L + D  +A 
Sbjct: 3  SPVLRIIVENLFYPVTL----EVLHQIFSKFGTVLKIITF-TKNNQFQALLQYADPMNAH 57

Query: 73 AAVEKMQGFPFYDK--PMRIQYAKTKS 97
           A   + G   Y+    +RI ++K  S
Sbjct: 58 HAKMALDGQNIYNACCTLRIDFSKLTS 84

This subgroup corresponds to the RRM2 of ROD1 coding protein Rod1, 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 and negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities. . Length = 103

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

 Score = 36.8 bits (86), Expect = 9e-04
 Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 9/77 (11%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEK 77
          +Y+ NL      +QL++     F ++G +      +  K K  A++ F++   A  A+E+
Sbjct: 4  LYVRNLPLSTTEEQLREL----FSEYGEVE-----RVKKIKDYAFVHFEERDDAVKAMEE 54

Query: 78 MQGFPFYDKPMRIQYAK 94
          M G      P+ +  AK
Sbjct: 55 MNGKELEGSPIEVSLAK 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|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 = 36.4 bits (85), Expect = 0.001
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVA 224
            N  LFV  +   TT   L+  FS+F   +EV +++        G  FV +     A  A
Sbjct: 1   GNK-LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAA 59

Query: 225 MQSLQSLKIGQQQLLITYAKK 245
           ++ L   ++  + + +  AK+
Sbjct: 60  IRDLNGKELEGRVIKVEKAKR 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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 10/66 (15%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP----------GIAFVEYGDEMQATV 223
           LFV+N+   TT   L+  F +  G + V + + K           G  FVE+  +  A  
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 224 AMQSLQ 229
           A++ LQ
Sbjct: 63  ALKRLQ 68

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAFKTLKHKGQAWLVFKDVASATAAV 75
          I++ NL+ KV   +LK+    VFK  G ++  +I   K  K +G   + F+    A  A+
Sbjct: 1  IFVANLDYKVGWKKLKE----VFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAI 56

Query: 76 EKMQGFPFYDKPMRIQ 91
              G   +D+PMR++
Sbjct: 57 SMFNGQMLFDRPMRVK 72

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 41 KQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQG 80
           +FG +  I   K    +G  ++ FK V +A   ++ + G
Sbjct: 33 SKFGPVEHIKVDKN-SPEGVVYVKFKTVEAAQKCIQALNG 71

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

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

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 7/78 (8%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTL-KHKGQAWLVFKDVASATAAVE 76
          + ++NLNE+        +  A+F  FG   +++  K L   K  A +   D   A  A+ 
Sbjct: 2  LLVSNLNEE------MVTPDALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALT 55

Query: 77 KMQGFPFYDKPMRIQYAK 94
           + G   + K +R+  +K
Sbjct: 56 HLNGIRLHGKKLRVTLSK 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 7/81 (8%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASATA 73
           +Y+ NL   V  + LK     +F QFG +     I   +T + +G  ++  +    A A
Sbjct: 1  NLYVGNLPYNVTEEDLKD----LFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANA 56

Query: 74 AVEKMQGFPFYDKPMRIQYAK 94
          A+EK+ G  F  + + +  A+
Sbjct: 57 AIEKLNGTDFGGRTLTVNEAR 77

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

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 24/71 (33%), Positives = 32/71 (45%), Gaps = 9/71 (12%)

Query: 172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQ 226
            ILFV N+P+DTT   L   F        VR++  K      G AFVE+      T A++
Sbjct: 1   FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60

Query: 227 ----SLQSLKI 233
                L+  KI
Sbjct: 61  LHHTLLKGRKI 71

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

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 12/83 (14%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----------GIAFVEYGDEMQAT 222
           LFV+N+   TT   L   F    GF   R V+ KP           G  FV +  + QA 
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFAR-VKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61

Query: 223 VAMQSLQSLKIGQQQLLITYAKK 245
            A++++    +    L++ ++ +
Sbjct: 62  AALKAMDGFVLDGHTLVVKFSHR 84

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 8/84 (9%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILE----ILAFKTLKHKGQAWLVFKDVASATA 73
          ++I NL+ +V     ++ L+  F  FG IL+    +    T   KG A++ +    ++ A
Sbjct: 4  LFIGNLDPEVD----EKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDA 59

Query: 74 AVEKMQGFPFYDKPMRIQYAKTKS 97
          A+E M G    ++P+ + YA  K 
Sbjct: 60 AIEAMNGQYLCNRPITVSYAFKKD 83

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

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

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQ 226
           LFV+N+P+D T  +L   FS+F   +    V  K      G  FV + D+      ++
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 61

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

>gnl|CDD|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 = 19/64 (29%), Positives = 33/64 (51%), Gaps = 4/64 (6%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
          T++I NL +      L+      F++FG I++I   K   +   A++ + D+AS   A+ 
Sbjct: 4  TLFIGNLEKTTTYSDLR----EAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMR 59

Query: 77 KMQG 80
          KM G
Sbjct: 60 KMDG 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|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 = 35.7 bits (83), Expect = 0.002
 Identities = 14/37 (37%), Positives = 20/37 (54%)

Query: 56 KHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY 92
          K KG A++ F   A+A A  EK++G  F  K   + Y
Sbjct: 40 KSKGFAYVEFASEAAAAAVKEKLEGREFNGKKCVVTY 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|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 173 ILFVQNVPHDTTPMALQMFFSQFP--GFKE-VRMVEAKPGIAFVEYGDEMQATVAMQSLQ 229
           +L V  +  D   M     F+ F   G    ++ +++KPG A V+ GD   A  A++ L 
Sbjct: 1   VLMVYGLDKDK--MNCDKLFNLFCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLN 58

Query: 230 SLKIGQQQLLITY 242
            + +  Q+L + +
Sbjct: 59  GVVLFGQKLEVNF 71

This subfamily corresponds to the RRM3 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). 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 polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RRMs. Length = 71

>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 = 21/71 (29%), Positives = 33/71 (46%), Gaps = 6/71 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV-----EAKPGIAFVEYGDEMQATVAMQSL 228
           LFV+N+P+      L+  FS+F    EV +          G A+V + D   A  A + L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 229 QSLKIGQQQLL 239
              K+ Q +L+
Sbjct: 65  DG-KVFQGRLI 74

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

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 25/97 (25%), Positives = 45/97 (46%), Gaps = 6/97 (6%)

Query: 13  SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAFKTLKHKGQAWLVFKDVAS 70
           S    I++ NL++ V      ++L   F +FG IL  ++   +  K +G  ++ F+   S
Sbjct: 86  SGVGNIFVKNLDKSVD----NKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEES 141

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTF 107
           A AA++K+ G    DK + +     K +  A     F
Sbjct: 142 AKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKF 178

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 5/55 (9%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRM-----VEAKPGIAFVEYGDE 218
           P ++ LFV N+PHD T   L+ FF +F    EVR+         P   FV + D 
Sbjct: 1   PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDP 55

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 5/50 (10%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV----EAKP-GIAFVEYGDE 218
           LFV  + +DTT   L+  F ++   K +R+V      KP G AF+E+  E
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHE 53

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|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 = 34.8 bits (81), Expect = 0.004
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 3/51 (5%)

Query: 33 KQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASATAAVEKMQG 80
          ++ + A+F+++G I E   I    T + KG A++ F     A  A+E + G
Sbjct: 13 EEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 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|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 34.8 bits (80), Expect = 0.004
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE----AKPGIAFVEYGDEMQATVAMQSLQ 229
           + V+N+P + T   ++  FS +   K VR+ +    +  G AFVE+    +A  AM +L+
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 230 SLKIGQQQLLITYA 243
              +  ++L++ YA
Sbjct: 63  DTHLLGRRLVLQYA 76

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 37.6 bits (87), Expect = 0.004
 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 13/84 (15%)

Query: 16  NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLK------HKGQAWLVFKDVA 69
           + IYI NL   +  DQ+K+ L    + FG   ++ AF  +K       KG A+  +KD +
Sbjct: 296 DRIYIGNLPLYLGEDQIKELL----ESFG---DLKAFNLIKDIATGLSKGYAFCEYKDPS 348

Query: 70  SATAAVEKMQGFPFYDKPMRIQYA 93
               A+  + G    D  + +Q A
Sbjct: 349 VTDVAIAALNGKDTGDNKLHVQRA 372

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	245
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.98
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.98
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	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
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.96
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.96
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.95
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.95
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.95
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.94
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.94
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.9
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.9
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.89
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.89
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.88
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.88
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.88
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.86
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.86
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.85
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.85
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.83
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.79
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.78
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.78
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.77
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.77
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.76
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.74
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.73
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.73
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.71
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.66
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.66
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.66
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.65
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.65
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.62
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.62
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.62
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.61
PLN03120	260	nucleic acid binding protein; Provisional	99.6
PLN03120	260	nucleic acid binding protein; Provisional	99.6
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.58
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.57
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.56
KOG0122	270	consensus Translation initiation factor 3, subunit	99.56
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.56
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.56
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.55
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.55
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.55
PLN03121	243	nucleic acid binding protein; Provisional	99.53
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.53
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.53
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.52
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.52
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.52
smart00362	72	RRM_2 RNA recognition motif.	99.5
PLN03121	243	nucleic acid binding protein; Provisional	99.5
PLN03213	759	repressor of silencing 3; Provisional	99.49
KOG0122	270	consensus Translation initiation factor 3, subunit	99.48
PLN03213	759	repressor of silencing 3; Provisional	99.48
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.48
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.47
smart00362	72	RRM_2 RNA recognition motif.	99.46
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.45
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.44
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.44
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.43
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.42
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.41
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.41
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.4
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.4
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.39
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.38
smart00360	71	RRM RNA recognition motif.	99.38
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.37
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.36
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.36
smart00360	71	RRM RNA recognition motif.	99.35
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.35
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.33
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.32
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.32
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.31
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.29
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.28
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.28
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	99.27
smart00361	70	RRM_1 RNA recognition motif.	99.25
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.22
smart00361	70	RRM_1 RNA recognition motif.	99.21
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.2
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.19
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.19
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.18
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	99.14
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.12
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.11
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.11
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.08
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.05
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.04
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.03
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.01
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.95
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.93
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.86
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.84
KOG4210	285	consensus Nuclear localization sequence binding pr	98.82
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.81
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.79
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.79
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.78
KOG0151	877	consensus Predicted splicing regulator, contains R	98.78
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.77
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.77
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.74
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.74
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.72
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.72
KOG0226	290	consensus RNA-binding proteins [General function p	98.68
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.64
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.61
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.61
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.61
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.59
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.56
KOG0151	877	consensus Predicted splicing regulator, contains R	98.51
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.51
KOG0226	290	consensus RNA-binding proteins [General function p	98.48
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.38
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.36
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.36
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.36
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.33
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.98
KOG2314	698	consensus Translation initiation factor 3, subunit	97.98
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.88
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.88
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.86
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.77
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.74
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.71
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.68
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.66
KOG3152	278	consensus TBP-binding protein, activator of basal	97.58
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.57
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.52
KOG2314	698	consensus Translation initiation factor 3, subunit	97.5
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.49
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.46
KOG4210	285	consensus Nuclear localization sequence binding pr	97.44
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.42
KOG3152	278	consensus TBP-binding protein, activator of basal	97.37
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.33
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.28
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.26
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	97.24
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.23
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.14
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.07
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.05
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.0
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.97
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.92
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.9
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.78
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.57
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.51
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.45
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.43
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	96.37
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.33
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.28
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.13
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	96.05
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.0
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	95.9
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.76
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.75
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.75
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.73
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.67
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	95.67
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	95.43
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	95.19
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.13
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.77
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	94.2
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.18
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.15
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	93.97
KOG2135	526	consensus Proteins containing the RNA recognition	93.93
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	92.48
KOG2591	684	consensus c-Mpl binding protein, contains La domai	92.06
KOG2135	526	consensus Proteins containing the RNA recognition	90.36
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	90.22
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	89.73
KOG2068	327	consensus MOT2 transcription factor [Transcription	89.31
KOG2318	650	consensus Uncharacterized conserved protein [Funct	87.85
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	86.65
PF14893	331	PNMA: PNMA	83.83
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	83.25
PRK14548	84	50S ribosomal protein L23P; Provisional	81.76

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=3.5e-33  Score=234.37  Aligned_cols=227  Identities=18%  Similarity=0.294  Sum_probs=146.8

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      +.++|||+|||.++++++    |+++|+.||+|.+|+++   .+|+++|||||+|.+.++|.+|++.|||..+.|+.|+|
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   77 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEE----IRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKV   77 (352)
T ss_pred             CCcEEEEeCCCCCCCHHH----HHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEE
Confidence            578999999999999999    77999999999998765   36789999999999999999999999999999999999


Q ss_pred             EEccccchHhhh----------------------cCCCc-------------------ccchhhhhhhhh---hhhc---
Q 025973           91 QYAKTKSDIIAK----------------------ADGTF-------------------VPRERRKRHEEK---GKKR---  123 (245)
Q Consensus        91 ~~~~~~~~~~~~----------------------~~~~~-------------------~~~~~~~~~~~~---~~~~---  123 (245)
                      .++.+.......                      .-+..                   ............   .+..   
T Consensus        78 ~~a~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~  157 (352)
T TIGR01661        78 SYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPS  157 (352)
T ss_pred             EeecccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccC
Confidence            998654421100                      00000                   000000000000   0000   


Q ss_pred             -----------cchh----hHhhh---cCCCCc--cccC-----------CC----------------------CCCCCC
Q 025973          124 -----------KDQH----DANQA---GMGLNP--AYAG-----------AY----------------------GATPPL  150 (245)
Q Consensus       124 -----------~~~~----~~~~~---~~~~~~--~~~~-----------~~----------------------~~~~~~  150 (245)
                                 ....    .....   ....+.  ..+.           ..                      ..+.+.
T Consensus       158 g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  237 (352)
T TIGR01661       158 GCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQ  237 (352)
T ss_pred             CCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhccccc
Confidence                       0000    00000   000000  0000           00                      000000


Q ss_pred             -----CCCCC-CCCCC-CC----CCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEE
Q 025973          151 -----SQIPY-PGGAK-SV----IPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVE  214 (245)
Q Consensus       151 -----~~~~~-~~~~~-~~----~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~  214 (245)
                           ...+. ..... ..    ........+.+|||+|||..+++++|+++|++||.|.+++++.++     +|||||+
T Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~  317 (352)
T TIGR01661       238 QHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVS  317 (352)
T ss_pred             ccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEE
Confidence                 00000 00000 00    000011223479999999999999999999999999999999874     7999999


Q ss_pred             eCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          215 YGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       215 f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      |.+.++|..|+..|||+.|+|++|+|+|+.
T Consensus       318 F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       318 MTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             ECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            999999999999999999999999999963

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=5.8e-33  Score=228.96  Aligned_cols=163  Identities=22%  Similarity=0.382  Sum_probs=143.2

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ......++|||+|||.++++++    |+++|+.||.|.+|++.   .+++++|||||+|.+.++|.+|++.||+..+.++
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~----L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr  177 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRE----LYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNK  177 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCc
Confidence            3455789999999999999999    77999999999988664   4778999999999999999999999999999999


Q ss_pred             eEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           87 PMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEA  166 (245)
Q Consensus        87 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (245)
                      .|+|.++++....                                                                   
T Consensus       178 ~i~V~~a~p~~~~-------------------------------------------------------------------  190 (346)
T TIGR01659       178 RLKVSYARPGGES-------------------------------------------------------------------  190 (346)
T ss_pred             eeeeecccccccc-------------------------------------------------------------------
Confidence            9999987532110                                                                   


Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCC--eEEE
Q 025973          167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQ--QQLL  239 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g--~~i~  239 (245)
                        ...++|||+|||..+|+++|+++|+.||.|..+.++.++     +|+|||+|.+.++|..|++.||+..+.+  ++|.
T Consensus       191 --~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~  268 (346)
T TIGR01659       191 --IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLT  268 (346)
T ss_pred             --cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEE
Confidence              123469999999999999999999999999999999864     5899999999999999999999998874  7999


Q ss_pred             EEEecC
Q 025973          240 ITYAKK  245 (245)
Q Consensus       240 v~~ak~  245 (245)
                      |.||+.
T Consensus       269 V~~a~~  274 (346)
T TIGR01659       269 VRLAEE  274 (346)
T ss_pred             EEECCc
Confidence            999863

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).

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=9.9e-32  Score=217.41  Aligned_cols=224  Identities=19%  Similarity=0.301  Sum_probs=164.7

Q ss_pred             ccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973            7 NQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus         7 ~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      .+.+.++.++.|||+.||.++.|++    |.-+|++.|.|-+++++.   +|.+||||||.|.+.+.|++|++.||+..|
T Consensus        75 weg~~p~~G~EVfvGkIPrD~~Ede----LvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Ei  150 (506)
T KOG0117|consen   75 WEGPPPPRGCEVFVGKIPRDVFEDE----LVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEI  150 (506)
T ss_pred             ccCCCCCCCceEEecCCCccccchh----hHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccc
Confidence            4556678899999999999999999    669999999999998775   689999999999999999999999999998


Q ss_pred             C-CceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhc---------------------------cchhhHhhhcCC
Q 025973           84 Y-DKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKR---------------------------KDQHDANQAGMG  135 (245)
Q Consensus        84 ~-g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~~~~~  135 (245)
                      . |+.|.|+.+..+.....   ++....+.+........+-                           .+.....+++..
T Consensus       151 r~GK~igvc~Svan~RLFi---G~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrK  227 (506)
T KOG0117|consen  151 RPGKLLGVCVSVANCRLFI---GNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRK  227 (506)
T ss_pred             cCCCEeEEEEeeecceeEe---ccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhh
Confidence            7 89999988755433211   1111111111111111110                           122223333444


Q ss_pred             CCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEe
Q 025973          136 LNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEY  215 (245)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f  215 (245)
                      +.+.....||...+..+.-.    ...........-+.|||+||+.++|+|.|...|+.||.|.+|+.++   .||||+|
T Consensus       228 l~~g~~klwgn~~tVdWAep----~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~r---DYaFVHf  300 (506)
T KOG0117|consen  228 LMPGKIKLWGNAITVDWAEP----EEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPR---DYAFVHF  300 (506)
T ss_pred             ccCCceeecCCcceeeccCc----ccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeeccc---ceeEEee
Confidence            44455555555444332211    1111112333557899999999999999999999999999998874   5999999


Q ss_pred             CCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          216 GDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       216 ~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.++|.+|+..+||+.+.|..|.|.+||
T Consensus       301 ~eR~davkAm~~~ngkeldG~~iEvtLAK  329 (506)
T KOG0117|consen  301 AEREDAVKAMKETNGKELDGSPIEVTLAK  329 (506)
T ss_pred             cchHHHHHHHHHhcCceecCceEEEEecC
Confidence            99999999999999999999999999997

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

Probab=99.98  E-value=2.1e-31  Score=230.77  Aligned_cols=170  Identities=21%  Similarity=0.336  Sum_probs=141.8

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ...++|||+|||+++++++    |+++|+.||.|.+|.+.   .+++++|||||+|.+.++|.+|++.|||..+.|+.|+
T Consensus       105 ~~~~rLfVGnLp~~~tEe~----Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~Ik  180 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDT----IRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIK  180 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHH----HHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceee
Confidence            4568999999999999999    77999999999998664   4788999999999999999999999999999999999


Q ss_pred             EEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           90 IQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAP  169 (245)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (245)
                      |.+.........     ..     ..                                                ......
T Consensus       181 V~rp~~~p~a~~-----~~-----~~------------------------------------------------~~~~~~  202 (612)
T TIGR01645       181 VGRPSNMPQAQP-----II-----DM------------------------------------------------VQEEAK  202 (612)
T ss_pred             eccccccccccc-----cc-----cc------------------------------------------------cccccc
Confidence            975322110000     00     00                                                000011


Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..++|||+||+..+++++|+++|+.||.|.++++.+++     +|||||+|.+.++|..|+..|||+.++|+.|+|.+|.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            34579999999999999999999999999999999853     7999999999999999999999999999999999874

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 Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.98  E-value=2.3e-31  Score=202.68  Aligned_cols=172  Identities=23%  Similarity=0.414  Sum_probs=146.5

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEE---EEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~---i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      --|||+.|+..++-+.    |++-|..||.|.+   |+++.++++|||+||.|.+.++|..||..|||..|.+|.|+-.|
T Consensus        63 fhvfvgdls~eI~~e~----lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNW  138 (321)
T KOG0148|consen   63 FHVFVGDLSPEIDNEK----LREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNW  138 (321)
T ss_pred             eeEEehhcchhcchHH----HHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccc
Confidence            4589999999999999    6699999999987   46667999999999999999999999999999999999999999


Q ss_pred             ccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 025973           93 AKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNN  172 (245)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  172 (245)
                      +..+....-   +     +..  ...+.                                           =....+.++
T Consensus       139 ATRKp~e~n---~-----~~l--tfdeV-------------------------------------------~NQssp~Nt  165 (321)
T KOG0148|consen  139 ATRKPSEMN---G-----KPL--TFDEV-------------------------------------------YNQSSPDNT  165 (321)
T ss_pred             cccCccccC---C-----CCc--cHHHH-------------------------------------------hccCCCCCc
Confidence            987752110   0     000  00000                                           001125788


Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      ++||+|++..+|+++|++.|++||.|.+|++.+++ ||+||.|.+.|+|..|+.++|++.++|..+++.|.|.
T Consensus       166 sVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q-GYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe  237 (321)
T KOG0148|consen  166 SVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ-GYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKE  237 (321)
T ss_pred             eEEeCCcCccccHHHHHHhcccCCcceEEEEeccc-ceEEEEecchhhHHHHHHHhcCceeCceEEEEecccc
Confidence            99999999999999999999999999999999997 9999999999999999999999999999999999874

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.97  E-value=5.1e-30  Score=191.72  Aligned_cols=215  Identities=50%  Similarity=0.820  Sum_probs=173.4

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .+..++.+|||.||......++|++.|+.+|++||.|..|...++.+.+|.|||.|.+.+.|..|+..|+|..|+|+.++
T Consensus         4 ~~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    4 MSVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             cccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            34566779999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCcccc--CCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           90 IQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYA--GAYGATPPLSQIPYPGGAKSVIPEAP  167 (245)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (245)
                      |.||..++..+....+.+....++...+......++.        ..++...  .....+.+            .. ...
T Consensus        84 iqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~--------~~ng~~~~~~~~~~p~p------------~~-~~~  142 (221)
T KOG4206|consen   84 IQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPL--------DTNGHFYNMNRMNLPPP------------FL-AQM  142 (221)
T ss_pred             eecccCccchhhccCceeccccCccccccccccCCcc--------cccccccccccccCCCC------------cc-ccC
Confidence            9999999987777666554444333222221111000        0000000  00111111            11 344


Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC-CeEEEEEEecC
Q 025973          168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITYAKK  245 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~ak~  245 (245)
                      .+++.++++.|||..++.+.|..+|..|...+.|++++.+++.|||+|.+...|..|.+.++|+.+- ...+.|++|+|
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~K  221 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAKK  221 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccCC
Confidence            5788999999999999999999999999999999999998899999999999999999999998887 99999999986

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

Probab=99.97  E-value=9.1e-30  Score=220.64  Aligned_cols=171  Identities=22%  Similarity=0.409  Sum_probs=142.4

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..+.++|||+|||..+++++    |.++|+.||.|..|.+..   +++++|||||+|.+.++|.+|+. |+|..+.|+.|
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~----l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i  160 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERD----LYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPI  160 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeee
Confidence            45588999999999999999    669999999999987654   67889999999999999999998 99999999999


Q ss_pred             EEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           89 RIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPA  168 (245)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (245)
                      .|.++............                                    .                     .....
T Consensus       161 ~v~~~~~~~~~~~~~~~------------------------------------~---------------------~~~~~  183 (457)
T TIGR01622       161 IVQSSQAEKNRAAKAAT------------------------------------H---------------------QPGDI  183 (457)
T ss_pred             EEeecchhhhhhhhccc------------------------------------c---------------------cCCCC
Confidence            99875432211000000                                    0                     00001


Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +...+|||+|||..+++++|+++|+.||.|..|.++.+.     +|||||+|.+.++|..|+..|||..|.|++|.|.||
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            235789999999999999999999999999999999753     689999999999999999999999999999999997


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       264 ~  264 (457)
T TIGR01622       264 Q  264 (457)
T ss_pred             c
Confidence            5

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=2.1e-29  Score=218.46  Aligned_cols=220  Identities=22%  Similarity=0.312  Sum_probs=148.5

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC--ceEEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD--KPMRIQY   92 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g--~~i~v~~   92 (245)
                      ..+|||+||++.+++++    |+++|+.||.|..|.+.++. .+++|||+|.+.++|.+|++.|||..+.|  ++|+|.|
T Consensus        96 ~~~v~v~nl~~~vt~~~----L~~~F~~~G~V~~v~i~~~~-~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~  170 (481)
T TIGR01649        96 VLRVIVENPMYPITLDV----LYQIFNPYGKVLRIVTFTKN-NVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEY  170 (481)
T ss_pred             eEEEEEcCCCCCCCHHH----HHHHHhccCCEEEEEEEecC-CceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEE
Confidence            34799999999999999    77999999999999776532 34799999999999999999999999975  4899999


Q ss_pred             ccccchHhhhcCCCcccchhhhhhhhhhh--------hccchhhHhhhcC----CCCccccCC----------CCCCCCC
Q 025973           93 AKTKSDIIAKADGTFVPRERRKRHEEKGK--------KRKDQHDANQAGM----GLNPAYAGA----------YGATPPL  150 (245)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~----~~~~~~~~~----------~~~~~~~  150 (245)
                      ++.........+.     +.|+.......        .............    .....+...          ...+++ 
T Consensus       171 sk~~~l~v~~~~~-----~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~-  244 (481)
T TIGR01649       171 AKPTRLNVKYNDD-----DSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPP-  244 (481)
T ss_pred             ecCCCceeEeccc-----CCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcccccccCCCc-
Confidence            9875543222221     11222211110        0000000000000    000000000          000000 


Q ss_pred             CCCCC------CCCC----CCCCCCCCCCCccEEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHH
Q 025973          151 SQIPY------PGGA----KSVIPEAPAPPNNILFVQNVPH-DTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEM  219 (245)
Q Consensus       151 ~~~~~------~~~~----~~~~~~~~~~~~~~l~v~nl~~-~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~  219 (245)
                      ...+.      ...+    .........+++.+|||+||+. .+|+++|+++|+.||.|.+|+++++++|+|||+|.+++
T Consensus       245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~  324 (481)
T TIGR01649       245 HGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPY  324 (481)
T ss_pred             ccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHH
Confidence            00000      0000    0001111234678999999997 79999999999999999999999988899999999999


Q ss_pred             HHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          220 QATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       220 ~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      +|..|+..|||..|.|++|+|+++++
T Consensus       325 ~A~~Ai~~lng~~l~g~~l~v~~s~~  350 (481)
T TIGR01649       325 QAQLALTHLNGVKLFGKPLRVCPSKQ  350 (481)
T ss_pred             HHHHHHHHhCCCEECCceEEEEEccc
Confidence            99999999999999999999999864

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=1.1e-29  Score=219.81  Aligned_cols=222  Identities=20%  Similarity=0.309  Sum_probs=146.5

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccC-C
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFY-D   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~-g   85 (245)
                      ...+...++|||+|||.+++|++    |+++|+.||.|.+|+++  .+|+++|||||+|.+.++|.+|++.||+..+. |
T Consensus        52 ~~~p~~~~~lFVgnLp~~~tEd~----L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~G  127 (578)
T TIGR01648        52 GVQPGRGCEVFVGKIPRDLYEDE----LVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPG  127 (578)
T ss_pred             CCCCCCCCEEEeCCCCCCCCHHH----HHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCC
Confidence            34455679999999999999999    77999999999998665  47889999999999999999999999998886 7


Q ss_pred             ceEEEEEccccchHhhhcCCCcccchhhhhhhhh-------------------hhhc--------cchhhHhhhcCCCCc
Q 025973           86 KPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEK-------------------GKKR--------KDQHDANQAGMGLNP  138 (245)
Q Consensus        86 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------~~~~--------~~~~~~~~~~~~~~~  138 (245)
                      +.|.|..+.........   ++.....+......                   ....        ++......+...+..
T Consensus       128 r~l~V~~S~~~~rLFVg---NLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~  204 (578)
T TIGR01648       128 RLLGVCISVDNCRLFVG---GIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMP  204 (578)
T ss_pred             ccccccccccCceeEee---cCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhc
Confidence            77777665432211100   00000000000000                   0000        011111111111100


Q ss_pred             cccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccC--CCeeEEEEecCCCeEEEEEeC
Q 025973          139 AYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQF--PGFKEVRMVEAKPGIAFVEYG  216 (245)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~--g~v~~v~l~~~~~g~afv~f~  216 (245)
                      .....++..+......    +............++|||+||+..+++++|+++|+.|  |.|.+|.++   ++||||+|.
T Consensus       205 gki~l~Gr~I~VdwA~----p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~---rgfAFVeF~  277 (578)
T TIGR01648       205 GRIQLWGHVIAVDWAE----PEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI---RDYAFVHFE  277 (578)
T ss_pred             cceEecCceEEEEeec----ccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee---cCeEEEEeC
Confidence            0001111111111000    0000011112345789999999999999999999999  999999876   379999999


Q ss_pred             CHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          217 DEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       217 ~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +.++|.+|+..|||..|.|+.|.|+||+
T Consensus       278 s~e~A~kAi~~lnG~~i~Gr~I~V~~Ak  305 (578)
T TIGR01648       278 DREDAVKAMDELNGKELEGSEIEVTLAK  305 (578)
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            9999999999999999999999999996

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.

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

Probab=99.97  E-value=4e-29  Score=216.73  Aligned_cols=194  Identities=19%  Similarity=0.369  Sum_probs=145.2

Q ss_pred             CCCCeEEEcCCCc-ccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           13 SPNNTIYINNLNE-KVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        13 ~~~~~l~V~nLp~-~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      .++++|||+|||. .+++++    |+++|+.||.|..|.++.+  .+|+|||+|.+.++|..|+..|||..+.|+.|+|.
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~----L~~lF~~yG~V~~vki~~~--~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDR----LFNLFCVYGNVERVKFMKN--KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHH----HHHHHHhcCCeEEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            4788999999997 699999    7799999999999988765  36999999999999999999999999999999999


Q ss_pred             EccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 025973           92 YAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPN  171 (245)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (245)
                      +++......... +.... .....  +.                    +..     ........+.   ........+++
T Consensus       347 ~s~~~~~~~~~~-~~~~~-~~~~~--~d--------------------~~~-----~~~~r~~~~~---~~~~~~~~~ps  394 (481)
T TIGR01649       347 PSKQQNVQPPRE-GQLDD-GLTSY--KD--------------------YSS-----SRNHRFKKPG---SANKNNIQPPS  394 (481)
T ss_pred             EcccccccCCCC-CcCcC-CCccc--cc--------------------ccC-----CccccCCCcc---cccccccCCCC
Confidence            986553311110 00000 00000  00                    000     0000000000   00001123577


Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCC--eeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeE------EEE
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPG--FKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQ------LLI  240 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~--v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~------i~v  240 (245)
                      .+|||+|||..+++++|+++|+.||.  |..+++.+.+   +++|||+|.+.++|..|+..|||+.+.++.      |+|
T Consensus       395 ~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv  474 (481)
T TIGR01649       395 ATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKV  474 (481)
T ss_pred             cEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEE
Confidence            88999999999999999999999998  8889887754   689999999999999999999999999885      999


Q ss_pred             EEec
Q 025973          241 TYAK  244 (245)
Q Consensus       241 ~~ak  244 (245)
                      +|||
T Consensus       475 ~fs~  478 (481)
T TIGR01649       475 SFST  478 (481)
T ss_pred             Eecc
Confidence            9997

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).

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

Probab=99.96  E-value=1.4e-28  Score=218.04  Aligned_cols=179  Identities=22%  Similarity=0.370  Sum_probs=145.7

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccC----C
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFY----D   85 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~----g   85 (245)
                      ....++|||+|||.++++++    |+++|+.||.|.++.+.+  +++++|||||.|.+.++|.+|++.||+..+.    |
T Consensus       175 ~~~~~~l~V~nl~~~~tee~----L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g  250 (562)
T TIGR01628       175 LKKFTNLYVKNLDPSVNEDK----LRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEG  250 (562)
T ss_pred             ccCCCeEEEeCCCCcCCHHH----HHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccc
Confidence            44567899999999999999    669999999999986654  6778999999999999999999999999999    9


Q ss_pred             ceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           86 KPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPE  165 (245)
Q Consensus        86 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (245)
                      +.+.|.++..+..+......        ......        .                                   ..
T Consensus       251 ~~l~v~~a~~k~er~~~~~~--------~~~~~~--------~-----------------------------------~~  279 (562)
T TIGR01628       251 KKLYVGRAQKRAEREAELRR--------KFEELQ--------Q-----------------------------------ER  279 (562)
T ss_pred             eeeEeecccChhhhHHHHHh--------hHHhhh--------h-----------------------------------hh
Confidence            99999887665442110000        000000        0                                   00


Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       166 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      .....+.+|||+||+..+++++|+++|+.||.|.+++++.+.    +|||||+|.+.++|.+|+..|||..|+|++|.|.
T Consensus       280 ~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~  359 (562)
T TIGR01628       280 KMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVA  359 (562)
T ss_pred             hcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEE
Confidence            001234569999999999999999999999999999998764    6899999999999999999999999999999999


Q ss_pred             EecC
Q 025973          242 YAKK  245 (245)
Q Consensus       242 ~ak~  245 (245)
                      +|++
T Consensus       360 ~a~~  363 (562)
T TIGR01628       360 LAQR  363 (562)
T ss_pred             eccC
Confidence            9863

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=2.1e-28  Score=216.89  Aligned_cols=156  Identities=23%  Similarity=0.413  Sum_probs=137.4

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      .|||+|||.+++|++    |+++|+.||.|.+|++.+   +++++|||||.|.+.++|.+|+..+|+..+.|+.|+|.|+
T Consensus         2 sl~VgnLp~~vte~~----L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s   77 (562)
T TIGR01628         2 SLYVGDLDPDVTEAK----LYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWS   77 (562)
T ss_pred             eEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecc
Confidence            699999999999999    779999999999987764   5778999999999999999999999999999999999986


Q ss_pred             cccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccE
Q 025973           94 KTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNI  173 (245)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (245)
                      .......                                                                   .....+
T Consensus        78 ~~~~~~~-------------------------------------------------------------------~~~~~~   90 (562)
T TIGR01628        78 QRDPSLR-------------------------------------------------------------------RSGVGN   90 (562)
T ss_pred             ccccccc-------------------------------------------------------------------ccCCCc
Confidence            4321100                                                                   012345


Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       174 l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      |||+|||..+++++|+++|+.||.|..|++..+.    +|||||+|.+.++|..|++.+||..+.|+.|.|...
T Consensus        91 vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~  164 (562)
T TIGR01628        91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRF  164 (562)
T ss_pred             eEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEecc
Confidence            9999999999999999999999999999998753    689999999999999999999999999999999764

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

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.96  E-value=5.4e-28  Score=183.51  Aligned_cols=226  Identities=19%  Similarity=0.320  Sum_probs=154.0

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ....+.|.|.-||..+|++|    |+.+|...|.|++|.+.+   +|.+.||+||.|.+++||.+|+..|||..+..++|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE----~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTI  113 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDE----LRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTI  113 (360)
T ss_pred             CcccceeeeeecccccCHHH----HHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceE
Confidence            44567899999999999999    679999999999986554   78899999999999999999999999999999999


Q ss_pred             EEEEccccchHhhhcCCCcccchhhhhhhhhhhhc-----------------------------cchhhHhhhcCCCCcc
Q 025973           89 RIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKR-----------------------------KDQHDANQAGMGLNPA  139 (245)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------------~~~~~~~~~~~~~~~~  139 (245)
                      +|.|+++.+..+....- |.+.-.+.....+...-                             +.......+..+++..
T Consensus       114 KVSyARPSs~~Ik~aNL-YvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~  192 (360)
T KOG0145|consen  114 KVSYARPSSDSIKDANL-YVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQ  192 (360)
T ss_pred             EEEeccCChhhhcccce-EEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCC
Confidence            99999988775443221 21111111111111000                             0000000000000000


Q ss_pred             ccCCCC------------------------------CCCCCCCCC--------------CCCCC-----------CCCCC
Q 025973          140 YAGAYG------------------------------ATPPLSQIP--------------YPGGA-----------KSVIP  164 (245)
Q Consensus       140 ~~~~~~------------------------------~~~~~~~~~--------------~~~~~-----------~~~~~  164 (245)
                      -+....                              .+.|..+.+              ....+           ....+
T Consensus       193 ~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp  272 (360)
T KOG0145|consen  193 KPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLP  272 (360)
T ss_pred             CCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccC
Confidence            000000                              000000000              00000           00011


Q ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEE
Q 025973          165 EAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLL  239 (245)
Q Consensus       165 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~  239 (245)
                      . .....-+|||-||.....|.-|+++|.+||.|.+|++++|-     ||||||.|.+.++|.+|+..|||..+++|.|.
T Consensus       273 ~-~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQ  351 (360)
T KOG0145|consen  273 G-GPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQ  351 (360)
T ss_pred             C-CCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEE
Confidence            1 11234579999999999999999999999999999999963     79999999999999999999999999999999


Q ss_pred             EEEe
Q 025973          240 ITYA  243 (245)
Q Consensus       240 v~~a  243 (245)
                      |+|-
T Consensus       352 VsFK  355 (360)
T KOG0145|consen  352 VSFK  355 (360)
T ss_pred             EEEe
Confidence            9984

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

Probab=99.96  E-value=3.2e-27  Score=207.35  Aligned_cols=190  Identities=16%  Similarity=0.233  Sum_probs=134.8

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccC--------CeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCc
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFG--------TILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFP   82 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G--------~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~   82 (245)
                      .....++|||+|||..+++++|+++|.++|...|        .|..+.+   +..+|||||+|.+.++|..|+. |+|..
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~---~~~kg~afVeF~~~e~A~~Al~-l~g~~  246 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI---NKEKNFAFLEFRTVEEATFAMA-LDSII  246 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE---CCCCCEEEEEeCCHHHHhhhhc-CCCeE
Confidence            3456789999999999999996655555444333        3444444   3457999999999999999996 99999


Q ss_pred             cCCceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCC
Q 025973           83 FYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSV  162 (245)
Q Consensus        83 ~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (245)
                      |.|+.|+|........... ....             ..                ...+...        ..  ......
T Consensus       247 ~~g~~l~v~r~~~~~~~~~-~~~~-------------~~----------------~~~~~~~--------~~--~~~~~~  286 (509)
T TIGR01642       247 YSNVFLKIRRPHDYIPVPQ-ITPE-------------VS----------------QKNPDDN--------AK--NVEKLV  286 (509)
T ss_pred             eeCceeEecCccccCCccc-cCCC-------------CC----------------CCCCccc--------cc--cccccc
Confidence            9999999865432211000 0000             00                0000000        00  000000


Q ss_pred             CCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeE
Q 025973          163 IPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQ  237 (245)
Q Consensus       163 ~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~  237 (245)
                      ..........+|||+|||..+++++|.++|+.||.|..+.++.+.     +|||||+|.+.++|..|+..|||..|+|++
T Consensus       287 ~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~  366 (509)
T TIGR01642       287 NSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNK  366 (509)
T ss_pred             ccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            001111244679999999999999999999999999999998752     799999999999999999999999999999


Q ss_pred             EEEEEec
Q 025973          238 LLITYAK  244 (245)
Q Consensus       238 i~v~~ak  244 (245)
                      |.|.+|.
T Consensus       367 l~v~~a~  373 (509)
T TIGR01642       367 LHVQRAC  373 (509)
T ss_pred             EEEEECc
Confidence            9999984

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

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=5.8e-28  Score=194.86  Aligned_cols=162  Identities=20%  Similarity=0.394  Sum_probs=139.8

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCcc-CC
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPF-YD   85 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~-~g   85 (245)
                      ......-++||+-+|..++|.|    |+.+|++||.|.+|.+.+   ++.++|||||.|.+.++|.+|+.+||+... .|
T Consensus        29 ~~d~~~vKlfVgqIprt~sE~d----lr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG  104 (510)
T KOG0144|consen   29 NPDGSAVKLFVGQIPRTASEKD----LRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPG  104 (510)
T ss_pred             CCCchhhhheeccCCccccHHH----HHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCC
Confidence            3446678999999999999999    669999999999985554   778999999999999999999999988444 34


Q ss_pred             --ceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCC
Q 025973           86 --KPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVI  163 (245)
Q Consensus        86 --~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (245)
                        ..|.|.|++...+++                                                               
T Consensus       105 ~~~pvqvk~Ad~E~er~---------------------------------------------------------------  121 (510)
T KOG0144|consen  105 MHHPVQVKYADGERERI---------------------------------------------------------------  121 (510)
T ss_pred             CCcceeecccchhhhcc---------------------------------------------------------------
Confidence              489999987655532                                                               


Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCe-eC--Ce
Q 025973          164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLK-IG--QQ  236 (245)
Q Consensus       164 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~-~~--g~  236 (245)
                           +..+.|||+-|+..+||.+++.+|++||.|++|.|.++.    +|||||.|.+.+.|..|++.|||.. +.  ..
T Consensus       122 -----~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~  196 (510)
T KOG0144|consen  122 -----VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQ  196 (510)
T ss_pred             -----ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCC
Confidence                 134569999999999999999999999999999999964    8999999999999999999999944 44  77


Q ss_pred             EEEEEEe
Q 025973          237 QLLITYA  243 (245)
Q Consensus       237 ~i~v~~a  243 (245)
                      +|.|.||
T Consensus       197 PLVVkFA  203 (510)
T KOG0144|consen  197 PLVVKFA  203 (510)
T ss_pred             ceEEEec
Confidence            8999998

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.95  E-value=1.4e-27  Score=172.20  Aligned_cols=161  Identities=24%  Similarity=0.396  Sum_probs=138.4

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      -...+|||+||+..++++-    |+++|-+.|+|..+++.+   +...+||||++|.+.|+|..|++.||++.++|++|+
T Consensus         7 nqd~tiyvgnld~kvs~~~----l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIr   82 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEEL----LYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIR   82 (203)
T ss_pred             CCCceEEEecCCHHHHHHH----HHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeE
Confidence            3468999999999999998    889999999999998776   455789999999999999999999999999999999


Q ss_pred             EEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           90 IQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAP  169 (245)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (245)
                      |.-+......                                                                    ..
T Consensus        83 v~kas~~~~n--------------------------------------------------------------------l~   94 (203)
T KOG0131|consen   83 VNKASAHQKN--------------------------------------------------------------------LD   94 (203)
T ss_pred             EEeccccccc--------------------------------------------------------------------cc
Confidence            9876411110                                                                    02


Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEecC-----CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKE-VRMVEA-----KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~-v~l~~~-----~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+..|||+||++.+.+..|.+.|+.||.+.. -.++++     .+|+||+.|.+.+.+.+|+..+||..+++++|.|++|
T Consensus        95 vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya  174 (203)
T KOG0131|consen   95 VGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYA  174 (203)
T ss_pred             ccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEE
Confidence            3456999999999999999999999999744 334442     3689999999999999999999999999999999999


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +|
T Consensus       175 ~k  176 (203)
T KOG0131|consen  175 FK  176 (203)
T ss_pred             Ee
Confidence            75

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

Probab=99.95  E-value=8.6e-26  Score=195.84  Aligned_cols=225  Identities=18%  Similarity=0.312  Sum_probs=143.3

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      +..++|||+|||..+++++    |.++|+.||.|..|.+..   +|.++|||||+|.+.++|.+|+..|||..+.|+.|.
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~  259 (457)
T TIGR01622       184 PNFLKLYVGNLHFNITEQE----LRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIK  259 (457)
T ss_pred             CCCCEEEEcCCCCCCCHHH----HHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEE
Confidence            3478999999999999999    669999999999886653   568899999999999999999999999999999999


Q ss_pred             EEEccccchHhhhcCCCcccchhhhhhhhhhh-hccchhhHhhhcCC------CCccc------c--CCCCCCCCCCC--
Q 025973           90 IQYAKTKSDIIAKADGTFVPRERRKRHEEKGK-KRKDQHDANQAGMG------LNPAY------A--GAYGATPPLSQ--  152 (245)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~------~~~~~------~--~~~~~~~~~~~--  152 (245)
                      |.|+......... ...+.............. ..............      .++..      .  ...+.......  
T Consensus       260 v~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  338 (457)
T TIGR01622       260 VGYAQDSTYLLDA-ANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSR  338 (457)
T ss_pred             EEEccCCCccccc-hhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccccccccccccc
Confidence            9997633221110 000000000000000000 00000000000000      00000      0  00000000000  


Q ss_pred             -----CCCCCCCCCCCCC-CCCCCccEEEEcCCCCCCC----------HHHHHHHhccCCCeeEEEEe-cCCCeEEEEEe
Q 025973          153 -----IPYPGGAKSVIPE-APAPPNNILFVQNVPHDTT----------PMALQMFFSQFPGFKEVRMV-EAKPGIAFVEY  215 (245)
Q Consensus       153 -----~~~~~~~~~~~~~-~~~~~~~~l~v~nl~~~~t----------~~~l~~~f~~~g~v~~v~l~-~~~~g~afv~f  215 (245)
                           .+.... ....+. ....++.+|+|.||....+          .+||++.|+.||.|..|.+. +...|++||+|
T Consensus       339 ~~~~~~~~~~~-~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~~~G~~fV~F  417 (457)
T TIGR01622       339 YATGALAIMAR-NSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKF  417 (457)
T ss_pred             ccccccccccC-CCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCCCceeEEEEE
Confidence                 000000 011111 1234678899999964443          36899999999999999998 44479999999


Q ss_pred             CCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          216 GDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       216 ~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++++|..|+..|||..|+|+.|.+.|.
T Consensus       418 ~~~e~A~~A~~~lnGr~f~gr~i~~~~~  445 (457)
T TIGR01622       418 SSVDAALAAFQALNGRYFGGKMITAAFV  445 (457)
T ss_pred             CCHHHHHHHHHHhcCcccCCeEEEEEEE
Confidence            9999999999999999999999999986

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

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=9.6e-27  Score=192.81  Aligned_cols=181  Identities=20%  Similarity=0.298  Sum_probs=143.6

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      .+|||++||++++.++    |.++|+.+|+|..+.+..   ++.++||+||.|.-.|+++.|+..+++..|.|+.|.|.+
T Consensus         6 ~TlfV~~lp~~~~~~q----L~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~   81 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQ----LEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDP   81 (678)
T ss_pred             ceEEEecCCCccchhH----HHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccc
Confidence            8999999999999999    779999999999876554   446799999999999999999999999999999999999


Q ss_pred             ccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 025973           93 AKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNN  172 (245)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  172 (245)
                      +..+........+.-.  ..+....+.                                      .+   .....+.+..
T Consensus        82 A~~R~r~e~~~~~e~~--~veK~~~q~--------------------------------------~~---~k~~v~~~k~  118 (678)
T KOG0127|consen   82 AKKRARSEEVEKGENK--AVEKPIEQK--------------------------------------RP---TKAKVDLPKW  118 (678)
T ss_pred             ccccccchhcccccch--hhhcccccC--------------------------------------Cc---chhhccCccc
Confidence            8776553211111000  000000000                                      00   0011112345


Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .|+|+|||.++.+.+|..+|+.||.|..|.|+..+    .|||||.|.+..+|..|+..+||..|.||+|-|.||
T Consensus       119 rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWA  193 (678)
T KOG0127|consen  119 RLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWA  193 (678)
T ss_pred             eEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeee
Confidence            69999999999999999999999999999998743    699999999999999999999999999999999998

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

Probab=99.95  E-value=6.1e-26  Score=199.27  Aligned_cols=186  Identities=19%  Similarity=0.267  Sum_probs=138.5

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .+.++|||+|||..+++++    |.++|+.||.|..+.+.   .+|.++|||||+|.+.++|..|+..|||..+.|+.|.
T Consensus       293 ~~~~~l~v~nlp~~~~~~~----l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~  368 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQ----IKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLH  368 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            4568999999999999999    66999999999987554   3688999999999999999999999999999999999


Q ss_pred             EEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           90 IQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAP  169 (245)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (245)
                      |.++.............      .     .            .      +....            ..............
T Consensus       369 v~~a~~~~~~~~~~~~~------~-----~------------~------~~~~~------------~~~~~~~~~~~~~~  407 (509)
T TIGR01642       369 VQRACVGANQATIDTSN------G-----M------------A------PVTLL------------AKALSQSILQIGGK  407 (509)
T ss_pred             EEECccCCCCCCccccc------c-----c------------c------ccccc------------cccchhhhccccCC
Confidence            99985432110000000      0     0            0      00000            00000000011123


Q ss_pred             CccEEEEcCCCCCC----------CHHHHHHHhccCCCeeEEEEecCC--------CeEEEEEeCCHHHHHHHHHHhCCC
Q 025973          170 PNNILFVQNVPHDT----------TPMALQMFFSQFPGFKEVRMVEAK--------PGIAFVEYGDEMQATVAMQSLQSL  231 (245)
Q Consensus       170 ~~~~l~v~nl~~~~----------t~~~l~~~f~~~g~v~~v~l~~~~--------~g~afv~f~~~~~A~~A~~~l~g~  231 (245)
                      ++.+|+|.||...-          ..++|+++|+.||.|..|.|++..        .|+|||+|.++++|..|+..|||.
T Consensus       408 ~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr  487 (509)
T TIGR01642       408 PTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGR  487 (509)
T ss_pred             CceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCC
Confidence            57889999996321          236899999999999999998641        489999999999999999999999


Q ss_pred             eeCCeEEEEEEe
Q 025973          232 KIGQQQLLITYA  243 (245)
Q Consensus       232 ~~~g~~i~v~~a  243 (245)
                      .|+|+.|.|.|.
T Consensus       488 ~~~gr~v~~~~~  499 (509)
T TIGR01642       488 KFNDRVVVAAFY  499 (509)
T ss_pred             EECCeEEEEEEe
Confidence            999999999985

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

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.94  E-value=2.5e-25  Score=184.46  Aligned_cols=226  Identities=24%  Similarity=0.319  Sum_probs=144.6

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      +.-+|.|+|||..+.+.+    |..+|+.||.|.+|.+.+  +|...|||||+|....+|.+|++.+|+..|.||+|.|.
T Consensus       116 ~k~rLIIRNLPf~~k~~d----Lk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVD  191 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPD----LKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVD  191 (678)
T ss_pred             ccceEEeecCCcccCcHH----HHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEe
Confidence            367899999999999999    669999999999998875  56677999999999999999999999999999999999


Q ss_pred             EccccchHhhhcCCCcccchhhhhhhhhhh-hccchh-----hHh---hhcC--CCCccccCCCCCCC----------CC
Q 025973           92 YAKTKSDIIAKADGTFVPRERRKRHEEKGK-KRKDQH-----DAN---QAGM--GLNPAYAGAYGATP----------PL  150 (245)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-----~~~---~~~~--~~~~~~~~~~~~~~----------~~  150 (245)
                      ||.++..-.......-...++....+.... ..++-.     ...   ....  +..+......+...          ++
T Consensus       192 WAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S  271 (678)
T KOG0127|consen  192 WAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESS  271 (678)
T ss_pred             eecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhcccccccccccccccccc
Confidence            997654311100000000000000000000 000000     000   0000  00000000000000          00


Q ss_pred             CCCCCCCCCCCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHH
Q 025973          151 SQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAM  225 (245)
Q Consensus       151 ~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~  225 (245)
                      +.......+..........-..+|||+|||+.+|+++|.++|+.||.|.+..++.++     +|.|||.|.++.+|+.++
T Consensus       272 ~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci  351 (678)
T KOG0127|consen  272 GKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCI  351 (678)
T ss_pred             ccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHH
Confidence            000000000000001111234789999999999999999999999999999888764     799999999999999999


Q ss_pred             HHh-----CC-CeeCCeEEEEEEe
Q 025973          226 QSL-----QS-LKIGQQQLLITYA  243 (245)
Q Consensus       226 ~~l-----~g-~~~~g~~i~v~~a  243 (245)
                      ...     .| ..+.||-|.|..|
T Consensus       352 ~~Aspa~e~g~~ll~GR~Lkv~~A  375 (678)
T KOG0127|consen  352 EAASPASEDGSVLLDGRLLKVTLA  375 (678)
T ss_pred             HhcCccCCCceEEEeccEEeeeec
Confidence            876     23 6678999999876

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.94  E-value=2.4e-26  Score=177.02  Aligned_cols=145  Identities=21%  Similarity=0.403  Sum_probs=134.1

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEccc
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKT   95 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~~   95 (245)
                      -+|||+|||..+++.+    |+.+|++||.|.+|.+.     |+||||..++...|..|+..||+..++|-.|.|+-++.
T Consensus         3 ~KLFIGNLp~~~~~~e----lr~lFe~ygkVlECDIv-----KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSks   73 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQE----LRSLFEQYGKVLECDIV-----KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKS   73 (346)
T ss_pred             cchhccCCCcccchHH----HHHHHHhhCceEeeeee-----cccceEEeecccccHHHHhhcccceecceEEEEEeccc
Confidence            3699999999999999    66999999999999876     47999999999999999999999999999999988765


Q ss_pred             cchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEE
Q 025973           96 KSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILF  175 (245)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  175 (245)
                      ++.                                                                       .+++|+
T Consensus        74 Ksk-----------------------------------------------------------------------~stkl~   82 (346)
T KOG0109|consen   74 KSK-----------------------------------------------------------------------ASTKLH   82 (346)
T ss_pred             cCC-----------------------------------------------------------------------Cccccc
Confidence            522                                                                       456799


Q ss_pred             EcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          176 VQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       176 v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      |+|+.+.++.++|+..|++||.|..+.+++   +|+||.|...++|..|++.|+++.|.|++++|+++
T Consensus        83 vgNis~tctn~ElRa~fe~ygpviecdivk---dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   83 VGNISPTCTNQELRAKFEKYGPVIECDIVK---DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             cCCCCccccCHHHhhhhcccCCceeeeeec---ceeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            999999999999999999999999999984   79999999999999999999999999999999986

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.90  E-value=1.6e-23  Score=178.77  Aligned_cols=164  Identities=24%  Similarity=0.416  Sum_probs=137.6

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CC----CeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TL----KHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~----~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      +|||.||+++++.++    |..+|..+|.|.++.+..  ++    .+.|||||+|.+.++|+.|++.|+|..+.|+.|.|
T Consensus       517 ~lfvkNlnf~Tt~e~----l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~l  592 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLED----LEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLEL  592 (725)
T ss_pred             hhhhhcCCcccchhH----HHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEE
Confidence            399999999999999    779999999999985443  22    24599999999999999999999999999999999


Q ss_pred             EEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           91 QYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP  170 (245)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (245)
                      .++..+........                                                            .+....
T Consensus       593 k~S~~k~~~~~gK~------------------------------------------------------------~~~kk~  612 (725)
T KOG0110|consen  593 KISENKPASTVGKK------------------------------------------------------------KSKKKK  612 (725)
T ss_pred             EeccCccccccccc------------------------------------------------------------cccccc
Confidence            99862222111000                                                            000012


Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC--C---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA--K---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~--~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.|+|+|||+..+..+++.+|..||.|.+|+|...  +   +|||||+|-++.+|..|+.+|.++++.||+|.++||+
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            457999999999999999999999999999999874  1   6899999999999999999999999999999999996

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=6.8e-23  Score=165.77  Aligned_cols=82  Identities=20%  Similarity=0.432  Sum_probs=74.0

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcC-CccCCc--eE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQG-FPFYDK--PM   88 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~-~~~~g~--~i   88 (245)
                      ..++|||+-|+..++|.|    ++++|++||.|++|.+.+  .+.+||||||.|++.|.|..|++.||| ..+.|+  +|
T Consensus       123 ~e~KLFvg~lsK~~te~e----vr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PL  198 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENE----VREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPL  198 (510)
T ss_pred             cchhhhhhhccccccHHH----HHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCce
Confidence            478999999999999999    779999999999998776  788999999999999999999999999 566776  99


Q ss_pred             EEEEccccchH
Q 025973           89 RIQYAKTKSDI   99 (245)
Q Consensus        89 ~v~~~~~~~~~   99 (245)
                      .|.|++++.+.
T Consensus       199 VVkFADtqkdk  209 (510)
T KOG0144|consen  199 VVKFADTQKDK  209 (510)
T ss_pred             EEEecccCCCc
Confidence            99999877653

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.89  E-value=2.6e-22  Score=166.74  Aligned_cols=147  Identities=22%  Similarity=0.410  Sum_probs=132.1

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEccc
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKT   95 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~~   95 (245)
                      ..||||   +++|+..    |++.|+.+|+|.+|++.++-.+-|||||.|.++++|.+|+..||...+.|+.|+|.|+..
T Consensus         2 ~sl~vg---~~v~e~~----l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~r   74 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAM----LFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQR   74 (369)
T ss_pred             CceecC---CcCChHH----HHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhcc
Confidence            468999   9999999    789999999999986665334889999999999999999999999999999999999633


Q ss_pred             cchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEE
Q 025973           96 KSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILF  175 (245)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  175 (245)
                      .                                                                         + ..+|
T Consensus        75 d-------------------------------------------------------------------------~-~~~~   80 (369)
T KOG0123|consen   75 D-------------------------------------------------------------------------P-SLVF   80 (369)
T ss_pred             C-------------------------------------------------------------------------C-ceee
Confidence            2                                                                         1 1199


Q ss_pred             EcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          176 VQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       176 v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      |.||+..++..+|.++|+.||+|.+|++..+.   +|| ||+|.++++|..|+..+||..+.|++|.|..+.
T Consensus        81 i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~  151 (369)
T KOG0123|consen   81 IKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFE  151 (369)
T ss_pred             ecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeecc
Confidence            99999999999999999999999999999865   789 999999999999999999999999999998764

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.89  E-value=5.5e-22  Score=151.53  Aligned_cols=229  Identities=20%  Similarity=0.344  Sum_probs=151.3

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCc-cCC--c
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFP-FYD--K   86 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~-~~g--~   86 (245)
                      ...+++|||+.|...-+|||    ++.+|..||.|.+|.+.+  +|.+||+|||.|.+.-+|..||..|||.. +-|  .
T Consensus        16 g~~drklfvgml~kqq~e~d----vrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASS   91 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDD----VRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASS   91 (371)
T ss_pred             CccchhhhhhhhcccccHHH----HHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCcc
Confidence            33689999999999999999    779999999999997775  88999999999999999999999999944 444  4


Q ss_pred             eEEEEEccccchHhhhc-------CCCcccchh-----hhhhhhh---------------hhhc--cch--hh--Hhhhc
Q 025973           87 PMRIQYAKTKSDIIAKA-------DGTFVPRER-----RKRHEEK---------------GKKR--KDQ--HD--ANQAG  133 (245)
Q Consensus        87 ~i~v~~~~~~~~~~~~~-------~~~~~~~~~-----~~~~~~~---------------~~~~--~~~--~~--~~~~~  133 (245)
                      .|.|.|++...++..+.       -+.+.+...     ..+...-               .++.  ...  .+  .....
T Consensus        92 SLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~a  171 (371)
T KOG0146|consen   92 SLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNA  171 (371)
T ss_pred             ceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhh
Confidence            89999998877654321       111111000     0000000               0000  000  00  00000


Q ss_pred             CCC-------------Cc---------------------cccCCCCCCCC-----CCCCCCCCCCCCC------------
Q 025973          134 MGL-------------NP---------------------AYAGAYGATPP-----LSQIPYPGGAKSV------------  162 (245)
Q Consensus       134 ~~~-------------~~---------------------~~~~~~~~~~~-----~~~~~~~~~~~~~------------  162 (245)
                      +++             ++                     ..+...|.+.+     -+..+++...+..            
T Consensus       172 ngl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~  251 (371)
T KOG0146|consen  172 NGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQ  251 (371)
T ss_pred             cccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHH
Confidence            000             00                     00000000000     0011111110000            


Q ss_pred             ----------------C---------CCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEE
Q 025973          163 ----------------I---------PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAF  212 (245)
Q Consensus       163 ----------------~---------~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~af  212 (245)
                                      .         -..+.+.++.|||..||....+.+|.++|-+||.|.+.++..|+     |=|+|
T Consensus       252 ~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGF  331 (371)
T KOG0146|consen  252 QYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGF  331 (371)
T ss_pred             HHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceee
Confidence                            0         01133467789999999999999999999999999999888875     56999


Q ss_pred             EEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          213 VEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       213 v~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      |.|+++.+|+.|+..|||+.|+-|+|+|++-+
T Consensus       332 VSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKR  363 (371)
T KOG0146|consen  332 VSFDNPASAQAAIQAMNGFQIGMKRLKVQLKR  363 (371)
T ss_pred             EecCCchhHHHHHHHhcchhhhhhhhhhhhcC
Confidence            99999999999999999999999999998753

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.88  E-value=1.3e-21  Score=157.40  Aligned_cols=217  Identities=25%  Similarity=0.333  Sum_probs=156.2

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC-C-ceEEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY-D-KPMRIQ   91 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~-g-~~i~v~   91 (245)
                      +--+++|.|+-+.++-|.    |+++|++||.|..|..... ...-.|+|+|.+.+.|..|...|+|..|+ | ++|+|.
T Consensus       149 ~vLr~iie~m~ypVslDV----LHqvFS~fG~VlKIiTF~K-nn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId  223 (492)
T KOG1190|consen  149 PVLRTIIENMFYPVSLDV----LHQVFSKFGFVLKIITFTK-NNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRID  223 (492)
T ss_pred             eeEEEEeccceeeeEHHH----HHHHHhhcceeEEEEEEec-ccchhhhhhccchhhHHHHHHhccCCcccCceeEEEee
Confidence            445788999999999999    8899999999999876542 22347999999999999999999998886 4 499999


Q ss_pred             EccccchHhhhcCCCcccchhhhhhhhhhhhc--cchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           92 YAKTKSDIIAKADGTFVPRERRKRHEEKGKKR--KDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAP  169 (245)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (245)
                      |++.......     |.+.++|++++.....-  ++..+..+++..-  ..+...|.+..  .......+....+....+
T Consensus       224 ~Sklt~LnvK-----ynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~--~~~~~~g~p~a--ip~~~~~a~~a~~~~~~~  294 (492)
T KOG1190|consen  224 FSKLTDLNVK-----YNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFG--SVPAVHGAPLA--IPSGAAGANAADGKIESP  294 (492)
T ss_pred             hhhcccceee-----ccccccccccCCCCCCCccccccchhhhcccc--ccccccCCccc--CCccchhhcccccccccC
Confidence            9876444222     55667777777765433  1112222221111  11111121111  111111111111111111


Q ss_pred             -CccEEEEcCCC-CCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 -PNNILFVQNVP-HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 -~~~~l~v~nl~-~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                       .+.+|.|.||. ..+|.+.|..+|+.||.|.+|++..+++..|+|+|.+..+|+.|+.+|+|..++|++|+|.++|
T Consensus       295 ~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  295 SANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             CCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence             26789999996 8999999999999999999999999988899999999999999999999999999999999987

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

Probab=99.88  E-value=1.3e-20  Score=163.86  Aligned_cols=80  Identities=21%  Similarity=0.405  Sum_probs=72.7

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ..++|||+|||.++++++    |+++|+.||.|.++++.+   +++++|||||+|.+.++|.+|+..||+..+.|+.|+|
T Consensus       203 ~~~rLfVgnLp~~vteed----Lk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV  278 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETD----IKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV  278 (612)
T ss_pred             ccceEEeecCCCCCCHHH----HHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            457999999999999999    669999999999987654   5778999999999999999999999999999999999


Q ss_pred             EEccccc
Q 025973           91 QYAKTKS   97 (245)
Q Consensus        91 ~~~~~~~   97 (245)
                      .++....
T Consensus       279 ~kAi~pP  285 (612)
T TIGR01645       279 GKCVTPP  285 (612)
T ss_pred             EecCCCc
Confidence            9987543

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.

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.88  E-value=2e-22  Score=160.08  Aligned_cols=166  Identities=22%  Similarity=0.349  Sum_probs=136.7

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEE---ecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEIL---AFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~---~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      -|+|||+.+++...||.    |+.-|..||+|.+|.   +.-+++.||||||+|+-+|.|+.|++.|||..+.||.|+|.
T Consensus       113 McRvYVGSIsfEl~EDt----iR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVg  188 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDT----IRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  188 (544)
T ss_pred             hHheeeeeeEEEechHH----HHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCcccccc
Confidence            37899999999999999    669999999999984   44589999999999999999999999999999999999997


Q ss_pred             EccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 025973           92 YAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPN  171 (245)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (245)
                      ....-.-    ...      --+....+                                                ...-
T Consensus       189 rPsNmpQ----AQp------iID~vqee------------------------------------------------Ak~f  210 (544)
T KOG0124|consen  189 RPSNMPQ----AQP------IIDMVQEE------------------------------------------------AKKF  210 (544)
T ss_pred             CCCCCcc----cch------HHHHHHHH------------------------------------------------HHhh
Confidence            5321100    000      00000000                                                0123


Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      +.|||..+-...+++||+.+|..||.|.+|.|.++.     +||||++|.+......|+..||=+.++|.-|+|.-
T Consensus       211 nRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk  286 (544)
T KOG0124|consen  211 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGK  286 (544)
T ss_pred             heEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccc
Confidence            569999999999999999999999999999999864     79999999999999999999999999999988854

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.86  E-value=1.7e-20  Score=135.98  Aligned_cols=173  Identities=17%  Similarity=0.251  Sum_probs=132.0

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      ..+++|||+|||.++-+.+    |+++|.+||.|.+|.+........||||+|++..+|..|+..-+|..+.|+.|+|++
T Consensus         4 r~~~~iyvGNLP~diReke----ieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEf   79 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKE----IEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEF   79 (241)
T ss_pred             cccceEEecCCCcchhhcc----HHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEe
Confidence            4578999999999999999    779999999999997664333467999999999999999999999999999999999


Q ss_pred             ccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 025973           93 AKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNN  172 (245)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  172 (245)
                      +..-.. .....+.+....+-.                             +             ........+.-.+..
T Consensus        80 prggr~-s~~~~G~y~gggrgG-----------------------------g-------------g~gg~rgppsrrSe~  116 (241)
T KOG0105|consen   80 PRGGRS-SSDRRGSYSGGGRGG-----------------------------G-------------GGGGRRGPPSRRSEY  116 (241)
T ss_pred             ccCCCc-ccccccccCCCCCCC-----------------------------C-------------CCCcccCCcccccce
Confidence            865432 111111111111000                             0             000000011113456


Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG  234 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~  234 (245)
                      .+.|++||.+-+++||+++...-|.|....+.++  |++.|+|...++..-|+..|....+.
T Consensus       117 RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD--g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  117 RVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD--GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             eEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc--cceeeeeeehhhHHHHHHhhcccccc
Confidence            7999999999999999999999999988888877  58999999999999999999886664

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.86  E-value=3.8e-21  Score=160.22  Aligned_cols=220  Identities=17%  Similarity=0.207  Sum_probs=143.3

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .|-.+|||+||.+.+++++    |+..|+.||.|..|...   ++|.++||+||+|.+.++|++|+..|||..+-|+.|+
T Consensus       276 ~p~~rl~vgnLHfNite~~----lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ik  351 (549)
T KOG0147|consen  276 GPMRRLYVGNLHFNITEDM----LRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIK  351 (549)
T ss_pred             cchhhhhhcccccCchHHH----HhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEE
Confidence            3444599999999999999    77999999999988544   3899999999999999999999999999999999999


Q ss_pred             EEEccccchHhhh---------cCCCcccchh---hhhhhhhhhhc-----cchhhHhhhcCCCCccccCCCCCCCCCCC
Q 025973           90 IQYAKTKSDIIAK---------ADGTFVPRER---RKRHEEKGKKR-----KDQHDANQAGMGLNPAYAGAYGATPPLSQ  152 (245)
Q Consensus        90 v~~~~~~~~~~~~---------~~~~~~~~~~---~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (245)
                      |............         .+....+...   .+....-....     ..+.........+........+... .. 
T Consensus       352 V~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~-~~-  429 (549)
T KOG0147|consen  352 VSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRV-RS-  429 (549)
T ss_pred             EEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCc-cc-
Confidence            9875433221100         0111111110   00000000000     0000000001111111111111110 00 


Q ss_pred             CCCCCCCCCCCCCCCCCCccEEEEcCCC--CCCC--------HHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHH
Q 025973          153 IPYPGGAKSVIPEAPAPPNNILFVQNVP--HDTT--------PMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQAT  222 (245)
Q Consensus       153 ~~~~~~~~~~~~~~~~~~~~~l~v~nl~--~~~t--------~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~  222 (245)
                       ..+..   ..+ ....++.++.++|+=  ...|        .+|+.+.+..||+|..|.+.++..|+.||.|.+.+.|.
T Consensus       430 -~~p~~---~~p-~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~  504 (549)
T KOG0147|consen  430 -VDPAD---ASP-AFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAG  504 (549)
T ss_pred             -cCccc---ccc-ccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHH
Confidence             00110   111 122577789999993  2222        37788999999999999999988899999999999999


Q ss_pred             HHHHHhCCCeeCCeEEEEEEe
Q 025973          223 VAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       223 ~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .|+..|||.+|.||.|.+.|-
T Consensus       505 ~a~~alhgrWF~gr~Ita~~~  525 (549)
T KOG0147|consen  505 TAVKALHGRWFAGRMITAKYL  525 (549)
T ss_pred             HHHHHHhhhhhccceeEEEEe
Confidence            999999999999999999883

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.85  E-value=1.3e-20  Score=156.64  Aligned_cols=161  Identities=25%  Similarity=0.405  Sum_probs=138.6

Q ss_pred             EEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEccc
Q 025973           18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKT   95 (245)
Q Consensus        18 l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~~   95 (245)
                      |||.||+++++.++    |++.|+.||.|++|++..  .| ++|| ||+|.+.+.|++|++.+||..+.|+.|.|.....
T Consensus        79 ~~i~nl~~~~~~~~----~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~  152 (369)
T KOG0123|consen   79 VFIKNLDESIDNKS----LYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFER  152 (369)
T ss_pred             eeecCCCcccCcHH----HHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccc
Confidence            99999999999999    889999999999997664  45 8999 9999999999999999999999999999988766


Q ss_pred             cchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEE
Q 025973           96 KSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILF  175 (245)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  175 (245)
                      +..+......                                                             ....-+.++
T Consensus       153 ~~er~~~~~~-------------------------------------------------------------~~~~~t~v~  171 (369)
T KOG0123|consen  153 KEEREAPLGE-------------------------------------------------------------YKKRFTNVY  171 (369)
T ss_pred             hhhhcccccc-------------------------------------------------------------hhhhhhhhh
Confidence            6553221000                                                             001123489


Q ss_pred             EcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          176 VQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       176 v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      +.|++..++++.|.++|+.||.|..+.++++.    ++|+||.|.++++|..|+..|++..++++.+.|..|.+
T Consensus       172 vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqk  245 (369)
T KOG0123|consen  172 VKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQK  245 (369)
T ss_pred             eeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCCccceeeccccc
Confidence            99999999999999999999999999999853    68999999999999999999999999999999988753

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.85  E-value=3.5e-20  Score=138.14  Aligned_cols=218  Identities=24%  Similarity=0.317  Sum_probs=135.6

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCC----eeeEEEEEecCHHHHHHHHHHHcCCccC--
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLK----HKGQAWLVFKDVASATAAVEKMQGFPFY--   84 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~----~kg~afV~F~~~~~A~~a~~~l~~~~~~--   84 (245)
                      ...+-++|||.+||.++...|    |+.+|..|-..+...+.-+++    .+.+||+.|.+..+|..|+.+|||+.|.  
T Consensus        30 ~~~~VRTLFVSGLP~DvKpRE----iynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE  105 (284)
T KOG1457|consen   30 EPGAVRTLFVSGLPNDVKPRE----IYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPE  105 (284)
T ss_pred             cccccceeeeccCCcccCHHH----HHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccc
Confidence            344579999999999999999    889999997777665554443    4589999999999999999999999997  


Q ss_pred             -CceEEEEEccccchHhhhcCCCc------ccchhhhhhhhhhhhccchhhHhhh-cCCCCcc---------ccCCC-CC
Q 025973           85 -DKPMRIQYAKTKSDIIAKADGTF------VPRERRKRHEEKGKKRKDQHDANQA-GMGLNPA---------YAGAY-GA  146 (245)
Q Consensus        85 -g~~i~v~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~---------~~~~~-~~  146 (245)
                       +.+|+|++++..........+.-      .....+....++.  ....+..... ...+.++         ..... ..
T Consensus       106 ~~stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~s--a~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l  183 (284)
T KOG1457|consen  106 TGSTLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKS--ADDQHDEGLSDPDELQEPGNADALKENDTTKSEAL  183 (284)
T ss_pred             cCceeEeeehhcCcccccCCCCCCCCCCccccccccChhhccc--chhhccccccCccccCCccccccCCCccccchhhh
Confidence             77999999987665433222221      0000000000000  0001111000 0000000         00000 00


Q ss_pred             CCCCCCCCCCCCC--CCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-CeEEEEEeCCHHHHHH
Q 025973          147 TPPLSQIPYPGGA--KSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-PGIAFVEYGDEMQATV  223 (245)
Q Consensus       147 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-~g~afv~f~~~~~A~~  223 (245)
                      ..+-.+.|.....  .+...........+|||-||..+++|++|+.+|+.|-.+...+|.... .-.||++|.+.+.|..
T Consensus       184 ~a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~  263 (284)
T KOG1457|consen  184 SAPDSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATD  263 (284)
T ss_pred             hhhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHH
Confidence            0000000000000  000111222345579999999999999999999999887766665422 3489999999999999


Q ss_pred             HHHHhCCCeeC
Q 025973          224 AMQSLQSLKIG  234 (245)
Q Consensus       224 A~~~l~g~~~~  234 (245)
                      |+.+|+|..+-
T Consensus       264 am~~lqg~~~s  274 (284)
T KOG1457|consen  264 AMNHLQGNLLS  274 (284)
T ss_pred             HHHHhhcceec
Confidence            99999998774

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.83  E-value=1e-18  Score=139.35  Aligned_cols=223  Identities=22%  Similarity=0.307  Sum_probs=154.3

Q ss_pred             CCCCCCCeEEEcCCC--cccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccC-C
Q 025973           10 NEISPNNTIYINNLN--EKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFY-D   85 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp--~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~-g   85 (245)
                      +...++..|.++=|.  +.+|-|.    |+.++...|.|+.|.+++ +|   =.|.|+|++.+.|++|.+.|||-.|+ |
T Consensus       115 es~~pN~VLl~TIlNp~YpItvDV----ly~Icnp~GkVlRIvIfkkng---VQAmVEFdsv~~AqrAk~alNGADIYsG  187 (494)
T KOG1456|consen  115 ESATPNKVLLFTILNPQYPITVDV----LYTICNPQGKVLRIVIFKKNG---VQAMVEFDSVEVAQRAKAALNGADIYSG  187 (494)
T ss_pred             CCCCCCeEEEEEeecCccccchhh----hhhhcCCCCceEEEEEEeccc---eeeEEeechhHHHHHHHhhccccccccc
Confidence            345567777766554  6778888    889999999999987664 33   48999999999999999999998887 4


Q ss_pred             -ceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhc--------cchhhHhhhcCCC---Cc---cccCCCCCCCCC
Q 025973           86 -KPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKR--------KDQHDANQAGMGL---NP---AYAGAYGATPPL  150 (245)
Q Consensus        86 -~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~---~~---~~~~~~~~~~~~  150 (245)
                       ++|+|+|+++......+.+...     |+++....+..        +...++.......   ..   .+.... ...+.
T Consensus       188 CCTLKIeyAkP~rlnV~knd~Dt-----wDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~-~~~p~  261 (494)
T KOG1456|consen  188 CCTLKIEYAKPTRLNVQKNDKDT-----WDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGD-RHGPP  261 (494)
T ss_pred             ceeEEEEecCcceeeeeecCCcc-----ccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccc-cCCCC
Confidence             4999999999877554443332     33333332111        1111111111100   00   011100 00111


Q ss_pred             CCCCCC--CCC---CCCCCCCCCCCccEEEEcCCC-CCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHH
Q 025973          151 SQIPYP--GGA---KSVIPEAPAPPNNILFVQNVP-HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVA  224 (245)
Q Consensus       151 ~~~~~~--~~~---~~~~~~~~~~~~~~l~v~nl~-~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A  224 (245)
                      ...|.+  ...   ....+.....++.++.|.+|. ..++.+.|.++|..||+|.+|++++.+.|.|+|++.|+.+.++|
T Consensus       262 ~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~  341 (494)
T KOG1456|consen  262 HPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERA  341 (494)
T ss_pred             CCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHH
Confidence            111110  000   001112344678899999998 67889999999999999999999999999999999999999999


Q ss_pred             HHHhCCCeeCCeEEEEEEecC
Q 025973          225 MQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       225 ~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      +.+||+..+.|.+|.|+++||
T Consensus       342 v~hLnn~~lfG~kl~v~~SkQ  362 (494)
T KOG1456|consen  342 VTHLNNIPLFGGKLNVCVSKQ  362 (494)
T ss_pred             HHHhccCccccceEEEeeccc
Confidence            999999999999999999987

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.79  E-value=1.7e-18  Score=148.21  Aligned_cols=208  Identities=21%  Similarity=0.267  Sum_probs=140.3

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      .....+.++|+|||..+..++    |...|..||.|..|.+.+.|   -.|+|+|.+..+|++|++.|....+...++.+
T Consensus       381 ~~rs~~vil~kNlpa~t~~~e----lt~~F~~fG~i~rvllp~~G---~~aiv~fl~p~eAr~Afrklaysr~k~~plyl  453 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEE----LTEAFLRFGEIGRVLLPPGG---TGAIVEFLNPLEARKAFRKLAYSRFKSAPLYL  453 (725)
T ss_pred             hhhhcceeeeccCccccccHH----HHHHhhcccccceeecCccc---ceeeeeecCccchHHHHHHhchhhhccCcccc
Confidence            345678999999999999999    77999999999999776554   36999999999999999999999888889988


Q ss_pred             EEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           91 QYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP  170 (245)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (245)
                      .|+.............+............   .+              ......+.... ...+....+...........
T Consensus       454 e~aP~dvf~~~pka~~~~~e~~~~~ee~~---~E--------------r~s~~d~~v~e-D~d~te~ss~a~~a~~~~~~  515 (725)
T KOG0110|consen  454 EWAPEDVFTEDPKADDLSAESRSKMEENP---SE--------------RVSAEDGQVEE-DKDPTEESSLARVAEDEETE  515 (725)
T ss_pred             ccChhhhccCCccccccccccccccccCc---ce--------------ecccccccccc-cCCccccccchhhhhccccc
Confidence            88754332100000000000000000000   00              00000000000 00000000000011111112


Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      + .||++||+..+|.++|..+|+.+|.|..+.|...+        .|||||+|.++++|..|++.|+|+.+.|+.|.|++
T Consensus       516 t-~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  516 T-KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             h-hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            2 29999999999999999999999999998887633        39999999999999999999999999999999999


Q ss_pred             ec
Q 025973          243 AK  244 (245)
Q Consensus       243 ak  244 (245)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            75

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.78  E-value=2e-17  Score=133.45  Aligned_cols=188  Identities=21%  Similarity=0.339  Sum_probs=143.2

Q ss_pred             CCeEEEcCCC-cccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           15 NNTIYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        15 ~~~l~V~nLp-~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      ++.|.|.||- ..+|.+.    |..+|+.||.|..|.+..+.+  -.|+|++.+...|..|++.|+|..++|+.|+|.++
T Consensus       297 n~vllvsnln~~~VT~d~----LftlFgvYGdVqRVkil~nkk--d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~S  370 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDV----LFTLFGVYGDVQRVKILYNKK--DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLS  370 (492)
T ss_pred             ceEEEEecCchhccchhH----HHHHHhhhcceEEEEeeecCC--cceeeeecchhHHHHHHHHhhcceecCceEEEeec
Confidence            6889999987 4678888    889999999999998876543  57999999999999999999999999999999999


Q ss_pred             cccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCc
Q 025973           94 KTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGG--AKSVIPEAPAPPN  171 (245)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~  171 (245)
                      +........+...     .+..+...                               ...+.+..  +.+.......|++
T Consensus       371 KH~~vqlp~egq~-----d~glT~dy-------------------------------~~spLhrfkkpgsKN~~ni~Pps  414 (492)
T KOG1190|consen  371 KHTNVQLPREGQE-----DQGLTKDY-------------------------------GNSPLHRFKKPGSKNYQNIFPPS  414 (492)
T ss_pred             cCccccCCCCCCc-----cccccccC-------------------------------CCCchhhccCcccccccccCCch
Confidence            8765533321110     01100000                               00111111  1122233455788


Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCe-eEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC-CeEEEEEEec
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGF-KEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v-~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~ak  244 (245)
                      .+|++.|+|.+++|++++..|..-|.. +-.++....+.+|++.+.+.|+|..|+-.++.+.++ +..|+|+|+|
T Consensus       415 atlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSk  489 (492)
T KOG1190|consen  415 ATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSK  489 (492)
T ss_pred             hheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceeecccCChhHhhhhccccccccCCCCceEEEEeec
Confidence            899999999999999999999988764 666666543459999999999999999999999998 6699999987

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.78  E-value=4.8e-19  Score=147.79  Aligned_cols=169  Identities=18%  Similarity=0.346  Sum_probs=136.3

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      .++||+--|+...++-+    |+++|+.+|.|..|++.   .++.++|.|||+|.+.++...|+. |.|..+.|-+|.|.
T Consensus       179 ~Rtvf~~qla~r~~pRd----L~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq  253 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRD----LEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQ  253 (549)
T ss_pred             HHHHHHHHHhhcCCchh----HHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEec
Confidence            57888888898999999    88999999999887554   367789999999999999999997 99999999999998


Q ss_pred             EccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 025973           92 YAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPN  171 (245)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (245)
                      .+.............                                                       ........+-
T Consensus       254 ~sEaeknr~a~~s~a-------------------------------------------------------~~~k~~~~p~  278 (549)
T KOG0147|consen  254 LSEAEKNRAANASPA-------------------------------------------------------LQGKGFTGPM  278 (549)
T ss_pred             ccHHHHHHHHhcccc-------------------------------------------------------ccccccccch
Confidence            754332211000000                                                       0000001122


Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ..|||+||-+++++++|+.+|.+||.|..|.+..+.     +||||++|.+.++|..|+..|||+.+.|+.|+|+..
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v  355 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVV  355 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEe
Confidence            229999999999999999999999999999999873     799999999999999999999999999999999753

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.77  E-value=2.5e-17  Score=130.39  Aligned_cols=196  Identities=16%  Similarity=0.245  Sum_probs=137.2

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE--------EEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCC
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--------ILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGF   81 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~--------i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~   81 (245)
                      +..++.|||.|||.++|-++    +.++|+.+|.|..        |.+.  ..|+.||=|++.|-..++...|+..|++.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE----~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~  206 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDE----FAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDED  206 (382)
T ss_pred             cccCceEEecCCCCcccHHH----HHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcc
Confidence            44577899999999999999    7799999998875        4333  36889999999999999999999999999


Q ss_pred             ccCCceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCC
Q 025973           82 PFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKS  161 (245)
Q Consensus        82 ~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (245)
                      .+.|+.|+|+.|+-+...      .+...++.........+ -...+....                  ...|..     
T Consensus       207 ~~rg~~~rVerAkfq~Kg------e~~~~~k~k~k~~~~kk-~~k~q~k~~------------------dw~pd~-----  256 (382)
T KOG1548|consen  207 ELRGKKLRVERAKFQMKG------EYDASKKEKGKCKDKKK-LKKQQQKLL------------------DWRPDR-----  256 (382)
T ss_pred             cccCcEEEEehhhhhhcc------CcCcccccccccccHHH-HHHHHHhhc------------------ccCCCc-----
Confidence            999999999998644331      11111111000000000 000000000                  000000     


Q ss_pred             CCCCCCCCCccEEEEcCCC----CCCC-------HHHHHHHhccCCCeeEEEEec-CCCeEEEEEeCCHHHHHHHHHHhC
Q 025973          162 VIPEAPAPPNNILFVQNVP----HDTT-------PMALQMFFSQFPGFKEVRMVE-AKPGIAFVEYGDEMQATVAMQSLQ  229 (245)
Q Consensus       162 ~~~~~~~~~~~~l~v~nl~----~~~t-------~~~l~~~f~~~g~v~~v~l~~-~~~g~afv~f~~~~~A~~A~~~l~  229 (245)
                       .........++|+++|+=    ...+       +++|..-++.||.|.+|.+.. .+.|.+-|.|.+.++|..+++.|+
T Consensus       257 -~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~  335 (382)
T KOG1548|consen  257 -DDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMD  335 (382)
T ss_pred             -cccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhc
Confidence             011122356789999983    2333       566778899999999998874 346999999999999999999999


Q ss_pred             CCeeCCeEEEEEE
Q 025973          230 SLKIGQQQLLITY  242 (245)
Q Consensus       230 g~~~~g~~i~v~~  242 (245)
                      |..|+||.|..+.
T Consensus       336 GR~fdgRql~A~i  348 (382)
T KOG1548|consen  336 GRWFDGRQLTASI  348 (382)
T ss_pred             CeeecceEEEEEE
Confidence            9999999998764

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.77  E-value=2e-18  Score=138.97  Aligned_cols=161  Identities=18%  Similarity=0.321  Sum_probs=134.8

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ..++|||++|+.+++++.    |+..|++||.|.++.+++   +++++||+||.|.+.+....++. .....+.|+.|.+
T Consensus         5 ~~~KlfiGgisw~ttee~----Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~   79 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEES----LREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEP   79 (311)
T ss_pred             CCcceeecCcCccccHHH----HHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccc
Confidence            679999999999999999    668999999999976554   78899999999999999999888 5667888999888


Q ss_pred             EEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           91 QYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP  170 (245)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (245)
                      ..+.+......-                                                               .....
T Consensus        80 k~av~r~~~~~~---------------------------------------------------------------~~~~~   96 (311)
T KOG4205|consen   80 KRAVSREDQTKV---------------------------------------------------------------GRHLR   96 (311)
T ss_pred             eeccCccccccc---------------------------------------------------------------ccccc
Confidence            777655431110                                                               00014


Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ...|||+.||..++++++++.|.+||.|..+.++.+.     +||+||.|.+++...+++. ..-+.|.|+++.|..|
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA  173 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRA  173 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeec
Confidence            5679999999999999999999999999888888764     7999999999999998886 5678899999999876

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.76  E-value=4.6e-18  Score=130.33  Aligned_cols=74  Identities=18%  Similarity=0.370  Sum_probs=69.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .-+||+.|...++-++|++.|.+||+|.+.++++|.     ||||||.|.+.++|..|++.|||.+|++|.|+--||-|
T Consensus        63 fhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   63 FHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             eeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            349999999999999999999999999999999973     89999999999999999999999999999999999754

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.74  E-value=5.5e-17  Score=118.15  Aligned_cols=75  Identities=20%  Similarity=0.399  Sum_probs=70.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++|||+|||..+++++|+++|++||.|.++.++.++     +|||||+|.++++|..|++.||+..|.|++|+|.+|+
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~  112 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN  112 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence            45679999999999999999999999999999998763     6999999999999999999999999999999999986

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.73  E-value=3.4e-17  Score=119.26  Aligned_cols=81  Identities=22%  Similarity=0.403  Sum_probs=73.3

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      -..+++|||+|||.++++++    |+++|+.||.|..|.+.   .+++++|||||+|.+.++|..|+..||+..+.|+.|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~----L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l  106 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDAS----LRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHI  106 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHH----HHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            45588999999999999999    67999999999987554   477899999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      +|.++..+
T Consensus       107 ~V~~a~~~  114 (144)
T PLN03134        107 RVNPANDR  114 (144)
T ss_pred             EEEeCCcC
Confidence            99998654

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.73  E-value=5.5e-18  Score=128.52  Aligned_cols=166  Identities=21%  Similarity=0.299  Sum_probs=129.2

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEccc
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKT   95 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~~   95 (245)
                      ..+||++||+.+.+.+    |+.+|..||.+..+.+.     .||+||+|.+..+|..|+..+|+..|.|-.+.|+++..
T Consensus         2 ~rv~vg~~~~~~~~~d----~E~~f~~yg~~~d~~mk-----~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERD----VERFFKGYGKIPDADMK-----NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhH----HHHHHhhccccccceee-----cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            4799999999999999    77999999999988665     37999999999999999999999999998899999864


Q ss_pred             cchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEE
Q 025973           96 KSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILF  175 (245)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  175 (245)
                      .....    +.-....+...                                             .............++
T Consensus        73 ~~~~~----g~~~~g~r~~~---------------------------------------------~~~~~~p~~s~~r~~  103 (216)
T KOG0106|consen   73 KRRGR----GRPRGGDRRSD---------------------------------------------SRRYRPPSRTHFRLI  103 (216)
T ss_pred             ccccc----CCCCCCCccch---------------------------------------------hhccCCcccccceee
Confidence            32211    00000000000                                             000000112456799


Q ss_pred             EcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          176 VQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       176 v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      |.|+...+.+.+|.++|+++|.+....+   ..+++||+|.+.++|..|+..++|..+.++.|.+..
T Consensus       104 ~~~~~~r~~~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  104 VRNLSLRVSWQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             eccchhhhhHHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            9999999999999999999999844433   358999999999999999999999999999998743

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.71  E-value=5e-16  Score=123.94  Aligned_cols=81  Identities=22%  Similarity=0.406  Sum_probs=70.7

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ...-.+|||..+.++.+|+||+    .+|+.||.|..|.+-+   .+..|||+|++|.+..+-..|+..||-..+.|..+
T Consensus       207 Ak~fnRiYVaSvHpDLSe~DiK----SVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyL  282 (544)
T KOG0124|consen  207 AKKFNRIYVASVHPDLSETDIK----SVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYL  282 (544)
T ss_pred             HHhhheEEeeecCCCccHHHHH----HHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceE
Confidence            3446899999999999999955    9999999999996654   45679999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      +|.-+..-
T Consensus       283 RVGk~vTP  290 (544)
T KOG0124|consen  283 RVGKCVTP  290 (544)
T ss_pred             ecccccCC
Confidence            99876543

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.66  E-value=4.7e-15  Score=122.64  Aligned_cols=166  Identities=13%  Similarity=0.173  Sum_probs=125.9

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .......|-+++||-++|++|    |.++|+.+ .|..+.+.+ +|+..|-|||+|.+.|++.+|++ .+...+..|-|.
T Consensus         6 e~~~~~~vr~rGLPwsat~~e----i~~Ff~~~-~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIE   79 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKE----ILDFFSNC-GIENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIE   79 (510)
T ss_pred             CCCcceEEEecCCCccccHHH----HHHHHhcC-ceeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEE
Confidence            345567899999999999999    66999988 577766555 69999999999999999999999 788889999999


Q ss_pred             EEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           90 IQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAP  169 (245)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (245)
                      |.-+........-               +.                                           .......
T Consensus        80 Vf~~~~~e~d~~~---------------~~-------------------------------------------~g~~s~~  101 (510)
T KOG4211|consen   80 VFTAGGAEADWVM---------------RP-------------------------------------------GGPNSSA  101 (510)
T ss_pred             EEccCCccccccc---------------cC-------------------------------------------CCCCCCC
Confidence            9776544331100               00                                           0000002


Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKE-VRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~-v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      ...+|-+++||..||++||.+||+..-.|.. |.+..+.    .|-|||.|++.+.|+.||. -|...|+-+=|.|-
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF  177 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVF  177 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEee
Confidence            4567999999999999999999998755544 4444443    6899999999999999998 46666766666553

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.66  E-value=6.4e-16  Score=129.87  Aligned_cols=80  Identities=18%  Similarity=0.414  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ..+.+|||+|||.++++++    |+++|++||.|.++++..   ++.++|||||+|.+.++|..|+..|||..+.|+.|+
T Consensus       267 ~~~~~lfV~NL~~~~~e~~----L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~  342 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETV----LWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQ  342 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHH----HHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            3455799999999999999    779999999999986553   788999999999999999999999999999999999


Q ss_pred             EEEcccc
Q 025973           90 IQYAKTK   96 (245)
Q Consensus        90 v~~~~~~   96 (245)
                      |.|...+
T Consensus       343 V~~~~~~  349 (352)
T TIGR01661       343 VSFKTNK  349 (352)
T ss_pred             EEEccCC
Confidence            9998665

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.66  E-value=5e-16  Score=99.42  Aligned_cols=68  Identities=31%  Similarity=0.536  Sum_probs=62.7

Q ss_pred             EEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        18 l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      |||+|||.++++++    |+++|+.||.|..+.+..  ++..+++|||+|.+.++|..|++.|||..+.|+.|+
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 LYVGNLPPDVTEEE----LRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHH----HHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHH----HHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            79999999999999    669999999998886665  578899999999999999999999999999999885

(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 ....

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.65  E-value=9.5e-16  Score=100.92  Aligned_cols=85  Identities=24%  Similarity=0.441  Sum_probs=78.0

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      =+++.++.|||+|||+++|.++    ++++|..||.|..|++-.+...+|.|||.|++..+|.+|+.+|+|..+.++.+.
T Consensus        13 lppevnriLyirNLp~~ITsee----mydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~   88 (124)
T KOG0114|consen   13 LPPEVNRILYIRNLPFKITSEE----MYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLV   88 (124)
T ss_pred             CChhhheeEEEecCCccccHHH----HHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEE
Confidence            3466789999999999999999    889999999999999988888899999999999999999999999999999999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |.+..+...
T Consensus        89 vlyyq~~~~   97 (124)
T KOG0114|consen   89 VLYYQPEDA   97 (124)
T ss_pred             EEecCHHHH
Confidence            999866543

>PF00076 RRM_1: RNA recognition motif

Probab=99.65  E-value=9.5e-16  Score=98.10  Aligned_cols=66  Identities=35%  Similarity=0.584  Sum_probs=62.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC----CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEE
Q 025973          174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA----KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLL  239 (245)
Q Consensus       174 l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~----~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~  239 (245)
                      |||+|||..+++++|+++|+.||.|..+.+..+    .+++|||+|.+.++|..|++.+||..++|++|+
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            799999999999999999999999999999985    268999999999999999999999999999985

(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 ....

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.62  E-value=1.4e-15  Score=109.73  Aligned_cols=75  Identities=25%  Similarity=0.401  Sum_probs=71.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..+.|||+||+..+++.+|..+|..||.+..|.+...+.|||||+|.++.+|..|+..|+|..|.|..|.|++++
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            356799999999999999999999999999999999889999999999999999999999999999999999864

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

Probab=99.62  E-value=2.7e-15  Score=130.68  Aligned_cols=138  Identities=14%  Similarity=0.189  Sum_probs=99.7

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhccc--CCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQF--GTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~--G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ....++|||+|||.++++++    |+++|+.|  |.|..|...     ++||||+|.+.++|.+|++.||+..|.|+.|+
T Consensus       230 ~~~~k~LfVgNL~~~~tee~----L~~~F~~f~~G~I~rV~~~-----rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~  300 (578)
T TIGR01648       230 MAKVKILYVRNLMTTTTEEI----IEKSFSEFKPGKVERVKKI-----RDYAFVHFEDREDAVKAMDELNGKELEGSEIE  300 (578)
T ss_pred             cccccEEEEeCCCCCCCHHH----HHHHHHhcCCCceEEEEee-----cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            34568999999999999999    66999999  999998654     47999999999999999999999999999999


Q ss_pred             EEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           90 IQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAP  169 (245)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (245)
                      |.|+++........-..- ...++......                                        .........+
T Consensus       301 V~~Akp~~~~~~~~~~rg-~gg~~~~~~~~----------------------------------------~~~~g~~~sp  339 (578)
T TIGR01648       301 VTLAKPVDKKSYVRYTRG-TGGRGKERQAA----------------------------------------RQSLGQVYDP  339 (578)
T ss_pred             EEEccCCCcccccccccc-cCCCccccccc----------------------------------------ccccCcccCc
Confidence            999976533110000000 00000000000                                        0001122234


Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCee
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFK  199 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~  199 (245)
                      .+.++++.|++...+++.+.++|..+|.+.
T Consensus       340 ~s~~~~~g~~~~~~~~~~~~~~f~~~g~~~  369 (578)
T TIGR01648       340 ASRSLAYEDYYYHPPYAPSLHFPRMPGPIR  369 (578)
T ss_pred             cccccccccccccccccchhhccccCcccc
Confidence            567899999999999999999999988764

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

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.62  E-value=1.1e-15  Score=110.21  Aligned_cols=80  Identities=20%  Similarity=0.434  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      .-+++|||+||+..+++.|    |+..|..||+|..||+-.  ...|||||+|++..+|..|+..|+|..|.|..|+|++
T Consensus         8 ~~~~kVYVGnL~~~a~k~e----LE~~F~~yG~lrsvWvAr--nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~   81 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRE----LERAFSKYGPLRSVWVAR--NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVEL   81 (195)
T ss_pred             CCCceEEeccCCCCcchHH----HHHHHHhcCcceeEEEee--cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEe
Confidence            4489999999999999999    779999999999998876  3469999999999999999999999999999999999


Q ss_pred             ccccch
Q 025973           93 AKTKSD   98 (245)
Q Consensus        93 ~~~~~~   98 (245)
                      +.....
T Consensus        82 S~G~~r   87 (195)
T KOG0107|consen   82 STGRPR   87 (195)
T ss_pred             ecCCcc
Confidence            876544

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.61  E-value=4.8e-15  Score=122.84  Aligned_cols=78  Identities=24%  Similarity=0.470  Sum_probs=72.2

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      .....++|||+|||..+|+++|+++|+.||.|.+|+|+.+.     +|||||+|.++++|..|+..|||..+.+++|+|.
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            34467789999999999999999999999999999998764     5899999999999999999999999999999999


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      ||+
T Consensus       183 ~a~  185 (346)
T TIGR01659       183 YAR  185 (346)
T ss_pred             ccc
Confidence            985

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).

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.60  E-value=4.4e-15  Score=115.73  Aligned_cols=76  Identities=21%  Similarity=0.263  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEcc
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAK   94 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~   94 (245)
                      .++|||+|||+.+++++    |+++|+.||.|..|.+..++..+|||||+|.+.++|..|+. |||..|.|+.|.|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~d----LrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERD----IKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            57999999999999999    67999999999999988777678999999999999999997 99999999999999976


Q ss_pred             c
Q 025973           95 T   95 (245)
Q Consensus        95 ~   95 (245)
                      .
T Consensus        79 ~   79 (260)
T PLN03120         79 D   79 (260)
T ss_pred             C
Confidence            4

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.60  E-value=7.4e-15  Score=114.45  Aligned_cols=73  Identities=29%  Similarity=0.307  Sum_probs=68.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++|||+|||+.+++++|+++|+.||.|.+|.|+.++  +|||||+|.++++|..|+. |||..|.|+.|.|.++.
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            4679999999999999999999999999999999874  6899999999999999996 99999999999999874

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.58  E-value=2.5e-13  Score=110.95  Aligned_cols=74  Identities=16%  Similarity=0.196  Sum_probs=66.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ..+.|||+|||..+||+.|++-|..||.|.+..++-.-+..+.|.|.++++|.+|+..|+|..+.|+.|.|.|+
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 KACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            34579999999999999999999999999998886544456799999999999999999999999999999984

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.57  E-value=2.2e-14  Score=91.86  Aligned_cols=66  Identities=35%  Similarity=0.604  Sum_probs=60.7

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEE
Q 025973          174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLL  239 (245)
Q Consensus       174 l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~  239 (245)
                      |+|+|||..+++++|.++|+.||.|..+.+..++    +++|||+|.++++|..|+..++|..|+|+.|+
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            7999999999999999999999999999999874    68999999999999999999999999999985

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 ....

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.56  E-value=2.4e-14  Score=121.10  Aligned_cols=182  Identities=21%  Similarity=0.308  Sum_probs=130.2

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeE---EEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL---EILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~---~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ...-+.++|++||...++++++    ++...||.+.   -|....+|.++||||.+|.+......|+..|||..+.+..+
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~----Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~l  361 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVK----ELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKL  361 (500)
T ss_pred             ccccchhhhccCcCccCHHHHH----HHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCcee
Confidence            3446789999999999999966    5555555554   45566678999999999999999999999999999999999


Q ss_pred             EEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           89 RIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPA  168 (245)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (245)
                      .|..+-............                                          .....+.-   .........
T Consensus       362 vvq~A~~g~~~~~~~~~~------------------------------------------~~~~~~~i---~~~~~q~~g  396 (500)
T KOG0120|consen  362 VVQRAIVGASNANVNFNI------------------------------------------SQSQVPGI---PLLMTQMAG  396 (500)
T ss_pred             EeehhhccchhccccCCc------------------------------------------cccccccc---hhhhcccCC
Confidence            998875443311100000                                          00000000   000011222


Q ss_pred             CCccEEEEcCCC--CCC-C-------HHHHHHHhccCCCeeEEEEecC-C-------CeEEEEEeCCHHHHHHHHHHhCC
Q 025973          169 PPNNILFVQNVP--HDT-T-------PMALQMFFSQFPGFKEVRMVEA-K-------PGIAFVEYGDEMQATVAMQSLQS  230 (245)
Q Consensus       169 ~~~~~l~v~nl~--~~~-t-------~~~l~~~f~~~g~v~~v~l~~~-~-------~g~afv~f~~~~~A~~A~~~l~g  230 (245)
                      .++.+|.+.|+=  ... .       .|+++.-++.||.|..|.+... .       .|..||+|.+.+++++|++.|+|
T Consensus       397 ~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~G  476 (500)
T KOG0120|consen  397 IPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTG  476 (500)
T ss_pred             CcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccC
Confidence            456677777772  211 2       2556778899999999998875 1       57899999999999999999999


Q ss_pred             CeeCCeEEEEEE
Q 025973          231 LKIGQQQLLITY  242 (245)
Q Consensus       231 ~~~~g~~i~v~~  242 (245)
                      ..|.|+++..+|
T Consensus       477 rKF~nRtVvtsY  488 (500)
T KOG0120|consen  477 RKFANRTVVASY  488 (500)
T ss_pred             ceeCCcEEEEEe
Confidence            999999999887

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.56  E-value=1.4e-14  Score=109.93  Aligned_cols=78  Identities=26%  Similarity=0.511  Sum_probs=71.9

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE---EecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i---~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      .++|-|.|||.+++|++    |+++|..||+|..|   +...+|.+||||||.|.+.++|.+|+..|||.-+..-.|+|+
T Consensus       189 ~~tvRvtNLsed~~E~d----L~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  189 EATVRVTNLSEDMREDD----LEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cceeEEecCccccChhH----HHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            56799999999999999    77999999999887   455699999999999999999999999999999999999999


Q ss_pred             Ecccc
Q 025973           92 YAKTK   96 (245)
Q Consensus        92 ~~~~~   96 (245)
                      |++++
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99875

>PF13893 RRM_5: RNA recognition motif

Probab=99.56  E-value=4.3e-14  Score=86.26  Aligned_cols=56  Identities=30%  Similarity=0.546  Sum_probs=52.4

Q ss_pred             HHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          188 LQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       188 l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      |.++|++||.|.++.+.+..+++|||+|.+.++|..|+..|||..|.|++|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999998876689999999999999999999999999999999997

(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 ....

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.56  E-value=1.1e-14  Score=99.60  Aligned_cols=73  Identities=21%  Similarity=0.330  Sum_probs=68.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      .+++|||+||...++|++|.++|+.+|.|+.|.+--++     .|||||+|.+.++|..|++.++|+.+..++|.+.|
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            56789999999999999999999999999988876654     69999999999999999999999999999999987

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.55  E-value=3e-14  Score=91.23  Aligned_cols=68  Identities=25%  Similarity=0.456  Sum_probs=59.3

Q ss_pred             EEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        18 l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      |||+|||..+++++    |.++|+.||.|..+.+..  .+..+++|||+|.+.++|..|+..+++..+.|+.|+
T Consensus         1 v~i~nlp~~~~~~~----l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEED----LRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHH----HHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHH----HHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999    669999999999886664  367899999999999999999999888999999874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.55  E-value=3.8e-14  Score=111.75  Aligned_cols=72  Identities=21%  Similarity=0.330  Sum_probs=68.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC---CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA---KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~---~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ++|+|+|||+..-+-||+.+|.+||.|.+|.|+.+   .||||||+|+++++|.+|-+.|||..+.||+|.|-.|
T Consensus        97 kRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   97 KRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             ceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            57999999999999999999999999999999985   3899999999999999999999999999999999876

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.55  E-value=4.7e-13  Score=109.40  Aligned_cols=217  Identities=18%  Similarity=0.267  Sum_probs=136.8

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhc-ccCCeEEE--EecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFK-QFGTILEI--LAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~-~~G~v~~i--~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ....+.+||+|||+++.=.+||    ++|. ..|.|..|  ....+|+.+|+|.|+|+++|.+++|++.||...+.||+|
T Consensus        41 ~~r~R~vfItNIpyd~rWqdLK----dLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l  116 (608)
T KOG4212|consen   41 AARDRSVFITNIPYDYRWQDLK----DLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGREL  116 (608)
T ss_pred             ccccceEEEecCcchhhhHhHH----HHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceE
Confidence            3445669999999999999955    7775 45888877  445689999999999999999999999999999999999


Q ss_pred             EEEEccccchH----hhhcCC-Ccccch----hhhhhhhhh---------hhccchhhHhhhcCCC--------CccccC
Q 025973           89 RIQYAKTKSDI----IAKADG-TFVPRE----RRKRHEEKG---------KKRKDQHDANQAGMGL--------NPAYAG  142 (245)
Q Consensus        89 ~v~~~~~~~~~----~~~~~~-~~~~~~----~~~~~~~~~---------~~~~~~~~~~~~~~~~--------~~~~~~  142 (245)
                      .|.--......    +.+.-+ .+....    .+...+.--         .+..+.... ......        +....+
T Consensus       117 ~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~-sr~~~t~t~~~~~~~~~~~~  195 (608)
T KOG4212|consen  117 VVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRL-SRRNNTNTMSNDYNNSSNYN  195 (608)
T ss_pred             EEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCccccccc-ccccCccccccccccchhhh
Confidence            99764332211    000000 000000    000000000         000000000 000000        001111


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCH
Q 025973          143 AYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDE  218 (245)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~  218 (245)
                      ..+..+.+..+. +        .-..|....+||.||...+....|.+.|.--|.|.+|.+--++    +|++.++|.++
T Consensus       196 lfgl~~~Flr~~-h--------~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hp  266 (608)
T KOG4212|consen  196 LFGLSASFLRSL-H--------IFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHP  266 (608)
T ss_pred             cccchhhhhhhc-c--------CCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecch
Confidence            111111111100 0        0112345569999999999999999999999999998887765    78999999999


Q ss_pred             HHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          219 MQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       219 ~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      -+|..|+..+++.-++.++..+.+
T Consensus       267 veavqaIsml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  267 VEAVQAISMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             HHHHHHHHhhccCCCccccceeec
Confidence            999999999998776777666544

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.53  E-value=5.2e-14  Score=108.03  Aligned_cols=77  Identities=21%  Similarity=0.248  Sum_probs=71.6

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      .+.+|||+||++.+++++    |+++|+.||.|.+|.+.+++..+++|||+|.+.++|..|+. |+|..|.++.|.|..+
T Consensus         4 ~g~TV~V~NLS~~tTE~d----LrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~   78 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKD----VYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRW   78 (243)
T ss_pred             CceEEEEecCCCCCCHHH----HHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeC
Confidence            467999999999999999    77999999999999999888888999999999999999997 9999999999999886


Q ss_pred             cc
Q 025973           94 KT   95 (245)
Q Consensus        94 ~~   95 (245)
                      ..
T Consensus        79 ~~   80 (243)
T PLN03121         79 GQ   80 (243)
T ss_pred             cc
Confidence            53

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.53  E-value=2.4e-14  Score=97.98  Aligned_cols=83  Identities=20%  Similarity=0.329  Sum_probs=72.6

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ...+++|||+||+..++|++    |+++|+.+|.|..|++-   .+.+.-|||||+|-+.++|..|++.+++..+..++|
T Consensus        33 ~r~S~tvyVgNlSfyttEEq----iyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~i  108 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQ----IYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPI  108 (153)
T ss_pred             HhhcceEEEeeeeeeecHHH----HHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccce
Confidence            45689999999999999999    89999999999988543   244567999999999999999999999999999999


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      ++.|-....+
T Consensus       109 r~D~D~GF~e  118 (153)
T KOG0121|consen  109 RIDWDAGFVE  118 (153)
T ss_pred             eeeccccchh
Confidence            9998654433

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.53  E-value=9.4e-14  Score=91.58  Aligned_cols=73  Identities=27%  Similarity=0.537  Sum_probs=68.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      .+..|||+|||+++|.++.-++|..||.|..|++-..+  +|.|||.|.+..+|.+|+++|+|+.+.++-|.|-|
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vly   91 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLY   91 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEe
Confidence            46789999999999999999999999999999987654  79999999999999999999999999999999876

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.52  E-value=4.1e-14  Score=111.60  Aligned_cols=81  Identities=17%  Similarity=0.355  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec-CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF-KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~-~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ..--++|||+|||+...+-|    |+.+|++||.|++|-+. ...-+|||+||.|++.+||.+|-++|||..+.||+|.|
T Consensus        93 ~~~pkRLhVSNIPFrFRdpD----L~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEV  168 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPD----LRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEV  168 (376)
T ss_pred             CCCCceeEeecCCccccCcc----HHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEE
Confidence            33458999999999999999    77999999999988433 44458999999999999999999999999999999999


Q ss_pred             EEcccc
Q 025973           91 QYAKTK   96 (245)
Q Consensus        91 ~~~~~~   96 (245)
                      ..+..+
T Consensus       169 n~ATar  174 (376)
T KOG0125|consen  169 NNATAR  174 (376)
T ss_pred             eccchh
Confidence            998765

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.52  E-value=1.4e-13  Score=111.42  Aligned_cols=143  Identities=24%  Similarity=0.309  Sum_probs=105.3

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      .++|||+|||.++++++    |+.+|..||.|..|.+..   ++.++|+|||.|.+.++|..|+..+++..|.|+.|.|.
T Consensus       115 ~~~l~v~nL~~~~~~~~----l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~  190 (306)
T COG0724         115 NNTLFVGNLPYDVTEED----LRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQ  190 (306)
T ss_pred             CceEEEeCCCCCCCHHH----HHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEee
Confidence            69999999999999999    779999999998775543   68899999999999999999999999999999999999


Q ss_pred             Eccc-cchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           92 YAKT-KSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP  170 (245)
Q Consensus        92 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (245)
                      ++.. ......   ....     .......                      .                ...........
T Consensus       191 ~~~~~~~~~~~---~~~~-----~~~~~~~----------------------~----------------~~~~~~~~~~~  224 (306)
T COG0724         191 KAQPASQPRSE---LSNN-----LDASFAK----------------------K----------------LSRGKALLLEK  224 (306)
T ss_pred             ccccccccccc---cccc-----cchhhhc----------------------c----------------ccccccccccc
Confidence            9654 000000   0000     0000000                      0                00001112235


Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK  207 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~  207 (245)
                      ...+++.|++..++..++...|..+|.+....+....
T Consensus       225 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (306)
T COG0724         225 SDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSK  261 (306)
T ss_pred             cceeeccccccccchhHHHHhccccccceeeeccCCC
Confidence            5679999999999999999999999999766666543

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.52  E-value=4.8e-13  Score=107.32  Aligned_cols=172  Identities=20%  Similarity=0.213  Sum_probs=131.2

Q ss_pred             cccccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHc--CC
Q 025973            4 EVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQ--GF   81 (245)
Q Consensus         4 ~~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~--~~   81 (245)
                      |-..+.-++.++-.|+|++|-..++|.+    |.+-.+.||+|..+..+..   +..|.|+|++++.|..++...-  ..
T Consensus        20 e~~~dphk~~~spvvhvr~l~~~v~ead----l~eal~~fG~i~yvt~~P~---~r~alvefedi~~akn~Vnfaa~n~i   92 (494)
T KOG1456|consen   20 EDNADPHKPNPSPVVHVRGLHQGVVEAD----LVEALSNFGPIAYVTCMPH---KRQALVEFEDIEGAKNCVNFAADNQI   92 (494)
T ss_pred             ccCCCCCCCCCCceEEEeccccccchhH----HHHHHhcCCceEEEEeccc---cceeeeeeccccchhhheehhccCcc
Confidence            3344556688899999999999999999    5577789999988876643   4689999999999999987432  23


Q ss_pred             ccCCceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCC
Q 025973           82 PFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKS  161 (245)
Q Consensus        82 ~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (245)
                      .+.|..-.+.++..+.....                                                            
T Consensus        93 ~i~gq~Al~NyStsq~i~R~------------------------------------------------------------  112 (494)
T KOG1456|consen   93 YIAGQQALFNYSTSQCIERP------------------------------------------------------------  112 (494)
T ss_pred             cccCchhhcccchhhhhccC------------------------------------------------------------
Confidence            33455555555433222100                                                            


Q ss_pred             CCCCCCCCCccEEEEcCCC--CCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC--CeE
Q 025973          162 VIPEAPAPPNNILFVQNVP--HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG--QQQ  237 (245)
Q Consensus       162 ~~~~~~~~~~~~l~v~nl~--~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~--g~~  237 (245)
                        .+....++++|.+.=|.  ..+|-+-|..++.+.|+|.+|.+++..-=.|.|+|.+.+.|++|..+|||.-|+  --+
T Consensus       113 --g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCT  190 (494)
T KOG1456|consen  113 --GDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCT  190 (494)
T ss_pred             --CCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhccccccccccee
Confidence              11222467777766553  788999999999999999999998864237999999999999999999999987  778


Q ss_pred             EEEEEec
Q 025973          238 LLITYAK  244 (245)
Q Consensus       238 i~v~~ak  244 (245)
                      |+|+|||
T Consensus       191 LKIeyAk  197 (494)
T KOG1456|consen  191 LKIEYAK  197 (494)
T ss_pred             EEEEecC
Confidence            9999997

>smart00362 RRM_2 RNA recognition motif

Probab=99.50  E-value=2.2e-13  Score=86.97  Aligned_cols=69  Identities=35%  Similarity=0.580  Sum_probs=64.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      +|+|+|||..+++++|+++|+.||.|.++.+..++   +|+|||+|.+.++|..|+..++|..+.|++|.|+
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            48999999999999999999999999999988765   6899999999999999999999999999999874

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.50  E-value=2.2e-13  Score=104.66  Aligned_cols=73  Identities=22%  Similarity=0.253  Sum_probs=67.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.+|+|+||+..+|+++|+++|+.||.|.+|.|+.+.  +++|||+|.++++|..|+. |||..|.+++|.|..+
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~   78 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRW   78 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeC
Confidence            45789999999999999999999999999999999875  5799999999999999995 9999999999999864

>PLN03213 repressor of silencing 3; Provisional

Probab=99.49  E-value=1.1e-13  Score=114.78  Aligned_cols=80  Identities=20%  Similarity=0.255  Sum_probs=71.7

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCH--HHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDV--ASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~--~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ...+.+||||||++.+++++    |..+|+.||.|..|.+.+ +|  ||||||+|.+.  .++.+|+..|||..+.|+.|
T Consensus         7 ~~~gMRIYVGNLSydVTEDD----LravFSeFGsVkdVEIpRETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~L   80 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDD----LLKIFSPMGTVDAVEFVRTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRL   80 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEecccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCcee
Confidence            44568999999999999999    779999999999987665 55  99999999987  78999999999999999999


Q ss_pred             EEEEccccc
Q 025973           89 RIQYAKTKS   97 (245)
Q Consensus        89 ~v~~~~~~~   97 (245)
                      +|.-+++.-
T Consensus        81 KVNKAKP~Y   89 (759)
T PLN03213         81 RLEKAKEHY   89 (759)
T ss_pred             EEeeccHHH
Confidence            999997653

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.48  E-value=5.5e-13  Score=101.30  Aligned_cols=75  Identities=23%  Similarity=0.339  Sum_probs=71.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++|-|.||+..+++.+|+++|.+||.|.++.|.+++     +|||||.|.+.++|++|+..|||+-+..-.|+|.|||
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            45679999999999999999999999999999999986     7999999999999999999999999999999999997

>PLN03213 repressor of silencing 3; Provisional

Probab=99.48  E-value=2.3e-13  Score=112.85  Aligned_cols=75  Identities=17%  Similarity=0.185  Sum_probs=69.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-CeEEEEEeCCH--HHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-PGIAFVEYGDE--MQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-~g~afv~f~~~--~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+..|||+||+..+++++|..+|+.||.|.+|.|++.. +|||||+|.+.  .++.+|+..|||..+.|+.|+|.-||
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            45679999999999999999999999999999999743 79999999987  68999999999999999999999987

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.48  E-value=1.4e-13  Score=103.76  Aligned_cols=76  Identities=28%  Similarity=0.472  Sum_probs=70.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHH----HhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          170 PNNILFVQNVPHDTTPMALQM----FFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~----~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ++.+|||.||++.+..++|+.    +|+.||.|.+|...+..  +|.|||.|.+.+.|..|+.+|+|+.|.|++++|+||
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA   87 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYA   87 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecc
Confidence            445899999999999999887    99999999999988764  799999999999999999999999999999999999


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus        88 ~s   89 (221)
T KOG4206|consen   88 KS   89 (221)
T ss_pred             cC
Confidence            73

>PF13893 RRM_5: RNA recognition motif

Probab=99.47  E-value=3.2e-13  Score=82.38  Aligned_cols=56  Identities=34%  Similarity=0.683  Sum_probs=50.7

Q ss_pred             HHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           36 LHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        36 l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      |+++|++||.|..|.+.++.  +++|||+|.+.++|..|++.|||..+.|++|+|.||
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            56899999999999887655  689999999999999999999999999999999985

(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 ....

>smart00362 RRM_2 RNA recognition motif

Probab=99.46  E-value=4.5e-13  Score=85.53  Aligned_cols=70  Identities=30%  Similarity=0.528  Sum_probs=62.9

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCC-CCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKT-LKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~-~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      +|||+|||..+++++    |+++|..||.|..+.+..+ +.++|+|||+|.+.++|..|+..+++..+.|+.+.|
T Consensus         1 ~v~i~~l~~~~~~~~----l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEED----LKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHH----HHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            589999999999999    6699999999999876653 567799999999999999999999999999998876

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.45  E-value=8e-15  Score=106.37  Aligned_cols=76  Identities=30%  Similarity=0.495  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEE---ecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEIL---AFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~---~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      -+.-|||+|||++.||.|    |.-+|++||.|..|.   +..||+++||||+.|++..+-..|+..|||..+.||+|+|
T Consensus        34 dsA~Iyiggl~~~LtEgD----il~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirV  109 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGD----ILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRV  109 (219)
T ss_pred             cceEEEECCCcccccCCc----EEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEe
Confidence            467899999999999999    559999999998874   4459999999999999999999999999999999999999


Q ss_pred             EEc
Q 025973           91 QYA   93 (245)
Q Consensus        91 ~~~   93 (245)
                      ...
T Consensus       110 DHv  112 (219)
T KOG0126|consen  110 DHV  112 (219)
T ss_pred             eec
Confidence            874

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.44  E-value=1.5e-13  Score=101.87  Aligned_cols=73  Identities=23%  Similarity=0.405  Sum_probs=69.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..|.|-||...++.++|..+|.+||.|-+|.|..++     +|||||.|.+-.+|+.|++.|+|..+.|+.|.|++|+
T Consensus        14 ~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   14 TSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             eeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            459999999999999999999999999999999875     7999999999999999999999999999999999986

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.44  E-value=5.3e-13  Score=104.11  Aligned_cols=79  Identities=22%  Similarity=0.361  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .-|-+||||+-|+++++|+.    |+..|+.||+|..|++.   .+|+++|||||+|+...+...|++..+|..|.|+.|
T Consensus        98 gDPy~TLFv~RLnydT~Esk----LrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri  173 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESK----LRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRI  173 (335)
T ss_pred             CCccceeeeeeccccccHHH----HHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEE
Confidence            45789999999999999999    66999999999988655   489999999999999999999999999999999999


Q ss_pred             EEEEcc
Q 025973           89 RIQYAK   94 (245)
Q Consensus        89 ~v~~~~   94 (245)
                      .|.+-.
T Consensus       174 ~VDvER  179 (335)
T KOG0113|consen  174 LVDVER  179 (335)
T ss_pred             EEEecc
Confidence            998853

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.43  E-value=1.3e-12  Score=100.23  Aligned_cols=75  Identities=24%  Similarity=0.469  Sum_probs=71.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..+.|+|--||..+|+++++.+|+..|+|.+|+|++|+     -||+||.|.++++|.+|+..|||..+..|+|+|+||+
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            44569999999999999999999999999999999987     4899999999999999999999999999999999996

>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=2.2e-12  Score=82.75  Aligned_cols=70  Identities=39%  Similarity=0.647  Sum_probs=65.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      +|+|+|||..+++++|.++|+.||.|..+.+..++    +++|||+|.+.++|..|+..+++..+.|+++.|.+
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            38999999999999999999999999999999865    68999999999999999999999999999999875

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).

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.41  E-value=2.8e-14  Score=103.60  Aligned_cols=73  Identities=21%  Similarity=0.427  Sum_probs=69.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      .+..|||+|||..+||.||..+||+||.|.+|.|++++     +||||+.|.+..+...|+..|||..|.||.|+|..
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            45679999999999999999999999999999999975     79999999999999999999999999999999975

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.41  E-value=4.7e-13  Score=101.24  Aligned_cols=75  Identities=24%  Similarity=0.351  Sum_probs=64.5

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE---EecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i---~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      -++|||+||+-.+..++    |+++|++||.|++.   .+..+|++|||+||.|.+.++|.+|.+. -+-.|.||+-.|.
T Consensus        12 ~TKifVggL~w~T~~~~----l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcn   86 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKET----LRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCN   86 (247)
T ss_pred             EEEEEEcCcccccchHH----HHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccc
Confidence            47899999999999999    77999999999984   3445899999999999999999999994 3345789988888


Q ss_pred             Ecc
Q 025973           92 YAK   94 (245)
Q Consensus        92 ~~~   94 (245)
                      .+.
T Consensus        87 lA~   89 (247)
T KOG0149|consen   87 LAS   89 (247)
T ss_pred             hhh
Confidence            764

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.40  E-value=5.2e-13  Score=112.44  Aligned_cols=79  Identities=24%  Similarity=0.469  Sum_probs=72.7

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEE---ecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEIL---AFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~---~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      +.|||||+|+++++++    |..+|+..|.|.+++   +..+|..+||||++|.+.++|..|++.|||..+.|++|+|.|
T Consensus        19 ~~v~vgnip~~~se~~----l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~   94 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQ----LLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNY   94 (435)
T ss_pred             cceEecCCCCcccHHH----HHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeec
Confidence            8999999999999999    779999999999874   446899999999999999999999999999999999999999


Q ss_pred             ccccch
Q 025973           93 AKTKSD   98 (245)
Q Consensus        93 ~~~~~~   98 (245)
                      +.....
T Consensus        95 ~~~~~~  100 (435)
T KOG0108|consen   95 ASNRKN  100 (435)
T ss_pred             ccccch
Confidence            875544

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.40  E-value=5.4e-13  Score=98.89  Aligned_cols=81  Identities=23%  Similarity=0.464  Sum_probs=74.0

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      +++..-..|.|-||.+-++.++    |+.+|+.||.|-+|.+.+   ++.++|||||.|....+|+.|+.+|+|..+.|+
T Consensus         8 Pdv~gm~SLkVdNLTyRTspd~----LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgR   83 (256)
T KOG4207|consen    8 PDVEGMTSLKVDNLTYRTSPDD----LRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGR   83 (256)
T ss_pred             CCcccceeEEecceeccCCHHH----HHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccc
Confidence            4555678899999999999999    779999999999997765   778999999999999999999999999999999


Q ss_pred             eEEEEEcc
Q 025973           87 PMRIQYAK   94 (245)
Q Consensus        87 ~i~v~~~~   94 (245)
                      .|.|+++.
T Consensus        84 elrVq~ar   91 (256)
T KOG4207|consen   84 ELRVQMAR   91 (256)
T ss_pred             eeeehhhh
Confidence            99999875

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.39  E-value=8.6e-13  Score=91.27  Aligned_cols=74  Identities=22%  Similarity=0.370  Sum_probs=69.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+-.|||.++-...++++|.+.|.-||.|+++.|--++     +|||+|+|.+..+|+.|+..+||..+-|.+|.|.|+
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            34579999999999999999999999999999998876     799999999999999999999999999999999996

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.38  E-value=8.4e-13  Score=91.30  Aligned_cols=77  Identities=19%  Similarity=0.381  Sum_probs=70.6

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ++-.|||+++...++|++    +.+.|..||.|..|++.   ++|-.||||+|+|...+.|++|+..+||..+.|..|.|
T Consensus        71 EGwIi~VtgvHeEatEed----i~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~V  146 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEED----IHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSV  146 (170)
T ss_pred             eeEEEEEeccCcchhHHH----HHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeE
Confidence            356799999999999999    77999999999998544   68899999999999999999999999999999999999


Q ss_pred             EEcc
Q 025973           91 QYAK   94 (245)
Q Consensus        91 ~~~~   94 (245)
                      .|+-
T Consensus       147 Dw~F  150 (170)
T KOG0130|consen  147 DWCF  150 (170)
T ss_pred             EEEE
Confidence            9973

>smart00360 RRM RNA recognition motif

Probab=99.38  E-value=3.1e-12  Score=81.27  Aligned_cols=66  Identities=35%  Similarity=0.564  Sum_probs=61.0

Q ss_pred             EcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          176 VQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       176 v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      |+|||..+++++|+++|+.||.|..+.+..++     +|+|||+|.+.++|..|+..+++..+.|++|.|.
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            57999999999999999999999999988864     4899999999999999999999999999999873

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.37  E-value=4.8e-12  Score=98.83  Aligned_cols=75  Identities=29%  Similarity=0.507  Sum_probs=70.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .|-+||||.-|+..++|+.|+..|+.||.|+.|.|+.++     +|||||+|.++-+..+|..+.+|..|.|+.|.|.+-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            356789999999999999999999999999999999974     799999999999999999999999999999999874

>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=99.36  E-value=5.9e-12  Score=80.72  Aligned_cols=72  Identities=28%  Similarity=0.576  Sum_probs=63.5

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCC--CeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTL--KHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~--~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      +|+|+|||..+++++    |.++|+.+|.|..+.+....  ..+++|||+|.+.++|..|+..+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~----i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEED----LRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHH----HHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            489999999999999    66999999999988766533  4579999999999999999999999999999998864

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).

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.36  E-value=6.8e-13  Score=99.25  Aligned_cols=81  Identities=28%  Similarity=0.557  Sum_probs=73.8

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      -..++|||++|..+++|.-    |...|-.||.|..|.+.   .+.+.+|||||+|.-.|+|..|+..||+..+.||+|+
T Consensus         8 ~~KrtlYVGGladeVtekv----LhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~Grtir   83 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKV----LHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIR   83 (298)
T ss_pred             ccceeEEeccchHHHHHHH----HHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEE
Confidence            3468999999999999999    77999999999998654   4788999999999999999999999999999999999


Q ss_pred             EEEccccc
Q 025973           90 IQYAKTKS   97 (245)
Q Consensus        90 v~~~~~~~   97 (245)
                      |.++++..
T Consensus        84 VN~AkP~k   91 (298)
T KOG0111|consen   84 VNLAKPEK   91 (298)
T ss_pred             EeecCCcc
Confidence            99998754

>smart00360 RRM RNA recognition motif

Probab=99.35  E-value=4.2e-12  Score=80.64  Aligned_cols=67  Identities=28%  Similarity=0.516  Sum_probs=59.9

Q ss_pred             EcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           20 INNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        20 V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      |+|||..+++++    |.++|+.||.|..+.+..   ++.++|+|||+|.+.++|..|+..+++..+.|+.++|
T Consensus         1 i~~l~~~~~~~~----l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEE----LRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHH----HHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            689999999999    669999999999886654   4667899999999999999999999999999998876

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.35  E-value=4.4e-12  Score=107.58  Aligned_cols=188  Identities=18%  Similarity=0.317  Sum_probs=131.3

Q ss_pred             cccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhccc-------C-CeEEEEecCCCCeeeEEEEEecCHHHHHHHHHH
Q 025973            6 ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQF-------G-TILEILAFKTLKHKGQAWLVFKDVASATAAVEK   77 (245)
Q Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~-------G-~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~   77 (245)
                      ...+.....+++++|+++|+.++++++..+....+..-       | .+..+.+.   ..+++||++|.+.+.|..|+. 
T Consensus       166 ~~~~~~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n---~~~nfa~ie~~s~~~at~~~~-  241 (500)
T KOG0120|consen  166 PMDSQATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLN---LEKNFAFIEFRSISEATEAMA-  241 (500)
T ss_pred             ccCcchhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeec---ccccceeEEecCCCchhhhhc-
Confidence            34455567789999999999999999553333332211       1 24444443   456899999999999999999 


Q ss_pred             HcCCccCCceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCC
Q 025973           78 MQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPG  157 (245)
Q Consensus        78 l~~~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (245)
                      +++..+.|..+++.-.........                                      .....+..     .+...
T Consensus       242 ~~~~~f~g~~~~~~r~~d~~~~p~--------------------------------------~~~~~~~~-----~~~~~  278 (500)
T KOG0120|consen  242 LDGIIFEGRPLKIRRPHDYQPVPG--------------------------------------ITLSPSQL-----GKVGL  278 (500)
T ss_pred             ccchhhCCCCceecccccccCCcc--------------------------------------chhhhccc-----cccCC
Confidence            899999999887744221111000                                      00000000     00000


Q ss_pred             CCCCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCe
Q 025973          158 GAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLK  232 (245)
Q Consensus       158 ~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~  232 (245)
                        ....+... ...+.++|+|||...++.++.++...||.++...++.+.     +||||++|.++..+..|+..|||..
T Consensus       279 --~~~~t~~~-~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~  355 (500)
T KOG0120|consen  279 --LPASTDVP-DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQ  355 (500)
T ss_pred             --cccccCcc-cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhh
Confidence              00001111 123459999999999999999999999999888888754     7999999999999999999999999


Q ss_pred             eCCeEEEEEEe
Q 025973          233 IGQQQLLITYA  243 (245)
Q Consensus       233 ~~g~~i~v~~a  243 (245)
                      +++++|.|+.|
T Consensus       356 lgd~~lvvq~A  366 (500)
T KOG0120|consen  356 LGDKKLVVQRA  366 (500)
T ss_pred             hcCceeEeehh
Confidence            99999999986

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.33  E-value=2.4e-12  Score=93.70  Aligned_cols=75  Identities=20%  Similarity=0.305  Sum_probs=69.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+|||+||+..++++.|+++|-+.|.|.++++.+++     .||||++|.++++|.-|+..||.-.++||+|+|.-|.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            45689999999999999999999999999999999875     6999999999999999999999888999999998763

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.32  E-value=1.1e-12  Score=98.07  Aligned_cols=75  Identities=20%  Similarity=0.381  Sum_probs=70.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..++|||++|...+++.-|...|=+||.|.+|.+.-+-     +|||||+|.-.++|.+|+..||+..+.||+|+|-|||
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            45789999999999999999999999999999998752     7999999999999999999999999999999999996

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.32  E-value=3.9e-12  Score=92.77  Aligned_cols=75  Identities=20%  Similarity=0.407  Sum_probs=68.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEec--CCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE--AKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~--~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+..|||+|||..+-+.+|.++|.+||.|..|.|-.  ....||||+|.++.+|.-|+.--+|..+.|..|+|.|++
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            456799999999999999999999999998887754  335799999999999999999999999999999999985

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.31  E-value=6.4e-12  Score=103.11  Aligned_cols=87  Identities=22%  Similarity=0.412  Sum_probs=74.0

Q ss_pred             ccccccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCc
Q 025973            3 PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFP   82 (245)
Q Consensus         3 p~~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~   82 (245)
                      |+...+...-..-+.|||+||+.++|++.    |..+|+.||.|+.|...++     ||||+|.+-++|.+|++.+||..
T Consensus       247 p~~e~ded~ms~VKvLYVRNL~~~tTeE~----lk~~F~~~G~veRVkk~rD-----YaFVHf~eR~davkAm~~~ngke  317 (506)
T KOG0117|consen  247 PEEEPDEDTMSKVKVLYVRNLMESTTEET----LKKLFNEFGKVERVKKPRD-----YAFVHFAEREDAVKAMKETNGKE  317 (506)
T ss_pred             cccCCChhhhhheeeeeeeccchhhhHHH----HHHHHHhccceEEeecccc-----eeEEeecchHHHHHHHHHhcCce
Confidence            43333333344568899999999999999    5599999999999977654     99999999999999999999999


Q ss_pred             cCCceEEEEEccccch
Q 025973           83 FYDKPMRIQYAKTKSD   98 (245)
Q Consensus        83 ~~g~~i~v~~~~~~~~   98 (245)
                      +.|..|.|.++++...
T Consensus       318 ldG~~iEvtLAKP~~k  333 (506)
T KOG0117|consen  318 LDGSPIEVTLAKPVDK  333 (506)
T ss_pred             ecCceEEEEecCChhh
Confidence            9999999999987655

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.29  E-value=9.4e-12  Score=104.92  Aligned_cols=73  Identities=27%  Similarity=0.454  Sum_probs=70.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..+||+|+|+.+++++|.++|+..|.|.+++++.|+     +||||++|.+.++|.+|++.|||..+.|++|+|.|+.
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 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYAS   96 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccc
Confidence            679999999999999999999999999999999875     7999999999999999999999999999999999985

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.28  E-value=2e-11  Score=98.69  Aligned_cols=74  Identities=36%  Similarity=0.563  Sum_probs=69.6

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..+|||+|||..+++++|.++|..||.|..+.+..++     +|+|||+|.++++|..|+..++|..|.|++|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            5789999999999999999999999999999988864     7999999999999999999999999999999999863

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.28  E-value=8.5e-12  Score=94.51  Aligned_cols=72  Identities=25%  Similarity=0.330  Sum_probs=64.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      -+.|||++|+-.+..++|+++|.+||+|.+..++.|+     ||||||+|.+.++|.+|++.- .-.|+||+-.|-+|
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnlA   88 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNLA   88 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccchh
Confidence            4579999999999999999999999999999999875     899999999999999999864 46788888777664

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.27  E-value=3.1e-12  Score=112.88  Aligned_cols=159  Identities=15%  Similarity=0.249  Sum_probs=133.8

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCC--CCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKT--LKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~--~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      -+...+++||++||+..+++.+    |+..|..+|.|.+|.+...  +...-||||.|.+...+-.|...+.+..|....
T Consensus       367 DD~~atrTLf~Gnl~~kl~ese----iR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~  442 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESE----IRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGT  442 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhh----hhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCc
Confidence            3467799999999999999999    6799999999999877654  333459999999999999998888887766555


Q ss_pred             EEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           88 MRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAP  167 (245)
Q Consensus        88 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (245)
                      +++.+...                                                                       .
T Consensus       443 ~r~glG~~-----------------------------------------------------------------------k  451 (975)
T KOG0112|consen  443 HRIGLGQP-----------------------------------------------------------------------K  451 (975)
T ss_pred             cccccccc-----------------------------------------------------------------------c
Confidence            54444221                                                                       1


Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC--CeEEEEEEec
Q 025973          168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG--QQQLLITYAK  244 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~--g~~i~v~~ak  244 (245)
                      ..+++.+++++|+.-+....|...|..||.|..|.+-.+. .||++.|.+...|++|+..|-|+.|+  .++|+|.||+
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq-~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~  529 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQ-PYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLAS  529 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCC-cceeeecccCccchhhHHHHhcCcCCCCCccccccccc
Confidence            1255679999999999999999999999999999988877 59999999999999999999999998  7889999985

>smart00361 RRM_1 RNA recognition motif

Probab=99.25  E-value=4.7e-11  Score=76.18  Aligned_cols=62  Identities=15%  Similarity=0.306  Sum_probs=50.7

Q ss_pred             hHHHHHHHHHhhcccCCeEEEE--ec-C-C--CCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           29 IDQLKQSLHAVFKQFGTILEIL--AF-K-T--LKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        29 ~~~l~~~l~~~F~~~G~v~~i~--~~-~-~--~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      +++|++.+...++.||.|..|.  .. + +  +.++|+|||.|.+.++|.+|+..|||..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            4675555555555999999873  22 2 3  788999999999999999999999999999999876

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.22  E-value=1.9e-11  Score=95.29  Aligned_cols=80  Identities=19%  Similarity=0.378  Sum_probs=72.3

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      +.++..++++|+|+||.+.++.+|    |+..|+.||+|.++.+.     ++|+||.|.-.++|..|++.|++..|.|++
T Consensus        71 SksKsk~stkl~vgNis~tctn~E----lRa~fe~ygpviecdiv-----kdy~fvh~d~~eda~~air~l~~~~~~gk~  141 (346)
T KOG0109|consen   71 SKSKSKASTKLHVGNISPTCTNQE----LRAKFEKYGPVIECDIV-----KDYAFVHFDRAEDAVEAIRGLDNTEFQGKR  141 (346)
T ss_pred             ccccCCCccccccCCCCccccCHH----HhhhhcccCCceeeeee-----cceeEEEEeeccchHHHHhcccccccccce
Confidence            344566899999999999999999    77999999999999776     479999999999999999999999999999


Q ss_pred             EEEEEcccc
Q 025973           88 MRIQYAKTK   96 (245)
Q Consensus        88 i~v~~~~~~   96 (245)
                      ++|..+..+
T Consensus       142 m~vq~stsr  150 (346)
T KOG0109|consen  142 MHVQLSTSR  150 (346)
T ss_pred             eeeeeeccc
Confidence            999998654

>smart00361 RRM_1 RNA recognition motif

Probab=99.21  E-value=8.6e-11  Score=74.94  Aligned_cols=57  Identities=14%  Similarity=0.193  Sum_probs=49.2

Q ss_pred             HHHHHHHhc----cCCCeeEEE-EecC-------CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          185 PMALQMFFS----QFPGFKEVR-MVEA-------KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       185 ~~~l~~~f~----~~g~v~~v~-l~~~-------~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      +++|+++|+    .||.|.++. ++.+       .+|+|||+|.++++|..|+..|||..+.|+.|.++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578888898    999998885 3321       27999999999999999999999999999999873

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.20  E-value=1e-10  Score=93.31  Aligned_cols=77  Identities=19%  Similarity=0.350  Sum_probs=67.8

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHh-CCCeeCCeEEEEEEec
Q 025973          167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL-QSLKIGQQQLLITYAK  244 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l-~g~~~~g~~i~v~~ak  244 (245)
                      .+...++|||++|.+.+++.+|+++|.+||.|..|.+...+ ++|||+|.+.+.|..|.... |...|.|.+|+|.|++
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-GCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc-ccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            34456789999999999999999999999999999999887 79999999999999777655 5577889999999975

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.19  E-value=1.2e-10  Score=94.04  Aligned_cols=181  Identities=15%  Similarity=0.197  Sum_probs=113.3

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhccc----CCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQF----GTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~----G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      .|-+++||+++++.+    +..+|...    |..+.|.+.  .+|+..|-|||.|..+++|+.|+. -|...+.-|.|.+
T Consensus       163 ivRmRGLPfdat~~d----Vv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~-khrq~iGqRYIEl  237 (508)
T KOG1365|consen  163 IVRMRGLPFDATALD----VVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALR-KHRQNIGQRYIEL  237 (508)
T ss_pred             EEEecCCCCCcchHH----HHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHH-HHHHHHhHHHHHH
Confidence            466789999999999    66888633    233445433  388889999999999999999999 4666565555544


Q ss_pred             EEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           91 QYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP  170 (245)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (245)
                      ..+....-...                             ....... +.....+.++      .+..+....+  ...+
T Consensus       238 FRSTaaEvqqv-----------------------------lnr~~s~-pLi~~~~sp~------~p~~p~~~~p--~~~~  279 (508)
T KOG1365|consen  238 FRSTAAEVQQV-----------------------------LNREVSE-PLIPGLTSPL------LPGGPARLVP--PTRS  279 (508)
T ss_pred             HHHhHHHHHHH-----------------------------HHhhccc-cccCCCCCCC------CCCCccccCC--CCCC
Confidence            22221111000                             0000000 0000000000      0000111111  1234


Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCC-eeE--EEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEE
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPG-FKE--VRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLI  240 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~-v~~--v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v  240 (245)
                      ..+|-+++||...+.+||.+||..|.. |..  |.++.+.    .|-|||+|.+.++|.+|....+.+....+-|.|
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEv  356 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEV  356 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEE
Confidence            568999999999999999999988764 333  5555542    689999999999999999988776665666655

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.19  E-value=6.6e-10  Score=93.18  Aligned_cols=156  Identities=22%  Similarity=0.312  Sum_probs=106.9

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---C--CCeee---EEEEEecCHHHHHHHHHHHcCCcc
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---T--LKHKG---QAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~--~~~kg---~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      ..-+++||||+||.+++|++    |...|..||.+..=+-.+   .  -..+|   |+|+.|+++.+.+.-+.+...   
T Consensus       256 ~~~S~KVFvGGlp~dise~~----i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---  328 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQ----INASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---  328 (520)
T ss_pred             cccccceeecCCCccccHHH----HHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---
Confidence            34478999999999999999    669999999885422211   1  12345   999999999888877765432   


Q ss_pred             CCc--eEEEEEccccchHh-----hhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCC
Q 025973           84 YDK--PMRIQYAKTKSDII-----AKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYP  156 (245)
Q Consensus        84 ~g~--~i~v~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (245)
                      ...  .++|.-...+....     ...+..|...                                              
T Consensus       329 ~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d----------------------------------------------  362 (520)
T KOG0129|consen  329 GEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLD----------------------------------------------  362 (520)
T ss_pred             cccceEEEEecCcccccceeEEeeEeccchhhhc----------------------------------------------
Confidence            322  23232221111100     0000000000                                              


Q ss_pred             CCCCCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHhc-cCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHH
Q 025973          157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFS-QFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQS  227 (245)
Q Consensus       157 ~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~-~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~  227 (245)
                             ......+.+||||++||..++.++|..+|. .||.|.++-|-.|.     +|-|-|.|.+..+-.+|+.+
T Consensus       363 -------~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  363 -------HNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             -------cCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence                   011123678999999999999999999999 79999999988773     79999999999999999974

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.18  E-value=7.5e-11  Score=102.84  Aligned_cols=75  Identities=23%  Similarity=0.444  Sum_probs=71.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..++||||+.|+.++++.||.++|..||.|.+|.++..+ ++|||.|....+|.+|+++|+...+.++.|+|.||-
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R-~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR-GCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC-ceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            357899999999999999999999999999999999987 899999999999999999999999999999999983

>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=99.14  E-value=3.5e-10  Score=72.10  Aligned_cols=75  Identities=20%  Similarity=0.394  Sum_probs=56.2

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccC-CeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEcc
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFG-TILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAK   94 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G-~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~   94 (245)
                      ..|+|.|||.+.+...|+..|.+++..+| .|.+|.       .+.|.|.|.+.+.|.+|.+.|+|....|+.|.|.|..
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~-------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS-------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe-------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            46899999999999999999999999995 777762       2689999999999999999999999999999999975


Q ss_pred             ccc
Q 025973           95 TKS   97 (245)
Q Consensus        95 ~~~   97 (245)
                      ...
T Consensus        76 ~~r   78 (90)
T PF11608_consen   76 KNR   78 (90)
T ss_dssp             -S-
T ss_pred             Ccc
Confidence            443

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.12  E-value=4.4e-09  Score=87.80  Aligned_cols=217  Identities=17%  Similarity=0.210  Sum_probs=121.0

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE-E--EecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE-I--LAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~-i--~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .....|-+++||+.|+++|    |.++|+-.-.|.. |  .+.+-++..|-|||+|++.++|++|+. -|...|..|-|.
T Consensus       101 ~~d~vVRLRGLPfscte~d----I~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIE  175 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEED----IVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIE  175 (510)
T ss_pred             CCCceEEecCCCccCcHHH----HHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEE
Confidence            3678999999999999999    6699998755544 3  334466788999999999999999999 688888888898


Q ss_pred             EEEccccchHhhhcCCC-cccc----hhhhhhhh---hhhhccchhhHhhhcCCCC--------ccccC-------CCCC
Q 025973           90 IQYAKTKSDIIAKADGT-FVPR----ERRKRHEE---KGKKRKDQHDANQAGMGLN--------PAYAG-------AYGA  146 (245)
Q Consensus        90 v~~~~~~~~~~~~~~~~-~~~~----~~~~~~~~---~~~~~~~~~~~~~~~~~~~--------~~~~~-------~~~~  146 (245)
                      |..+............. ...+    ......+.   -..................        +....       ..+.
T Consensus       176 vF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~  255 (510)
T KOG4211|consen  176 VFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGR  255 (510)
T ss_pred             eehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccccccccc
Confidence            87765443322111000 0000    00000000   0000000000000000000        00000       0000


Q ss_pred             CCCCCCC-CCCCCCCCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCe-eEEEEecCC--CeEEEEEeCCHHHHH
Q 025973          147 TPPLSQI-PYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGF-KEVRMVEAK--PGIAFVEYGDEMQAT  222 (245)
Q Consensus       147 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v-~~v~l~~~~--~g~afv~f~~~~~A~  222 (245)
                      .+..... ..+.................+..++||...++.++.++|+..-.+ ..|.+-++-  +|-|+|+|.|.++|.
T Consensus       256 ~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~~v~i~ig~dGr~TGEAdveF~t~edav  335 (510)
T KOG4211|consen  256 DPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPYRVHIEIGPDGRATGEADVEFATGEDAV  335 (510)
T ss_pred             ccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCceeEEEEeCCCCccCCcceeecccchhhH
Confidence            0000000 001111111111222233679999999999999999999986554 333333332  789999999999999


Q ss_pred             HHHHHhCCCeeCC
Q 025973          223 VAMQSLQSLKIGQ  235 (245)
Q Consensus       223 ~A~~~l~g~~~~g  235 (245)
                      .|+.. ++..+..
T Consensus       336 ~Amsk-d~anm~h  347 (510)
T KOG4211|consen  336 GAMGK-DGANMGH  347 (510)
T ss_pred             hhhcc-CCcccCc
Confidence            99963 5555543

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=99.11  E-value=2e-11  Score=91.45  Aligned_cols=143  Identities=19%  Similarity=0.202  Sum_probs=107.9

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .+..+..++|||.|+...++|+-    |.++|.+.|+|..|.+..  +++.| ||||.|.++.+...|+..+||..+.++
T Consensus         3 aaaae~drtl~v~n~~~~v~eel----L~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~   77 (267)
T KOG4454|consen    3 AAAAEMDRTLLVQNMYSGVSEEL----LSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEED   77 (267)
T ss_pred             CCCcchhhHHHHHhhhhhhhHHH----HHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccc
Confidence            34577899999999999999998    779999999999987664  55666 999999999999999999999999999


Q ss_pred             eEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           87 PMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEA  166 (245)
Q Consensus        87 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (245)
                      .+.|.+-...+-                                                                    
T Consensus        78 e~q~~~r~G~sh--------------------------------------------------------------------   89 (267)
T KOG4454|consen   78 EEQRTLRCGNSH--------------------------------------------------------------------   89 (267)
T ss_pred             hhhcccccCCCc--------------------------------------------------------------------
Confidence            888765221100                                                                    


Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeC
Q 025973          167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIG  234 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~  234 (245)
                           .     -|+..++++.+..+|+.-|.+..+++..+.    +.++|+.+...-+.-.++...++....
T Consensus        90 -----a-----pld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~  151 (267)
T KOG4454|consen   90 -----A-----PLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLELF  151 (267)
T ss_pred             -----c-----hhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCcC
Confidence                 0     033456777777778887877777666532    457788777766666777666654433

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.11  E-value=3.5e-10  Score=84.22  Aligned_cols=82  Identities=20%  Similarity=0.334  Sum_probs=70.6

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhccc-CCeEEEEe---cCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQF-GTILEILA---FKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~-G~v~~i~~---~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .......++|..+|....+.+    +..+|.++ |.|..+++   .+||++||||||+|++.+.|.-|-+.||+..|.|+
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~----~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~  120 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETE----ILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEH  120 (214)
T ss_pred             ccCCccceeecccccchhHHH----HhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhh
Confidence            345567899999999999999    55777877 67777665   46999999999999999999999999999999999


Q ss_pred             eEEEEEcccc
Q 025973           87 PMRIQYAKTK   96 (245)
Q Consensus        87 ~i~v~~~~~~   96 (245)
                      .|.|.+-.+.
T Consensus       121 lL~c~vmppe  130 (214)
T KOG4208|consen  121 LLECHVMPPE  130 (214)
T ss_pred             eeeeEEeCch
Confidence            9999886654

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.08  E-value=1.6e-10  Score=92.40  Aligned_cols=81  Identities=22%  Similarity=0.381  Sum_probs=74.0

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE---EecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i---~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .+|.++|||-.|.+-+++++    |+-+|+.||.|.+|   ++.++|.+..||||+|.+.+++.+|+-.|+++.|.+++|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeD----LeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRI  311 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDED----LEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRI  311 (479)
T ss_pred             CCCcceEEEEecCCcccccc----hhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceE
Confidence            57889999999999999999    77999999999885   566788899999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      +|.|+..-
T Consensus       312 HVDFSQSV  319 (479)
T KOG0415|consen  312 HVDFSQSV  319 (479)
T ss_pred             Eeehhhhh
Confidence            99997543

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.05  E-value=4.2e-10  Score=90.09  Aligned_cols=78  Identities=22%  Similarity=0.456  Sum_probs=72.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCC-----eEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~-----g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      ..||.++|||--|.+-++.+||.-+|+.||.|..+.++++++     .||||+|.+.++...|...|++.-|..++|.|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            456889999999999999999999999999999999999862     399999999999999999999999999999999


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      |+.
T Consensus       315 FSQ  317 (479)
T KOG0415|consen  315 FSQ  317 (479)
T ss_pred             hhh
Confidence            974

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.04  E-value=2.8e-10  Score=87.81  Aligned_cols=83  Identities=27%  Similarity=0.376  Sum_probs=72.6

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEE---ecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEIL---AFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~---~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ..+++|+|||-.||.+..+.|    |.++|-.||.|.+-+   ++-+..+|.|+||.|.|+.+|+.||.+|||..|.=++
T Consensus       281 eGPeGCNlFIYHLPQEFgDaE----liQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKR  356 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAE----LIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKR  356 (371)
T ss_pred             cCCCcceEEEEeCchhhccHH----HHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhh
Confidence            367799999999999999999    669999999998743   3348889999999999999999999999999999889


Q ss_pred             EEEEEccccc
Q 025973           88 MRIQYAKTKS   97 (245)
Q Consensus        88 i~v~~~~~~~   97 (245)
                      |+|..-+++.
T Consensus       357 LKVQLKRPkd  366 (371)
T KOG0146|consen  357 LKVQLKRPKD  366 (371)
T ss_pred             hhhhhcCccc
Confidence            9988765543

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.03  E-value=6.6e-10  Score=97.07  Aligned_cols=77  Identities=23%  Similarity=0.451  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEcc
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAK   94 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~   94 (245)
                      ++||||++|+..+++.|    |.++|+.||.|.+|.+..   .+++|||.+.+-.+|.+|+..|+...+.++.|+|.|+.
T Consensus       421 SrTLwvG~i~k~v~e~d----L~~~feefGeiqSi~li~---~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQD----LANLFEEFGEIQSIILIP---PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeccccchhhHHH----HHHHHHhcccceeEeecc---CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            79999999999999999    669999999999998764   46999999999999999999999999999999999987


Q ss_pred             ccch
Q 025973           95 TKSD   98 (245)
Q Consensus        95 ~~~~   98 (245)
                      .+..
T Consensus       494 g~G~  497 (894)
T KOG0132|consen  494 GKGP  497 (894)
T ss_pred             cCCc
Confidence            5543

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=99.01  E-value=4.5e-10  Score=94.88  Aligned_cols=179  Identities=18%  Similarity=0.226  Sum_probs=117.1

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .+..-+.++|+|-|||..+++++    |+.+|+.||.|.+|+  .+...+|..||+|-|+.+|+.|+++|++..+.|+.|
T Consensus        69 ~~~~~~~~~L~v~nl~~~Vsn~~----L~~~f~~yGeir~ir--~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~  142 (549)
T KOG4660|consen   69 SEKDMNQGTLVVFNLPRSVSNDT----LLRIFGAYGEIREIR--ETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRI  142 (549)
T ss_pred             CcccCccceEEEEecCCcCCHHH----HHHHHHhhcchhhhh--cccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhh
Confidence            34456689999999999999999    779999999999964  344567999999999999999999999999999988


Q ss_pred             EEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           89 RIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPA  168 (245)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (245)
                      +............   +   .   .                         .+....+.++.           ...+....
T Consensus       143 k~~~~~~~~~~~~---~---~---~-------------------------~~~~~~~~p~a-----------~s~pgg~~  177 (549)
T KOG4660|consen  143 KRPGGARRAMGLQ---S---G---T-------------------------SFLNHFGSPLA-----------NSPPGGWP  177 (549)
T ss_pred             cCCCcccccchhc---c---c---c-------------------------hhhhhccchhh-----------cCCCCCCc
Confidence            7222111111000   0   0   0                         00001111110           00111111


Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                       ... ++ +.|++..+...+...++.+|.+.. ...+...-.-|+.|.+..++..++..+ |+.+.++...++++
T Consensus       178 -~~~-~~-g~l~P~~s~~~~~~~~~~~~~~~~-~~~~~~~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S  247 (549)
T KOG4660|consen  178 -RGQ-LF-GMLSPTRSSILLEHISSVDGSSPG-RETPLLNHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFS  247 (549)
T ss_pred             -CCc-ce-eeeccchhhhhhhcchhccCcccc-ccccchhhhhhhhhccccchhhcccCC-ceecCCCCceEEec
Confidence             111 22 227777777778888888988766 544443346788888888887666633 67777776666654

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.95  E-value=1.1e-08  Score=68.62  Aligned_cols=81  Identities=26%  Similarity=0.339  Sum_probs=65.5

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE---EecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC----Cce
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY----DKP   87 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i---~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~----g~~   87 (245)
                      .++|+|+|||...+.++|.+.|.+.|.  |...=+   .+.+++-+.|||||-|.+++.|.+....++|..+.    .+.
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~--g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kv   78 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFK--GKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKV   78 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhcc--CcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcE
Confidence            378999999999999999988877653  444333   34457778999999999999999999999998875    458


Q ss_pred             EEEEEccccc
Q 025973           88 MRIQYAKTKS   97 (245)
Q Consensus        88 i~v~~~~~~~   97 (245)
                      +.|.||.-+.
T Consensus        79 c~i~yAriQG   88 (97)
T PF04059_consen   79 CEISYARIQG   88 (97)
T ss_pred             EEEehhHhhC
Confidence            8888886554

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.93  E-value=1.2e-09  Score=92.40  Aligned_cols=76  Identities=26%  Similarity=0.415  Sum_probs=69.2

Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEE
Q 025973          164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLL  239 (245)
Q Consensus       164 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~  239 (245)
                      +...+-++.+|+|-|||..+++++|+.+|+.||+|+.|+.-+.+.|..||+|.|..+|.+|++.|++..+.|+.|+
T Consensus        68 p~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   68 PSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3333446678999999999999999999999999999998888889999999999999999999999999999887

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.86  E-value=8e-09  Score=82.69  Aligned_cols=77  Identities=26%  Similarity=0.418  Sum_probs=67.0

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHH-cCCccCCceEEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKM-QGFPFYDKPMRI   90 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l-~~~~~~g~~i~v   90 (245)
                      ....++|||+||-..++|.+    |+++|-+||.|.+|.+..   .+++|||+|.+-+.|..|.+.. +...+.|.+|.|
T Consensus       225 D~~I~tLyIg~l~d~v~e~d----IrdhFyqyGeirsi~~~~---~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQD----IRDHFYQYGEIRSIRILP---RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             ccceeEEEecccccchhHHH----HHHHHhhcCCeeeEEeec---ccccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            44578999999999999999    679999999999997764   3579999999999999998766 457778999999


Q ss_pred             EEccc
Q 025973           91 QYAKT   95 (245)
Q Consensus        91 ~~~~~   95 (245)
                      .|+.+
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99887

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.84  E-value=1.5e-08  Score=75.58  Aligned_cols=73  Identities=23%  Similarity=0.424  Sum_probs=65.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccC-CCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQF-PGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~-g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      ....+++..+|.-+.+..+...|.++ |.|..+++.+++     +|||||+|.+++.|..|-+.||++-|.++.|.|.+
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            44579999999999999999999998 667888887754     79999999999999999999999999999999876

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.82  E-value=6.4e-09  Score=83.96  Aligned_cols=168  Identities=17%  Similarity=0.236  Sum_probs=122.3

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE---EecCCCCeeeEEEEEecCHHHHHHHHHHHcC-CccCCceE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAAVEKMQG-FPFYDKPM   88 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i---~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~-~~~~g~~i   88 (245)
                      ...++.|++++...+.+.+    .-.++..+|.+...   .......++|++++.|...+.+..|+. +.+ ....++.+
T Consensus        86 ~~~~~~f~g~~s~~~e~~~----~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~-~s~~~~~~~~~~  160 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESE----DDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALE-ESGSKVLDGNKG  160 (285)
T ss_pred             cccccccccccccchhhcc----ccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHH-hhhccccccccc
Confidence            3588999999999988887    44788888866654   233467789999999999999999999 454 34444444


Q ss_pred             EEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           89 RIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPA  168 (245)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (245)
                      .............                                                          .........
T Consensus       161 ~~dl~~~~~~~~~----------------------------------------------------------n~~~~~~~~  182 (285)
T KOG4210|consen  161 EKDLNTRRGLRPK----------------------------------------------------------NKLSRLSSG  182 (285)
T ss_pred             cCccccccccccc----------------------------------------------------------chhcccccC
Confidence            3322221110000                                                          000011112


Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ++....+++|++..+++++|..+|..+|.|..+++..++     +|+|++.|.+...+..++.. +...++++++.+.+.
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            233445599999999999999999999999999998754     68999999999999999987 888899999988775


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       262 ~  262 (285)
T KOG4210|consen  262 E  262 (285)
T ss_pred             C
Confidence            3

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.81  E-value=3.4e-10  Score=99.86  Aligned_cols=137  Identities=22%  Similarity=0.298  Sum_probs=111.2

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      ..++||+||++.+.+.+    |...|..+|.+..+.+.   ..++.+|+||+.|...++|.+|+....+. +.|      
T Consensus       667 ~~~~fvsnl~~~~~~~d----l~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~-~~g------  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEED----LSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSC-FFG------  735 (881)
T ss_pred             HHHHHHhhcchhhcCch----hhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhh-hhh------
Confidence            46789999999999999    66899999888776433   36778899999999999999999944332 221      


Q ss_pred             EccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 025973           92 YAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPN  171 (245)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (245)
                                                                                                     .
T Consensus       736 -------------------------------------------------------------------------------K  736 (881)
T KOG0128|consen  736 -------------------------------------------------------------------------------K  736 (881)
T ss_pred             -------------------------------------------------------------------------------h
Confidence                                                                                           1


Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      ..++|+|.|+..|.+.|+.+++.+|++.+..++..+    +|.|+|.|.++.+|.+++...+...+.-+.+.|.
T Consensus       737 ~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~  810 (881)
T KOG0128|consen  737 ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQ  810 (881)
T ss_pred             hhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCcccc
Confidence            239999999999999999999999999988877643    7899999999999999998887766654444443

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.79  E-value=4.2e-09  Score=85.45  Aligned_cols=194  Identities=13%  Similarity=0.114  Sum_probs=115.1

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCC------CeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTL------KHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~------~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      .|.|.||++.++.++    ++.+|...|.|.++.++.+-      .....|||.|.+...+..|.. |.++.|-++.|.|
T Consensus         9 vIqvanispsat~dq----m~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv   83 (479)
T KOG4676|consen    9 VIQVANISPSATKDQ----MQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIV   83 (479)
T ss_pred             eeeecccCchhhHHH----HHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEE
Confidence            899999999999999    77999999999999777622      244699999999999999998 6666666775555


Q ss_pred             EE-ccccch-HhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCC-CCcccc--CCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           91 QY-AKTKSD-IIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMG-LNPAYA--GAYGATPPLSQIPYPGGAKSVIPE  165 (245)
Q Consensus        91 ~~-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~  165 (245)
                      -+ ...-.. ...     |............           +...+ +++..+  ..+..+... .. .|..++.....
T Consensus        84 ~p~~~~~~p~r~a-----f~~l~~~navprl-----------l~pdg~Lp~~~~lt~~nh~p~ai-lk-tP~Lp~~~~A~  145 (479)
T KOG4676|consen   84 RPYGDEVIPDRFA-----FVELADQNAVPRL-----------LPPDGVLPGDRPLTKINHSPNAI-LK-TPELPPQAAAK  145 (479)
T ss_pred             EecCCCCCccHHH-----HHhcCcccccccc-----------cCCCCccCCCCccccccCCccce-ec-CCCCChHhhhh
Confidence            44 322111 100     0000000000000           00000 000000  000000000 00 00000000000


Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC-CCeEEEEEeCCHHHHHHHHHHhCCCeeC
Q 025973          166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-KPGIAFVEYGDEMQATVAMQSLQSLKIG  234 (245)
Q Consensus       166 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~-~~g~afv~f~~~~~A~~A~~~l~g~~~~  234 (245)
                      ....-..+++|.+|+..+-..++...|..+|.|.+-...-. ...+|.++|........|++ ++|..+.
T Consensus       146 kleeirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  146 KLEEIRRTREVQSLISAAILPESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             hhHHHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            00012357999999999999999999999999987666543 24588899999889999998 5676654

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.79  E-value=1.3e-07  Score=71.56  Aligned_cols=74  Identities=26%  Similarity=0.450  Sum_probs=63.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC------CeEEEEEeCCHHHHHHHHHHhCCCeeC---CeEEEEE
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK------PGIAFVEYGDEMQATVAMQSLQSLKIG---QQQLLIT  241 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~------~g~afv~f~~~~~A~~A~~~l~g~~~~---g~~i~v~  241 (245)
                      -++|||.+||..+..-+|..+|..|-.-....|-...      +.+|||.|.+...|..|+.+|||..|+   +.+|+|+
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            4689999999999999999999988665444443321      359999999999999999999999998   9999999


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      +||
T Consensus       114 lAK  116 (284)
T KOG1457|consen  114 LAK  116 (284)
T ss_pred             ehh
Confidence            997

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.78  E-value=1.3e-08  Score=86.42  Aligned_cols=80  Identities=13%  Similarity=0.319  Sum_probs=68.7

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCC---CCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKT---LKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~---~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      -+++|||.+|+..+--.+    |..+|+.||.|....+..+   .-.+.|+||.+++.++|.+||..||.+.++|+.|.|
T Consensus       404 ~gRNlWVSGLSstTRAtD----LKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISV  479 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATD----LKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISV  479 (940)
T ss_pred             cccceeeeccccchhhhH----HHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeee
Confidence            378999999999999999    5599999999987655432   234569999999999999999999999999999999


Q ss_pred             EEccccc
Q 025973           91 QYAKTKS   97 (245)
Q Consensus        91 ~~~~~~~   97 (245)
                      +-++...
T Consensus       480 EkaKNEp  486 (940)
T KOG4661|consen  480 EKAKNEP  486 (940)
T ss_pred             eecccCc
Confidence            9987543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.78  E-value=3.5e-08  Score=85.77  Aligned_cols=78  Identities=19%  Similarity=0.328  Sum_probs=71.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEE
Q 025973          167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQL  238 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i  238 (245)
                      .+|.++.|||+||+++++++.|...|..||.|..++++..+        +.||||.|-+..+|.+|+..|+|..+.+..+
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~  249 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEM  249 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeee
Confidence            34566779999999999999999999999999999998743        5799999999999999999999999999999


Q ss_pred             EEEEec
Q 025973          239 LITYAK  244 (245)
Q Consensus       239 ~v~~ak  244 (245)
                      ++.|+|
T Consensus       250 K~gWgk  255 (877)
T KOG0151|consen  250 KLGWGK  255 (877)
T ss_pred             eecccc
Confidence            999986

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.77  E-value=3.7e-08  Score=85.45  Aligned_cols=193  Identities=12%  Similarity=0.086  Sum_probs=125.6

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE--EecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI--LAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i--~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      -++.+-+.+++...++.+    ++++|.-. .|..+  ..++ .+...|.++|.|....++++|++ -|...+..|.+.+
T Consensus       310 d~~y~~~~gm~fn~~~nd----~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~~~R~~q~  383 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFND----GRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDDVNRPFQT  383 (944)
T ss_pred             hhheeeecccccccccch----hhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHh-cCchhhhhcceee
Confidence            367788899999999999    55777633 33332  2222 33346899999999999999999 5777778888888


Q ss_pred             EEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           91 QYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP  170 (245)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (245)
                      ..+........   +.+....                        .+......++.+........+....  .+. ....
T Consensus       384 ~P~g~~~~~~a---~~~~~~~------------------------~~~~~~~~hg~p~~~pr~~~~~gq~--vp~-P~~a  433 (944)
T KOG4307|consen  384 GPPGNLGRNGA---PPFQAGV------------------------PPPVIQNNHGRPIAPPRAMVRPGQN--VPF-PGGA  433 (944)
T ss_pred             cCCCccccccC---ccccccC------------------------CCCcccccCCCCCCCcccccCCCCC--CCC-CCCc
Confidence            77643322111   1100000                        0011122222222222222221111  111 1234


Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKE-VRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~-v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      +.+|||..||..+++.++.++|+....|.+ |.|.+..    ++.|||.|..++++..|+..-+.+.++.+-|+|.-
T Consensus       434 g~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  434 GGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             cceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            568999999999999999999998766655 7776643    67999999999999999987777777788888853

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.77  E-value=1.4e-07  Score=82.06  Aligned_cols=70  Identities=21%  Similarity=0.340  Sum_probs=61.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCe-eEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGF-KEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v-~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      +|-+.|+|+.++.+||.+||.-|-.+ .+|.+-.+.    +|-|.|.|++.++|.+|...|++..|..+++++.+
T Consensus       869 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  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            89999999999999999999999665 555555432    78999999999999999999999999999998864

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.74  E-value=1.2e-07  Score=63.63  Aligned_cols=73  Identities=18%  Similarity=0.245  Sum_probs=61.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhcc--CCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeC----CeEEEE
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQ--FPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIG----QQQLLI  240 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~--~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~----g~~i~v  240 (245)
                      +||.|+|+|...|.++|.+++..  .|....+.|+-|-     .|||||.|.+++.|..-.+.++|..+.    .|...|
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            57999999999999999988864  3556666666542     699999999999999999999998875    777888


Q ss_pred             EEec
Q 025973          241 TYAK  244 (245)
Q Consensus       241 ~~ak  244 (245)
                      +||+
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            8885

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.74  E-value=2.5e-08  Score=84.79  Aligned_cols=75  Identities=19%  Similarity=0.282  Sum_probs=68.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+..|+|.+|...+-..+|+++|++||+|.-.+++.+-     +=|+||+|.+.++|.+++.+||.+.++|+.|.|.-||
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            34569999999999999999999999999888888753     3499999999999999999999999999999999886

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.72  E-value=1.1e-09  Score=89.56  Aligned_cols=148  Identities=22%  Similarity=0.329  Sum_probs=116.5

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccC-CeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcC-CccCCceEEEEEc
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFG-TILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQG-FPFYDKPMRIQYA   93 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G-~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~-~~~~g~~i~v~~~   93 (245)
                      ..+|++||.+.++.++    |+.+|...- +...-.+++    .|||||.+.+..-|.+|++.++| ..+.|.++.+.++
T Consensus         2 nklyignL~p~~~psd----l~svfg~ak~~~~g~fl~k----~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~s   73 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSD----LESVFGDAKIPGSGQFLVK----SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHH----HHHHhccccCCCCcceeee----cceeeccCCchhhhhhhHHhhchhhhhcCceeeccch
Confidence            4689999999999999    778887551 110111122    37999999999999999999988 6778999988886


Q ss_pred             cccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccE
Q 025973           94 KTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNI  173 (245)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (245)
                      .++.-+                                                                       ++.
T Consensus        74 v~kkqr-----------------------------------------------------------------------srk   82 (584)
T KOG2193|consen   74 VPKKQR-----------------------------------------------------------------------SRK   82 (584)
T ss_pred             hhHHHH-----------------------------------------------------------------------hhh
Confidence            544321                                                                       233


Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       174 l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      +-|+|+|...-++-|..+...||.+..+..+...  .-..-|.|.+.+.+..|+.++||..+.+..++|.|
T Consensus        83 ~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Y  153 (584)
T KOG2193|consen   83 IQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGY  153 (584)
T ss_pred             hhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhccc
Confidence            7889999999999999999999999887765432  23456889999999999999999999988888776

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.72  E-value=5.3e-08  Score=76.07  Aligned_cols=79  Identities=24%  Similarity=0.361  Sum_probs=70.1

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE--EecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI--LAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i--~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      ..+|+|.|||+.++++|    |.++|..||.+..+  ++.+.|.+.|.|-|.|...++|..|++.+|++.+.|+.|++..
T Consensus        83 ~~~v~v~NL~~~V~~~D----l~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDAD----LKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             cceeeeecCCcCcchHH----HHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            47899999999999999    66999999977664  6667999999999999999999999999999999999999888


Q ss_pred             ccccc
Q 025973           93 AKTKS   97 (245)
Q Consensus        93 ~~~~~   97 (245)
                      .....
T Consensus       159 i~~~~  163 (243)
T KOG0533|consen  159 ISSPS  163 (243)
T ss_pred             ecCcc
Confidence            65443

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.68  E-value=1.7e-08  Score=77.55  Aligned_cols=70  Identities=20%  Similarity=0.459  Sum_probs=63.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEE
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLI  240 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v  240 (245)
                      ...||++.|...++.+.|...|.+|-....-++++++     +||+||.|.++.++.+|+..|+|..++.++|++
T Consensus       190 DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpikl  264 (290)
T KOG0226|consen  190 DFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKL  264 (290)
T ss_pred             cceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHh
Confidence            4569999999999999999999999888777888764     799999999999999999999999999998875

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.64  E-value=5.7e-08  Score=81.83  Aligned_cols=78  Identities=22%  Similarity=0.293  Sum_probs=64.6

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .....|||+|||.++++++    |.++|..||.|.+..+..   .+++..||||+|.+.+.+..|+. .+...+.++++.
T Consensus       286 ~~~~~i~V~nlP~da~~~~----l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~-Asp~~ig~~kl~  360 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAE----LEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIE-ASPLEIGGRKLN  360 (419)
T ss_pred             ecccceEeecCCCCCCHHH----HHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhh-cCccccCCeeEE
Confidence            3355599999999999999    779999999999864432   34455899999999999999999 578888999999


Q ss_pred             EEEccc
Q 025973           90 IQYAKT   95 (245)
Q Consensus        90 v~~~~~   95 (245)
                      |+--..
T Consensus       361 Veek~~  366 (419)
T KOG0116|consen  361 VEEKRP  366 (419)
T ss_pred             EEeccc
Confidence            976443

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.61  E-value=3.8e-08  Score=75.25  Aligned_cols=69  Identities=20%  Similarity=0.425  Sum_probs=64.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+||++||..+.+.+|..+|..||.+.++.+.   .||+||+|.++.+|.-|+..+|+..|.|.++.|.||+
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk---~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r   71 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK---NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHAR   71 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee---cccceeccCchhhhhcccchhcCceecceeeeeeccc
Confidence            48999999999999999999999999888774   3799999999999999999999999998889999986

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.61  E-value=1.9e-07  Score=72.97  Aligned_cols=72  Identities=19%  Similarity=0.282  Sum_probs=66.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ..|+|.|||..++.+||+++|..||.++.+-+.+++    .|.|-|.|...++|.+|++.+||..+.|++|++...
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             ceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            569999999999999999999999999999999875    579999999999999999999999999999988754

>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=98.61  E-value=3e-07  Score=58.85  Aligned_cols=68  Identities=16%  Similarity=0.377  Sum_probs=47.8

Q ss_pred             cEEEEcCCCCCCCHHHH----HHHhccCCC-eeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          172 NILFVQNVPHDTTPMAL----QMFFSQFPG-FKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l----~~~f~~~g~-v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..|+|.|||.......|    +.++..+|. |..|.     .+.|+|.|.+++.|.+|...|+|-.+.|.+|.|+|..
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~-----~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS-----GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe-----CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            46999999988887664    566667765 55552     3689999999999999999999999999999999974

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.59  E-value=2.1e-07  Score=74.74  Aligned_cols=75  Identities=20%  Similarity=0.250  Sum_probs=68.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCee--------EEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFK--------EVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQ  237 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~--------~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~  237 (245)
                      .++.|||.|||..+|-+++..+|+.+|.|.        .|+|+++.    +|-|++.|--.++...|+..|++..|.|+.
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            455699999999999999999999999883        47888764    789999999999999999999999999999


Q ss_pred             EEEEEec
Q 025973          238 LLITYAK  244 (245)
Q Consensus       238 i~v~~ak  244 (245)
                      |+|+.|+
T Consensus       213 ~rVerAk  219 (382)
T KOG1548|consen  213 LRVERAK  219 (382)
T ss_pred             EEEehhh
Confidence            9999885

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.56  E-value=1.1e-07  Score=77.13  Aligned_cols=81  Identities=17%  Similarity=0.326  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEE---ecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEIL---AFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~---~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      ..+|||++||.++++.+    |++.|++||.|..+.   +..+...+||+||.|.+.+++.++.. ..-..|.|+.+.|.
T Consensus        97 tkkiFvGG~~~~~~e~~----~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevk  171 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEED----FKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVK  171 (311)
T ss_pred             eeEEEecCcCCCCchHH----HhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEe
Confidence            55999999999999999    669999999887753   33467789999999999999999988 67889999999999


Q ss_pred             EccccchHh
Q 025973           92 YAKTKSDII  100 (245)
Q Consensus        92 ~~~~~~~~~  100 (245)
                      .|.++....
T Consensus       172 rA~pk~~~~  180 (311)
T KOG4205|consen  172 RAIPKEVMQ  180 (311)
T ss_pred             eccchhhcc
Confidence            998877643

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.51  E-value=1.8e-07  Score=81.47  Aligned_cols=80  Identities=23%  Similarity=0.424  Sum_probs=70.4

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--C----CCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--T----LKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~----~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      .+.+++|||+||++.++++.    |...|..||+|.+|+++-  +    ...+.++||-|.+-.+|.+|++.|+|..+.+
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~----ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~  246 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENF----LLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVME  246 (877)
T ss_pred             CCcccceeeecCCccccHHH----HHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeee
Confidence            45689999999999999999    669999999999986663  2    2356799999999999999999999999999


Q ss_pred             ceEEEEEccc
Q 025973           86 KPMRIQYAKT   95 (245)
Q Consensus        86 ~~i~v~~~~~   95 (245)
                      ..+++.|++.
T Consensus       247 ~e~K~gWgk~  256 (877)
T KOG0151|consen  247 YEMKLGWGKA  256 (877)
T ss_pred             eeeeeccccc
Confidence            9999999854

>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=98.51  E-value=3.4e-07  Score=62.84  Aligned_cols=69  Identities=20%  Similarity=0.260  Sum_probs=45.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCC-----eeCCeEEEEE
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSL-----KIGQQQLLIT  241 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~-----~~~g~~i~v~  241 (245)
                      .+|.|.+++..++.++|++.|+.||.|.+|.+..+. ..|+|.|.+++.|..|+..+...     .+.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~-~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD-TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT--SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC-CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            468999999999999999999999999999999987 48999999999999999877543     4445555443

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.48  E-value=2e-07  Score=71.80  Aligned_cols=75  Identities=27%  Similarity=0.387  Sum_probs=64.4

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccC---CeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFG---TILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G---~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      -+-+||.+.|..+++++.    |...|.+|-   .-..|+..++|+++||+||.|.+..++..|+..|+|..++.+.|++
T Consensus       189 ~DfRIfcgdlgNevnd~v----l~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpikl  264 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDV----LARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKL  264 (290)
T ss_pred             ccceeecccccccccHHH----HHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHh
Confidence            368999999999999998    556666664   3445788899999999999999999999999999999999988866


Q ss_pred             EE
Q 025973           91 QY   92 (245)
Q Consensus        91 ~~   92 (245)
                      .-
T Consensus       265 Rk  266 (290)
T KOG0226|consen  265 RK  266 (290)
T ss_pred             hh
Confidence            43

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.38  E-value=7.5e-07  Score=69.74  Aligned_cols=74  Identities=22%  Similarity=0.317  Sum_probs=67.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..+.++|+|++..+|.+++..+|+.||.+..+.+..++     +||+||+|.+.+.+..|+. |||..|.|+.|.|++.+
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeee
Confidence            34569999999999999999999999999988888764     7899999999999999999 99999999999998854

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.36  E-value=2.8e-05  Score=63.59  Aligned_cols=156  Identities=20%  Similarity=0.230  Sum_probs=102.6

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhccc----CCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQF----GTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~----G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..+..|-.++||-..++.+|.    .+|.-.    |.+.-+ ..-.|+..|.|.|.|.+.|.-.-|++ .|...+.++.|
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia----~ff~gl~ia~gg~aKO-G~~qgrRnge~lvrf~d~e~Rdlalk-Rhkhh~g~ryi  131 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIA----RFFKGLNIANGGRALC-LNAQGRRNGEALVRFVDPEGRDLALK-RHKHHMGTRYI  131 (508)
T ss_pred             CcceEEEecCCCCCcccCCHH----HHHhhhhccccceeee-ehhhhccccceEEEecCchhhhhhhH-hhhhhccCCce
Confidence            345677789999999998844    666533    222222 22346667899999999999999999 68888888988


Q ss_pred             EEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           89 RIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPA  168 (245)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (245)
                      .|.-+...+.-.. ..+.                                                  ....  .+....
T Consensus       132 evYka~ge~f~~i-agg~--------------------------------------------------s~e~--~~flsk  158 (508)
T KOG1365|consen  132 EVYKATGEEFLKI-AGGT--------------------------------------------------SNEA--APFLSK  158 (508)
T ss_pred             eeeccCchhheEe-cCCc--------------------------------------------------cccC--CCCCCc
Confidence            8866544332100 0000                                                  0000  000000


Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccC----CCeeEEEEecC---C-CeEEEEEeCCHHHHHHHHHH
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQF----PGFKEVRMVEA---K-PGIAFVEYGDEMQATVAMQS  227 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~----g~v~~v~l~~~---~-~g~afv~f~~~~~A~~A~~~  227 (245)
                      ...-.+-+++||+.+++.++..||.+.    |....|.++..   + +|-|||.|..+++|+.||..
T Consensus       159 ~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  159 ENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             ccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH
Confidence            012346788999999999999999632    24455665542   3 79999999999999999974

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.36  E-value=8.8e-07  Score=69.37  Aligned_cols=81  Identities=16%  Similarity=0.258  Sum_probs=69.2

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeE--EEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~--~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      .....+.+||+|+.+.++.++    +...|+.||.|.  .|...+ .++.||||||+|.+.+.+..|+. |++..+.|+.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~----~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~  171 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTK----IELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPA  171 (231)
T ss_pred             hccCCceEEEeccccccccch----hhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccc
Confidence            345578999999999999999    669999999996  343333 56789999999999999999999 9999999999


Q ss_pred             EEEEEcccc
Q 025973           88 MRIQYAKTK   96 (245)
Q Consensus        88 i~v~~~~~~   96 (245)
                      +.|.+....
T Consensus       172 i~vt~~r~~  180 (231)
T KOG4209|consen  172 IEVTLKRTN  180 (231)
T ss_pred             ceeeeeeee
Confidence            999886554

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.36  E-value=2.2e-07  Score=70.08  Aligned_cols=73  Identities=19%  Similarity=0.161  Sum_probs=66.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      ...+|||.|+...++++.|.++|-.-|.|..|.|..++   ..||||.|.++....-|++.+||-.+.+..|.+++
T Consensus         8 ~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    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhccc
Confidence            45679999999999999999999999999999998865   23999999999999999999999999999998876

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.33  E-value=1.2e-06  Score=73.96  Aligned_cols=69  Identities=33%  Similarity=0.545  Sum_probs=59.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEec----CC-CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE----AK-PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~----~~-~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      .|||+|||..++..+|.++|..||.|+...|..    ++ ..||||+|.+.+++..|+++ +-..+++++|.|.-
T Consensus       290 ~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Vee  363 (419)
T KOG0116|consen  290 GIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEE  363 (419)
T ss_pred             ceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEe
Confidence            499999999999999999999999997766654    21 26999999999999999985 57888999999974

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.98  E-value=3.3e-05  Score=53.03  Aligned_cols=74  Identities=18%  Similarity=0.296  Sum_probs=44.0

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCC-----ccCCceEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGF-----PFYDKPMR   89 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~-----~~~g~~i~   89 (245)
                      ++.|+|.|++.+++.++    |...|+.||.|..|.+.+.   -..|||.|.+.++|+.|+..+...     .+.+..+.
T Consensus         1 G~il~~~g~~~~~~re~----iK~~f~~~g~V~yVD~~~G---~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~   73 (105)
T PF08777_consen    1 GCILKFSGLGEPTSRED----IKEAFSQFGEVAYVDFSRG---DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVT   73 (105)
T ss_dssp             --EEEEEE--SS--HHH----HHHHT-SS--EEEEE--TT----SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEE
T ss_pred             CeEEEEecCCCCcCHHH----HHHHHHhcCCcceEEecCC---CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEE
Confidence            36799999999999999    5599999999998877652   247999999999999999877543     55566666


Q ss_pred             EEEccc
Q 025973           90 IQYAKT   95 (245)
Q Consensus        90 v~~~~~   95 (245)
                      +.....
T Consensus        74 ~~vLeG   79 (105)
T PF08777_consen   74 LEVLEG   79 (105)
T ss_dssp             EE---H
T ss_pred             EEECCC
Confidence            655433

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.98  E-value=4.3e-05  Score=65.50  Aligned_cols=83  Identities=17%  Similarity=0.299  Sum_probs=69.9

Q ss_pred             CCCCCeEEEcCCCc--ccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccC-Cc
Q 025973           12 ISPNNTIYINNLNE--KVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFY-DK   86 (245)
Q Consensus        12 ~~~~~~l~V~nLp~--~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~-g~   86 (245)
                      .--...|.|.|+|-  ....+-|+..|..+|+.+|+|..+.+.  ..|.++||.|++|.+..+|..|++.|||..+. ++
T Consensus        55 eg~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   55 EGFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CCcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            35578999999994  455678888899999999999887665  45669999999999999999999999998887 66


Q ss_pred             eEEEEEcc
Q 025973           87 PMRIQYAK   94 (245)
Q Consensus        87 ~i~v~~~~   94 (245)
                      +..|..-+
T Consensus       135 tf~v~~f~  142 (698)
T KOG2314|consen  135 TFFVRLFK  142 (698)
T ss_pred             eEEeehhh
Confidence            88886643

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.88  E-value=7.6e-05  Score=53.52  Aligned_cols=78  Identities=22%  Similarity=0.399  Sum_probs=59.1

Q ss_pred             CCCCCeEEEcCCC-----cccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           12 ISPNNTIYINNLN-----EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        12 ~~~~~~l~V~nLp-----~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .+|..+|.|.=+.     .....++|...|.+.|..||.|.-|++..     +.-+|.|.+-++|.+|+. ++|..+.|+
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~-----~~mwVTF~dg~sALaals-~dg~~v~g~   97 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG-----DTMWVTFRDGQSALAALS-LDGIQVNGR   97 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET-----TCEEEEESSCHHHHHHHH-GCCSEETTE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC-----CeEEEEECccHHHHHHHc-cCCcEECCE
Confidence            5667777777665     34567778888889999999998888775     368999999999999999 999999999


Q ss_pred             eEEEEEccc
Q 025973           87 PMRIQYAKT   95 (245)
Q Consensus        87 ~i~v~~~~~   95 (245)
                      .|+|..-.+
T Consensus        98 ~l~i~LKtp  106 (146)
T PF08952_consen   98 TLKIRLKTP  106 (146)
T ss_dssp             EEEEEE---
T ss_pred             EEEEEeCCc
Confidence            999987443

; PDB: 1UFW_A 2DNR_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.88  E-value=3.7e-05  Score=61.91  Aligned_cols=83  Identities=20%  Similarity=0.416  Sum_probs=64.8

Q ss_pred             CCCeEEEcCCCcccChHHHHHHH--HHhhcccCCeEEEEecCCC---Ce-eeE--EEEEecCHHHHHHHHHHHcCCccCC
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSL--HAVFKQFGTILEILAFKTL---KH-KGQ--AWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l--~~~F~~~G~v~~i~~~~~~---~~-kg~--afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      ...-+||-+||+.+..++...-|  .++|.+||.|..|.+.+.-   .+ .+.  .||.|.+.|+|..|+...+|..+.|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            35668999999988777633323  4799999999998766421   11 122  3999999999999999999999999


Q ss_pred             ceEEEEEcccc
Q 025973           86 KPMRIQYAKTK   96 (245)
Q Consensus        86 ~~i~v~~~~~~   96 (245)
                      |.|+..|...+
T Consensus       193 r~lkatYGTTK  203 (480)
T COG5175         193 RVLKATYGTTK  203 (480)
T ss_pred             ceEeeecCchH
Confidence            99999997654

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.86  E-value=1.7e-05  Score=64.31  Aligned_cols=77  Identities=22%  Similarity=0.302  Sum_probs=66.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKE--------VRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQ  235 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~--------v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g  235 (245)
                      ....++||-+||+.+++.+|.++|.++|.|+.        |.+..++     |+-|.|.|.++..|+.|+..+++..|.+
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            45567999999999999999999999998732        4444443     7899999999999999999999999999


Q ss_pred             eEEEEEEecC
Q 025973          236 QQLLITYAKK  245 (245)
Q Consensus       236 ~~i~v~~ak~  245 (245)
                      .+|+|.+|.+
T Consensus       144 n~ikvs~a~~  153 (351)
T KOG1995|consen  144 NTIKVSLAER  153 (351)
T ss_pred             CCchhhhhhh
Confidence            9999998864

>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=97.77  E-value=0.0002  Score=48.40  Aligned_cols=70  Identities=14%  Similarity=0.135  Sum_probs=50.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEE------------EecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCe-EE
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVR------------MVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQ-QL  238 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~------------l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~-~i  238 (245)
                      .-|.|-+.|.. .-..+.+.|++||.|.+..            -.+...++..|.|+++.+|.+||+ -||..|.|. .+
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mv   84 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMV   84 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEE
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEE
Confidence            45888888877 5667788899999997664            222334799999999999999998 699999864 55


Q ss_pred             EEEEe
Q 025973          239 LITYA  243 (245)
Q Consensus       239 ~v~~a  243 (245)
                      -|.+.
T Consensus        85 GV~~~   89 (100)
T PF05172_consen   85 GVKPC   89 (100)
T ss_dssp             EEEE-
T ss_pred             EEEEc
Confidence            57665

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.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.74  E-value=0.0001  Score=43.85  Aligned_cols=52  Identities=17%  Similarity=0.313  Sum_probs=41.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHH
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAM  225 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~  225 (245)
                      +.|-|.+.+....+. +..+|..||.|..+.+.... ...+|.|.+..+|.+||
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            357788888665544 55588899999998887444 69999999999999985

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.71  E-value=4.6e-05  Score=61.94  Aligned_cols=88  Identities=26%  Similarity=0.331  Sum_probs=74.6

Q ss_pred             cccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE--------EE---ecCCCCeeeEEEEEecCHHHHHHH
Q 025973            6 ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--------IL---AFKTLKHKGQAWLVFKDVASATAA   74 (245)
Q Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~--------i~---~~~~~~~kg~afV~F~~~~~A~~a   74 (245)
                      ....++..-..+|||-+||..+++++    |..+|.++|.|..        |.   ...|+..|+-|.|.|.+...|+.|
T Consensus        57 ~~~~~~~s~~~ti~v~g~~d~~~~~~----~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaa  132 (351)
T KOG1995|consen   57 ASSMADKSDNETIFVWGCPDSVCEND----NADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAA  132 (351)
T ss_pred             cCccccccccccceeeccCccchHHH----HHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhh
Confidence            34556677788999999999999999    7799999997753        32   224778999999999999999999


Q ss_pred             HHHHcCCccCCceEEEEEccccc
Q 025973           75 VEKMQGFPFYDKPMRIQYAKTKS   97 (245)
Q Consensus        75 ~~~l~~~~~~g~~i~v~~~~~~~   97 (245)
                      +.-+++..|.|.+|+|.++....
T Consensus       133 i~~~agkdf~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  133 IEWFAGKDFCGNTIKVSLAERRT  155 (351)
T ss_pred             hhhhccccccCCCchhhhhhhcc
Confidence            99999999999999998886554

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.68  E-value=0.00014  Score=43.19  Aligned_cols=52  Identities=19%  Similarity=0.325  Sum_probs=42.5

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHH
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAV   75 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~   75 (245)
                      +.|-|.|.+.+..+.     +..+|..||.|..+....   ...+.||.|.+..+|.+|+
T Consensus         2 ~wI~V~Gf~~~~~~~-----vl~~F~~fGeI~~~~~~~---~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-----VLEHFASFGEIVDIYVPE---STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-----HHHHHHhcCCEEEEEcCC---CCcEEEEEECCHHHHHhhC
Confidence            567889999887765     446889999999987762   3479999999999999985

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.66  E-value=0.00039  Score=44.69  Aligned_cols=61  Identities=15%  Similarity=0.278  Sum_probs=46.0

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcC
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQG   80 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~   80 (245)
                      ..+..+...||+ .|..+...|    |.++|+.||.|.--++..+     .|||...+.+.|..++..+..
T Consensus         4 ~~P~RdHVFhlt-FPkeWK~~D----I~qlFspfG~I~VsWi~dT-----SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    4 PQPSRDHVFHLT-FPKEWKTSD----IYQLFSPFGQIYVSWINDT-----SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             ---SGCCEEEEE---TT--HHH----HHHHCCCCCCEEEEEECTT-----EEEEEECCCHHHHHHHHHHTT
T ss_pred             CCCCcceEEEEe-CchHhhhhh----HHHHhccCCcEEEEEEcCC-----cEEEEeecHHHHHHHHHHhcc
Confidence            445567788888 999999999    7799999999977677654     699999999999999987753

; 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 TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.58  E-value=4.1e-05  Score=59.39  Aligned_cols=67  Identities=19%  Similarity=0.338  Sum_probs=59.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-------------C----eEEEEEeCCHHHHHHHHHHhCCCee
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-------------P----GIAFVEYGDEMQATVAMQSLQSLKI  233 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-------------~----g~afv~f~~~~~A~~A~~~l~g~~~  233 (245)
                      ..+||++|||+.+...-|+++|+.||.|-+|.|.+..             +    .-|-|+|.+-..|.++...||+.+|
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~I  153 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPI  153 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCcc
Confidence            4589999999999999999999999999999998842             0    1478999999999999999999999


Q ss_pred             CCeE
Q 025973          234 GQQQ  237 (245)
Q Consensus       234 ~g~~  237 (245)
                      +|++
T Consensus       154 ggkk  157 (278)
T KOG3152|consen  154 GGKK  157 (278)
T ss_pred             CCCC
Confidence            9875

>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=97.57  E-value=0.0003  Score=47.55  Aligned_cols=75  Identities=16%  Similarity=0.220  Sum_probs=52.2

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec-C---------CCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF-K---------TLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~-~---------~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      ..+-|.|=|.|+..+..     +-+.|++||.|.+.... +         .....+.-.|.|.+..+|.+|+. .||..+
T Consensus         5 ~~~wVtVFGfp~~~~~~-----Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~   78 (100)
T PF05172_consen    5 SETWVTVFGFPPSASNQ-----VLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIF   78 (100)
T ss_dssp             GCCEEEEE---GGGHHH-----HHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEE
T ss_pred             CCeEEEEEccCHHHHHH-----HHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEE
Confidence            34568888999886654     44899999999887411 1         01234689999999999999999 799999


Q ss_pred             CCc-eEEEEEcc
Q 025973           84 YDK-PMRIQYAK   94 (245)
Q Consensus        84 ~g~-~i~v~~~~   94 (245)
                      .|. .+-|.+.+
T Consensus        79 ~g~~mvGV~~~~   90 (100)
T PF05172_consen   79 SGSLMVGVKPCD   90 (100)
T ss_dssp             TTCEEEEEEE-H
T ss_pred             cCcEEEEEEEcH
Confidence            986 56677764

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.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.52  E-value=6.3e-05  Score=62.45  Aligned_cols=65  Identities=23%  Similarity=0.332  Sum_probs=56.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC---C---------------CeEEEEEeCCHHHHHHHHHHhCC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA---K---------------PGIAFVEYGDEMQATVAMQSLQS  230 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~---~---------------~g~afv~f~~~~~A~~A~~~l~g  230 (245)
                      -++.+|.+.|||....-+.|.++|+.+|.|+.|++..-   .               +-+|+|+|.+.+.|.+|.+.++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            36789999999999999999999999999999999863   0               34799999999999999998865


Q ss_pred             Cee
Q 025973          231 LKI  233 (245)
Q Consensus       231 ~~~  233 (245)
                      ..-
T Consensus       309 e~~  311 (484)
T KOG1855|consen  309 EQN  311 (484)
T ss_pred             hhh
Confidence            443

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.50  E-value=0.00025  Score=60.99  Aligned_cols=72  Identities=19%  Similarity=0.302  Sum_probs=58.8

Q ss_pred             CccEEEEcCCCCC--CC----HHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeC-CeEE
Q 025973          170 PNNILFVQNVPHD--TT----PMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIG-QQQL  238 (245)
Q Consensus       170 ~~~~l~v~nl~~~--~t----~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~-g~~i  238 (245)
                      -..+++|-|+|--  ..    ..-|..+|+++|++....+..+.    +||.|++|.+..+|..|++.|||+.|. +++.
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            3567999999832  11    34467899999999988888653    799999999999999999999999998 7777


Q ss_pred             EEE
Q 025973          239 LIT  241 (245)
Q Consensus       239 ~v~  241 (245)
                      .|-
T Consensus       137 ~v~  139 (698)
T KOG2314|consen  137 FVR  139 (698)
T ss_pred             Eee
Confidence            664

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.49  E-value=0.0013  Score=47.33  Aligned_cols=71  Identities=23%  Similarity=0.340  Sum_probs=52.9

Q ss_pred             CCCccEEEEcCCC-----CCCCH----HHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEE
Q 025973          168 APPNNILFVQNVP-----HDTTP----MALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQL  238 (245)
Q Consensus       168 ~~~~~~l~v~nl~-----~~~t~----~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i  238 (245)
                      .|+..++.|.=+.     .....    .+|.+.|..||.+.-|+++-+   .-.|.|.+-+.|.+|+. ++|..++|+.|
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~---~mwVTF~dg~sALaals-~dg~~v~g~~l   99 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD---TMWVTFRDGQSALAALS-LDGIQVNGRTL   99 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT---CEEEEESSCHHHHHHHH-GCCSEETTEEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC---eEEEEECccHHHHHHHc-cCCcEECCEEE
Confidence            3566677776444     12223    367888999999988888754   57899999999999997 89999999999


Q ss_pred             EEEE
Q 025973          239 LITY  242 (245)
Q Consensus       239 ~v~~  242 (245)
                      +|.+
T Consensus       100 ~i~L  103 (146)
T PF08952_consen  100 KIRL  103 (146)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            9986

; PDB: 1UFW_A 2DNR_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.46  E-value=0.00042  Score=55.96  Aligned_cols=74  Identities=15%  Similarity=0.356  Sum_probs=61.1

Q ss_pred             CccEEEEcCCCCCCCHHHH------HHHhccCCCeeEEEEecCC------Ce--EEEEEeCCHHHHHHHHHHhCCCeeCC
Q 025973          170 PNNILFVQNVPHDTTPMAL------QMFFSQFPGFKEVRMVEAK------PG--IAFVEYGDEMQATVAMQSLQSLKIGQ  235 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l------~~~f~~~g~v~~v~l~~~~------~g--~afv~f~~~~~A~~A~~~l~g~~~~g  235 (245)
                      ..+.+||-+|+..+..|+.      .++|.+||.|+.|.+-+.-      .+  -.++.|.+-++|.+++...+|..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            3456899999988877773      5889999999988776521      12  24999999999999999999999999


Q ss_pred             eEEEEEEe
Q 025973          236 QQLLITYA  243 (245)
Q Consensus       236 ~~i~v~~a  243 (245)
                      |.|+..|.
T Consensus       193 r~lkatYG  200 (480)
T COG5175         193 RVLKATYG  200 (480)
T ss_pred             ceEeeecC
Confidence            99999885

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.44  E-value=9.5e-05  Score=59.99  Aligned_cols=80  Identities=23%  Similarity=0.353  Sum_probs=68.2

Q ss_pred             CCCeEE-EcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           14 PNNTIY-INNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        14 ~~~~l~-V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      +..++| |++|+..+++++    |+.+|..+|.|..+++..   ++.++|+|||.|.+...+..++.. +...+.++++.
T Consensus       183 ~s~~~~~~~~~~f~~~~d~----~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~  257 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDD----LKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLR  257 (285)
T ss_pred             ccccceeecccccccchHH----HhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccc
Confidence            344555 999999999999    668999999999987664   788999999999999999999996 78888899999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      +.+..+...
T Consensus       258 ~~~~~~~~~  266 (285)
T KOG4210|consen  258 LEEDEPRPK  266 (285)
T ss_pred             cccCCCCcc
Confidence            998776544

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.42  E-value=7.5e-05  Score=58.05  Aligned_cols=58  Identities=12%  Similarity=0.222  Sum_probs=49.5

Q ss_pred             HHHHHHhc-cCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          186 MALQMFFS-QFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       186 ~~l~~~f~-~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +++...|+ +||.|..+++-.+.    .|.++|.|...++|.+|++.||+.+|.|++|...+.
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 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            45556666 89999888776643    689999999999999999999999999999998874

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.37  E-value=0.00011  Score=56.98  Aligned_cols=69  Identities=16%  Similarity=0.304  Sum_probs=57.0

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCC-----------CCee----eEEEEEecCHHHHHHHHHHH
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKT-----------LKHK----GQAWLVFKDVASATAAVEKM   78 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~-----------~~~k----g~afV~F~~~~~A~~a~~~l   78 (245)
                      ..-.||+++||+.++..-    |+++++.||.|-.|.+.+.           |.++    .-|+|+|.+-..|..+...|
T Consensus        73 k~GVvylS~IPp~m~~~r----lReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~L  148 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVR----LREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELL  148 (278)
T ss_pred             cceEEEeccCCCccCHHH----HHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHh
Confidence            457899999999999998    6688899999988866542           1112    25789999999999999999


Q ss_pred             cCCccCCc
Q 025973           79 QGFPFYDK   86 (245)
Q Consensus        79 ~~~~~~g~   86 (245)
                      |+..|.|+
T Consensus       149 nn~~Iggk  156 (278)
T KOG3152|consen  149 NNTPIGGK  156 (278)
T ss_pred             CCCccCCC
Confidence            99999876

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.33  E-value=0.00074  Score=53.57  Aligned_cols=73  Identities=16%  Similarity=0.215  Sum_probs=57.1

Q ss_pred             CccEEEEcCCC--CCC---CHHHHHHHhccCCCeeEEEEecCC------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEE
Q 025973          170 PNNILFVQNVP--HDT---TPMALQMFFSQFPGFKEVRMVEAK------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQL  238 (245)
Q Consensus       170 ~~~~l~v~nl~--~~~---t~~~l~~~f~~~g~v~~v~l~~~~------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i  238 (245)
                      ++++|.++|+-  -.+   -++++...+.+||.|-+|.++-..      .--.||+|..+++|.+|+-.|||..|+|+.+
T Consensus       280 ptkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v  359 (378)
T KOG1996|consen  280 PTKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVV  359 (378)
T ss_pred             chHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceee
Confidence            34456777762  233   345678889999999888777543      1247999999999999999999999999999


Q ss_pred             EEEE
Q 025973          239 LITY  242 (245)
Q Consensus       239 ~v~~  242 (245)
                      +.+|
T Consensus       360 ~A~F  363 (378)
T KOG1996|consen  360 SACF  363 (378)
T ss_pred             ehee
Confidence            9887

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.28  E-value=0.00047  Score=62.42  Aligned_cols=78  Identities=22%  Similarity=0.361  Sum_probs=68.4

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC--ceE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD--KPM   88 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g--~~i   88 (245)
                      ...+++.+|+++|+..+....    |...|..||+|..|.+...   -.||||+|++...|+.|++.|-|..|.|  +.+
T Consensus       451 kst~ttr~~sgglg~w~p~~~----l~r~fd~fGpir~Idy~hg---q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~  523 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSR----LNREFDRFGPIRIIDYRHG---QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRL  523 (975)
T ss_pred             ccccceeeccCCCCCCChHHH----HHHHhhccCcceeeecccC---CcceeeecccCccchhhHHHHhcCcCCCCCccc
Confidence            677899999999999999888    7799999999988876643   3699999999999999999999999984  589


Q ss_pred             EEEEccc
Q 025973           89 RIQYAKT   95 (245)
Q Consensus        89 ~v~~~~~   95 (245)
                      .|.|+..
T Consensus       524 rvdla~~  530 (975)
T KOG0112|consen  524 RVDLASP  530 (975)
T ss_pred             ccccccC
Confidence            9988753

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.26  E-value=0.001  Score=51.83  Aligned_cols=62  Identities=16%  Similarity=0.177  Sum_probs=51.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC-C---CeEEEEEeCCHHHHHHHHHHhCCCee
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-K---PGIAFVEYGDEMQATVAMQSLQSLKI  233 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~-~---~g~afv~f~~~~~A~~A~~~l~g~~~  233 (245)
                      ..|+|.||..-++.+.+..-|+.||.|..-.++.| +   .+-++|.|.....|..|+...+..-|
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~   97 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGF   97 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCcc
Confidence            45999999999999999999999999966554443 2   56899999999999999988854333

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=97.24  E-value=0.0032  Score=44.77  Aligned_cols=79  Identities=25%  Similarity=0.337  Sum_probs=59.5

Q ss_pred             CCCCCCCeEEEcCCCcccCh-HHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           10 NEISPNNTIYINNLNEKVKI-DQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~-~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ...+|-.+|.|+=|...+.. +|++ .+.+..+.||+|.+|...  |  +..|.|.|.+..+|.+|+.+++. ...|..+
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~-sV~~~Ls~fGpI~SVT~c--G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLK-SVIQRLSVFGPIQSVTLC--G--RQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHH-HHHHHHHhcCCcceeeec--C--CceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            34567778888877766644 3333 344667999999998665  3  46799999999999999998776 5668888


Q ss_pred             EEEEcc
Q 025973           89 RIQYAK   94 (245)
Q Consensus        89 ~v~~~~   94 (245)
                      ++.|-.
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            888743

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.23  E-value=0.00042  Score=59.99  Aligned_cols=78  Identities=17%  Similarity=0.291  Sum_probs=63.8

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHhcc-CCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC---CeEEEEEE
Q 025973          167 PAPPNNILFVQNVPHDTTPMALQMFFSQ-FPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG---QQQLLITY  242 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~-~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~---g~~i~v~~  242 (245)
                      ....+++|+|.||-...|..+|+.++.. .|.|....|-+- +.-|||.|.+.++|.....+|||-.+-   ++.|.+.|
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            4567889999999999999999999995 455654433222 468999999999999999999998774   88999999


Q ss_pred             ecC
Q 025973          243 AKK  245 (245)
Q Consensus       243 ak~  245 (245)
                      +.+
T Consensus       519 ~~~  521 (718)
T KOG2416|consen  519 VRA  521 (718)
T ss_pred             cch
Confidence            753

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.14  E-value=1.8e-05  Score=70.83  Aligned_cols=161  Identities=17%  Similarity=0.109  Sum_probs=111.0

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCC---eeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLK---HKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~---~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      .....+...+.++.+...+.++   ....|..+|.|+.|+....|.   ...++++.++...++..|.. ..+-.+.++.
T Consensus       567 ~~~~~~e~~s~~v~p~~~~ke~---~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~  642 (881)
T KOG0128|consen  567 APLERREKESTNVYPEQQKKEI---QRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRS  642 (881)
T ss_pred             hhhhhhhhcccCCCcchhhHHh---hHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCcc
Confidence            3455677788888887777652   678999999999997665222   22378888888888888877 5666667776


Q ss_pred             EEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           88 MRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAP  167 (245)
Q Consensus        88 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (245)
                      ..|..+.+......   -                                                        ......
T Consensus       643 ~av~~ad~~~~~~~---~--------------------------------------------------------kvs~n~  663 (881)
T KOG0128|consen  643 AAVGLADAEEKEEN---F--------------------------------------------------------KVSPNE  663 (881)
T ss_pred             ccCCCCCchhhhhc---c--------------------------------------------------------CcCchH
Confidence            66655544321000   0                                                        000000


Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEe--cC--C-CeEEEEEeCCHHHHHHHHHHhCCCeeC
Q 025973          168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV--EA--K-PGIAFVEYGDEMQATVAMQSLQSLKIG  234 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~--~~--~-~g~afv~f~~~~~A~~A~~~l~g~~~~  234 (245)
                      .....++|++||+..+.+++|...|+.+|.+..+.+.  .+  + +|+|++.|..++++.+|+....++.++
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            0123469999999999999999999999987665554  22  2 799999999999999999855444443

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.07  E-value=0.00069  Score=58.69  Aligned_cols=84  Identities=20%  Similarity=0.314  Sum_probs=65.4

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhc-ccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC--
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFK-QFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY--   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~-~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~--   84 (245)
                      +.+-.++++.|||.||-...|..+|+    .+.. ..|.|.+.|+.+   -|..|||.|.+.++|.....+|||+.+-  
T Consensus       437 SPsR~~~SnvlhI~nLvRPFTlgQLk----elL~rtgg~Vee~WmDk---IKShCyV~yss~eEA~atr~AlhnV~WP~s  509 (718)
T KOG2416|consen  437 SPSRKEPSNVLHIDNLVRPFTLGQLK----ELLGRTGGNVEEFWMDK---IKSHCYVSYSSVEEAAATREALHNVQWPPS  509 (718)
T ss_pred             CCCCCCccceEeeecccccchHHHHH----HHHhhccCchHHHHHHH---hhcceeEecccHHHHHHHHHHHhccccCCC
Confidence            33456779999999999999999955    6666 345666665543   3568999999999999999999998885  


Q ss_pred             -CceEEEEEccccch
Q 025973           85 -DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 -g~~i~v~~~~~~~~   98 (245)
                       ++.|.+.|......
T Consensus       510 NPK~L~adf~~~del  524 (718)
T KOG2416|consen  510 NPKHLIADFVRADEL  524 (718)
T ss_pred             CCceeEeeecchhHH
Confidence             56888888765433

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.05  E-value=0.0067  Score=39.10  Aligned_cols=57  Identities=23%  Similarity=0.378  Sum_probs=42.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQS  230 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g  230 (245)
                      ...+.+|. .|......||.++|++||.|. |.-+.+  .-|||...+.+.|..|+..+..
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d--TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND--TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT--TEEEEEECCCHHHHHHHHHHTT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC--CcEEEEeecHHHHHHHHHHhcc
Confidence            45667776 899999999999999999963 333334  3799999999999999988753

; 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.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.00  E-value=0.0011  Score=54.66  Aligned_cols=69  Identities=20%  Similarity=0.320  Sum_probs=58.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      +|.|.||.++.|.+++..+|...|+|..+.|+++.        .-.|||.|.+...+..|- +|.++.|-++.|.|-.
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p   85 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRP   85 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEe
Confidence            79999999999999999999999999999999842        248999999988877776 5778888777776653

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.97  E-value=0.00082  Score=56.03  Aligned_cols=67  Identities=25%  Similarity=0.263  Sum_probs=55.3

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCC----------------eeeEEEEEecCHHHHHHHH
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLK----------------HKGQAWLVFKDVASATAAV   75 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~----------------~kg~afV~F~~~~~A~~a~   75 (245)
                      ..++++|.+-|||.+-.-+.    |..+|+.+|.|..|++.+.|.                .+-+|+|+|...+.|.+|.
T Consensus       228 el~srtivaenLP~Dh~~en----l~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~  303 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYEN----LSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAR  303 (484)
T ss_pred             ccccceEEEecCCcchHHHH----HHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHH
Confidence            35899999999998877766    779999999999998876521                2458999999999999999


Q ss_pred             HHHcCCc
Q 025973           76 EKMQGFP   82 (245)
Q Consensus        76 ~~l~~~~   82 (245)
                      +.|+...
T Consensus       304 e~~~~e~  310 (484)
T KOG1855|consen  304 ELLNPEQ  310 (484)
T ss_pred             Hhhchhh
Confidence            9776533

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.92  E-value=0.0007  Score=52.78  Aligned_cols=54  Identities=19%  Similarity=0.354  Sum_probs=46.4

Q ss_pred             ccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEccc
Q 025973           42 QFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKT   95 (245)
Q Consensus        42 ~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~~   95 (245)
                      +||.|+++.+..  .-...|.+||.|...++|.+|+..||+-.|.|++|+.+++.-
T Consensus        92 kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   92 KYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            899999875443  334679999999999999999999999999999999999653

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.90  E-value=0.0034  Score=53.68  Aligned_cols=66  Identities=18%  Similarity=0.357  Sum_probs=54.8

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhc-ccCCeEEEEecCC---CCeeeEEEEEecCHHHHHHHHHH
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFK-QFGTILEILAFKT---LKHKGQAWLVFKDVASATAAVEK   77 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~-~~G~v~~i~~~~~---~~~kg~afV~F~~~~~A~~a~~~   77 (245)
                      ......+.+|||||+||.-++-.+    |..+|+ -||.|..+-+..+   +-.+|-|=|.|++..+-.+||++
T Consensus       363 ~sq~lDprrTVFVGgvprpl~A~e----LA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  363 HNQPIDPRRTVFVGGLPRPLTAEE----LAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCcccCccceEEecCCCCcchHHH----HHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            445678899999999999999999    667777 7899988755543   44679999999999999999984

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.78  E-value=0.01  Score=42.29  Aligned_cols=73  Identities=18%  Similarity=0.220  Sum_probs=55.0

Q ss_pred             CCccEEEEcCCC----CCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVP----HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~----~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ++-.+|.|+=|.    ..-+...+...++.||.|.+|.+.-  +.-|.|.|.+..+|-.|+.+++. ...|..+.+.|-.
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWqq  160 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQQ  160 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC--CceEEEEehhhHHHHHHHHhhcC-CCCCceEEeeccc
Confidence            445568887554    3334455667778999999887753  35799999999999999999865 6678888888743

>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=96.57  E-value=0.057  Score=37.26  Aligned_cols=79  Identities=16%  Similarity=0.189  Sum_probs=53.8

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhccc-CCeEEEEecCCCC-eeeEEEEEecCHHHHHHHHHHHcCCccC---Cc
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQF-GTILEILAFKTLK-HKGQAWLVFKDVASATAAVEKMQGFPFY---DK   86 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~-G~v~~i~~~~~~~-~kg~afV~F~~~~~A~~a~~~l~~~~~~---g~   86 (245)
                      ...+..|.|--.|+.++..+.   |..+.+.+ ..|..+++.+++. ++--+.+.|.+.++|......+||..|.   ..
T Consensus         9 ~~~~~~~~~l~vp~~~~~~d~---l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE   85 (110)
T PF07576_consen    9 DERRSTLCCLAVPPYMTPSDF---LLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPE   85 (110)
T ss_pred             CCCCceEEEEEeCcccccHHH---HHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCc
Confidence            344555555555655555431   33444444 4566778887765 5667889999999999999999998886   44


Q ss_pred             eEEEEEc
Q 025973           87 PMRIQYA   93 (245)
Q Consensus        87 ~i~v~~~   93 (245)
                      .++|-|.
T Consensus        86 ~ChvvfV   92 (110)
T PF07576_consen   86 TCHVVFV   92 (110)
T ss_pred             eeEEEEE
Confidence            5666554

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.51  E-value=0.008  Score=47.89  Aligned_cols=69  Identities=16%  Similarity=0.275  Sum_probs=53.5

Q ss_pred             ChHHHHHHHHHhhcccCCeEEEEecCCC----CeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEcccc
Q 025973           28 KIDQLKQSLHAVFKQFGTILEILAFKTL----KHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTK   96 (245)
Q Consensus        28 ~~~~l~~~l~~~F~~~G~v~~i~~~~~~----~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~~~   96 (245)
                      -+++|...+..-++.||.|..|.+....    ..----||+|++.++|.+|+-.|||..|.||.+.-.|....
T Consensus       295 vd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~e  367 (378)
T KOG1996|consen  295 VDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLE  367 (378)
T ss_pred             ccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHH
Confidence            3455555577889999999987665421    11125899999999999999999999999999988886543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.45  E-value=0.024  Score=34.61  Aligned_cols=52  Identities=17%  Similarity=0.322  Sum_probs=42.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccC----CCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHh
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQF----PGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL  228 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~----g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l  228 (245)
                      .|+|++++ .++-++|..+|..|    + ..+|.-+.+.  -|-|.|.+.+.|.+||.+|
T Consensus         7 avhirGvd-~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt--ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    7 AVHIRGVD-ELSTDDIKAYFSEYFDEEG-PFRIEWIDDT--SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eEEEEcCC-CCCHHHHHHHHHHhcccCC-CceEEEecCC--cEEEEECCHHHHHHHHHcC
Confidence            49999986 58888999999988    3 3556666664  5899999999999999865

>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=96.43  E-value=0.013  Score=44.37  Aligned_cols=60  Identities=15%  Similarity=0.146  Sum_probs=46.6

Q ss_pred             CHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhC--CCeeCCeEEEEEEec
Q 025973          184 TPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQ--SLKIGQQQLLITYAK  244 (245)
Q Consensus       184 t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~--g~~~~g~~i~v~~ak  244 (245)
                      ..+.|+.+|..|+.+..+...+.- +-..|.|.+.+.|..|...|+  +..|.|..++|-|+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF-rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF-RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT-TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC-CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            458899999999998877777765 368999999999999999999  999999999999874

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.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=96.37  E-value=0.0058  Score=55.33  Aligned_cols=71  Identities=17%  Similarity=0.249  Sum_probs=61.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC--CeEEEEEEec
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG--QQQLLITYAK  244 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~--g~~i~v~~ak  244 (245)
                      +..+.|.+-..+-..|..+|+.||.|.+.+..++- ..|.|+|...+.|..|+.+++|..+.  |-+.+|.|||
T Consensus       300 ~~~~~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  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL-NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAK  372 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc-cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecc
Confidence            34455556677888899999999999999888776 68999999999999999999998876  8899999987

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.33  E-value=0.0045  Score=51.71  Aligned_cols=68  Identities=24%  Similarity=0.351  Sum_probs=53.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCe--eEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCe-eCCeEEEEEEe
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGF--KEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLK-IGQQQLLITYA  243 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v--~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~-~~g~~i~v~~a  243 (245)
                      .+|++||...++.+||..+|... .+  ..-.++  +.||+||.+.+...|.+|.+.++|.. +.|+++.|..+
T Consensus         3 klyignL~p~~~psdl~svfg~a-k~~~~g~fl~--k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~s   73 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDA-KIPGSGQFLV--KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHS   73 (584)
T ss_pred             cccccccCCCCChHHHHHHhccc-cCCCCcceee--ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccch
Confidence            48999999999999999999743 11  111122  25899999999999999999999954 67999988764

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.28  E-value=0.0056  Score=49.91  Aligned_cols=76  Identities=17%  Similarity=0.153  Sum_probs=58.9

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      .-.+||+||--.+|++||.+.|...--  ..+.+|.+.   .+|.+||||+|...+.....+-++.|-...++|..-.|.
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 KYCCYVGNLLWYTTDADLLKALQSTGL--AQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhH--HHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            456899999999999997766654311  145555544   378999999999999999999999999999998854444


Q ss_pred             E
Q 025973           92 Y   92 (245)
Q Consensus        92 ~   92 (245)
                      .
T Consensus       158 ~  158 (498)
T KOG4849|consen  158 S  158 (498)
T ss_pred             c
Confidence            3

>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=96.13  E-value=0.01  Score=44.78  Aligned_cols=80  Identities=14%  Similarity=0.203  Sum_probs=47.8

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcc-cCCe---EEEE--ecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCc
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQ-FGTI---LEIL--AFK---TLKHKGQAWLVFKDVASATAAVEKMQGFP   82 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~-~G~v---~~i~--~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~   82 (245)
                      .....+|.|++||+..|+++    ++...+. ++.-   ..+.  ...   .......|||.|.+.+++......++|..
T Consensus         4 ~~~~~KvVIR~LPP~Lteee----F~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~   79 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEE----FWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHV   79 (176)
T ss_dssp             -----EEEEEEE-TTS-HHH----HCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEE
T ss_pred             cccCceEEEeCCCCCCCHHH----HHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcE
Confidence            45567999999999999999    5555554 4444   2222  111   11123579999999999999999999977


Q ss_pred             cCCc-----eEEEEEccc
Q 025973           83 FYDK-----PMRIQYAKT   95 (245)
Q Consensus        83 ~~g~-----~i~v~~~~~   95 (245)
                      |.+.     .-.|++|.-
T Consensus        80 F~D~kg~~~~~~VE~Apy   97 (176)
T PF03467_consen   80 FVDSKGNEYPAVVEFAPY   97 (176)
T ss_dssp             EE-TTS-EEEEEEEE-SS
T ss_pred             EECCCCCCcceeEEEcch
Confidence            7532     555666543

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.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=96.05  E-value=0.042  Score=44.11  Aligned_cols=75  Identities=9%  Similarity=0.078  Sum_probs=58.0

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc-eEEEEEc
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK-PMRIQYA   93 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~-~i~v~~~   93 (245)
                      ..=|-|=++|+....-     |-.+|++||.|.......+|   ++-+|.|.+.-+|++|+. .||..|.|. .|-|...
T Consensus       197 D~WVTVfGFppg~~s~-----vL~~F~~cG~Vvkhv~~~ng---NwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpC  267 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQVSI-----VLNLFSRCGEVVKHVTPSNG---NWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPC  267 (350)
T ss_pred             cceEEEeccCccchhH-----HHHHHHhhCeeeeeecCCCC---ceEEEEecchhHHHHhhh-hcCeeeccceEEeeeec
Confidence            5556677888776543     34899999999886555554   799999999999999999 799999887 6677776


Q ss_pred             cccch
Q 025973           94 KTKSD   98 (245)
Q Consensus        94 ~~~~~   98 (245)
                      ..+.-
T Consensus       268 tDksv  272 (350)
T KOG4285|consen  268 TDKSV  272 (350)
T ss_pred             CCHHH
Confidence            55543

>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=96.00  E-value=0.13  Score=35.50  Aligned_cols=65  Identities=12%  Similarity=0.213  Sum_probs=50.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEecCCC---eEEEEEeCCHHHHHHHHHHhCCCeeC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPG-FKEVRMVEAKP---GIAFVEYGDEMQATVAMQSLQSLKIG  234 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~-v~~v~l~~~~~---g~afv~f~~~~~A~~A~~~l~g~~~~  234 (245)
                      ...++.+-..|.-++-++|..+.+.+-. |..++++++..   =.++++|.+.++|..-...+||+.|.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            3445555555666777778777776654 67888988753   37899999999999999999999886

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=95.90  E-value=0.037  Score=43.41  Aligned_cols=73  Identities=21%  Similarity=0.282  Sum_probs=56.7

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEE--EEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC----CceEE
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY----DKPMR   89 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~--i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~----g~~i~   89 (245)
                      ..|+|.||+..++.+.    +.+-|+.||+|..  +.....++..+-++|.|.+.-.|.+|...+..--|.    ++...
T Consensus        32 a~l~V~nl~~~~sndl----l~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~  107 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDL----LEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVG  107 (275)
T ss_pred             ceEEEEecchhhhhHH----HHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccC
Confidence            6799999999999999    7799999999975  334445667788999999999999999987543332    44555


Q ss_pred             EEE
Q 025973           90 IQY   92 (245)
Q Consensus        90 v~~   92 (245)
                      |..
T Consensus       108 VeP  110 (275)
T KOG0115|consen  108 VEP  110 (275)
T ss_pred             CCh
Confidence            544

>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=95.76  E-value=0.048  Score=34.77  Aligned_cols=59  Identities=19%  Similarity=0.263  Sum_probs=36.9

Q ss_pred             CCCCHHHHHHHhccCCCe-----eEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          181 HDTTPMALQMFFSQFPGF-----KEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       181 ~~~t~~~l~~~f~~~g~v-----~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +.++..+|..++...+.|     -.|.+.   ..|+||+-.. +.|..++..|++..+.|+++.|..|
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 DGLTPRDIVGAICNEAGIPGRDIGRIDIF---DNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE----SS-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEe---eeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            678888999888877654     455554   3589999886 6899999999999999999999876

; PDB: 2G0C_A 3MOJ_B.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.75  E-value=0.11  Score=31.65  Aligned_cols=55  Identities=25%  Similarity=0.349  Sum_probs=37.4

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccC--CeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHH
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFG--TILEILAFKTLKHKGQAWLVFKDVASATAAVEKM   78 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G--~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l   78 (245)
                      ..|+|+|+.. ++-++|+.++..+|..-+  .|+-|.+       ..|=|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdD-------tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDD-------TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecC-------CcEEEEECCHHHHHHHHHcC
Confidence            5699999966 555676766655543224  3333322       25889999999999999754

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.75  E-value=0.019  Score=50.71  Aligned_cols=68  Identities=19%  Similarity=0.259  Sum_probs=59.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLI  240 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v  240 (245)
                      ++..++||+|+...+..+-+..+...+|.|..++...    |||+.|..+.-+.+|+..++-..++|..+.+
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~----fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK----FGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh----hcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            4566799999999999999999999999998776653    9999999999999999999888888877654

>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=95.73  E-value=0.019  Score=43.28  Aligned_cols=64  Identities=9%  Similarity=0.063  Sum_probs=45.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhcc-CCCe---eEEEEecCC-------CeEEEEEeCCHHHHHHHHHHhCCCeeC
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQ-FPGF---KEVRMVEAK-------PGIAFVEYGDEMQATVAMQSLQSLKIG  234 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~-~g~v---~~v~l~~~~-------~g~afv~f~~~~~A~~A~~~l~g~~~~  234 (245)
                      ...|.||+||+.+|+++++..+++ ++.-   .++.-..+.       ..-|+|.|.+.++.......++|+.|-
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~   81 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFV   81 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEE
Confidence            457999999999999999998887 6665   233211221       346999999999999999999997774

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.

>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=95.67  E-value=0.024  Score=42.99  Aligned_cols=62  Identities=19%  Similarity=0.379  Sum_probs=44.8

Q ss_pred             HHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHc--CCccCCceEEEEEccc
Q 025973           31 QLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQ--GFPFYDKPMRIQYAKT   95 (245)
Q Consensus        31 ~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~--~~~~~g~~i~v~~~~~   95 (245)
                      ++++.|+.+|..++.+......++-   +-..|.|.+.++|.+|...|+  +..+.|..++|.|+..
T Consensus         7 ~~~~~l~~l~~~~~~~~~~~~L~sF---rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    7 DNLAELEELFSTYDPPVQFSPLKSF---RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             --HHHHHHHHHTT-SS-EEEEETTT---TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hhHHHHHHHHHhcCCceEEEEcCCC---CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            4455588999999988887666543   468899999999999999999  8999999999999843

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=95.67  E-value=0.09  Score=32.61  Aligned_cols=56  Identities=11%  Similarity=0.209  Sum_probs=45.7

Q ss_pred             CCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEE
Q 025973          181 HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLI  240 (245)
Q Consensus       181 ~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v  240 (245)
                      ..++-++++..+..|+   +.++..+++| =+|.|.+..+|.+.....+|..+.+.+|..
T Consensus        10 ~~~~v~d~K~~Lr~y~---~~~I~~d~tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYR---WDRIRDDRTG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCC---cceEEecCCE-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4678899999999985   3444556665 488999999999999999999999888764

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=95.43  E-value=0.065  Score=45.42  Aligned_cols=65  Identities=17%  Similarity=0.336  Sum_probs=57.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFP-GFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIG  234 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g-~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~  234 (245)
                      ++++|+|-.+|..++-.||..|+..+- .|.+++++++.   +-..++.|.+.++|......+||..|.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            378899999999999999999998764 47999999875   347899999999999999999999886

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=95.19  E-value=0.1  Score=44.26  Aligned_cols=78  Identities=18%  Similarity=0.227  Sum_probs=60.1

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhccc-CCeEEEEecCCCC-eeeEEEEEecCHHHHHHHHHHHcCCccC---Cc
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQF-GTILEILAFKTLK-HKGQAWLVFKDVASATAAVEKMQGFPFY---DK   86 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~-G~v~~i~~~~~~~-~kg~afV~F~~~~~A~~a~~~l~~~~~~---g~   86 (245)
                      ..+++.|+|-.+|..++-.||.    .++..+ -.|..|++.++|. ++-..+|.|.+.++|....+.+||..|.   ..
T Consensus        71 ~~~~~mLcilaVP~~mt~~Dll----~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e  146 (493)
T KOG0804|consen   71 ASSSTMLCILAVPAYMTSHDLL----RFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPE  146 (493)
T ss_pred             CCCCcEEEEEeccccccHHHHH----HHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCcc
Confidence            4448999999999999999955    544444 4677787777665 4557889999999999999999998887   33


Q ss_pred             eEEEEEc
Q 025973           87 PMRIQYA   93 (245)
Q Consensus        87 ~i~v~~~   93 (245)
                      .+++-|.
T Consensus       147 ~Chll~V  153 (493)
T KOG0804|consen  147 VCHLLYV  153 (493)
T ss_pred             ceeEEEE
Confidence            5555554

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.13  E-value=0.0071  Score=49.19  Aligned_cols=84  Identities=17%  Similarity=0.309  Sum_probs=63.9

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCC--C----eeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTL--K----HKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~--~----~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ..+-+||-+|+.....+++.+.- ..|.+||.|..|...++-  .    .--.+||.|...++|..|+...+|....|+.
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~-eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~  154 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERT-EYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRA  154 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCc-ccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhh
Confidence            35678999999887665543222 689999999998766532  0    1125899999999999999999999999999


Q ss_pred             EEEEEccccch
Q 025973           88 MRIQYAKTKSD   98 (245)
Q Consensus        88 i~v~~~~~~~~   98 (245)
                      ++..+...+-.
T Consensus       155 lka~~gttkyc  165 (327)
T KOG2068|consen  155 LKASLGTTKYC  165 (327)
T ss_pred             hHHhhCCCcch
Confidence            88888765443

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.77  E-value=0.063  Score=46.68  Aligned_cols=69  Identities=12%  Similarity=0.274  Sum_probs=56.6

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhcc--CCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCC--CeeCCeEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQ--FPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQS--LKIGQQQLLI  240 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~--~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g--~~~~g~~i~v  240 (245)
                      ..++++++.||..+..|+++.+|..  +-.+++|.+-.+.  -=||+|.+..+|+.|...|..  +.|-||+|+.
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~--nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND--NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC--ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            4568999999999999999999985  5677888777654  468999999999999988865  5677887754

>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=94.20  E-value=2.5  Score=34.22  Aligned_cols=85  Identities=14%  Similarity=0.299  Sum_probs=62.7

Q ss_pred             cccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCC----------CeeeEEEEEecCHHHHHHHH
Q 025973            6 ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTL----------KHKGQAWLVFKDVASATAAV   75 (245)
Q Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~----------~~kg~afV~F~~~~~A~~a~   75 (245)
                      ...+.|.-.+|.|...|+..+++--+    +...|-.||+|++|.+..+.          +......+.|-+.+.|....
T Consensus         6 LPkGdD~YrTRSLLfeNv~~sidLh~----Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFY   81 (309)
T PF10567_consen    6 LPKGDDEYRTRSLLFENVNNSIDLHS----FLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFY   81 (309)
T ss_pred             cCCCCccceeHHHHHhhccccccHHH----HHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHH
Confidence            34577888899999999998888777    55899999999999776544          23457889999988876554


Q ss_pred             ----HHHcC--CccCCceEEEEEcc
Q 025973           76 ----EKMQG--FPFYDKPMRIQYAK   94 (245)
Q Consensus        76 ----~~l~~--~~~~g~~i~v~~~~   94 (245)
                          ++|..  ..+....+.+.|..
T Consensus        82 NnvLQrLsEfK~~L~S~~L~lsFV~  106 (309)
T PF10567_consen   82 NNVLQRLSEFKTKLKSESLTLSFVS  106 (309)
T ss_pred             HHHHHHHHHHHHhcCCcceeEEEEE
Confidence                22332  34456677777754

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.

>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=94.18  E-value=0.24  Score=30.70  Aligned_cols=55  Identities=20%  Similarity=0.332  Sum_probs=42.2

Q ss_pred             ccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           26 KVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        26 ~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      .++-.+|+    ..+..|+ -..|+..++|     =||.|.+.++|.++....+|..+.+.+|.+
T Consensus        11 ~~~v~d~K----~~Lr~y~-~~~I~~d~tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFK----KRLRKYR-WDRIRDDRTG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHH----HHHhcCC-cceEEecCCE-----EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            44666755    5566774 4467777665     689999999999999999999888877655

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=94.15  E-value=0.034  Score=50.61  Aligned_cols=71  Identities=24%  Similarity=0.409  Sum_probs=56.9

Q ss_pred             EcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC--CceEEEEEccccc
Q 025973           20 INNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY--DKPMRIQYAKTKS   97 (245)
Q Consensus        20 V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~--g~~i~v~~~~~~~   97 (245)
                      +.|.+-..+...    |..+|+.||.|.+.|..++-   +.|.|.|.+.+.|..|..+++|....  |-+.+|.+++.-.
T Consensus       303 ~~nn~v~~tSss----L~~l~s~yg~v~s~wtlr~~---N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  303 LENNAVNLTSSS----LATLCSDYGSVASAWTLRDL---NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             hhcccccchHHH----HHHHHHhhcchhhheecccc---cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            334444556666    77999999999999886653   68999999999999999999996664  8899999987543

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=93.97  E-value=0.13  Score=42.28  Aligned_cols=68  Identities=19%  Similarity=0.228  Sum_probs=55.6

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEE
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFP--GFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQL  238 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g--~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i  238 (245)
                      .-++||+||---+|.+||.+..+..|  .+.+++++-++     ||||+|...+.......++.|-.+.|+|..-
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P  154 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSP  154 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCC
Confidence            34799999999999999998888766  35667776654     8999999999888889999888888886543

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=93.93  E-value=0.034  Score=47.29  Aligned_cols=72  Identities=15%  Similarity=0.194  Sum_probs=57.5

Q ss_pred             CccEEEEcCCCCCC-CHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          170 PNNILFVQNVPHDT-TPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       170 ~~~~l~v~nl~~~~-t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ....|-+.-.|... +..+|..+|..||.|..|.+-... .-|.|+|.+..+|-.|.. .++..|.++.|+|-|=
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~-~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~wh  443 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS-LHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWH  443 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCch-hhheeeeeccccccchhc-cccceecCceeEEEEe
Confidence            34445555555433 678999999999999988886653 469999999999988876 6899999999999884

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=92.48  E-value=0.29  Score=39.47  Aligned_cols=62  Identities=13%  Similarity=0.088  Sum_probs=46.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeE
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQ  237 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~  237 (245)
                      -+-|.++|..- -.-|..+|++||.|.+.....+ -.+-.|.|.+.-+|.+||. -||+.|+|..
T Consensus       199 WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~~n-gNwMhirYssr~~A~KALs-kng~ii~g~v  260 (350)
T KOG4285|consen  199 WVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTPSN-GNWMHIRYSSRTHAQKALS-KNGTIIDGDV  260 (350)
T ss_pred             eEEEeccCccc-hhHHHHHHHhhCeeeeeecCCC-CceEEEEecchhHHHHhhh-hcCeeeccce
Confidence            35566666433 3456788999999876655533 3589999999999999998 5899998654

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=92.06  E-value=0.39  Score=42.02  Aligned_cols=67  Identities=18%  Similarity=0.306  Sum_probs=50.5

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcc--cCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcC--CccCCceE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQ--FGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQG--FPFYDKPM   88 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~--~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~--~~~~g~~i   88 (245)
                      ..|.|.++-||..+-+++++    .+|+.  +-++++|.+-.+    .-=||.|++..||+.|++.|..  ..|.|+.|
T Consensus       174 kRcIvilREIpettp~e~Vk----~lf~~encPk~iscefa~N----~nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVK----ALFKGENCPKVISCEFAHN----DNWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             ceeEEEEeecCCCChHHHHH----HHhccCCCCCceeeeeeec----CceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            36778899999999999955    88874  557778755432    2368999999999999988754  45566644

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=90.36  E-value=0.17  Score=43.30  Aligned_cols=75  Identities=19%  Similarity=0.240  Sum_probs=58.5

Q ss_pred             CCeEEEcCCCcccCh-HHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           15 NNTIYINNLNEKVKI-DQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~-~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      .+.|-+.-.|+..+. .+    |...|.+||.|..|.+...   .-.|.|.|.+-.+|-+|.. .++-.|+|+.|+|.|.
T Consensus       372 hs~l~lek~~~glnt~a~----ln~hfA~fG~i~n~qv~~~---~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~wh  443 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIAD----LNPHFAQFGEIENIQVDYS---SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWH  443 (526)
T ss_pred             cchhhhhccCCCCchHhh----hhhhhhhcCccccccccCc---hhhheeeeeccccccchhc-cccceecCceeEEEEe
Confidence            445555666665543 44    7799999999999866543   2469999999999999988 7999999999999998


Q ss_pred             cccc
Q 025973           94 KTKS   97 (245)
Q Consensus        94 ~~~~   97 (245)
                      ++..
T Consensus       444 nps~  447 (526)
T KOG2135|consen  444 NPSP  447 (526)
T ss_pred             cCCc
Confidence            7643

>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=90.22  E-value=1.8  Score=27.47  Aligned_cols=63  Identities=14%  Similarity=0.144  Sum_probs=31.8

Q ss_pred             cccChHHHHHHHHHhhccc-CCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           25 EKVKIDQLKQSLHAVFKQF-GTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        25 ~~~~~~~l~~~l~~~F~~~-G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      ..++..+|..+|.....-- ..|-.|.+..     .|+||+-... .|..++..|++..+.|+.+.|+.|
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-----NFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S-----S-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee-----eEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3456667543333322111 1444566654     4899998754 899999999999999999999764

; PDB: 2G0C_A 3MOJ_B.

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=89.73  E-value=0.35  Score=31.83  Aligned_cols=24  Identities=13%  Similarity=0.203  Sum_probs=20.6

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhc
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFS  193 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~  193 (245)
                      +.++|.|.|||....+++|++...
T Consensus        51 s~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen   51 SKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             cCCEEEEeCCCCCCChhhheeeEE
Confidence            567899999999999999987654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=89.31  E-value=0.11  Score=42.43  Aligned_cols=72  Identities=14%  Similarity=0.319  Sum_probs=55.8

Q ss_pred             cEEEEcCCCCCCCHHHH---HHHhccCCCeeEEEEecCC--------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEE
Q 025973          172 NILFVQNVPHDTTPMAL---QMFFSQFPGFKEVRMVEAK--------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLI  240 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l---~~~f~~~g~v~~v~l~~~~--------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v  240 (245)
                      +.+|+-+|+..+..+.+   ...|.+||.|..|....+.        .--++|.|...++|..|+...+|+...|+.|+.
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            45777777766655544   3678899999888887743        113799999999999999999999999998777


Q ss_pred             EEe
Q 025973          241 TYA  243 (245)
Q Consensus       241 ~~a  243 (245)
                      .++
T Consensus       158 ~~g  160 (327)
T KOG2068|consen  158 SLG  160 (327)
T ss_pred             hhC
Confidence            654

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.85  E-value=3.7  Score=36.39  Aligned_cols=67  Identities=18%  Similarity=0.247  Sum_probs=57.0

Q ss_pred             CccEEEEcCCC-CCCCHHHHHHHhccC----CCeeEEEEecCC-------------C-----------------------
Q 025973          170 PNNILFVQNVP-HDTTPMALQMFFSQF----PGFKEVRMVEAK-------------P-----------------------  208 (245)
Q Consensus       170 ~~~~l~v~nl~-~~~t~~~l~~~f~~~----g~v~~v~l~~~~-------------~-----------------------  208 (245)
                      .++.|-|-||+ ..+..+||..+|+.|    |.|.+|.|++..             +                       
T Consensus       173 ~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~~~  252 (650)
T KOG2318|consen  173 ETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEEED  252 (650)
T ss_pred             ccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhhhh
Confidence            56779999999 899999999998865    579999998831             1                       


Q ss_pred             ----------------eEEEEEeCCHHHHHHHHHHhCCCeeCCe
Q 025973          209 ----------------GIAFVEYGDEMQATVAMQSLQSLKIGQQ  236 (245)
Q Consensus       209 ----------------g~afv~f~~~~~A~~A~~~l~g~~~~g~  236 (245)
                                      =||.|+|.+.+.|......++|..|...
T Consensus       253 ~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS  296 (650)
T KOG2318|consen  253 VDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESS  296 (650)
T ss_pred             HHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccc
Confidence                            1799999999999999999999999833

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=86.65  E-value=0.58  Score=41.82  Aligned_cols=73  Identities=11%  Similarity=0.160  Sum_probs=59.6

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ++.++.-+|||+|+...+..+-    +......+|.|.++...      -|+|..|....-+..|+..++...+.|..+.
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~----~~~il~~~g~v~s~kr~------~fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~  104 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEF----WKSILAKSGFVPSWKRD------KFGFCEFLKHIGDLRASRLLTELNIDDQKLI  104 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHH----HHHHHhhCCcchhhhhh------hhcccchhhHHHHHHHHHHhcccCCCcchhh
Confidence            4567789999999999999887    45777888988775332      2999999999999999998998888887665


Q ss_pred             EEE
Q 025973           90 IQY   92 (245)
Q Consensus        90 v~~   92 (245)
                      +..
T Consensus       105 ~~~  107 (668)
T KOG2253|consen  105 ENV  107 (668)
T ss_pred             ccc
Confidence            544

>PF14893 PNMA: PNMA

Probab=83.83  E-value=1  Score=37.47  Aligned_cols=55  Identities=13%  Similarity=0.280  Sum_probs=41.3

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE--EecCCCCeeeEEEEEecCH
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI--LAFKTLKHKGQAWLVFKDV   68 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i--~~~~~~~~kg~afV~F~~~   68 (245)
                      -+-+.|.|.|||.+|++++|.+.|...+...|...-.  .+.+.-. ...|+|+|...
T Consensus        16 ~~~r~lLv~giP~dc~~~ei~e~l~~~l~plg~yrvl~~~f~~~~~-~~aalve~~e~   72 (331)
T PF14893_consen   16 DPQRALLVLGIPEDCEEAEIEEALQAALSPLGRYRVLGKMFRREEN-AKAALVEFAED   72 (331)
T ss_pred             ChhhhheeecCCCCCCHHHHHHHHHHhhcccccceehhhHhhhhcc-cceeeeecccc
Confidence            3456789999999999999999999989888866433  3333322 34799999744

>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=83.25  E-value=3.3  Score=33.51  Aligned_cols=73  Identities=12%  Similarity=0.245  Sum_probs=56.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC------------CeEEEEEeCCHHHHHH----HHHHhCC--Ce
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK------------PGIAFVEYGDEMQATV----AMQSLQS--LK  232 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~------------~g~afv~f~~~~~A~~----A~~~l~g--~~  232 (245)
                      ++-|.+.|+...++-......|-.||.|.+|+++.+.            .-...+.|-+.+.+..    .++.|+.  +.
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            3459999999999999999999999999999999864            2368889988877653    4444543  44


Q ss_pred             eCCeEEEEEEe
Q 025973          233 IGQQQLLITYA  243 (245)
Q Consensus       233 ~~g~~i~v~~a  243 (245)
                      +....|.+.|.
T Consensus        95 L~S~~L~lsFV  105 (309)
T PF10567_consen   95 LKSESLTLSFV  105 (309)
T ss_pred             cCCcceeEEEE
Confidence            66777777774

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.

>PRK14548 50S ribosomal protein L23P; Provisional

Probab=81.76  E-value=6  Score=25.83  Aligned_cols=56  Identities=11%  Similarity=0.195  Sum_probs=41.7

Q ss_pred             EEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHH
Q 025973           19 YINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE   76 (245)
Q Consensus        19 ~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~   76 (245)
                      |.=-.+.+++..+|++.++.+|..  .|..|..........-|||.+....+|...-.
T Consensus        24 y~F~V~~~anK~eIK~AvE~lf~V--kV~~VnT~~~~~~~KKA~V~L~~g~~A~~va~   79 (84)
T PRK14548         24 LTFIVDRRATKPDIKRAVEELFDV--KVEKVNTLITPKGEKKAYVKLAEEYDAEEIAS   79 (84)
T ss_pred             EEEEECCCCCHHHHHHHHHHHhCC--ceEEEEeEEcCCCcEEEEEEeCCCCcHHHHHH
Confidence            333478899999999999999864  67777655433333469999999888887654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	245
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		5e-53
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		1e-36
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		2e-36
1m5k_C	100	Crystal Structure Of A Hairpin Ribozyme In The Cata		2e-35
2nz4_A	94	Structural Investigation Of The Glms Ribozyme Bound		2e-34
1u6b_A	98	Crystal Structure Of A Self-Splicing Group I Intron		3e-34
1urn_A	97	U1a MutantRNA COMPLEX + GLYCEROL Length = 97		3e-34
3k0j_A	96	Crystal Structure Of The E. Coli Thim Riboswitch In		3e-34
3bo2_A	95	A Relaxed Active Site Following Exon Ligation By A		3e-34
3iwn_C	91	Co-Crystal Structure Of A Bacterial C-Di-Gmp Ribosw		9e-34
3l3c_A	90	Crystal Structure Of The Bacillus Anthracis Glms Ri		9e-34
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		2e-33
1drz_A	97	U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOM		1e-32
3cul_A	98	Aminoacyl-Trna Synthetase Ribozyme Length = 98		1e-32
1cx0_A	95	Hepatitis Delta Virus Ribozyme Length = 95		1e-32
1a9n_B	96	Crystal Structure Of The Spliceosomal U2b''-U2a' Pr		5e-31
2k3k_A	104	Solution Structure Of Drosophila Melanogaster Snf R		2e-28
2u1a_A	88	Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20		9e-17
2b0g_A	83	Solution Structure Of Drosophila Melanogaster Snf R		5e-16
2a3j_A	127	Structure Of Urndesign, A Complete Computational Re		5e-09
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		3e-06
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		2e-05
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		3e-05
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		5e-05
2lcw_A	116	Solution Structure Of FusTLS RRM DOMAIN Length = 11		7e-05
2cpe_A	113	Solution Structure Of The Rna Recognition Motif Of		2e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		2e-04
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		2e-04
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		5e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		5e-04

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score =  204 bits (518), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 118/278 (42%), Positives = 152/278 (54%), Gaps = 43/278 (15%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPXXXXXXXXXXXXXXXDQHDAN 130
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GTFV                      
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKA 124
Query: 131 QAGMGLNPXXXXXXXXT---PPLSQIPY-------------------------------- 155
             G G  P            PP++Q P                                 
Sbjct: 125 VQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGA 184
Query: 156 -------PGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP 208
                  PG      P +  PPN+ILF+ N+P +T  + L M F+QFPGFKEVR+V  + 
Sbjct: 185 MPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH 244
Query: 209 GIAFVEYGDEMQATVAMQSLQSLKIGQQQLL-ITYAKK 245
            IAFVE+ +E+QA  A  +LQ  KI Q   + I++AKK
Sbjct: 245 DIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score =  149 bits (376), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 68/98 (69%), Positives = 84/98 (85%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFV 108
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GTFV
Sbjct: 64  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 101

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score =  149 bits (375), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 68/98 (69%), Positives = 84/98 (85%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFV 108
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GTFV
Sbjct: 64  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 101

>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The Catalytically-Active Conformation Length = 100

Iteration: 1
 Score =  145 bits (366), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 66/96 (68%), Positives = 82/96 (85%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGT 106
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GT
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGT 100

>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its Catalytic Cofactor Length = 94

Iteration: 1
 Score =  142 bits (357), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 64/92 (69%), Positives = 80/92 (86%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 1   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 60
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 61  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 92

>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With Both Exons Length = 98

Iteration: 1
 Score =  141 bits (356), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 64/92 (69%), Positives = 80/92 (86%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 96

>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL Length = 97

Iteration: 1
 Score =  141 bits (356), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 64/92 (69%), Positives = 80/92 (86%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 64  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 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 =  141 bits (356), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 64/92 (69%), Positives = 80/92 (86%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 64  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95

>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I Intron Length = 95

Iteration: 1
 Score =  141 bits (355), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 64/92 (69%), Positives = 80/92 (86%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 2   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 61
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 62  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 93

>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch Length = 91

Iteration: 1
 Score =  140 bits (352), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 63/89 (70%), Positives = 79/89 (88%)
Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
           PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+SAT 
Sbjct: 3   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 74  AVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           A+  MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 63  ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 91

>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme Bound To Glc6p Length = 90

Iteration: 1
 Score =  140 bits (352), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 63/89 (70%), Positives = 79/89 (88%)
Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
           PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+SAT 
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 74  AVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           A+  MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 90

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score =  139 bits (349), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 63/91 (69%), Positives = 79/91 (86%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIA 101
           AT A+  MQGFPFYDKPMRIQYAKT SDIIA
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIA 95

>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC Ribozyme Complex Length = 97

Iteration: 1
 Score =  136 bits (342), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 62/92 (67%), Positives = 78/92 (84%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSS 63
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           AT A+   QGFPFYDKP RIQYAKT SDIIAK
Sbjct: 64  ATNALRSXQGFPFYDKPXRIQYAKTDSDIIAK 95

>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme Length = 98

Iteration: 1
 Score =  136 bits (342), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 62/92 (67%), Positives = 78/92 (84%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSS 64
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           AT A+   QGFPFYDKP RIQYAKT SDIIAK
Sbjct: 65  ATNALRSXQGFPFYDKPXRIQYAKTDSDIIAK 96

>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme Length = 95

Iteration: 1
 Score =  136 bits (342), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 62/92 (67%), Positives = 78/92 (84%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 2   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSS 61
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           AT A+   QGFPFYDKP RIQYAKT SDIIAK
Sbjct: 62  ATNALRSXQGFPFYDKPXRIQYAKTDSDIIAK 93

>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 =  130 bits (328), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 56/95 (58%), Positives = 82/95 (86%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           +I PN+TIYINN+N+K+K ++LK+SL+A+F QFG +++I+A KT+K +GQA+++FK++ S
Sbjct: 2   DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 61
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADG 105
           +T A+ ++QGFPFY KPMRIQYAKT SDII+K  G
Sbjct: 62  STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRG 96

>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1 Length = 104

Iteration: 1
 Score =  122 bits (306), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 61/97 (62%), Positives = 82/97 (84%)
Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E+ PN TIYINNLNEK+K ++LK+SL+A+F QFG IL+I+A KTLK +GQA+++FK++ S
Sbjct: 2   EMLPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGS 61
Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTF 107
           A+ A+  MQGFPFYDKPM+I Y+K+ SDI+AK  GTF
Sbjct: 62  ASNALRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTF 98

>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20 Structures Length = 88

Iteration: 1
 Score = 83.6 bits (205), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 41/83 (49%), Positives = 57/83 (68%), Gaps = 1/83 (1%)
Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATV 223
           P +  PPN+ILF+ N+P +T  + L M F+QFPGFKEVR+V  +  IAFVE+ +E+QA  
Sbjct: 6   PLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGA 65
Query: 224 AMQSLQSLKIGQQQLL-ITYAKK 245
           A  +LQ  KI Q   + I++AKK
Sbjct: 66  ARDALQGFKITQNNAMKISFAKK 88

>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2 Length = 83

Iteration: 1
 Score = 81.3 bits (199), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 40/78 (51%), Positives = 53/78 (67%), Gaps = 1/78 (1%)
Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL 228
           PPN ILF+ N+P +T  M L M F+QFPGFKEVR+V  +  IAFVE+  E+Q+  A ++L
Sbjct: 6   PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEAL 65
Query: 229 QSLKIG-QQQLLITYAKK 245
           Q  KI     + IT+AKK
Sbjct: 66  QGFKITPTHAMKITFAKK 83

>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign Of Human U1a Protein Length = 127

Iteration: 1
 Score = 57.8 bits (138), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 32/105 (30%), Positives = 59/105 (56%), Gaps = 1/105 (0%)
Query: 3   PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAW 62
           P++ +      P+  + I N+N +V  ++L+  L+A+    G IL+I+   +  + G+A+
Sbjct: 17  PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAY 76
Query: 63  LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTF 107
           +VF    SA A VE  QG+PF   P+ I +++T    +A+ DG+ 
Sbjct: 77  IVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAE-DGSL 120

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/89 (28%), Positives = 46/89 (51%), Gaps = 7/89 (7%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVA 69
          S ++ +Y+ +L+  +  D L+     +F+ FG I  I+  K   T + KG  ++ F D  
Sbjct: 3  SGSSGLYVGSLHFNITEDMLR----GIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSE 58
Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A  A+E++ GF    +PMR+ +   + D
Sbjct: 59 CARRALEQLNGFELAGRPMRVGHVTERLD 87

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 7/89 (7%)
Query: 9  GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVF 65
          G+  +    +Y+  L E+V      + LHA F  FG I +I   L ++T KH+G A++ F
Sbjct: 1  GSMATTKRVLYVGGLAEEVD----DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 56
Query: 66 KDVASATAAVEKMQGFPFYDKPMRIQYAK 94
          +    A AA++ M     + + +R+  AK
Sbjct: 57 ELAEDAAAAIDNMNESELFGRTIRVNLAK 85

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 7/85 (8%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVA 69
          +    +Y+  L E+V      + LHA F  FG I +I   L ++T KH+G A++ F+   
Sbjct: 10 TTKRVLYVGGLAEEVD----DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65
Query: 70 SATAAVEKMQGFPFYDKPMRIQYAK 94
           A AA++ M     + + +R+  AK
Sbjct: 66 DAAAAIDNMNESELFGRTIRVNLAK 90

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 7/85 (8%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVA 69
          +    +Y+  L E+V      + LHA F  FG I +I   L ++T KH+G A++ F+   
Sbjct: 3  TTKRVLYVGGLAEEVD----DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 58
Query: 70 SATAAVEKMQGFPFYDKPMRIQYAK 94
           A AA++ M     + + +R+  AK
Sbjct: 59 DAAAAIDNMNESELFGRTIRVNLAK 83

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 7/84 (8%)
Query: 18  IYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAA 74
           +Y+ +L+  +  D L+     +F+ FG I  I   +  +T + KG  ++ F D   A  A
Sbjct: 29  LYVGSLHFNITEDMLR----GIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 75  VEKMQGFPFYDKPMRIQYAKTKSD 98
           +E++ GF    +PM++ +   ++D
Sbjct: 85  LEQLNGFELAGRPMKVGHVTERTD 108

>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN Length = 116

Iteration: 1
 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 31/97 (31%), Positives = 46/97 (47%), Gaps = 15/97 (15%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE-----------ILAFKTLKHKGQA 61
          S NNTI++  L E V I    +S+   FKQ G I                 +T K KG+A
Sbjct: 5  SDNNTIFVQGLGENVTI----ESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 62 WLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           + F D  SA AA++   G  F   P+++ +A  ++D
Sbjct: 61 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD 97

>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing Sarcoma(Ews) Protein Length = 113

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 15/98 (15%)
Query: 10  NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTI----------LEI-LAFKTLKHK 58
           +E S N+ IY+  LN+ V +D L       FKQ G +          + I L  +T K K
Sbjct: 10  DEDSDNSAIYVQGLNDSVTLDDLAD----FFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65
Query: 59  GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTK 96
           G A + ++D  +A AAVE   G  F    +++  A+ K
Sbjct: 66  GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 103

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 13  SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVA 69
           +    +Y+  L E+V      + LHA F  FG I +I   L ++T KH+G A++ F+   
Sbjct: 61  TTKRVLYVGGLAEEVD----DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 116
Query: 70  SATAAVEKMQGFPFYDKPMRIQYA 93
            A AA++ M     + + +R+  A
Sbjct: 117 DAAAAIDNMNESELFGRTIRVNLA 140

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 8/93 (8%)
Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIA 211
           G + S  P A + P+  LFV+ +  DTT   L+     F G    R+V  +      G  
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFG 57
Query: 212 FVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           FV++  E  A  A ++++  +I   ++ + +AK
Sbjct: 58  FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAV 75
          ++I  LN +     LK    AVF + G I E+L  K  T K +G A++ F++ A A  A 
Sbjct: 10 LFIGGLNRETNEKMLK----AVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65
Query: 76 EKMQGFPFYDKPMRIQYAKTKS 97
          + M G   + K ++++ AK  S
Sbjct: 66 KDMNGKSLHGKAIKVEQAKKPS 87

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 7/79 (8%)
Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAA 74
          +Y+  L E+V      + LHA F  FG I +I   L ++T KH+G A++ F+    A AA
Sbjct: 5  LYVGGLAEEVD----DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 75 VEKMQGFPFYDKPMRIQYA 93
          ++ M     + + +R+  A
Sbjct: 61 IDNMNESELFGRTIRVNLA 79

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	245
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-61
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-44
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	9e-41
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-37
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-35
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-12
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-32
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-07
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-31
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-25
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-07
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-24
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-10
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-19
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-16
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	4e-12
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-06
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-15
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-15
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-04
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-14
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-11
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-14
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-08
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-11
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	1e-13
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-07
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-09
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-13
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-04
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-12
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-07
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	6e-08
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-12
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-05
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	6e-12
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	6e-12
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-07
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	7e-12
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-10
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-11
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-09
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-05
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-11
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-06
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-11
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-11
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-05
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-11
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-11
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-11
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-09
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-11
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-11
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-11
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-11
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-04
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	7e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-10
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-05
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-08
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-10
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	9e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-05
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-05
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	9e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-06
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-10
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-04
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-10
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-10
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-06
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-10
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-10
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-07
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-10
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-10
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-08
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	5e-08
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	8e-10
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-08
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	9e-10
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	9e-10
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-06
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	2e-07
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-07
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-07
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-09
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-08
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-07
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-09
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	9e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-09
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-05
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-06
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-09
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-07
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	5e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-09
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-08
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-06
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-05
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-04
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	6e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-06
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-09
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-06
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-09
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-04
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-05
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-08
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-04
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-08
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-06
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-08
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-04
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-08
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	6e-06
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-08
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	7e-06
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-08
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-05
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-08
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-07
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-08
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-07
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	8e-08
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-06
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	8e-08
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-05
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	8e-08
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	7e-07
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	9e-08
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	6e-06
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-07
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-07
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-07
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-04
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-07
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-07
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-07
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-05
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-07
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	9e-06
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-07
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-07
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-06
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-04
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	6e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	6e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	6e-04
1x4e_A	85	RNA binding motif, single-stranded interacting pro	8e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	6e-05
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	9e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-06
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-06
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-04
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-06
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	8e-06
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-06
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-04
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-06
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-06
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	6e-06
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	6e-06
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	7e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	9e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	8e-06
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	9e-06
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-05
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-05
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-05
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-05
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-05
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	5e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-05
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	6e-05
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-04
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	7e-05
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-04
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-04
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-04
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	2e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-04
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	8e-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 =  192 bits (489), Expect = 5e-61
 Identities = 123/278 (44%), Positives = 159/278 (57%), Gaps = 43/278 (15%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDAN 130
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK  GTFV R+R++   +   +        
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKA 124

Query: 131 QAGMGLNPAYAGAYGAT-----------------------PPLSQIPYPGGAKSVIPEA- 166
             G G  P      G                         PP   IP PG A   IP   
Sbjct: 125 VQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGA 184

Query: 167 ------------------PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP 208
                               PPN+ILF+ N+P +T  + L M F+QFPGFKEVR+V  + 
Sbjct: 185 MPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH 244

Query: 209 GIAFVEYGDEMQATVAMQSLQSLKIGQQQLL-ITYAKK 245
            IAFVE+ +E+QA  A  +LQ  KI Q   + I++AKK
Sbjct: 245 DIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 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 = 54.9 bits (131), Expect = 3e-09
 Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 6/88 (6%)

Query: 164 PEAPAPPNNILFVQNVPHDTTP----MALQMFFSQFPGFKEVRMVEAKP--GIAFVEYGD 217
                 PN+ +++ N+           +L   FSQF    ++ +  +    G AFV + +
Sbjct: 2   AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKE 61

Query: 218 EMQATVAMQSLQSLKIGQQQLLITYAKK 245
              AT A++S+Q      + + I YAK 
Sbjct: 62  VSSATNALRSMQGFPFYDKPMRIQYAKT 89

>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 =  144 bits (365), Expect = 1e-44
 Identities = 64/92 (69%), Positives = 80/92 (86%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E  PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+S
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           AT A+  MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 64  ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95

>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 = 4e-09
 Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 169 PPNNILFVQNVPHDTTP----MALQMFFSQFPGFKEVR-MVEAKP-GIAFVEYGDEMQAT 222
            PN+ +++ N+           +L   FS+F    ++      K  G AFV + +   AT
Sbjct: 6   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65

Query: 223 VAMQSLQSLKIGQQQLLITYAKK 245
            A++S+Q      + + I YAK 
Sbjct: 66  NALRSMQGFPFYDKPMRIQYAKT 88

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score =  135 bits (341), Expect = 9e-41
 Identities = 34/115 (29%), Positives = 61/115 (53%), Gaps = 4/115 (3%)

Query: 2   EPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQA 61
            P++ +      P+  + I N+N +V  ++L+  L+A+    G IL+I+   +  + G+A
Sbjct: 16  SPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKA 75

Query: 62  WLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRH 116
           ++VF    SA A VE  QG+PF   P+ I +++T    +A+ DG+    E    H
Sbjct: 76  YIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAE-DGSL---EHHHHH 126

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 53.4 bits (128), Expect = 2e-09
 Identities = 13/106 (12%), Positives = 36/106 (33%), Gaps = 9/106 (8%)

Query: 146 ATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTP----MALQMFFSQFPGFKEV 201
           A      +  P    +        P+ ++ + N+  +         L    S      ++
Sbjct: 7   AKFERQHMDSPDLGSTP---PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDI 63

Query: 202 RMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
            +  +    G A++ +  +  A   +++ Q        L+IT+++ 
Sbjct: 64  VVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSET 109

>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 =  129 bits (326), Expect = 1e-37
 Identities = 39/233 (16%), Positives = 85/233 (36%), Gaps = 41/233 (17%)

Query: 15  NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAA 74
           N+ + ++NLN + ++    QSL  +F  +G +  +        K  A +   D   A  A
Sbjct: 3   NSVLLVSNLNPE-RVTP--QSLFILFGVYGDVQRVKILF--NKKENALVQMADGNQAQLA 57

Query: 75  VEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGM 134
           +  + G   + KP+RI  +K ++  + +         +   +    + +K          
Sbjct: 58  MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKN----- 112

Query: 135 GLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQ 194
                                         +   PP+  L + N+P   +   L++ FS 
Sbjct: 113 -----------------------------FQNIFPPSATLHLSNIPPSVSEEDLKVLFSS 143

Query: 195 FPGF-KEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLL-ITYAKK 245
             G  K  +  +    +A ++ G   +A  A+  L +  +G+   L ++++K 
Sbjct: 144 NGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 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 = 63.8 bits (155), Expect = 1e-12
 Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 6/95 (6%)

Query: 3   PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAW 62
           P   N  N   P+ T++++N+   V  + LK     +F   G +++   F   K +  A 
Sbjct: 108 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKV----LFSSNGGVVKGFKFFQ-KDRKMAL 162

Query: 63  LVFKDVASATAAVEKMQGFPFYD-KPMRIQYAKTK 96
           +    V  A  A+  +      +   +R+ ++K+ 
Sbjct: 163 IQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197

>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 =  123 bits (310), Expect = 8e-35
 Identities = 43/245 (17%), Positives = 92/245 (37%), Gaps = 41/245 (16%)

Query: 3   PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAW 62
             +A  G   + N+ + ++NLN + ++    QSL  +F  +G +  +        K  A 
Sbjct: 22  GRIAIPGLAGAGNSVLLVSNLNPE-RVTP--QSLFILFGVYGDVQRVKILF--NKKENAL 76

Query: 63  LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKK 122
           +   D   A  A+  + G   + KP+RI  +K ++          V   R  + ++   K
Sbjct: 77  VQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN----------VQLPREGQEDQGLTK 126

Query: 123 RKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHD 182
                  ++     +  +   +                        PP+  L + N+P  
Sbjct: 127 DYGNSPLHRFKKPGSKNFQNIF------------------------PPSATLHLSNIPPS 162

Query: 183 TTPMALQMFFSQFPGF-KEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLL-I 240
            +   L++ FS   G  K  +  +    +A ++ G   +A  A+  L +  +G+   L +
Sbjct: 163 VSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV 222

Query: 241 TYAKK 245
           +++K 
Sbjct: 223 SFSKS 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 = 63.1 bits (153), Expect = 3e-12
 Identities = 28/110 (25%), Positives = 48/110 (43%), Gaps = 6/110 (5%)

Query: 137 NPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNV-PHDTTPMALQMFFSQF 195
           +  +  + G  P  S +         IP      N++L V N+ P   TP +L + F  +
Sbjct: 5   HHHHHHSSGLVPRGSHMGRIA-----IPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVY 59

Query: 196 PGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
              + V+++  K   A V+  D  QA +AM  L   K+  + + IT +K 
Sbjct: 60  GDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH 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 = 62.3 bits (151), Expect = 5e-12
 Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 6/95 (6%)

Query: 3   PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAW 62
           P   N  N   P+ T++++N+   V  + LK     +F   G +++   F   K +  A 
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKV----LFSSNGGVVKGFKFFQ-KDRKMAL 193

Query: 63  LVFKDVASATAAVEKMQGFPFYD-KPMRIQYAKTK 96
           +    V  A  A+  +      +   +R+ ++K+ 
Sbjct: 194 IQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>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 =  114 bits (287), Expect = 2e-32
 Identities = 26/114 (22%), Positives = 48/114 (42%), Gaps = 12/114 (10%)

Query: 2   EPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTI--------LEILAFK 53
              V        PN  IY+ NL + V+   LK     +F ++            +I   K
Sbjct: 32  TLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKY----IFGRYVDFSSETQRIMFDIRLMK 87

Query: 54  TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTF 107
             + KGQA++   +  +A  A+++  G+  + KPM +Q+A++        +G  
Sbjct: 88  EGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR 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 = 47.9 bits (114), Expect = 2e-07
 Identities = 14/88 (15%), Positives = 35/88 (39%), Gaps = 10/88 (11%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQF-----PGFKEVRMVEAKP-----GIAFVEYG 216
           P  PN  ++V+N+        L+  F ++        + +  +         G AF+   
Sbjct: 41  PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLP 100

Query: 217 DEMQATVAMQSLQSLKIGQQQLLITYAK 244
           +E  A  A++      +  + +++ +A+
Sbjct: 101 NEKAAAKALKEANGYVLFGKPMVVQFAR 128

>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 =  110 bits (278), Expect = 3e-31
 Identities = 23/99 (23%), Positives = 42/99 (42%), Gaps = 8/99 (8%)

Query: 3   PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKG 59
           P  ++      PN  +Y+ NL+ +V    L      +F +F             T + +G
Sbjct: 14  PMFSSYNPG-EPNKVLYLKNLSPRVTERDLVS----LFARFQEKKGPPIQFRMMTGRMRG 68

Query: 60  QAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           QA++ F +   A  A+  + G+  Y K + I++ K K  
Sbjct: 69  QAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ 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 = 19/83 (22%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQA 221
           P  PN +L+++N+    T   L   F++F   K   +          G AF+ + ++  A
Sbjct: 21  PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIA 80

Query: 222 TVAMQSLQSLKIGQQQLLITYAK 244
             A+  +   K+  + L+I + K
Sbjct: 81  WQALHLVNGYKLYGKILVIEFGK 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 = 97.9 bits (243), Expect = 3e-25
 Identities = 29/238 (12%), Positives = 66/238 (27%), Gaps = 42/238 (17%)

Query: 13  SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
           + +  + +  L++  K++     +  VF  +G + ++   K     G A +   D  +  
Sbjct: 2   ADSPVLMVYGLDQS-KMNC--DRVFNVFCLYGNVEKVKFMK--SKPGAAMVEMADGYAVD 56

Query: 73  AAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQA 132
            A+  +     + + M +  +K  +               +    E G         ++ 
Sbjct: 57  RAITHLNNNFMFGQKMNVCVSKQPA-----------IMPGQSYGLEDGSCSYKDFSESRN 105

Query: 133 GMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFF 192
                P  A                            P+N+L   N P + T        
Sbjct: 106 NRFSTPEQA---------------------AKNRIQHPSNVLHFFNAPLEVTEENFFEIC 144

Query: 193 SQF--PGFKEVRMVEAKP---GIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
            +        V++   K        +E+  +  A   +  L   ++        Y  K
Sbjct: 145 DELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLK 202

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 60.1 bits (145), Expect = 3e-11
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 168 APPNNILFVQNVPHD-TTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQ 226
              + +L V  +         +   F  +   ++V+ +++KPG A VE  D      A+ 
Sbjct: 1   GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAIT 60

Query: 227 SLQSLKIGQQQLLITYAKK 245
            L +  +  Q++ +  +K+
Sbjct: 61  HLNNNFMFGQKMNVCVSKQ 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 = 48.5 bits (115), Expect = 4e-07
 Identities = 12/93 (12%), Positives = 29/93 (31%), Gaps = 7/93 (7%)

Query: 3   PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTI--LEILAFK-TLKHKG 59
           PE A +     P+N ++  N   +V  +   +    +  + G      +  F    +   
Sbjct: 111 PEQAAKNRIQHPSNVLHFFNAPLEVTEENFFE----ICDELGVKRPTSVKVFSGKSERSS 166

Query: 60  QAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY 92
              L +   + A   +  +  +   +      Y
Sbjct: 167 SGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199

>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 = 93.6 bits (233), Expect = 1e-24
 Identities = 27/118 (22%), Positives = 55/118 (46%), Gaps = 13/118 (11%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
            N  +YI NL  K+  +++      +F ++G I +I    T + +G A++V++D+  A  
Sbjct: 7   VNRILYIRNLPYKITAEEMYD----IFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 62

Query: 74  AVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQ 131
           AV+ + GF   ++ + + Y                 +   K+ EE+ K  K+++  N 
Sbjct: 63  AVDHLSGFNVSNRYLVVLYYNANRAF---------QKMDTKKKEEQLKLLKEKYGINT 111

>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 = 55.1 bits (133), Expect = 3e-10
 Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 2/80 (2%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVA 224
           P   N IL+++N+P+  T   +   F ++   +++R+       G A+V Y D   A  A
Sbjct: 4   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 63

Query: 225 MQSLQSLKIGQQQLLITYAK 244
           +  L    +  + L++ Y  
Sbjct: 64  VDHLSGFNVSNRYLVVLYYN 83

>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 = 82.0 bits (203), Expect = 2e-19
 Identities = 39/247 (15%), Positives = 76/247 (30%), Gaps = 69/247 (27%)

Query: 13  SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--------ILAFKTLKHKGQAWLV 64
           +    +Y+ N+   +  + +       F     +          +LA +  + K  A+L 
Sbjct: 2   AMARRLYVGNIPFGITEEAMMD----FFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 57

Query: 65  FKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRK 124
           F+ V   T A+    G  F  + ++I+                                 
Sbjct: 58  FRSVDETTQAMA-FDGIIFQGQSLKIRRPH------------------------------ 86

Query: 125 DQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTT 184
                              Y   P +S+ P       V    P   + + F+  +P+   
Sbjct: 87  ------------------DYQPLPGMSENPSVYVPGVVSTVVPDSAHKL-FIGGLPNYLN 127

Query: 185 PMALQMFFSQFPGFKEVRMV------EAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQL 238
              ++   + F   K   +V       +K G AF EY D      A+  L  +++G ++L
Sbjct: 128 DDQVKELLTSFGPLKAFNLVKDSATGLSK-GYAFCEYVDINVTDQAIAGLNGMQLGDKKL 186

Query: 239 LITYAKK 245
           L+  A  
Sbjct: 187 LVQRASV 193

>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 = 60.0 bits (146), Expect = 3e-11
 Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 7/95 (7%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAF--KTLKHKGQAW 62
                     + ++I  L   +  DQ+K+    +   FG +    L     T   KG A+
Sbjct: 105 VVSTVVPDSAHKLFIGGLPNYLNDDQVKE----LLTSFGPLKAFNLVKDSATGLSKGYAF 160

Query: 63  LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKS 97
             + D+     A+  + G    DK + +Q A   +
Sbjct: 161 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA 195

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 72.1 bits (177), Expect = 1e-16
 Identities = 20/97 (20%), Positives = 38/97 (39%), Gaps = 9/97 (9%)

Query: 2  EPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQA 61
            E  +  ++   +  ++I  L + V    L +      ++FG I  +     +  K QA
Sbjct: 8  HMENYDDPHKTPASPVVHIRGLIDGVVEADLVE----ALQEFGPISYV---VVMPKKRQA 60

Query: 62 WLVFKDVASATAAVEKMQGFPFY--DKPMRIQYAKTK 96
           + F+DV  A  AV        Y    P  + Y+ ++
Sbjct: 61 LVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ 97

>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 = 4e-12
 Identities = 13/79 (16%), Positives = 28/79 (35%), Gaps = 3/79 (3%)

Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQS 227
            P + ++ ++ +        L     +F     V ++  K   A VE+ D + A  A+  
Sbjct: 18  TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK-RQALVEFEDVLGACNAVNY 76

Query: 228 LQS--LKIGQQQLLITYAK 244
                + I      + Y+ 
Sbjct: 77  AADNQIYIAGHPAFVNYST 95

>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 = 74.2 bits (183), Expect = 6e-16
 Identities = 38/272 (13%), Positives = 76/272 (27%), Gaps = 43/272 (15%)

Query: 1   MEPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQ 60
           +   + +   +      I I  L   V   ++      +   +  +         K+KG 
Sbjct: 8   IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHD----LLSDYE-LKYC---FVDKYKGT 59

Query: 61  AWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKS-------------DIIAKADGTF 107
           A++   +   A AA+         ++ + +Q   T +                 +    F
Sbjct: 60  AFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPF 119

Query: 108 --VPRERRKRHEEKGKKR-------KDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGG 158
             + R      E  G+ +         +  A +A   L        G       + Y   
Sbjct: 120 GSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL-------GKPLGPRTL-YVHW 171

Query: 159 AKSVIPEAPAPPNNILFVQNVPHDTTPM-ALQMFFSQFPGFKEVRMVEAKPGI----AFV 213
             +         +  L V  +P     + AL    S        ++   + G     A +
Sbjct: 172 TDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVL 231

Query: 214 EYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
           EY     A  A Q    L +G   L +++   
Sbjct: 232 EYETAEMAEEAQQQADGLSLGGSHLRVSFCAP 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 = 53.8 bits (130), Expect = 7e-09
 Identities = 11/95 (11%), Positives = 29/95 (30%), Gaps = 7/95 (7%)

Query: 7   NQGNEISPNNTIYINNLNEKVK-IDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWL 63
                +  +  + ++ L      +D L +          +     +   +  + KG A L
Sbjct: 176 QLTPALLHSRCLCVDRLPPGFNDVDALCR----ALSAVHSPTFCQLACGQDGQLKGFAVL 231

Query: 64  VFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            ++    A  A ++  G       +R+ +      
Sbjct: 232 EYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP 266

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 69.7 bits (171), Expect = 1e-15
 Identities = 18/109 (16%), Positives = 37/109 (33%), Gaps = 21/109 (19%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVAS 70
           P   +    LN+ V+    +  L  + +++G + E+       T KH G A ++F     
Sbjct: 5   PLKEVTFARLNDNVR----ETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG 60

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEK 119
           A   V+ +         +  Q                   ++R ++ E 
Sbjct: 61  AKETVKNLHLTSVMGNIIHAQLDI--------------KGQQRMKYYEL 95

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 43.9 bits (104), Expect = 3e-06
 Identities = 10/82 (12%), Positives = 26/82 (31%), Gaps = 5/82 (6%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATV 223
            P   +    +  +     L+    ++   +EV ++         G+A V +     A  
Sbjct: 4   IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63

Query: 224 AMQSLQSLKIGQQQLLITYAKK 245
            +++L    +    +      K
Sbjct: 64  TVKNLHLTSVMGNIIHAQLDIK 85

>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 = 68.0 bits (167), Expect = 3e-15
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 9/85 (10%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
          P   +++  L           +L   F +FG+I  I     +K    A++ ++ + +A A
Sbjct: 16 PTTRLWVGGLGPNTS----LAALAREFDRFGSIRTI---DHVKGDSFAYIQYESLDAAQA 68

Query: 74 AVEKMQGFPF--YDKPMRIQYAKTK 96
          A  KM+GFP    D+ +R+ +AK+ 
Sbjct: 69 ACAKMRGFPLGGPDRRLRVDFAKSG 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 = 51.5 bits (124), Expect = 4e-09
 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 1/67 (1%)

Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQS 227
           A P   L+V  +  +T+  AL   F +F   + +  V+     A+++Y     A  A   
Sbjct: 14  ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD-SFAYIQYESLDAAQAACAK 72

Query: 228 LQSLKIG 234
           ++   +G
Sbjct: 73  MRGFPLG 79

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 67.5 bits (165), Expect = 5e-15
 Identities = 20/96 (20%), Positives = 42/96 (43%), Gaps = 6/96 (6%)

Query: 3  PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAW 62
             +  G        +Y+ NL    ++  LK+      ++ G++   L ++    + +A+
Sbjct: 7  GPGSPPGEGAPLAADVYVGNLPRDARVSDLKR----ALRELGSVPLRLTWQ--GPRRRAF 60

Query: 63 LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
          L + D A+A  AV  +QG       +R+  A+ + D
Sbjct: 61 LHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 58.3 bits (141), Expect = 1e-11
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV-EAKPGIAFVEYGDEMQAT 222
           P   AP    ++V N+P D     L+    +  G   +R+  +     AF+ Y D   A 
Sbjct: 12  PGEGAPLAADVYVGNLPRDARVSDLKRALREL-GSVPLRLTWQGPRRRAFLHYPDSAAAQ 70

Query: 223 VAMQSLQSLKIGQQQLLITYAKK 245
            A+  LQ L++G   L +  A++
Sbjct: 71  QAVSCLQGLRLGTDTLRVALARQ 93

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 69.6 bits (171), Expect = 1e-14
 Identities = 39/248 (15%), Positives = 80/248 (32%), Gaps = 70/248 (28%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAW 62
           A +   ++  + +Y+ ++  ++  D ++Q     F  FG I  I       T+KHKG A+
Sbjct: 19  AQRQGALAIMSRVYVGSIYYELGEDTIRQ----AFAPFGPIKSIDMSWDSVTMKHKGFAF 74

Query: 63  LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKK 122
           + ++   +A  A+E+M       + +++              G      + +   ++  +
Sbjct: 75  VEYEVPEAAQLALEQMNSVMLGGRNIKV--------------GRPSNIGQAQPIIDQLAE 120

Query: 123 RKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHD 182
                                                           N I +V +V  D
Sbjct: 121 EARAF-------------------------------------------NRI-YVASVHQD 136

Query: 183 TTPMALQMFFSQFPGFKEVRMV----EAKP-GIAFVEYGDEMQATVAMQSLQSLKIGQQQ 237
            +   ++  F  F   K   +       K  G  F+EY     +  A+ S+    +G Q 
Sbjct: 137 LSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQY 196

Query: 238 LLITYAKK 245
           L +  A  
Sbjct: 197 LRVGKAVT 204

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 60.0 bits (146), Expect = 3e-11
 Identities = 25/98 (25%), Positives = 44/98 (44%), Gaps = 7/98 (7%)

Query: 2   EPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHK 58
           +P +     E    N IY+ ++++ +  D +K     VF+ FG I      +   T KHK
Sbjct: 112 QPIIDQLAEEARAFNRIYVASVHQDLSDDDIKS----VFEAFGKIKSATLARDPTTGKHK 167

Query: 59  GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTK 96
           G  ++ ++   S+  AV  M  F    + +R+  A T 
Sbjct: 168 GYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 16/99 (16%), Positives = 39/99 (39%), Gaps = 5/99 (5%)

Query: 145 GATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV 204
                ++     G   +   +      + ++V ++ ++     ++  F+ F   K + M 
Sbjct: 2   SHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMS 61

Query: 205 EAKP-----GIAFVEYGDEMQATVAMQSLQSLKIGQQQL 238
                    G AFVEY     A +A++ + S+ +G + +
Sbjct: 62  WDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNI 100

>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 = 66.4 bits (162), Expect = 2e-14
 Identities = 20/89 (22%), Positives = 39/89 (43%), Gaps = 9/89 (10%)

Query: 10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVA 69
          +++S +  +++  L E V    L +      ++FGTI  +     +  K QA + F+++ 
Sbjct: 10 HKVSVSPVVHVRGLCESVVEADLVE----ALEKFGTICYV---MMMPFKRQALVEFENID 62

Query: 70 SATAAVEKMQGFPFY--DKPMRIQYAKTK 96
          SA   V      P Y   +     Y+ +K
Sbjct: 63 SAKECVTFAADVPVYIAGQQAFFNYSTSK 91

>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 = 3e-11
 Identities = 14/80 (17%), Positives = 26/80 (32%), Gaps = 3/80 (3%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQ 226
               + ++ V+ +        L     +F     V M+  K   A VE+ +   A   + 
Sbjct: 11  KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK-RQALVEFENIDSAKECVT 69

Query: 227 SLQS--LKIGQQQLLITYAK 244
                 + I  QQ    Y+ 
Sbjct: 70  FAADVPVYIAGQQAFFNYST 89

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 66.6 bits (162), Expect = 3e-14
 Identities = 23/106 (21%), Positives = 41/106 (38%), Gaps = 10/106 (9%)

Query: 3   PEVANQGNEISPNNT--IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQ 60
               N  +    N    + I N    + +D L    + V    G +  I+ FK  ++  Q
Sbjct: 11  TRPGNTDDPSGGNKVLLLSIQNPLYPITVDVL----YTVCNPVGKVQRIVIFK--RNGIQ 64

Query: 61  AWLVFKDVASATAAVEKMQGFPFYDK--PMRIQYAKTKSDIIAKAD 104
           A + F+ V  A  A   + G   Y     ++I+YA+     + + D
Sbjct: 65  AMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIRND 110

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 50.5 bits (120), Expect = 2e-08
 Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 4/85 (4%)

Query: 164 PEAPAPPNNILF--VQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQA 221
            + P+  N +L   +QN  +  T   L    +     + + + +     A VE+   + A
Sbjct: 16  TDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCA 75

Query: 222 TVAMQSLQSLKI--GQQQLLITYAK 244
             A  +L    I  G   L I YA+
Sbjct: 76  QKAKAALNGADIYAGCCTLKIEYAR 100

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 64.6 bits (158), Expect = 7e-14
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 8/88 (9%)

Query: 10  NEISPNNT-IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDV 68
               P  T  YI N+        L      +F+ FG IL+    K    KG  ++ +   
Sbjct: 21  RSAPPRVTTAYIGNIPHFATEADLIP----LFQNFGFILDF---KHYPEKGCCFIKYDTH 73

Query: 69  ASATAAVEKMQGFPFYDKPMRIQYAKTK 96
             A   +  +  FPF  + +R  + K +
Sbjct: 74  EQAAVCIVALANFPFQGRNLRTGWGKER 101

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 58.9 bits (143), Expect = 1e-11
 Identities = 23/105 (21%), Positives = 40/105 (38%), Gaps = 6/105 (5%)

Query: 141 AGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKE 200
           +   G  P ++          +I  AP P     ++ N+PH  T   L   F  F    +
Sbjct: 2   SQTIGLPPQVNPQAVD----HIIRSAP-PRVTTAYIGNIPHFATEADLIPLFQNFGFILD 56

Query: 201 VRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
            +    K G  F++Y    QA V + +L +     + L   + K+
Sbjct: 57  FKHYPEK-GCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE 100

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 65.0 bits (158), Expect = 1e-13
 Identities = 27/104 (25%), Positives = 49/104 (47%), Gaps = 10/104 (9%)

Query: 6   ANQGNEISPNNTI---YINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAW 62
            + G  ++  + +    + NL   V +D     LH +F +FGT+L+I+ F    ++ QA 
Sbjct: 16  VDAGMAMAGQSPVLRIIVENLFYPVTLD----VLHQIFSKFGTVLKIITFTK-NNQFQAL 70

Query: 63  LVFKDVASATAAVEKMQGFPFYDKP--MRIQYAKTKSDIIAKAD 104
           L + D  SA  A   + G   Y+    +RI ++K  S  +   +
Sbjct: 71  LQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNN 114

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 46.9 bits (111), Expect = 4e-07
 Identities = 21/98 (21%), Positives = 37/98 (37%), Gaps = 7/98 (7%)

Query: 154 PYPGGAKSVIPE--APAPPNNILFVQ--NVPHDTTPMALQMFFSQF-PGFKEVRMVEAKP 208
                + + +    A A  + +L +   N+ +  T   L   FS+F    K +   +   
Sbjct: 7   LALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ 66

Query: 209 GIAFVEYGDEMQATVAMQSLQSLKI--GQQQLLITYAK 244
             A ++Y D + A  A  SL    I      L I ++K
Sbjct: 67  FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 104

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.1 bits (154), Expect = 3e-13
 Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 8/98 (8%)

Query: 2   EPEVANQGNEISPNN-TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQ 60
           +    +  N+ SP N T+Y   +   +    ++Q     F  FG I+EI   +    KG 
Sbjct: 11  QLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQ----TFSPFGQIMEI---RVFPEKGY 63

Query: 61  AWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           +++ F    SA  A+  + G       ++  + K   D
Sbjct: 64  SFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD 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 = 51.6 bits (124), Expect = 5e-09
 Identities = 21/103 (20%), Positives = 42/103 (40%), Gaps = 6/103 (5%)

Query: 142 GAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEV 201
           G+ G++    Q+ +      V+ ++  P N  ++   +    T   ++  FS F    E+
Sbjct: 1   GSSGSSGNTKQLRFED----VVNQSS-PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEI 55

Query: 202 RMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           R+   K G +FV +     A  A+ S+    I    +   + K
Sbjct: 56  RVFPEK-GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK 97

>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 = 62.7 bits (153), Expect = 4e-13
 Identities = 17/94 (18%), Positives = 39/94 (41%), Gaps = 11/94 (11%)

Query: 7  NQGNEISP--NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLV 64
          + G   +P   NT+Y+   +    +      L   F  FG I+++        +  A++ 
Sbjct: 5  SSGERRAPRKGNTLYVYGED----MTP--TLLRGAFSPFGNIIDL---SMDPPRNCAFVT 55

Query: 65 FKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
          ++ + SA  AV ++ G       +++  A+ +  
Sbjct: 56 YEKMESADQAVAELNGTQVESVQLKVNIARKQPM 89

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 45.7 bits (109), Expect = 6e-07
 Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 4/83 (4%)

Query: 164 PEAPAPPNN-ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQAT 222
            E  AP     L+V     D TP  L+  FS F    ++ M   +   AFV Y     A 
Sbjct: 7   GERRAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPR-NCAFVTYEKMESAD 63

Query: 223 VAMQSLQSLKIGQQQLLITYAKK 245
            A+  L   ++   QL +  A+K
Sbjct: 64  QAVAELNGTQVESVQLKVNIARK 86

>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 = 65.8 bits (161), Expect = 7e-13
 Identities = 28/251 (11%), Positives = 73/251 (29%), Gaps = 81/251 (32%)

Query: 9   GNEIS----PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTL---KHKGQA 61
            NEI        T+++ N         ++     + +    +   +   +L     +  A
Sbjct: 107 QNEIIVSHLTECTLWMTNFPPSYTQRNIRD----LLQDINVVALSIRLPSLRFNTSRRFA 162

Query: 62  WLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGK 121
           ++       A   VEK+ G       +  + +               P E+ KR +    
Sbjct: 163 YIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN--------------PLEKSKRTDSATL 208

Query: 122 KRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPH 181
           + ++                                                + ++N+  
Sbjct: 209 EGRE------------------------------------------------IMIRNLST 220

Query: 182 DTTP-MALQMFFSQFPGFKEVRMVEAKP------GIAFVEYGDEMQATVAMQSLQSLKIG 234
           +      L+  F  F   +++ +   +         AF+ + ++  A  A+Q +    +G
Sbjct: 221 ELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLG 279

Query: 235 QQQLLITYAKK 245
            +++ ++ A K
Sbjct: 280 NREISVSLADK 290

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 51.1 bits (123), Expect = 6e-08
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 8/84 (9%)

Query: 17  TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK----TLKHKGQAWLVFKDVASAT 72
            I I NL+ ++  + L   L   F+ FG+I +I           +   A++VF++  SA 
Sbjct: 212 EIMIRNLSTELLDENL---LRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 268

Query: 73  AAVEKMQGFPFYDKPMRIQYAKTK 96
            A++ M      ++ + +  A  K
Sbjct: 269 RALQ-MNRSLLGNREISVSLADKK 291

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 9/66 (13%), Positives = 22/66 (33%), Gaps = 3/66 (4%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP---GIAFVEYGDEMQATVAMQSLQS 230
           + V+N+P       +  +F        V + ++       A +E+     A  A+     
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 103

Query: 231 LKIGQQ 236
           +    +
Sbjct: 104 VVGQNE 109

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 62.9 bits (153), Expect = 2e-12
 Identities = 21/100 (21%), Positives = 46/100 (46%), Gaps = 6/100 (6%)

Query: 1   MEPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAFKTLKHK 58
           +       G  +     + ++NL+  V    +++    +F +FGT+    +   ++ +  
Sbjct: 74  LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQE----LFAEFGTLKKAAVDYDRSGRSL 129

Query: 59  GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           G A + F+  A A  A+++ +G P   +PM IQ   ++ D
Sbjct: 130 GTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 169

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 23/152 (15%), Positives = 43/152 (28%), Gaps = 14/152 (9%)

Query: 98  DIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPG 157
           DII            R +          ++    A  G N     +     P        
Sbjct: 25  DIIK---------LNRNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLF 75

Query: 158 GAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP----GIAFV 213
            +     E        L V N+    +   +Q  F++F   K+  +   +     G A V
Sbjct: 76  DSGCGGGEGVETGAK-LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADV 134

Query: 214 EYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
            +     A  AM+  + + +  + + I     
Sbjct: 135 HFERRADALKAMKQYKGVPLDGRPMDIQLVAS 166

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 61.3 bits (149), Expect = 2e-12
 Identities = 32/115 (27%), Positives = 46/115 (40%), Gaps = 15/115 (13%)

Query: 13  SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-----------TLKHKGQA 61
           S NNTI++  L E V I+ +       FKQ G I                  T K KG+A
Sbjct: 5   SDNNTIFVQGLGENVTIESVAD----YFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60

Query: 62  WLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRH 116
            + F D  SA AA++   G  F   P+++ +A  ++D            E    H
Sbjct: 61  TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEHHHHH 115

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 16/90 (17%), Positives = 33/90 (36%), Gaps = 13/90 (14%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQF--------PGFKEVRMVEAKP-----GIAFVEY 215
             NN +FVQ +  + T  ++  +F Q          G   + +   +      G A V +
Sbjct: 5   SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64

Query: 216 GDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
            D   A  A+      +     + +++A +
Sbjct: 65  DDPPSAKAAIDWFDGKEFSGNPIKVSFATR 94

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 60.2 bits (146), Expect = 3e-12
 Identities = 12/91 (13%), Positives = 31/91 (34%), Gaps = 4/91 (4%)

Query: 8  QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKD 67
             +      + I N+   ++ + L      +  Q+G +       T        + +  
Sbjct: 8  SVPKRQRIRKLQIRNIPPHLQWEVLDS----LLVQYGVVESCEQVNTDSETAVVNVTYSS 63

Query: 68 VASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
             A  A++K+ GF   +  +++ Y   +  
Sbjct: 64 KDQARQALDKLNGFQLENFTLKVAYIPDEMA 94

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 49.4 bits (118), Expect = 2e-08
 Identities = 16/90 (17%), Positives = 28/90 (31%), Gaps = 3/90 (3%)

Query: 158 GAKSVIPEAPAPPN-NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP--GIAFVE 214
           G+       P       L ++N+P       L     Q+   +    V       +  V 
Sbjct: 1   GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVT 60

Query: 215 YGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           Y  + QA  A+  L   ++    L + Y  
Sbjct: 61  YSSKDQARQALDKLNGFQLENFTLKVAYIP 90

>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 = 60.5 bits (147), Expect = 4e-12
 Identities = 21/100 (21%), Positives = 46/100 (46%), Gaps = 6/100 (6%)

Query: 1   MEPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAFKTLKHK 58
           +       G  +     + ++NL+  V    +++    +F +FGT+    +   ++ +  
Sbjct: 21  LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQE----LFAEFGTLKKAAVDYDRSGRSL 76

Query: 59  GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           G A + F+  A A  A+++ +G P   +PM IQ   ++ D
Sbjct: 77  GTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 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 = 40.4 bits (95), Expect = 7e-05
 Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 5/86 (5%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP----GIAFVEYGDEM 219
            E        L V N+    +   +Q  F++F   K+  +   +     G A V +    
Sbjct: 29  GEGVETGAK-LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRA 87

Query: 220 QATVAMQSLQSLKIGQQQLLITYAKK 245
            A  AM+  + + +  + + I     
Sbjct: 88  DALKAMKQYKGVPLDGRPMDIQLVAS 113

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 59.2 bits (144), Expect = 6e-12
 Identities = 24/87 (27%), Positives = 38/87 (43%), Gaps = 8/87 (9%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          S  N +YI NL+  V  D L+Q    +F      L     + L   G A++ + D   A 
Sbjct: 6  SGMNKLYIGNLSPAVTADDLRQ----LFGDRKLPLAG---QVLLKSGYAFVDYPDQNWAI 58

Query: 73 AAVEKMQG-FPFYDKPMRIQYAKTKSD 98
           A+E + G    + K M + Y+ +K  
Sbjct: 59 RAIETLSGKVELHGKIMEVDYSVSKKL 85

>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 = 46.1 bits (110), Expect = 4e-07
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQ 229
             N L++ N+    T   L+  F           V  K G AFV+Y D+  A  A+++L 
Sbjct: 7   GMNKLYIGNLSPAVTADDLRQLFGDR-KLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLS 65

Query: 230 -SLKIGQQQLLITYAK 244
             +++  + + + Y+ 
Sbjct: 66  GKVELHGKIMEVDYSV 81

>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 = 61.3 bits (148), Expect = 6e-12
 Identities = 27/107 (25%), Positives = 49/107 (45%), Gaps = 10/107 (9%)

Query: 3   PEVANQGNEISPNNTI---YINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKG 59
               + G  ++  + +    + NL   V +D     LH +F +FGT+L+I+ F    ++ 
Sbjct: 31  AAAVDAGMAMAGQSPVLRIIVENLFYPVTLD----VLHQIFSKFGTVLKIITFTK-NNQF 85

Query: 60  QAWLVFKDVASATAAVEKMQGFPFYDKP--MRIQYAKTKSDIIAKAD 104
           QA L + D  SA  A   + G   Y+    +RI ++K  S  +   +
Sbjct: 86  QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNN 132

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 49.3 bits (117), Expect = 1e-07
 Identities = 23/118 (19%), Positives = 41/118 (34%), Gaps = 11/118 (9%)

Query: 138 PAYAGAYGATPPLSQIPYPGGAKSVIPEA------PAPPNNILFVQ--NVPHDTTPMALQ 189
             +  A  A   ++ +     A +    A       A  + +L +   N+ +  T   L 
Sbjct: 5   HHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLH 64

Query: 190 MFFSQFPGFKEVRMVEAKPGI-AFVEYGDEMQATVAMQSLQSLKI--GQQQLLITYAK 244
             FS+F    ++          A ++Y D + A  A  SL    I      L I ++K
Sbjct: 65  QIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 122

>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 = 59.3 bits (143), Expect = 7e-12
 Identities = 16/87 (18%), Positives = 36/87 (41%), Gaps = 4/87 (4%)

Query: 13 SPNNTIYINNLNEKV-KIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASA 71
          S ++ +     N+ V    + +    ++F+ +        FK+ K   +  + F +  SA
Sbjct: 3  SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK---RVRINFSNPLSA 59

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            A  ++    F  K M++ +A+T   
Sbjct: 60 ADARLRLHKTEFLGKEMKLYFAQTLHI 86

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 58.4 bits (142), Expect = 1e-11
 Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 1/89 (1%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYG 216
           G + S   E       IL+V+N+   T+   ++  F+        R+ + +   AFV + 
Sbjct: 1   GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR-DYAFVHFS 59

Query: 217 DEMQATVAMQSLQSLKIGQQQLLITYAKK 245
           +   A  AM++L    +    + +T AK 
Sbjct: 60  NREDAVEAMKALNGKVLDGSPIEVTLAKP 88

>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 = 54.6 bits (132), Expect = 3e-10
 Identities = 14/86 (16%), Positives = 30/86 (34%), Gaps = 7/86 (8%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          S    +Y+ NL      + +++     F            +  K +  A++ F +   A 
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEK----EFNNIKPGAVE---RVKKIRDYAFVHFSNREDAV 65

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A++ + G      P+ +  AK    
Sbjct: 66 EAMKALNGKVLDGSPIEVTLAKPVDK 91

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 61.1 bits (149), Expect = 1e-11
 Identities = 30/141 (21%), Positives = 53/141 (37%), Gaps = 27/141 (19%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLV 64
            +     S    I+I NL++ +  D   ++L+  F  FG IL   +       KG  ++ 
Sbjct: 94  RDPSLRKSGVGNIFIKNLDKSI--DN--KALYDTFSAFGNILSCKVVCDENGSKGYGFVH 149

Query: 65  FKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRK 124
           F+   +A  A+EKM G    D+ + +   K++ +             R      + K+  
Sbjct: 150 FETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE-------------REAELGARAKEFY 196

Query: 125 DQHDANQAGMGLNPAYAGAYG 145
                        P YAG+ G
Sbjct: 197 PYD---------VPDYAGSSG 208

>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 = 54.2 bits (131), Expect = 3e-09
 Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 7/91 (7%)

Query: 6  ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAW 62
           N      P  ++Y+ +L+  V    L +     F   G IL I   +   T +  G A+
Sbjct: 6  MNPSAPSYPMASLYVGDLHPDVTEAMLYE----KFSPAGPILSIRVCRDMITRRSLGYAY 61

Query: 63 LVFKDVASATAAVEKMQGFPFYDKPMRIQYA 93
          + F+  A A  A++ M       KP+RI ++
Sbjct: 62 VNFQQPADAERALDTMNFDVIKGKPVRIMWS 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 = 46.9 bits (112), Expect = 1e-06
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV--EAKP-GIAFVEYGDEMQATVAMQSLQS 230
           +F++N+       AL   FS F      ++V  E    G  FV +  +  A  A++ +  
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165

Query: 231 LKIGQQQLLITYAKK 245
           + +  +++ +   K 
Sbjct: 166 MLLNDRKVFVGRFKS 180

>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 = 41.9 bits (99), Expect = 6e-05
 Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 5/92 (5%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIA 211
           G   S+ P AP+ P   L+V ++  D T   L   FS       +R+          G A
Sbjct: 1   GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA 60

Query: 212 FVEYGDEMQATVAMQSLQSLKIGQQQLLITYA 243
           +V +     A  A+ ++    I  + + I ++
Sbjct: 61  YVNFQQPADAERALDTMNFDVIKGKPVRIMWS 92

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 7/91 (7%)

Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKD 67
              N TI + NL+E  +   L++    +F+ FG+I          T + KG A++ F  
Sbjct: 11 RADDNATIRVTNLSEDTRETDLQE----LFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 66

Query: 68 VASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
             A  A+  + GF +    + +++AK  ++
Sbjct: 67 REDAARAIAGVSGFGYDHLILNVEWAKPSTN 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 = 44.1 bits (105), Expect = 2e-06
 Identities = 22/94 (23%), Positives = 35/94 (37%), Gaps = 7/94 (7%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV------EAKPGI 210
           G + S  P   A  N  + V N+  DT    LQ  F  F     + +       ++K G 
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSK-GF 59

Query: 211 AFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           AF+ +     A  A+  +         L + +AK
Sbjct: 60  AFISFHRREDAARAIAGVSGFGYDHLILNVEWAK 93

>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 = 58.0 bits (141), Expect = 2e-11
 Identities = 24/114 (21%), Positives = 44/114 (38%), Gaps = 18/114 (15%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAW 62
           +   +E + + T+Y+  L+EKV    L +    +F Q G ++     K   T +H+G  +
Sbjct: 6   SGPISERNQDATVYVGGLDEKVSEPLLWE----LFLQAGPVVNTHMPKDRVTGQHQGYGF 61

Query: 63  LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRH 116
           + F     A  A++ M     Y KP+R+  A   +                   
Sbjct: 62  VEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN-----------KNLSGPSS 104

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 17/93 (18%), Positives = 33/93 (35%), Gaps = 5/93 (5%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV-----EAKPGIA 211
           G + S  P +    +  ++V  +    +   L   F Q        M          G  
Sbjct: 1   GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60

Query: 212 FVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           FVE+  E  A  A++ +  +K+  + + +  A 
Sbjct: 61  FVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS 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 = 59.5 bits (145), Expect = 2e-11
 Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 6/91 (6%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
                ++    T+   NL+  +  D+LK+    VF+    I   L  +  K KG A++ F
Sbjct: 90  GRDSKKVRAARTLLAKNLSFNITEDELKE----VFEDALEI--RLVSQDGKSKGIAYIEF 143

Query: 66  KDVASATAAVEKMQGFPFYDKPMRIQYAKTK 96
           K  A A   +E+ QG     + + + Y   K
Sbjct: 144 KSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 16/106 (15%), Positives = 41/106 (38%), Gaps = 8/106 (7%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAFKTLKHKGQAWL 63
             +G+E +    ++I NLN    + +LK        +        ++  +T  ++   ++
Sbjct: 4   MVEGSESTTPFNLFIGNLNPNKSVAELKV----AISELFAKNDLAVVDVRTGTNRKFGYV 59

Query: 64  VFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGT-FV 108
            F+       A+E + G   +   ++++  K +     +A  T   
Sbjct: 60  DFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLA 104

>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 = 44.5 bits (106), Expect = 6e-06
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 6/85 (7%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA--KP-GIAFVEYGDEMQ 220
                     L  +N+  + T   L+  F       E+R+V    K  GIA++E+  E  
Sbjct: 92  DSKKVRAARTLLAKNLSFNITEDELKEVFEDA---LEIRLVSQDGKSKGIAYIEFKSEAD 148

Query: 221 ATVAMQSLQSLKIGQQQLLITYAKK 245
           A   ++  Q  +I  + + + Y  +
Sbjct: 149 AEKNLEEKQGAEIDGRSVSLYYTGE 173

>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 = 43.7 bits (104), Expect = 1e-05
 Identities = 12/86 (13%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP----GIAFVEYGDEM 219
             + +     LF+ N+  + +   L++  S+     ++ +V+ +        +V++    
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 65

Query: 220 QATVAMQSLQSLKIGQQQLLITYAKK 245
               A++ L  LK+   ++ +   K 
Sbjct: 66  DLEKALE-LTGLKVFGNEIKLEKPKG 90

>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 = 58.3 bits (141), Expect = 2e-11
 Identities = 19/122 (15%), Positives = 43/122 (35%), Gaps = 16/122 (13%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
            + G+       I   NL       ++++     F +FG++  +L  +       A + F
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQE----TFSRFGSLGRVLLPEG---GITAIVEF 53

Query: 66  KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKD 125
            +   A  A   +    F+  P+ +++A           G F    ++K  + +    K 
Sbjct: 54  LEPLEARKAFRHLAYSKFHHVPLYLEWAP---------IGVFGAAPQKKDSQHEQPAEKA 104

Query: 126 QH 127
           + 
Sbjct: 105 ES 106

>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 = 56.7 bits (137), Expect = 7e-11
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQS 230
             ++  +N+P  T    +Q  FS+F     V + E     A VE+ + ++A  A + L  
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-ITAIVEFLEPLEARKAFRHLAY 68

Query: 231 LKIGQQQLLITYAKK 245
            K     L + +A  
Sbjct: 69  SKFHHVPLYLEWAPI 83

>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 = 57.7 bits (140), Expect = 3e-11
 Identities = 14/86 (16%), Positives = 40/86 (46%), Gaps = 7/86 (8%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          +  + +++ NL   +  +++++    +F+++G   E+      K KG  ++  +    A 
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRK----LFEKYGKAGEV---FIHKDKGFGFIRLETRTLAE 65

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A  ++   P   K +R+++A   + 
Sbjct: 66 IAKVELDNMPLRGKQLRVRFACHSAS 91

>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 = 51.5 bits (124), Expect = 5e-09
 Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 1/89 (1%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYG 216
           G + S   E      + LFV N+P D T   ++  F ++    EV + + K G  F+   
Sbjct: 1   GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-GFGFIRLE 59

Query: 217 DEMQATVAMQSLQSLKIGQQQLLITYAKK 245
               A +A   L ++ +  +QL + +A  
Sbjct: 60  TRTLAEIAKVELDNMPLRGKQLRVRFACH 88

>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 = 57.2 bits (139), Expect = 3e-11
 Identities = 19/106 (17%), Positives = 45/106 (42%), Gaps = 14/106 (13%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAF--KTLKHKGQAWLVFKDVAS 70
           P+  +Y+ ++      +Q+      +    G ++ + + F  +T + KG A++ F+D+ S
Sbjct: 1   PSRVVYLGSIPYDQTEEQILD----LCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLES 56

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRH 116
           + +AV  + G+    + ++  Y+           G     E    H
Sbjct: 57  SASAVRNLNGYQLGSRFLKCGYSSNS-----DISGV--SLEHHHHH 95

>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 = 43.8 bits (104), Expect = 2e-06
 Identities = 16/81 (19%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE----AKP-GIAFVEYGDEMQATVA 224
           P+ ++++ ++P+D T   +    S       ++M+      +  G AF+E+ D   +  A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 225 MQSLQSLKIGQQQLLITYAKK 245
           +++L   ++G + L   Y+  
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSN 81

>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 = 57.2 bits (139), Expect = 3e-11
 Identities = 26/90 (28%), Positives = 46/90 (51%), Gaps = 8/90 (8%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE----ILAFKTLKHKGQAWLVFKDV 68
          S ++ I+I NL+ ++  D+  + L+  F  FG IL+    +    T   KG A++ F   
Sbjct: 3  SGSSGIFIGNLDPEI--DE--KLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASF 58

Query: 69 ASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           ++ AA+E M G    ++P+ + YA  K  
Sbjct: 59 DASDAAIEAMNGQYLCNRPITVSYAFKKDS 88

>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 = 57.6 bits (139), Expect = 4e-11
 Identities = 11/87 (12%), Positives = 35/87 (40%), Gaps = 7/87 (8%)

Query: 16  NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK------TLKHKGQAWLVFKDVA 69
           N +++  L++++   ++ +     F +FG I +++         +      A++ +    
Sbjct: 16  NLVFVVGLSQRLADPEVLKR-PEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74

Query: 70  SATAAVEKMQGFPFYDKPMRIQYAKTK 96
            A  A++ +       + ++     TK
Sbjct: 75  DALRAIQCVNNVVVDGRTLKASLGTTK 101

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 56.9 bits (138), Expect = 7e-11
 Identities = 27/112 (24%), Positives = 49/112 (43%), Gaps = 11/112 (9%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAFKTLKHKGQAWL 63
           +         +T+++ NL+ KV   +LK+    VF   G ++  +IL  K  K +G   +
Sbjct: 6   SGALQAGRLGSTVFVANLDYKVGWKKLKE----VFSMAGVVVRADILEDKDGKSRGIGTV 61

Query: 64  VFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKR 115
            F+    A  A+    G   +D+PM ++  +          G F P ER ++
Sbjct: 62  TFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP-----KGDFFPPERPQQ 108

>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 = 37.7 bits (88), Expect = 6e-04
 Identities = 14/93 (15%), Positives = 32/93 (34%), Gaps = 4/93 (4%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGI----AF 212
           G + S          + +FV N+ +      L+  FS         ++E K G       
Sbjct: 1   GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGT 60

Query: 213 VEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
           V +   ++A  A+       +  + + +   ++
Sbjct: 61  VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDER 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 = 56.5 bits (137), Expect = 7e-11
 Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 5/94 (5%)

Query: 6  ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLV 64
          +    +     T+Y+ NL+  V    + Q    +F Q G      +  +   +    ++ 
Sbjct: 6  SGMMEDDGQPRTLYVGNLSRDVTEVLILQ----LFSQIGPCKSCKMITEHTSNDPYCFVE 61

Query: 65 FKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
          F +   A AA+  M G     K +++ +A T S 
Sbjct: 62 FYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS 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 = 46.1 bits (110), Expect = 5e-07
 Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 3/91 (3%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV---EAKPGIAFV 213
           G + S            L+V N+  D T + +   FSQ    K  +M+    +     FV
Sbjct: 1   GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFV 60

Query: 214 EYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           E+ +   A  A+ ++   KI  +++ + +A 
Sbjct: 61  EFYEHRDAAAALAAMNGRKILGKEVKVNWAT 91

>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 = 55.6 bits (135), Expect = 1e-10
 Identities = 26/89 (29%), Positives = 45/89 (50%), Gaps = 7/89 (7%)

Query: 9  GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVF 65
          G+  +    +Y+  L E+V      + LHA F  FG I +    L ++T KH+G A++ F
Sbjct: 1  GSMATTKRVLYVGGLAEEVD----DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 56

Query: 66 KDVASATAAVEKMQGFPFYDKPMRIQYAK 94
          +    A AA++ M     + + +R+  AK
Sbjct: 57 ELAEDAAAAIDNMNESELFGRTIRVNLAK 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 = 39.8 bits (94), Expect = 5e-05
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 5/82 (6%)

Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQAT 222
           A    +L+V  +  +     L   F  F    ++++          G AFVE+     A 
Sbjct: 4   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 223 VAMQSLQSLKIGQQQLLITYAK 244
            A+ ++   ++  + + +  AK
Sbjct: 64  AAIDNMNESELFGRTIRVNLAK 85

>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 = 56.2 bits (135), Expect = 1e-10
 Identities = 13/82 (15%), Positives = 36/82 (43%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
           + ++N++ ++   +L+Q L   F + G +  +       ++ +A +  +++  A  AV 
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVN 70

Query: 77 KMQGFPFYDKPMRIQYAKTKSD 98
           +  +    K + +  A   S 
Sbjct: 71 SLHRYKIGSKKILVSLATGASG 92

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 56.2 bits (136), Expect = 1e-10
 Identities = 19/93 (20%), Positives = 43/93 (46%), Gaps = 9/93 (9%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
            ++      N  +++      V+  +L +    +F  FG + E+         G A++ F
Sbjct: 22  HHRQEGELSNTRLFVRPFPLDVQESELNE----IFGPFGPMKEVK-----ILNGFAFVEF 72

Query: 66  KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           ++  SA  A+E++ G  F ++P+ + Y+K  + 
Sbjct: 73  EEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 3/90 (3%)

Query: 156 PGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEY 215
           P G+     +     N  LFV+  P D     L   F  F G   ++ V+   G AFVE+
Sbjct: 16  PRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPF-G--PMKEVKILNGFAFVEF 72

Query: 216 GDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
            +   A  A++ +       Q L + Y+K 
Sbjct: 73  EEAESAAKAIEEVHGKSFANQPLEVVYSKL 102

>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 = 56.1 bits (136), Expect = 1e-10
 Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 7/96 (7%)

Query: 6  ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAW 62
          +      +    +Y+  L E+V    L       F  FG I +    L ++T KH+G A+
Sbjct: 3  SGSSGMATTKRVLYVGGLAEEVDDKVLHA----AFIPFGDITDIQIPLDYETEKHRGFAF 58

Query: 63 LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
          + F+    A AA++ M     + + +R+  AK    
Sbjct: 59 VEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI 94

>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 = 42.6 bits (101), Expect = 9e-06
 Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 5/87 (5%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDE 218
               A    +L+V  +  +     L   F  F    ++++          G AFVE+   
Sbjct: 5   SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64

Query: 219 MQATVAMQSLQSLKIGQQQLLITYAKK 245
             A  A+ ++   ++  + + +  AK 
Sbjct: 65  EDAAAAIDNMNESELFGRTIRVNLAKP 91

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 55.5 bits (134), Expect = 1e-10
 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 15 NNTIYINNL--NEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASA 71
          ++ I ++N+      ++++LK  +H +F +FG I       +  K KG  +L +   A A
Sbjct: 1  DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 60

Query: 72 TAAVEKMQGFPFYDK 86
            AV+   G+    +
Sbjct: 61 VDAVKNADGYKLDKQ 75

>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 = 56.1 bits (135), Expect = 2e-10
 Identities = 18/97 (18%), Positives = 35/97 (36%), Gaps = 9/97 (9%)

Query: 2   EPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQA 61
              + +  +   P+  I+I  L   V   ++      +   FG +  +     LK K QA
Sbjct: 18  GSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVIS----LGLPFGKVTNL---LMLKGKNQA 70

Query: 62  WLVFKDVASATAAVEKMQGFPFY--DKPMRIQYAKTK 96
           ++      +A   V            +P+ IQ++  K
Sbjct: 71  FIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK 107

>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 = 56.1 bits (135), Expect = 2e-10
 Identities = 15/81 (18%), Positives = 32/81 (39%), Gaps = 3/81 (3%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAM 225
           +   P+ ++ ++ +P D T   +      F     + M++ K   AF+E   E  A   +
Sbjct: 26  SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMV 84

Query: 226 QSLQS--LKIGQQQLLITYAK 244
               S    +  Q + I ++ 
Sbjct: 85  NYYTSVTPVLRGQPIYIQFSN 105

>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 = 57.2 bits (139), Expect = 2e-10
 Identities = 17/89 (19%), Positives = 39/89 (43%), Gaps = 7/89 (7%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVA 69
          + N  + +N L + +   +L      +F+  G I     +  +KT    G A++ F    
Sbjct: 1  ASNTNLIVNYLPQDMTDRELYA----LFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEM 56

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           +  A++ + G    +K +++ YA+   +
Sbjct: 57 DSQRAIKVLNGITVRNKRLKVSYARPGGE 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 = 47.6 bits (114), Expect = 4e-07
 Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 9/93 (9%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILA-FKTLKHKGQAW 62
           A  G E   +  +Y+ NL   +  DQL      +F ++G+I++  IL    T + +G A+
Sbjct: 80  ARPGGESIKDTNLYVTNLPRTITDDQLDT----IFGKYGSIVQKNILRDKLTGRPRGVAF 135

Query: 63  LVFKDVASATAAVEKMQG--FPFYDKPMRIQYA 93
           + +     A  A+  +         +P+ ++ A
Sbjct: 136 VRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 41.4 bits (98), Expect = 6e-05
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           L V  +P D T   L   F         R++         G AFV++  EM +  A++ L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 229 QSLKIGQQQLLITYAKK 245
             + +  ++L ++YA+ 
Sbjct: 66  NGITVRNKRLKVSYARP 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 = 41.0 bits (97), Expect = 7e-05
 Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 7/87 (8%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVR-MVEAKP----GIAFVEYGDE 218
           P   +  +  L+V N+P   T   L   F ++    +   + +       G+AFV Y   
Sbjct: 82  PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 141

Query: 219 MQATVAMQSL--QSLKIGQQQLLITYA 243
            +A  A+ +L     + G Q L +  A
Sbjct: 142 EEAQEAISALNNVIPEGGSQPLSVRLA 168

>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 = 55.3 bits (134), Expect = 2e-10
 Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFKDVAS 70
            + T+++ NL  +V+ + L +    +F Q G + +  I   +  K K   ++ FK   S
Sbjct: 14 EADRTVFVGNLEARVREEILYE----LFLQAGPLTKVTICKDREGKPKSFGFVCFKHPES 69

Query: 71 ATAAVEKMQGFPFYDKPMRIQYA 93
           + A+  + G   Y +P+ +   
Sbjct: 70 VSYAIALLNGIRLYGRPINVSGP 92

>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 = 48.8 bits (117), Expect = 4e-08
 Identities = 16/89 (17%), Positives = 32/89 (35%), Gaps = 4/89 (4%)

Query: 159 AKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV---EAKP-GIAFVE 214
             S +  A    +  +FV N+        L   F Q     +V +    E KP    FV 
Sbjct: 4   GSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVC 63

Query: 215 YGDEMQATVAMQSLQSLKIGQQQLLITYA 243
           +      + A+  L  +++  + + ++  
Sbjct: 64  FKHPESVSYAIALLNGIRLYGRPINVSGP 92

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 55.3 bits (134), Expect = 2e-10
 Identities = 18/89 (20%), Positives = 40/89 (44%), Gaps = 10/89 (11%)

Query: 10 NEISPNNTIYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDV 68
          + I P + ++I NL  + V     K+ L  +F  +G I++I     +K     ++ F + 
Sbjct: 5  HNIPPKSRLFIGNLPLKNVS----KEDLFRIFSPYGHIMQI----NIK-NAFGFIQFDNP 55

Query: 69 ASATAAVEKMQGFPFYDKPMRIQYAKTKS 97
           S   A+E       + K + ++ + + +
Sbjct: 56 QSVRDAIECESQEMNFGKKLILEVSSSNA 84

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 44.9 bits (107), Expect = 9e-07
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 169 PPNNILFVQNVP-HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQS 227
           PP + LF+ N+P  + +   L   FS + G   +  +  K    F+++ +      A++ 
Sbjct: 8   PPKSRLFIGNLPLKNVSKEDLFRIFSPY-G--HIMQINIKNAFGFIQFDNPQSVRDAIEC 64

Query: 228 LQSLKIGQQQLLITYAK 244
                   ++L++  + 
Sbjct: 65  ESQEMNFGKKLILEVSS 81

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 55.2 bits (133), Expect = 2e-10
 Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 9/85 (10%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
          P+  ++I  L  +V   ++      +   FG +  I     LK K QA+L      +A  
Sbjct: 14 PSRVLHIRKLPGEVTETEVIA----LGLPFGKVTNI---LMLKGKNQAFLELATEEAAIT 66

Query: 74 AVEKMQGFPFY--DKPMRIQYAKTK 96
           V        +  ++P+ IQY+  K
Sbjct: 67 MVNYYSAVTPHLRNQPIYIQYSNHK 91

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 54.8 bits (132), Expect = 3e-10
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 3/81 (3%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQ 226
              P+ +L ++ +P + T   +      F     + M++ K   AF+E   E  A   + 
Sbjct: 11  DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-NQAFLELATEEAAITMVN 69

Query: 227 --SLQSLKIGQQQLLITYAKK 245
             S  +  +  Q + I Y+  
Sbjct: 70  YYSAVTPHLRNQPIYIQYSNH 90

>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 = 55.4 bits (134), Expect = 2e-10
 Identities = 29/92 (31%), Positives = 41/92 (44%), Gaps = 15/92 (16%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-----------TLKHKGQA 61
          S NNTI++  L E V I+ +       FKQ G I                  T K KG+A
Sbjct: 11 SDNNTIFVQGLGENVTIESVAD----YFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 66

Query: 62 WLVFKDVASATAAVEKMQGFPFYDKPMRIQYA 93
           + F D  SA AA++   G  F   P+++ +A
Sbjct: 67 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 43.1 bits (102), Expect = 5e-06
 Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 13/78 (16%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQF--------PGFKEVRMVEAKP-----GI 210
                  NN +FVQ +  + T  ++  +F Q          G   + +   +      G 
Sbjct: 6   HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65

Query: 211 AFVEYGDEMQATVAMQSL 228
           A V + D   A  A+   
Sbjct: 66  ATVSFDDPPSAKAAIDWF 83

>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 = 55.0 bits (133), Expect = 3e-10
 Identities = 20/89 (22%), Positives = 42/89 (47%), Gaps = 6/89 (6%)

Query: 9   GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAFKTLKHKGQAWLVFK 66
           G  +     + ++NL+  V    +++    +F +FGT+    +   ++ +  G A + F+
Sbjct: 23  GAGVETGGKLLVSNLDFGVSDADIQE----LFAEFGTLKKAAVHYDRSGRSLGTADVHFE 78

Query: 67  DVASATAAVEKMQGFPFYDKPMRIQYAKT 95
             A A  A+++  G P   +PM IQ   +
Sbjct: 79  RKADALKAMKQYNGVPLDGRPMNIQLVTS 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 = 37.6 bits (88), Expect = 5e-04
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 4/82 (4%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP----GIAFVEYGDEMQA 221
           A       L V N+    +   +Q  F++F   K+  +   +     G A V +  +  A
Sbjct: 24  AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADA 83

Query: 222 TVAMQSLQSLKIGQQQLLITYA 243
             AM+    + +  + + I   
Sbjct: 84  LKAMKQYNGVPLDGRPMNIQLV 105

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 55.9 bits (135), Expect = 3e-10
 Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 7/91 (7%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAW 62
              G   +    +Y+  L E+V    L       F  FG I +I       T KH+G A+
Sbjct: 54  GGSGGSATTKRVLYVGGLAEEVDDKVLHA----AFIPFGDITDIQIPLDYETEKHRGFAF 109

Query: 63  LVFKDVASATAAVEKMQGFPFYDKPMRIQYA 93
           + F+    A AA++ M     + + +R+  A
Sbjct: 110 VEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 41.3 bits (97), Expect = 5e-05
 Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 5/77 (6%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE----AKP-GIA 211
           G   S      A    +L+V  +  +     L   F  F    ++++       K  G A
Sbjct: 49  GSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 108

Query: 212 FVEYGDEMQATVAMQSL 228
           FVE+     A  A+ ++
Sbjct: 109 FVEFELAEDAAAAIDNM 125

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 54.9 bits (132), Expect = 3e-10
 Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 9/85 (10%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
          P+  I+I  L   V   ++      +   FG +  +     LK K QA++      +A  
Sbjct: 15 PSRVIHIRKLPIDVTEGEVIS----LGLPFGKVTNL---LMLKGKNQAFIEMNTEEAANT 67

Query: 74 AVEKMQGFP--FYDKPMRIQYAKTK 96
           V            +P+ IQ++  K
Sbjct: 68 MVNYYTSVTPVLRGQPIYIQFSNHK 92

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 53.3 bits (128), Expect = 1e-09
 Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 3/80 (3%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQ 226
              P+ ++ ++ +P D T   +      F     + M++ K   AF+E   E  A   + 
Sbjct: 12  SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMVN 70

Query: 227 SLQS--LKIGQQQLLITYAK 244
              S    +  Q + I ++ 
Sbjct: 71  YYTSVTPVLRGQPIYIQFSN 90

>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 = 54.6 bits (132), Expect = 3e-10
 Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 9/91 (9%)

Query: 6  ANQGNEISPNNT-IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLV 64
          ++  +      T +Y+  L + +    L+      F QFG I  I     ++ +  A++ 
Sbjct: 2  SSGSSGEDKTITTLYVGGLGDTITETDLRN----HFYQFGEIRTI---TVVQRQQCAFIQ 54

Query: 65 FKDVASATAAVEKM-QGFPFYDKPMRIQYAK 94
          F    +A  A EK         + + +++ +
Sbjct: 55 FATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 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 = 51.1 bits (123), Expect = 5e-09
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQ-S 227
                L+V  +    T   L+  F QF   + + +V+ +   AF+++     A VA + S
Sbjct: 10  KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ-QCAFIQFATRQAAEVAAEKS 68

Query: 228 LQSLKIGQQQLLITYAK 244
              L +  ++L + + +
Sbjct: 69  FNKLIVNGRRLNVKWGR 85

>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 = 56.0 bits (135), Expect = 3e-10
 Identities = 21/132 (15%), Positives = 46/132 (34%), Gaps = 3/132 (2%)

Query: 113 RKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNN 172
            +  +    ++  +  AN  G+     Y  A           +             P + 
Sbjct: 18  TEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMH---RDSCPLDC 74

Query: 173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLK 232
            ++V N+ ++     L+  F  +   + V +    PG AFVE+ D   A  A++ L    
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 134

Query: 233 IGQQQLLITYAK 244
           +   ++ +  + 
Sbjct: 135 LCGCRVRVELSN 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 = 44.9 bits (106), Expect = 3e-06
 Identities = 16/85 (18%), Positives = 36/85 (42%), Gaps = 7/85 (8%)

Query: 13  SPNNT-IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASA 71
            P +  +Y+ NL       +L++     F  +G +  +   +     G A++ F+D   A
Sbjct: 70  CPLDCKVYVGNLGNNGNKTELER----AFGYYGPLRSVWVAR--NPPGFAFVEFEDPRDA 123

Query: 72  TAAVEKMQGFPFYDKPMRIQYAKTK 96
             AV ++ G       +R++ +  +
Sbjct: 124 ADAVRELDGRTLCGCRVRVELSNGE 148

>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 = 56.4 bits (136), Expect = 3e-10
 Identities = 17/125 (13%), Positives = 49/125 (39%), Gaps = 21/125 (16%)

Query: 2   EPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHK 58
           + E+            +++ +++E+ + D++++     F  +G I      L  +T   K
Sbjct: 59  DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQE----KFCDYGEIKNIHLNLDRRTGFSK 114

Query: 59  GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEE 118
           G A + ++    A AA E + G     + +++ +                 +  ++  + 
Sbjct: 115 GYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF--------------VKGPKRVKKS 160

Query: 119 KGKKR 123
           + ++R
Sbjct: 161 EKRRR 165

>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 = 51.0 bits (122), Expect = 2e-08
 Identities = 27/143 (18%), Positives = 46/143 (32%), Gaps = 21/143 (14%)

Query: 108 VPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAP 167
           + R + K    KG+      +  +A                P  Q    G          
Sbjct: 23  IVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEG---------- 72

Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV------EAKPGIAFVEYGDEMQA 221
                ILFV ++  +     +Q  F  +   K + +        +K G A VEY    QA
Sbjct: 73  ----WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK-GYALVEYETHKQA 127

Query: 222 TVAMQSLQSLKIGQQQLLITYAK 244
             A ++L   +I  Q + + +  
Sbjct: 128 LAAKEALNGAEIMGQTIQVDWCF 150

>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 = 54.6 bits (132), Expect = 4e-10
 Identities = 16/96 (16%), Positives = 39/96 (40%), Gaps = 9/96 (9%)

Query: 8  QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFK---TLKHKGQAWL 63
          Q  +    + I + N+  +    ++++    +F  FG +  + L  K   T  H+G  ++
Sbjct: 8  QVPKKQTTSKILVRNIPFQANQREIRE----LFSTFGELKTVRLPKKMTGTGAHRGFGFV 63

Query: 64 VFKDVASATAAVEKM-QGFPFYDKPMRIQYAKTKSD 98
           F     A  A   +      Y + + +++A ++  
Sbjct: 64 DFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT 99

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 46.1 bits (110), Expect = 4e-07
 Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 7/95 (7%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP------GI 210
           G + S          + + V+N+P       ++  FS F   K VR+ +         G 
Sbjct: 1   GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 211 AFVEYGDEMQATVAMQSL-QSLKIGQQQLLITYAK 244
            FV++  +  A  A  +L  S  +  ++L++ +A 
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWAD 95

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 56.1 bits (136), Expect = 4e-10
 Identities = 17/89 (19%), Positives = 35/89 (39%), Gaps = 6/89 (6%)

Query: 160 KSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV-----EAKPGIAFVE 214
           +    +     + + F+  +P+      ++   + F   K   +V         G AF E
Sbjct: 84  RPHDYQPLPGAHKL-FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 142

Query: 215 YGDEMQATVAMQSLQSLKIGQQQLLITYA 243
           Y D      A+  L  +++G ++LL+  A
Sbjct: 143 YVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 55.7 bits (135), Expect = 6e-10
 Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 7/91 (7%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAF--KTLKHKGQAW 62
            +    +   + ++I  L   +  DQ+K+    +   FG +    L     T   KG A+
Sbjct: 85  PHDYQPLPGAHKLFIGGLPNYLNDDQVKE----LLTSFGPLKAFNLVKDSATGLSKGYAF 140

Query: 63  LVFKDVASATAAVEKMQGFPFYDKPMRIQYA 93
             + D+     A+  + G    DK + +Q A
Sbjct: 141 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 15/95 (15%), Positives = 33/95 (34%), Gaps = 13/95 (13%)

Query: 12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--------ILAFKTLKHKGQAWL 63
          +     +Y+ N+   +  + +       F     +          +LA +  + K  A+L
Sbjct: 1  LGSARRLYVGNIPFGITEEAMMD----FFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 56

Query: 64 VFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           F+ V   T A+    G  F  + ++I+       
Sbjct: 57 EFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQP 90

>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 = 44.1 bits (105), Expect = 6e-06
 Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 10/63 (15%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP----------GIAFVEYGDEMQATV 223
           L+V N+P   T  A+  FF+       +      P            AF+E+    + T 
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 224 AMQ 226
           AM 
Sbjct: 67  AMA 69

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 54.0 bits (130), Expect = 5e-10
 Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 8/85 (9%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          S ++ I + NL +        Q +H + K +     +      ++K  A++   +   A 
Sbjct: 3  SGSSGILVKNLPQDSN----CQEVHDLLKDYD----LKYCYVDRNKRTAFVTLLNGEQAQ 54

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKS 97
           A++    + F  K + +Q   T +
Sbjct: 55 NAIQMFHQYSFRGKDLIVQLQPTDA 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 = 48.2 bits (115), Expect = 5e-08
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 2/71 (2%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
           + V+N+P D+    +      +   K    V+     AFV   +  QA  A+Q       
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDY-DLKYCY-VDRNKRTAFVTLLNGEQAQNAIQMFHQYSF 65

Query: 234 GQQQLLITYAK 244
             + L++    
Sbjct: 66  RGKDLIVQLQP 76

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 54.2 bits (131), Expect = 5e-10
 Identities = 22/93 (23%), Positives = 43/93 (46%), Gaps = 4/93 (4%)

Query: 156 PGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE---AKP-GIA 211
             G+  V   + +   + LF+  +P   T   L+         K++R+V     KP G+A
Sbjct: 2   SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLA 61

Query: 212 FVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           +VEY +E QA+ A+  +  + I +  + +  + 
Sbjct: 62  YVEYENESQASQAVMKMDGMTIKENIIKVAISN 94

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 50.4 bits (121), Expect = 1e-08
 Identities = 16/85 (18%), Positives = 43/85 (50%), Gaps = 6/85 (7%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFKDVASA 71
            + ++I+ L      ++L++    + K  GT+ +  ++  +  K KG A++ +++ + A
Sbjct: 16 EKHKLFISGLPFSCTKEELEE----ICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQA 71

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTK 96
          + AV KM G    +  +++  + + 
Sbjct: 72 SQAVMKMDGMTIKENIIKVAISNSG 96

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 54.2 bits (131), Expect = 6e-10
 Identities = 19/94 (20%), Positives = 40/94 (42%), Gaps = 4/94 (4%)

Query: 1  MEPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQ 60
          M      +G   + +  IY+ NL   ++     + +  VF ++G I +I           
Sbjct: 8  MSGGGVIRGPAGNNDCRIYVGNLPPDIR----TKDIEDVFYKYGAIRDIDLKNRRGGPPF 63

Query: 61 AWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAK 94
          A++ F+D   A  AV    G+ +    +R+++ +
Sbjct: 64 AFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 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 = 48.9 bits (117), Expect = 5e-08
 Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 2/81 (2%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATV 223
                +  ++V N+P D     ++  F ++   +++ +   +  P  AFVE+ D   A  
Sbjct: 17  PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAED 76

Query: 224 AMQSLQSLKIGQQQLLITYAK 244
           A+           +L + + +
Sbjct: 77  AVYGRDGYDYDGYRLRVEFPR 97

>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 = 53.4 bits (129), Expect = 8e-10
 Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 6/85 (7%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
             T+   NL+  +  D+LK+    VF+    I   L  +  K KG A++ FK  A A  
Sbjct: 15 AARTLLAKNLSFNITEDELKE----VFEDALEI--RLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 74 AVEKMQGFPFYDKPMRIQYAKTKSD 98
           +E+ QG     + + + Y   K  
Sbjct: 69 NLEEKQGAEIDGRSVSLYYTGEKGG 93

>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 = 50.3 bits (121), Expect = 1e-08
 Identities = 15/81 (18%), Positives = 29/81 (35%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATV 223
                     L  +N+  + T   L+  F      + V       GIA++E+  E  A  
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 224 AMQSLQSLKIGQQQLLITYAK 244
            ++  Q  +I  + + + Y  
Sbjct: 69  NLEEKQGAEIDGRSVSLYYTG 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 = 54.3 bits (131), Expect = 9e-10
 Identities = 19/114 (16%), Positives = 41/114 (35%), Gaps = 21/114 (18%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVAS 70
               +++  ++E+   +     +H  F ++G I      L  +T   KG   + ++    
Sbjct: 21  EGWILFVTGVHEEATEE----DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 76

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRK 124
           A AA+E + G     +P+ + +                 R   K     G++R 
Sbjct: 77  AQAAMEGLNGQDLMGQPISVDWCF--------------VRGPPKGKRRGGRRRS 116

>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 = 50.8 bits (122), Expect = 2e-08
 Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 7/85 (8%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV------EAKPGIAFVEYGDEM 219
             +    ILFV  V  + T   +   F+++   K + +         K G   VEY    
Sbjct: 17  QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK-GYTLVEYETYK 75

Query: 220 QATVAMQSLQSLKIGQQQLLITYAK 244
           +A  AM+ L    +  Q + + +  
Sbjct: 76  EAQAAMEGLNGQDLMGQPISVDWCF 100

>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 = 54.0 bits (130), Expect = 9e-10
 Identities = 29/104 (27%), Positives = 44/104 (42%), Gaps = 15/104 (14%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-----------T 54
           +   +E S N+ IY+  LN+ V +D L       FKQ G +                  T
Sbjct: 6   SGDPDEDSDNSAIYVQGLNDSVTLDDLAD----FFKQCGVVKMNKRTGQPMIHIYLDKET 61

Query: 55  LKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            K KG A + ++D  +A AAVE   G  F    +++  A+ K  
Sbjct: 62  GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105

>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 = 44.3 bits (105), Expect = 3e-06
 Identities = 19/85 (22%), Positives = 28/85 (32%), Gaps = 13/85 (15%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQF--------PGFKEVRMVEAKP 208
           G + S         N+ ++VQ +    T   L  FF Q          G   + +   K 
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 209 -----GIAFVEYGDEMQATVAMQSL 228
                G A V Y D   A  A++  
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWF 85

>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 = 25/87 (28%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDE 218
           P A       LFV  V +DTT   L+  F  +   K + MV +K      G AF+EY  E
Sbjct: 95  PNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE 154

Query: 219 MQATVAMQSLQSLKIGQQQLLITYAKK 245
                A +     KI  +++L+   + 
Sbjct: 155 RDMHSAYKHADGKKIDGRRVLVDVERG 181

>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 = 50.2 bits (119), Expect = 2e-07
 Identities = 15/123 (12%), Positives = 41/123 (33%), Gaps = 7/123 (5%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVAS 70
              T+++  +N      +L++     F+ +G I  I      ++ K +G A++ ++    
Sbjct: 101 AFKTLFVARVNYDTTESKLRR----EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERD 156

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDAN 130
             +A +   G     + + +   + ++    +           +R       R    D  
Sbjct: 157 MHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDT 216

Query: 131 QAG 133
              
Sbjct: 217 SRY 219

>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 = 53.1 bits (128), Expect = 2e-09
 Identities = 16/86 (18%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVAS 70
               +++ +++E+ + D++++     F  +G I      L  +T   KG A + ++    
Sbjct: 25  EGWILFVTSIHEEAQEDEIQE----KFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 80

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTK 96
           A AA E + G     + +++ +   K
Sbjct: 81  ALAAKEALNGAEIMGQTIQVDWCFVK 106

>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 = 46.1 bits (110), Expect = 5e-07
 Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 7/85 (8%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV------EAKPGIAFVEYGDEM 219
             +    ILFV ++  +     +Q  F  +   K + +        +K G A VEY    
Sbjct: 21  QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK-GYALVEYETHK 79

Query: 220 QATVAMQSLQSLKIGQQQLLITYAK 244
           QA  A ++L   +I  Q + + +  
Sbjct: 80  QALAAKEALNGAEIMGQTIQVDWCF 104

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 52.6 bits (127), Expect = 2e-09
 Identities = 14/86 (16%), Positives = 35/86 (40%), Gaps = 7/86 (8%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVAS 70
               +++  ++E+   + +       F ++G I      L  +T   KG   + ++    
Sbjct: 22  EGWILFVTGVHEEATEEDIHD----KFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 77

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTK 96
           A AA+E + G     +P+ + +   +
Sbjct: 78  AQAAMEGLNGQDLMGQPISVDWCFVR 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 17/81 (20%), Positives = 30/81 (37%), Gaps = 5/81 (6%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE----AKP-GIAFVEYGDEMQATV 223
               ILFV  V  + T   +   F+++   K + +          G   VEY    +A  
Sbjct: 21  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 80

Query: 224 AMQSLQSLKIGQQQLLITYAK 244
           AM+ L    +  Q + + +  
Sbjct: 81  AMEGLNGQDLMGQPISVDWCF 101

>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 = 54.0 bits (130), Expect = 2e-09
 Identities = 24/133 (18%), Positives = 50/133 (37%), Gaps = 15/133 (11%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAW 62
             Q   +  + T+Y+ NL+     +Q+ +    +F + G I +I   L        G  +
Sbjct: 30  EEQEKLLKKSCTLYVGNLSFYTTEEQIYE----LFSKSGDIKKIIMGLDKMKKTACGFCF 85

Query: 63  LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKK 122
           + +   A A  A+  + G    D+ +R  +     +      G    + R +  ++    
Sbjct: 86  VEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQD---- 141

Query: 123 RKDQHDANQAGMG 135
               +DA + G G
Sbjct: 142 ----YDAGRGGYG 150

>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 = 51.7 bits (124), Expect = 1e-08
 Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 5/86 (5%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDE 218
            E     +  L+V N+   TT   +   FS+    K++ M   K      G  FVEY   
Sbjct: 32  QEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSR 91

Query: 219 MQATVAMQSLQSLKIGQQQLLITYAK 244
             A  AM+ +   ++  + +   +  
Sbjct: 92  ADAENAMRYINGTRLDDRIIRTDWDA 117

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 52.8 bits (127), Expect = 2e-09
 Identities = 24/95 (25%), Positives = 40/95 (42%), Gaps = 10/95 (10%)

Query: 5   VANQGNEISPNNTIYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWL 63
           V N+ +  S N+ ++I NLN   VK    K  +  +F ++G +          HKG A++
Sbjct: 17  VTNKNDPKSINSRVFIGNLNTALVK----KSDVETIFSKYGRVAGCSV-----HKGYAFV 67

Query: 64  VFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            + +   A AAV    G     + + I  A     
Sbjct: 68  QYSNERHARAAVLGENGRVLAGQTLDINMAGEPKP 102

>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 = 46.2 bits (110), Expect = 4e-07
 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 167 PAPPNNILFVQNVPHD-TTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAM 225
           P   N+ +F+ N+         ++  FS++ G   V       G AFV+Y +E  A  A+
Sbjct: 23  PKSINSRVFIGNLNTALVKKSDVETIFSKY-G--RVAGCSVHKGYAFVQYSNERHARAAV 79

Query: 226 QSLQSLKIGQQQLLITYAK 244
                  +  Q L I  A 
Sbjct: 80  LGENGRVLAGQTLDINMAG 98

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 52.3 bits (126), Expect = 2e-09
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 12/93 (12%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWL------V-F 65
          S ++ ++I NLN     + LK     VF + G I         K+K    L      V +
Sbjct: 3  SGSSGLFIKNLNFSTTEETLKG----VFSKVGAIKSC-TISKKKNKAGVLLSMGFGFVEY 57

Query: 66 KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
          K    A  A++++QG       + ++ ++  + 
Sbjct: 58 KKPEQAQKALKQLQGHTVDGHKLEVRISERATK 90

>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 = 44.9 bits (107), Expect = 9e-07
 Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 9/88 (10%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVR-MVEAKPGIA-------FVEYGD 217
             +  +  LF++N+   TT   L+  FS+    K      +             FVEY  
Sbjct: 1   GSSGSSG-LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKK 59

Query: 218 EMQATVAMQSLQSLKIGQQQLLITYAKK 245
             QA  A++ LQ   +   +L +  +++
Sbjct: 60  PEQAQKALKQLQGHTVDGHKLEVRISER 87

>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 = 52.2 bits (126), Expect = 3e-09
 Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 7/94 (7%)

Query: 6  ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAW 62
           + G ++    T+ ++NL  +   D L++    VF+++G + +        T   +G A+
Sbjct: 4  GSSGPDVDGMITLKVDNLTYRTSPDSLRR----VFEKYGRVGDVYIPREPHTKAPRGFAF 59

Query: 63 LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTK 96
          + F D   A  A   M G     + +R+Q A+  
Sbjct: 60 VRFHDRRDAQDAEAAMDGAELDGRELRVQVARYG 93

>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 = 44.5 bits (106), Expect = 1e-06
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 8/93 (8%)

Query: 158 GAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV------EAKPGIA 211
           G+              L V N+ + T+P +L+  F ++    +V +         + G A
Sbjct: 1   GSSGSSGPDVDGMIT-LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPR-GFA 58

Query: 212 FVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           FV + D   A  A  ++   ++  ++L +  A+
Sbjct: 59  FVRFHDRRDAQDAEAAMDGAELDGRELRVQVAR 91

>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 = 52.3 bits (126), Expect = 3e-09
 Identities = 19/91 (20%), Positives = 40/91 (43%), Gaps = 9/91 (9%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFKDVAS 70
            +  +++  LN++   + + +    +F+ FG I E  +L       KG A++ F     
Sbjct: 13 GRDRKLFVGMLNKQQSEEDVLR----LFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTE 68

Query: 71 ATAAVEKMQG---FPFYDKPMRIQYAKTKSD 98
          A AA+  + G    P     + +++A T  +
Sbjct: 69 AQAAIHALHGSQTMPGASSSLVVKFADTDKE 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 = 41.9 bits (99), Expect = 1e-05
 Identities = 19/96 (19%), Positives = 37/96 (38%), Gaps = 7/96 (7%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAF 212
           G + S   E+    +  LFV  +    +   +   F  F    E  ++        G AF
Sbjct: 1   GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAF 60

Query: 213 VEYGDEMQATVAMQSL---QSLKIGQQQLLITYAKK 245
           V++    +A  A+ +L   Q++      L++ +A  
Sbjct: 61  VKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADT 96

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 51.9 bits (125), Expect = 3e-09
 Identities = 19/90 (21%), Positives = 38/90 (42%), Gaps = 11/90 (12%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQF--PGFKEVRMVEAKP-----GIAFVEYGDEM 219
                + + ++N+   T   ++    S +       +R+++ K      G AFV+    M
Sbjct: 5   HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64

Query: 220 QATVAMQSLQ----SLKIGQQQLLITYAKK 245
            A+  +Q LQ     LKI  + + + +AK 
Sbjct: 65  DASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 14/90 (15%), Positives = 33/90 (36%), Gaps = 13/90 (14%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGT--ILEILAFK---TLKHKGQAWLVFKDV 68
            +TI + N+           S+      + +  +  I   K   T +++G A++     
Sbjct: 8  HMDTIILRNIAPHTV----VDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSA 63

Query: 69 ASATAAVEKMQG----FPFYDKPMRIQYAK 94
            A+  ++ +Q          K + + +AK
Sbjct: 64 MDASQLLQILQSLHPPLKIDGKTIGVDFAK 93

>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 = 52.3 bits (126), Expect = 3e-09
 Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 9/86 (10%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          +    +++ NL   V  + L++     F QFG +  +      K K  A++ F +   A 
Sbjct: 9  AKVKVLFVRNLANTVTEEILEK----AFSQFGKLERVK-----KLKDYAFIHFDERDGAV 59

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A+E+M G     + + I +AK    
Sbjct: 60 KAMEEMNGKDLEGENIEIVFAKPPDQ 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 = 46.5 bits (111), Expect = 4e-07
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQS 227
                +LFV+N+ +  T   L+  FSQF   + V+ ++     AF+ + +   A  AM+ 
Sbjct: 8   MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK---DYAFIHFDERDGAVKAMEE 64

Query: 228 LQSLKIGQQQLLITYAKK 245
           +    +  + + I +AK 
Sbjct: 65  MNGKDLEGENIEIVFAKP 82

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 52.0 bits (125), Expect = 3e-09
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 13 SPNNTIYINNL--NEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVA 69
            ++ I ++N+      ++++LK  +H +F +FG I       +  K KG  +L +   A
Sbjct: 13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPA 72

Query: 70 SATAAVEKMQGFPF 83
           A  AV+   G+  
Sbjct: 73 HAVDAVKNADGYKL 86

>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 = 52.1 bits (125), Expect = 4e-09
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 9/88 (10%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQF-PGFKEVRMVE------AKPGIAFVEYGDE 218
           + +  N  LF+  +P       +    ++   G  +V +           G AFVEY   
Sbjct: 3   SGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62

Query: 219 MQATVAMQSLQS--LKIGQQQLLITYAK 244
             A +A + L    +++   Q+ + +A+
Sbjct: 63  RAAAMARRKLMPGRIQLWGHQIAVDWAE 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 = 49.0 bits (117), Expect = 5e-08
 Identities = 12/92 (13%), Positives = 38/92 (41%), Gaps = 11/92 (11%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEIL-----AFKTLKHKGQAWLVFKDV 68
           N  ++I  + +  K +++ +       +    +  +     A   +K++G A++ ++  
Sbjct: 7  GNCRLFIGGIPKMKKREEILE----EIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62

Query: 69 ASATAAVEKMQ--GFPFYDKPMRIQYAKTKSD 98
           +A  A  K+       +   + + +A+ + D
Sbjct: 63 RAAAMARRKLMPGRIQLWGHQIAVDWAEPEID 94

>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 = 51.5 bits (124), Expect = 4e-09
 Identities = 16/86 (18%), Positives = 37/86 (43%), Gaps = 10/86 (11%)

Query: 13 SPNNTIYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASA 71
             + ++I NL  + V     K+ L  +F  +G I++I     +K     ++ F +  S 
Sbjct: 20 HMKSRLFIGNLPLKNVS----KEDLFRIFSPYGHIMQI----NIK-NAFGFIQFDNPQSV 70

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKS 97
            A+E       + K + ++ + + +
Sbjct: 71 RDAIEXESQEMNFGKKLILEVSSSNA 96

>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 = 45.0 bits (107), Expect = 1e-06
 Identities = 12/79 (15%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 167 PAPPNNILFVQNVP-HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAM 225
            +   + LF+ N+P  + +   L   FS + G   +  +  K    F+++ +      A+
Sbjct: 18  GSHMKSRLFIGNLPLKNVSKEDLFRIFSPY-G--HIMQINIKNAFGFIQFDNPQSVRDAI 74

Query: 226 QSLQSLKIGQQQLLITYAK 244
           +         ++L++  + 
Sbjct: 75  EXESQEMNFGKKLILEVSS 93

>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 = 54.0 bits (129), Expect = 5e-09
 Identities = 24/170 (14%), Positives = 46/170 (27%), Gaps = 13/170 (7%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGT--ILEILAFK---TLKHKGQ 60
                       +YI NL      + L +         G   ILEI  F+     + KG 
Sbjct: 59  NVVYTYTGKRIALYIGNLTWWTTDEDLTE----AVHSLGVNDILEIKFFENRANGQSKGF 114

Query: 61  AWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKG 120
           A +     AS+   ++ +     + +   +     +      +      R+  +  +  G
Sbjct: 115 ALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQF----LSQFEMQSRKTTQSGQMSG 170

Query: 121 KKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP 170
           + +      +                        +PG A    P  P P 
Sbjct: 171 EGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPA 220

>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 = 50.9 bits (121), Expect = 6e-08
 Identities = 30/148 (20%), Positives = 46/148 (31%), Gaps = 10/148 (6%)

Query: 108 VPRERRKRHEEKGKKRKDQHD---ANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIP 164
           V  E  +  E  G  + D +D   +  A  G  P         PP        GA   + 
Sbjct: 2   VGEEFNQEAEYGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVV 61

Query: 165 EAPAPPNNILFVQNVPHDTTPMALQMFFSQF--PGFKEVRMVEAKP-----GIAFVEYGD 217
                    L++ N+   TT   L             E++  E +      G A V  G 
Sbjct: 62  YTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGS 121

Query: 218 EMQATVAMQSLQSLKIGQQQLLITYAKK 245
           E  +   M  L   ++  Q  ++T   K
Sbjct: 122 EASSKKLMDLLPKRELHGQNPVVTPVNK 149

>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 = 51.5 bits (124), Expect = 5e-09
 Identities = 17/94 (18%), Positives = 39/94 (41%), Gaps = 7/94 (7%)

Query: 6  ANQGNEIS--PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWL 63
           + GN      + T+ ++NL+     + L++    VF++   I ++   +  K KG A++
Sbjct: 4  GSSGNSTWSGESKTLVLSNLSYSATEETLQE----VFEKATFI-KVPQNQNGKSKGYAFI 58

Query: 64 VFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKS 97
           F     A  A+          + +R++    + 
Sbjct: 59 EFASFEDAKEALNSCNKREIEGRAIRLELQGPRG 92

>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 = 49.2 bits (118), Expect = 3e-08
 Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 7/92 (7%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA---KP-GIAF 212
           G + S      +  +  L + N+ +  T   LQ  F +      +++ +    K  G AF
Sbjct: 1   GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAF 57

Query: 213 VEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           +E+     A  A+ S    +I  + + +    
Sbjct: 58  IEFASFEDAKEALNSCNKREIEGRAIRLELQG 89

>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 = 53.0 bits (128), Expect = 6e-09
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 7/87 (8%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASA 71
             + +N L + +  ++ +     +F   G I      +   T +  G  ++ + D   A
Sbjct: 2  KTNLIVNYLPQNMTQEEFRS----LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDA 57

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            A+  + G     K +++ YA+  S 
Sbjct: 58 EKAINTLNGLRLQTKTIKVSYARPSSA 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 = 46.0 bits (110), Expect = 1e-06
 Identities = 17/93 (18%), Positives = 41/93 (44%), Gaps = 9/93 (9%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAW 62
           A   +    +  +Y++ L +   + Q  + L  +F Q+G I+    ++   T   +G  +
Sbjct: 79  ARPSSASIRDANLYVSGLPKT--MTQ--KELEQLFSQYGRIITSRILVDQVTGVSRGVGF 134

Query: 63  LVFKDVASATAAVEKMQG--FPFYDKPMRIQYA 93
           + F     A  A++ + G       +P+ +++A
Sbjct: 135 IRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           L+V  +P   T   L+  FSQ+      R++  +      G+ F+ +   ++A  A++ L
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 229 --QSLKIGQQQLLITYA 243
             Q      + + + +A
Sbjct: 151 NGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 40.6 bits (96), Expect = 1e-04
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           L V  +P + T    +  F      +  ++V  K      G  FV Y D   A  A+ +L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 229 QSLKIGQQQLLITYAKK 245
             L++  + + ++YA+ 
Sbjct: 65  NGLRLQTKTIKVSYARP 81

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 51.0 bits (123), Expect = 6e-09
 Identities = 18/86 (20%), Positives = 31/86 (36%), Gaps = 5/86 (5%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASA 71
          S    I++ NL        LK      F + G +L   +  +  K KG   + F+    A
Sbjct: 6  SGACQIFVRNLPFDFTWKMLKD----KFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKS 97
            A   M G     + + ++  +  S
Sbjct: 62 ERACRMMNGMKLSGREIDVRIDRNAS 87

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 51.1 bits (123), Expect = 6e-09
 Identities = 17/71 (23%), Positives = 31/71 (43%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
           ++V N+        L+  FS +   + V +    PG AFVE+ D   A  A++ L    I
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62

Query: 234 GQQQLLITYAK 244
              ++ +  + 
Sbjct: 63  CGSRVRVELST 73

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 20/102 (19%), Positives = 38/102 (37%), Gaps = 14/102 (13%)

Query: 18  IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKH--KGQAWLVFKDVASATAAV 75
           +Y+ NL       +L++     F  +G +  +     +     G A++ F+D   A  AV
Sbjct: 3   VYVGNLGTGAGKGELER----AFSYYGPLRTV----WIARNPPGFAFVEFEDPRDAEDAV 54

Query: 76  EKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHE 117
             + G       +R++ +        +      P  RRK  E
Sbjct: 55  RGLDGKVICGSRVRVELSTGMP----RRSRFDRPPARRKLLE 92

>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 = 52.5 bits (127), Expect = 7e-09
 Identities = 21/95 (22%), Positives = 41/95 (43%), Gaps = 7/95 (7%)

Query: 17  TIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAFKTLKHKGQAWLVFKDVASATAA 74
            +Y+ NL++ +  D LKQ     F+  G I   +I+  K  K+   A++ +     A  A
Sbjct: 2   VLYVGNLDKAITEDILKQ----YFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIA 57

Query: 75  VEKMQGFPFYDKPMRIQYAKTKSDIIAKADGT-FV 108
           ++ + G    +  ++I +A       +      FV
Sbjct: 58  LQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFV 92

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 51.0 bits (123), Expect = 2e-08
 Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 7/84 (8%)

Query: 13  SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVA 69
                +++ +LN  V  D   ++L   FK F + L    +   +T   +G  ++ F    
Sbjct: 85  DDTFNLFVGDLNVNV--DD--ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQD 140

Query: 70  SATAAVEKMQGFPFYDKPMRIQYA 93
            A  A++ MQG     +P+RI +A
Sbjct: 141 DAQNAMDSMQGQDLNGRPLRINWA 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 = 44.8 bits (107), Expect = 3e-06
 Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 7/88 (7%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV------EAKPGIAFVEYGD 217
            ++ +     LFV ++  +     L+  F  FP +    ++       ++ G  FV +  
Sbjct: 80  QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR-GYGFVSFTS 138

Query: 218 EMQATVAMQSLQSLKIGQQQLLITYAKK 245
           +  A  AM S+Q   +  + L I +A K
Sbjct: 139 QDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>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 = 51.6 bits (124), Expect = 8e-09
 Identities = 25/90 (27%), Positives = 43/90 (47%), Gaps = 6/90 (6%)

Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFKDV 68
          E      ++I  LN +     LK     VF + G I E  ++  +T K +G A++ F++ 
Sbjct: 3  EADHPGKLFIGGLNRETNEKMLKA----VFGKHGPISEVLLIKDRTSKSRGFAFITFENP 58

Query: 69 ASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
          A A  A + M G   + K ++++ AK  S 
Sbjct: 59 ADAKNAAKDMNGKSLHGKAIKVEQAKKPSF 88

>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 = 39.2 bits (92), Expect = 2e-04
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 4/82 (4%)

Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATV 223
           A     LF+  +  +T    L+  F +     EV +++ +     G AF+ + +   A  
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKN 63

Query: 224 AMQSLQSLKIGQQQLLITYAKK 245
           A + +    +  + + +  AKK
Sbjct: 64  AAKDMNGKSLHGKAIKVEQAKK 85

>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 = 52.6 bits (127), Expect = 9e-09
 Identities = 31/239 (12%), Positives = 72/239 (30%), Gaps = 81/239 (33%)

Query: 17  TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-----TLKHKGQAWLVFKDVASA 71
            +++  +        L++    +F+Q+G + EI   +       + KG  ++ F    +A
Sbjct: 5   KMFVGQVPRTWSEKDLRE----LFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 72  TAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQ 131
             A   +               K              P +  K +  + +K         
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMK--------------PADSEKNNAVEDRK--------- 97

Query: 132 AGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMF 191
                                                     LF+  +    T   +++ 
Sbjct: 98  ------------------------------------------LFIGMISKKCTENDIRVM 115

Query: 192 FSQFPGFKEVRMVEAKPGI----AFVEYGDEMQATVAMQSL---QSLKIGQQQLLITYA 243
           FS F   +E R++    G+    AFV +     A  A++++   Q+++     +++ +A
Sbjct: 116 FSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 48.4 bits (116), Expect = 3e-07
 Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 9/91 (9%)

Query: 8   QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVF 65
           + N    +  ++I  +++K   + ++     +F  FG I E  IL       +G A++ F
Sbjct: 88  EKNNAVEDRKLFIGMISKKCTENDIRV----MFSSFGQIEECRILRGPDGLSRGCAFVTF 143

Query: 66  KDVASATAAVEKMQG---FPFYDKPMRIQYA 93
              A A  A++ M           PM +++A
Sbjct: 144 TTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 7/79 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-------GIAFVEYGDEMQATVAMQ 226
           +FV  VP   +   L+  F Q+    E+ ++  +        G  FV +     A  A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 227 SLQSLKIGQQQLLITYAKK 245
           +L ++K+          K 
Sbjct: 66  ALHNMKVLPGMHHPIQMKP 84

>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 = 50.8 bits (122), Expect = 1e-08
 Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 7/96 (7%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAW 62
           A    E      ++I +L ++     L Q    +F  FG ++     +  +T   K   +
Sbjct: 16  AGSQKEGPEGANLFIYHLPQEFGDQDLLQ----MFMPFGNVVSAKVFIDKQTNLSKCFGF 71

Query: 63  LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           + + +  SA AA++ M GF    K +++Q  ++K+D
Sbjct: 72  VSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 107

>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 = 39.2 bits (92), Expect = 2e-04
 Identities = 24/109 (22%), Positives = 45/109 (41%), Gaps = 10/109 (9%)

Query: 142 GAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEV 201
           G+ G++    Q     GA     E P   N  LF+ ++P +     L   F  F      
Sbjct: 1   GSSGSSGLTQQ---SIGAAGSQKEGPEGAN--LFIYHLPQEFGDQDLLQMFMPFGNVVSA 55

Query: 202 R-MVEAKPGI----AFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
           +  ++ +  +     FV Y + + A  A+QS+   +IG ++L +   + 
Sbjct: 56  KVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 50.3 bits (121), Expect = 1e-08
 Identities = 18/91 (19%), Positives = 39/91 (42%), Gaps = 7/91 (7%)

Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKD 67
            S +  +++ NL+     + L++    +F  +G + E    +   T K KG A++ F  
Sbjct: 4  GSSGSGRLFVRNLSYTSSEEDLEK----LFSAYGPLSELHYPIDSLTKKPKGFAFVTFMF 59

Query: 68 VASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
             A  A  ++ G  F  + + +  +  K +
Sbjct: 60 PEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE 90

>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 = 45.7 bits (109), Expect = 6e-07
 Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 5/85 (5%)

Query: 165 EAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEM 219
            + +  +  LFV+N+ + ++   L+  FS +    E+            G AFV +    
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 220 QATVAMQSLQSLKIGQQQLLITYAK 244
            A  A   +       + L +  + 
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPST 86

>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 = 50.9 bits (122), Expect = 2e-08
 Identities = 19/86 (22%), Positives = 42/86 (48%), Gaps = 7/86 (8%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVAS 70
           PN  + +  L+       L++    VF ++G I +   +   ++ + +G A++ F++V  
Sbjct: 45  PNCCLGVFGLSLYTTERDLRE----VFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 100

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTK 96
           A  A E+  G     + +R+ ++ TK
Sbjct: 101 AKEAKERANGMELDGRRIRVDFSITK 126

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 49.0 bits (117), Expect = 6e-08
 Identities = 20/106 (18%), Positives = 42/106 (39%), Gaps = 7/106 (6%)

Query: 145 GATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV 204
                        G++ V   A   PN  L V  +   TT   L+  FS++    +V +V
Sbjct: 20  HMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV 79

Query: 205 ------EAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
                  ++ G AFV + +   A  A +    +++  +++ + ++ 
Sbjct: 80  YDQQSRRSR-GFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI 124

>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 = 50.0 bits (120), Expect = 2e-08
 Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 5/94 (5%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKE-VRMV---EAKP-GIA 211
           G + S    +  P   I+ VQN+P   +   +  FF  +      V +    +  P G A
Sbjct: 1   GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 212 FVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
            V +    +AT A+  L    IG +++ +     
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 7/98 (7%)

Query: 3  PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTL---KHKG 59
             +   +       I + N+   V ID++       F  +  I   +  K        G
Sbjct: 3  SGSSGASSGKPGPTIIKVQNMPFTVSIDEILD----FFYGYQVIPGSVCLKYNEKGMPTG 58

Query: 60 QAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKS 97
          +A + F+    ATAAV  +   P   + +++      S
Sbjct: 59 EAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96

>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 = 49.9 bits (120), Expect = 2e-08
 Identities = 25/89 (28%), Positives = 46/89 (51%), Gaps = 7/89 (7%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVA 69
          S ++ +Y+ +L+  +  D L+     +F+ FG I  I+  K   T + KG  ++ F D  
Sbjct: 3  SGSSGLYVGSLHFNITEDMLRG----IFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSE 58

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A  A+E++ GF    +PMR+ +   + D
Sbjct: 59 CARRALEQLNGFELAGRPMRVGHVTERLD 87

>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 = 12/82 (14%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQAT 222
           +  ++ L+V ++  + T   L+  F  F     + +++        G  F+ + D   A 
Sbjct: 2   SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61

Query: 223 VAMQSLQSLKIGQQQLLITYAK 244
            A++ L   ++  + + + +  
Sbjct: 62  RALEQLNGFELAGRPMRVGHVT 83

>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 = 52.8 bits (127), Expect = 2e-08
 Identities = 14/83 (16%), Positives = 37/83 (44%), Gaps = 7/83 (8%)

Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
            +    +++ NL   +  +  K+    +F+++G   E+      + +G  ++  +    
Sbjct: 18 TYTQRCRLFVGNLPTDITEEDFKR----LFERYGEPSEV---FINRDRGFGFIRLESRTL 70

Query: 71 ATAAVEKMQGFPFYDKPMRIQYA 93
          A  A  ++ G     +P+RI++A
Sbjct: 71 AEIAKAELDGTILKSRPLRIRFA 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 = 43.5 bits (103), Expect = 2e-05
 Identities = 21/139 (15%), Positives = 45/139 (32%), Gaps = 19/139 (13%)

Query: 10  NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFKD 67
              +    + + NL+  V  + L+Q+    F QFG + +  ++     +  G+ ++ F  
Sbjct: 91  RFATHGAALTVKNLSPVVSNELLEQA----FSQFGPVEKAVVVVDDRGRATGKGFVEFAA 146

Query: 68  VASATAAVEKMQGFPFYD-KPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQ 126
              A  A+E+     F      R    +                +      EK  ++  Q
Sbjct: 147 KPPARKALERCGDGAFLLTTTPRPVIVEPME-----------QFDDEDGLPEKLMQKTQQ 195

Query: 127 HDANQAGMGLNPAYAGAYG 145
           +   +       A  G + 
Sbjct: 196 Y-HKEREQPPRFAQPGTFE 213

>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 = 40.8 bits (96), Expect = 2e-04
 Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 1/82 (1%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATV 223
            E        LFV N+P D T    +  F ++    EV +   + G  F+       A +
Sbjct: 15  GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR-GFGFIRLESRTLAEI 73

Query: 224 AMQSLQSLKIGQQQLLITYAKK 245
           A   L    +  + L I +A  
Sbjct: 74  AKAELDGTILKSRPLRIRFATH 95

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 52.5 bits (125), Expect = 2e-08
 Identities = 24/120 (20%), Positives = 44/120 (36%), Gaps = 15/120 (12%)

Query: 8   QGNEISPNNTIYINNLNEKVKIDQLK-----QSLHAVFKQFGTILEILAFKTLKHKGQAW 62
            G+    N T+Y+  ++  +    LK       +  VF + G I  I   + ++ K   +
Sbjct: 127 IGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRI---RYVESKNCGF 183

Query: 63  LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDII----AKADGTFVPRERRKRHEE 118
           + FK  A+A  A E M          +    + +   +    A  D        +KR +E
Sbjct: 184 VKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDP---DPAAQKRLQE 240

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 40.5 bits (94), Expect = 2e-04
 Identities = 18/128 (14%), Positives = 39/128 (30%), Gaps = 15/128 (11%)

Query: 127 HDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPM 186
            + +   + L       +G           GG  S         N  L+V  +       
Sbjct: 95  DEEDIGKLALRTEVLDCFGREKFADYREDMGGIGS-----FRKKNKTLYVGGIDGALNSK 149

Query: 187 A---------LQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQ 237
                     ++  FS+      +R VE+K    FV++  +  A  A +++ +  +    
Sbjct: 150 HLKPAQIESRIRFVFSRLGDIDRIRYVESK-NCGFVKFKYQANAEFAKEAMSNQTLLLPS 208

Query: 238 LLITYAKK 245
                 ++
Sbjct: 209 DKEWDDRR 216

>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 = 49.5 bits (119), Expect = 2e-08
 Identities = 17/86 (19%), Positives = 38/86 (44%), Gaps = 7/86 (8%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVA 69
           PN  + +  L+       L++    VF ++G I ++       + + +G A++ F++V 
Sbjct: 13 DPNCCLGVFGLSLYTTERDLRE----VFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKT 95
           A  A E+  G     + +R+    +
Sbjct: 69 DAKEAKERANGMELDGRRIRVSGPSS 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 = 48.7 bits (117), Expect = 5e-08
 Identities = 20/93 (21%), Positives = 39/93 (41%), Gaps = 5/93 (5%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIA 211
           G + S    A   PN  L V  +   TT   L+  FS++    +V +V  +      G A
Sbjct: 1   GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60

Query: 212 FVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           FV + +   A  A +    +++  +++ ++   
Sbjct: 61  FVYFENVDDAKEAKERANGMELDGRRIRVSGPS 93

>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 = 49.6 bits (119), Expect = 2e-08
 Identities = 21/87 (24%), Positives = 42/87 (48%), Gaps = 5/87 (5%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASA 71
          S    ++++N+  + +   L+Q    +F QFG IL++ + F     KG  ++ F++ A A
Sbjct: 13 STPKRLHVSNIPFRFRDPDLRQ----MFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 68

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            A EK+ G     + + +  A  +  
Sbjct: 69 DRAREKLHGTVVEGRKIEVNNATARVM 95

>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 = 43.0 bits (102), Expect = 6e-06
 Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 4/90 (4%)

Query: 159 AKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV---EAKPGIAFVEY 215
             S   E+ + P  +  V N+P       L+  F QF    +V ++       G  FV +
Sbjct: 4   GSSGNSESKSTPKRL-HVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF 62

Query: 216 GDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
            +   A  A + L    +  +++ +  A  
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNATA 92

>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 = 49.2 bits (118), Expect = 3e-08
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 5/94 (5%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKE-VRMV---EAKP-GIA 211
           G + S    +  P   ++ VQN+P   +   +  FF  +      V +    +  P G A
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 212 FVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
            V +    +AT A+  L    IG +++ ++    
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS 94

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 42.7 bits (101), Expect = 7e-06
 Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 7/96 (7%)

Query: 3  PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTL---KHKG 59
             +   +       I + N+   V ID++       F  +  I   +  K        G
Sbjct: 3  SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILD----FFYGYQVIPGSVCLKYNEKGMPTG 58

Query: 60 QAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKT 95
          +A + F+    ATAAV  +   P   + +++    +
Sbjct: 59 EAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS 94

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 48.7 bits (117), Expect = 4e-08
 Identities = 16/89 (17%), Positives = 30/89 (33%), Gaps = 8/89 (8%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEIL----AFKTLKHKGQAWLVFKDVA 69
              ++I  L   V  D + +    +F  +G I  I            KG A++ F++  
Sbjct: 3  KPTKVHIGRLTRNVTKDHIME----IFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPD 58

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A  A++ M G     + +          
Sbjct: 59 EAEKALKHMDGGQIDGQEITATAVLAPWP 87

>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 = 40.2 bits (95), Expect = 4e-05
 Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 6/84 (7%)

Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP------GIAFVEYGDEMQA 221
           +     + +  +  + T   +   FS +   K + M   +       G A+VE+ +  +A
Sbjct: 1   SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60

Query: 222 TVAMQSLQSLKIGQQQLLITYAKK 245
             A++ +   +I  Q++  T    
Sbjct: 61  EKALKHMDGGQIDGQEITATAVLA 84

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 19/89 (21%), Positives = 43/89 (48%), Gaps = 7/89 (7%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKD 67
           ++    ++ ++NL  +   D L++    VF+++G + +        T + +G A++ F D
Sbjct: 43  DVEGMTSLKVDNLTYRTSPDTLRR----VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 98

Query: 68  VASATAAVEKMQGFPFYDKPMRIQYAKTK 96
              A  A++ M G     + +R+Q A+  
Sbjct: 99  KRDAEDAMDAMDGAVLDGRELRVQMARYG 127

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 24/109 (22%), Positives = 46/109 (42%), Gaps = 7/109 (6%)

Query: 142 GAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEV 201
           G++ A+    Q    G      P         L V N+ + T+P  L+  F ++    +V
Sbjct: 18  GSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV 77

Query: 202 RMV------EAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
            +       E++ G AFV + D+  A  AM ++    +  ++L +  A+
Sbjct: 78  YIPRDRYTKESR-GFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 125

>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 = 48.4 bits (116), Expect = 5e-08
 Identities = 19/91 (20%), Positives = 41/91 (45%), Gaps = 7/91 (7%)

Query: 6  ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAW 62
             G      +T+Y++NL   +  + L +    +F ++G ++++   K   T K KG A+
Sbjct: 7  GMSGGLAPSKSTVYVSNLPFSLTNNDLYR----IFSKYGKVVKVTIMKDKDTRKSKGVAF 62

Query: 63 LVFKDVASATAAVEKMQGFPFYDKPMRIQYA 93
          ++F D  SA      +     + + ++   A
Sbjct: 63 ILFLDKDSAQNCTRAINNKQLFGRVIKASIA 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 = 45.7 bits (109), Expect = 5e-07
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 159 AKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFV 213
             S +    AP  + ++V N+P   T   L   FS++    +V +++ K      G+AF+
Sbjct: 4   GSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFI 63

Query: 214 EYGDEMQATVAMQSL 228
            + D+  A    +++
Sbjct: 64  LFLDKDSAQNCTRAI 78

>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 = 49.5 bits (118), Expect = 8e-08
 Identities = 19/89 (21%), Positives = 43/89 (48%), Gaps = 7/89 (7%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKD 67
           ++    ++ ++NL  +   D L++    VF+++G + +        T + +G A++ F D
Sbjct: 66  DVEGMTSLKVDNLTYRTSPDTLRR----VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121

Query: 68  VASATAAVEKMQGFPFYDKPMRIQYAKTK 96
              A  A++ M G     + +R+Q A+  
Sbjct: 122 KRDAEDAMDAMDGAVLDGRELRVQMARYG 150

>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 = 3e-06
 Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 5/96 (5%)

Query: 154 PYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----P 208
               G+              L V N+ + T+P  L+  F ++    +V +   +      
Sbjct: 53  TVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR 112

Query: 209 GIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           G AFV + D+  A  AM ++    +  ++L +  A+
Sbjct: 113 GFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 148

>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 = 48.5 bits (116), Expect = 8e-08
 Identities = 23/100 (23%), Positives = 44/100 (44%), Gaps = 7/100 (7%)

Query: 2   EPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHK 58
                N     +    +Y+ +L+  +  D L+     +F+ FG I  I       T + K
Sbjct: 13  AAMANNLQKGSAGPMRLYVGSLHFNITEDMLRG----IFEPFGRIESIQLMMDSETGRSK 68

Query: 59  GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           G  ++ F D   A  A+E++ GF    +PM++ +   ++D
Sbjct: 69  GYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>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 = 2e-05
 Identities = 13/90 (14%), Positives = 37/90 (41%), Gaps = 6/90 (6%)

Query: 160 KSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVE 214
            + + +  A P  + +V ++  + T   L+  F  F   + ++++         G  F+ 
Sbjct: 16  ANNLQKGSAGPMRL-YVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74

Query: 215 YGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           + D   A  A++ L   ++  + + + +  
Sbjct: 75  FSDSECAKKALEQLNGFELAGRPMKVGHVT 104

>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 = 48.4 bits (116), Expect = 8e-08
 Identities = 18/110 (16%), Positives = 45/110 (40%), Gaps = 21/110 (19%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVAS 70
              ++++ N+  +   +QLK     +F + G ++    +   +T K KG  +  ++D  +
Sbjct: 7   SLRSVFVGNIPYEATEEQLKD----IFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKG 120
           A +A+  + G  F  + +R+  A                 + ++  +  G
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAA--------------SEKNKEELKSLG 98

>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 = 45.3 bits (108), Expect = 7e-07
 Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE----AKP-GIAFVEYGDE 218
           P       ++ FV N+P++ T   L+  FS+       R+V      KP G  F EY D+
Sbjct: 2   PAVDRSLRSV-FVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 219 MQATVAMQSLQSLKIGQQQLLITYAK 244
             A  AM++L   +   + L +  A 
Sbjct: 61  ETALSAMRNLNGREFSGRALRVDNAA 86

>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 = 48.0 bits (115), Expect = 9e-08
 Identities = 24/93 (25%), Positives = 43/93 (46%), Gaps = 8/93 (8%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIA 211
           G + S  P A + P+  LFV+ +  DTT   L+  F         R+V  +      G  
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFG 57

Query: 212 FVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           FV++  E  A  A ++++  +I   ++ + +AK
Sbjct: 58  FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90

>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 = 42.6 bits (101), Expect = 6e-06
 Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 4/86 (4%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
           P+ T+++  L+E    + LK+     F        +   +T   KG  ++ F     A 
Sbjct: 13 QPSKTLFVKGLSEDTTEETLKE----SFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAK 68

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSD 98
          AA E M+        + + +AK K +
Sbjct: 69 AAKEAMEDGEIDGNKVTLDWAKPKGE 94

>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 = 47.6 bits (114), Expect = 1e-07
 Identities = 16/97 (16%), Positives = 40/97 (41%), Gaps = 7/97 (7%)

Query: 4  EVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTI--LEILAFKTLKHKGQA 61
          E   +G+E +    ++I NLN    + +LK        +      L ++  +T  ++   
Sbjct: 6  EDPVEGSESTTPFNLFIGNLNPNKSVAELKV----AISELFAKNDLAVVDVRTGTNRKFG 61

Query: 62 WLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
          ++ F+       A+E + G   +   ++++  K +  
Sbjct: 62 YVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDG 97

>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 = 44.9 bits (107), Expect = 1e-06
 Identities = 14/91 (15%), Positives = 36/91 (39%), Gaps = 6/91 (6%)

Query: 159 AKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP----GIAFVE 214
              V       P N+ F+ N+  + +   L++  S+     ++ +V+ +        +V+
Sbjct: 6   EDPVEGSESTTPFNL-FIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVD 64

Query: 215 YGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
           +        A++ L  LK+   ++ +   K 
Sbjct: 65  FESAEDLEKALE-LTGLKVFGNEIKLEKPKG 94

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 47.8 bits (114), Expect = 1e-07
 Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 15 NNTIYINNL--NEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVA 69
          +  I +N        K+  LK++L ++F + G ++ +   +   T K KG  ++    + 
Sbjct: 6  DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMN 65

Query: 70 SATAAVEKMQGFPF 83
           A   ++   G   
Sbjct: 66 DAKKIIKSFHGKRL 79

>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 = 48.0 bits (115), Expect = 1e-07
 Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 5/87 (5%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASA 71
            +  I+I NL++   ID   ++L+  F  FG IL   +       KG  ++ F+   +A
Sbjct: 3  LGSGNIFIKNLDKS--IDN--KALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAA 58

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            A+EKM G    D+ + +   K++ +
Sbjct: 59 ERAIEKMNGMLLNDRKVFVGRFKSRKE 85

>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 = 38.8 bits (91), Expect = 2e-04
 Identities = 17/83 (20%), Positives = 33/83 (39%), Gaps = 4/83 (4%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV---EAKPGIAFVEYGDEMQAT 222
            P    NI F++N+       AL   FS F      ++V       G  FV +  +  A 
Sbjct: 1   GPLGSGNI-FIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAE 59

Query: 223 VAMQSLQSLKIGQQQLLITYAKK 245
            A++ +  + +  +++ +   K 
Sbjct: 60  RAIEKMNGMLLNDRKVFVGRFKS 82

>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 = 47.2 bits (113), Expect = 1e-07
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 3/71 (4%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
           LF+ N+P + T   ++  F Q+ G  +V   +      FV   D+  A  A+++L   K+
Sbjct: 11  LFIGNLPREATEQEIRSLFEQY-G--KVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKL 67

Query: 234 GQQQLLITYAK 244
               + +  +K
Sbjct: 68  HGVNINVEASK 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 = 46.8 bits (112), Expect = 2e-07
 Identities = 16/86 (18%), Positives = 39/86 (45%), Gaps = 9/86 (10%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          S    ++I NL  +    +++     +F+Q+G +LE      +  K   ++  +D  +A 
Sbjct: 6  SGMVKLFIGNLPREATEQEIRS----LFEQYGKVLEC----DII-KNYGFVHIEDKTAAE 56

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A+  +  +  +   + ++ +K KS 
Sbjct: 57 DAIRNLHHYKLHGVNINVEASKNKSK 82

>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 = 1e-07
 Identities = 20/96 (20%), Positives = 37/96 (38%), Gaps = 8/96 (8%)

Query: 3   PEVANQGNEISPNNT-IYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHK 58
              A       P    ++I +L ++     L       F  FG ++     +  +T   K
Sbjct: 27  AAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLAS----TFLPFGNVISAKVFIDKQTSLSK 82

Query: 59  GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAK 94
              ++ F +  SA  A++ M GF    K +++Q  K
Sbjct: 83  CFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 22/116 (18%), Positives = 49/116 (42%), Gaps = 6/116 (5%)

Query: 135 GLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNI-LFVQNVPHDTTPMALQMFFS 193
           GL    + +  +T PL+ +     A +   +    P    LF+ ++P + T   L   F 
Sbjct: 3   GLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFL 62

Query: 194 QFPGFKEVR-MVEAKPGI----AFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
            F      +  ++ +  +     FV + +   A VA++++   ++G ++L +   K
Sbjct: 63  PFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 5/85 (5%)

Query: 13  SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASA 71
           S    ++++N+  + +   L+Q    +F QFG IL++ + F     KG  ++ F++ A A
Sbjct: 27  SQPKRLHVSNIPFRFRDPDLRQ----MFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 82

Query: 72  TAAVEKMQGFPFYDKPMRIQYAKTK 96
             A EK+ G     + + +  A  +
Sbjct: 83  DRAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 4/85 (4%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV---EAKPGIAFVEYGDEMQ 220
            E  + P   L V N+P       L+  F QF    +V ++       G  FV + +   
Sbjct: 23  TENKSQPKR-LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD 81

Query: 221 ATVAMQSLQSLKIGQQQLLITYAKK 245
           A  A + L    +  +++ +  A  
Sbjct: 82  ADRAREKLHGTVVEGRKIEVNNATA 106

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 47.2 bits (113), Expect = 1e-07
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 3/79 (3%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAM 225
           +    +  L V N+    T   L+  F ++ G   V   +     AFV       A  A+
Sbjct: 5   SSGKASTKLHVGNISPTCTNQELRAKFEEY-G--PVIECDIVKDYAFVHMERAEDAVEAI 61

Query: 226 QSLQSLKIGQQQLLITYAK 244
           + L + +   +++ +  + 
Sbjct: 62  RGLDNTEFQGKRMHVQLST 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 = 45.7 bits (109), Expect = 5e-07
 Identities = 13/84 (15%), Positives = 35/84 (41%), Gaps = 9/84 (10%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
           +  +++ N++      +L+      F+++G ++E         K  A++  +    A  
Sbjct: 9  ASTKLHVGNISPTCTNQELRA----KFEEYGPVIECD-----IVKDYAFVHMERAEDAVE 59

Query: 74 AVEKMQGFPFYDKPMRIQYAKTKS 97
          A+  +    F  K M +Q + ++ 
Sbjct: 60 AIRGLDNTEFQGKRMHVQLSTSRL 83

>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 = 47.2 bits (113), Expect = 2e-07
 Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 7/89 (7%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVA 69
          S    +++  L+       L+Q    VF ++G I E++  K   T + +G  ++ F+++ 
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQ----VFSKYGQISEVVVVKDRETQRSRGFGFVTFENID 65

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A  A+  M G     + +R+  A   SD
Sbjct: 66 DAKDAMMAMNGKSVDGRQIRVDQAGKSSD 94

>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 = 22/90 (24%), Positives = 38/90 (42%), Gaps = 5/90 (5%)

Query: 161 SVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEY 215
           S      A     LFV  +  DT   +L+  FS++    EV +V+ +      G  FV +
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 216 GDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
            +   A  AM ++    +  +Q+ +  A K
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAGK 91

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 48.4 bits (115), Expect = 2e-07
 Identities = 20/133 (15%), Positives = 39/133 (29%), Gaps = 12/133 (9%)

Query: 125 DQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSV-----IPEAPAPPNNILFVQNV 179
             H ++   +G    Y  +    PP+ Q P P                      ++V + 
Sbjct: 4   HHHHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSF 63

Query: 180 PHDTTPMALQMFFSQF--PGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSLQSLK 232
              TT   L             E++  E +      G A V    E      ++ L    
Sbjct: 64  SWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKV 123

Query: 233 IGQQQLLITYAKK 245
           +  +++ +  A +
Sbjct: 124 LNGEKVDVRPATR 136

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 43.8 bits (103), Expect = 9e-06
 Identities = 15/98 (15%), Positives = 35/98 (35%), Gaps = 9/98 (9%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGT--ILEILAFK---TLKHKGQ 60
                  +    +Y+ + +      QL Q    V +  G   ++E+   +     + KG 
Sbjct: 46  YTYSGLRNRRAAVYVGSFSWWTTDQQLIQ----VIRSIGVYDVVELKFAENRANGQSKGY 101

Query: 61  AWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A +V     S    +E + G     + + ++ A  ++ 
Sbjct: 102 AEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNL 139

>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 = 46.4 bits (111), Expect = 2e-07
 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 3/80 (3%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAM 225
             +     +FV NV    T   L+  F +  G   V   +     AFV    E  A  A+
Sbjct: 4   GSSGNTWKIFVGNVSAACTSQELRSLFERR-G--RVIECDVVKDYAFVHMEKEADAKAAI 60

Query: 226 QSLQSLKIGQQQLLITYAKK 245
             L   ++  +++ +  + K
Sbjct: 61  AQLNGKEVKGKRINVELSTK 80

>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 = 44.9 bits (107), Expect = 1e-06
 Identities = 14/86 (16%), Positives = 35/86 (40%), Gaps = 9/86 (10%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
               I++ N++      +L+     +F++ G ++E         K  A++  +  A A 
Sbjct: 7  GNTWKIFVGNVSAACTSQELRS----LFERRGRVIECD-----VVKDYAFVHMEKEADAK 57

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSD 98
          AA+ ++ G     K + ++ +     
Sbjct: 58 AAIAQLNGKEVKGKRINVELSTKGQK 83

>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 = 47.0 bits (112), Expect = 2e-07
 Identities = 18/102 (17%), Positives = 41/102 (40%), Gaps = 13/102 (12%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAW 62
           +   ++++   T++I NL+   + + L +    V +QFG +  +       T   KG A+
Sbjct: 6   SGLPSDVTEGKTVFIRNLSFDSEEEALGE----VLQQFGDLKYVRVVLHPDTEHSKGCAF 61

Query: 63  LVFKDVASATAAVEKMQ------GFPFYDKPMRIQYAKTKSD 98
             F    +A   +          G     + +++  A T+ +
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103

>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 = 44.3 bits (105), Expect = 3e-06
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 5/79 (6%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIA 211
           G + S    +       +F++N+  D+   AL     QF   K VR+V         G A
Sbjct: 1   GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60

Query: 212 FVEYGDEMQATVAMQSLQS 230
           F ++  +  A   + +   
Sbjct: 61  FAQFMTQEAAQKCLAAASL 79

>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 = 47.0 bits (112), Expect = 3e-07
 Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKE-VRMV---EAKP-GIA 211
           G + S              + N+P   T M +  F    P  +  V ++     +  G A
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60

Query: 212 FVEYGDEMQATVAMQ 226
            V++ +E  A  + +
Sbjct: 61  LVQFKNEDDARKSER 75

>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 = 47.5 bits (114), Expect = 4e-07
 Identities = 17/99 (17%), Positives = 44/99 (44%), Gaps = 8/99 (8%)

Query: 1   MEPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAF--KTLKH 57
           ++P+ A   +E      I++  +   V+  + ++     F Q+GTI++  L     T + 
Sbjct: 73  IDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEE----FFSQWGTIIDAQLMLDKDTGQS 128

Query: 58  KGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTK 96
           +G  ++ +    +     +  +   F D+ + I+ A+ +
Sbjct: 129 RGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR 166

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 39.8 bits (94), Expect = 2e-04
 Identities = 17/72 (23%), Positives = 25/72 (34%), Gaps = 5/72 (6%)

Query: 160 KSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVE 214
           K  IP         +FV  +  D  P   + FFSQ+    + +++  K      G  FV 
Sbjct: 76  KRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVT 135

Query: 215 YGDEMQATVAMQ 226
           Y          Q
Sbjct: 136 YDSADAVDRVCQ 147

>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 = 46.1 bits (110), Expect = 5e-07
 Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 8/94 (8%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP------GI 210
           G + S     P  P    F+ N+P+D T  +++ FF        VR+           G 
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGF 59

Query: 211 AFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
            + E+ D      A+ SL    +G +++ +  A 
Sbjct: 60  GYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVAD 92

>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 = 38.4 bits (90), Expect = 3e-04
 Identities = 19/89 (21%), Positives = 36/89 (40%), Gaps = 8/89 (8%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVA 69
          SP  T ++ NL   V  + +K+     F+        L  +     + KG  +  F+D+ 
Sbjct: 13 SPPYTAFLGNLPYDVTEESIKE----FFRGLNISAVRLPREPSNPERLKGFGYAEFEDLD 68

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
          S  +A+  +      +K +R+  A    D
Sbjct: 69 SLLSAL-SLNEESLGNKRIRVDVADQAQD 96

>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 = 46.1 bits (110), Expect = 5e-07
 Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 5/82 (6%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASATAAVE 76
          +Y+ NL++ +  ++L++     F  FGTI    +  +  + KG  ++ F     AT AV 
Sbjct: 18 LYVKNLDDGIDDERLRK----AFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVT 73

Query: 77 KMQGFPFYDKPMRIQYAKTKSD 98
          +M G     KP+ +  A+ K +
Sbjct: 74 EMNGRIVATKPLYVALAQRKEE 95

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVR-MVEA---KPGIAFVEYGDEMQATVAMQSLQ 229
           L+V+N+        L+  FS F      + M+E    K G  FV +    +AT A+  + 
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSK-GFGFVCFSSPEEATKAVTEMN 76

Query: 230 SLKIGQQQLLITYAKK 245
              +  + L +  A++
Sbjct: 77  GRIVATKPLYVALAQR 92

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 45.7 bits (109), Expect = 6e-07
 Identities = 21/93 (22%), Positives = 37/93 (39%), Gaps = 7/93 (7%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE----AKP-GIA 211
           G + S   E P  P    +V N+P +T    +   F      + VR+V      K  G  
Sbjct: 1   GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFC 59

Query: 212 FVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           +VE+ +      A+ +     +G + L +  A+
Sbjct: 60  YVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAE 91

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 46.0 bits (109), Expect = 6e-07
 Identities = 15/85 (17%), Positives = 26/85 (30%), Gaps = 8/85 (9%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
            N + ++ L        LK       ++ G +     +  +   G   + F      T 
Sbjct: 15 SENRVVVSGLPPSGSWQDLKD----HMREAGDVC----YADVYRDGTGVVEFVRKEDMTY 66

Query: 74 AVEKMQGFPFYDKPMRIQYAKTKSD 98
          AV K+    F        Y + K D
Sbjct: 67 AVRKLDNTKFRSHEGETAYIRVKVD 91

>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 = 37.5 bits (87), Expect = 6e-04
 Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 6/80 (7%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQF--PGFKEVRMVEAKPGIAFVEYGDEMQATVA 224
                N + V  +P   +   L+    +     + +V     + G   VE+  +   T A
Sbjct: 12  SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY----RDGTGVVEFVRKEDMTYA 67

Query: 225 MQSLQSLKIGQQQLLITYAK 244
           ++ L + K    +    Y +
Sbjct: 68  VRKLDNTKFRSHEGETAYIR 87

>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 = 8e-07
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 7/80 (8%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVA 69
          S ++ +YI  L        L +    + + +G I+   A     T K KG  ++ F   +
Sbjct: 3  SGSSGLYIRGLQPGTTDQDLVK----LCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPS 58

Query: 70 SATAAVEKMQGFPFYDKPMR 89
          +A  AV  ++      +  +
Sbjct: 59 AAQKAVTALKASGVQAQMAK 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 = 39.8 bits (94), Expect = 6e-05
 Identities = 12/78 (15%), Positives = 28/78 (35%), Gaps = 6/78 (7%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQ 220
             +  +  L+++ +   TT   L      +      + +  K      G  FV++     
Sbjct: 1   GSSGSSG-LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSA 59

Query: 221 ATVAMQSLQSLKIGQQQL 238
           A  A+ +L++  +  Q  
Sbjct: 60  AQKAVTALKASGVQAQMA 77

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 44.9 bits (107), Expect = 9e-07
 Identities = 18/85 (21%), Positives = 38/85 (44%), Gaps = 5/85 (5%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQ 220
            P   +  +FV ++  + T  A+   F+ F    + R+V+        G  FV + ++  
Sbjct: 1   GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60

Query: 221 ATVAMQSLQSLKIGQQQLLITYAKK 245
           A  A+Q +    +G +Q+   +A +
Sbjct: 61  AENAIQQMGGQWLGGRQIRTNWATR 85

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 43.3 bits (103), Expect = 3e-06
 Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 7/87 (8%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVA 69
            +  +++ +L+ ++    +       F  FG I +    K   T K KG  ++ F +  
Sbjct: 4  GSHFHVFVGDLSPEITTAAIAA----AFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 59

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTK 96
           A  A+++M G     + +R  +A  K
Sbjct: 60 DAENAIQQMGGQWLGGRQIRTNWATRK 86

>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 = 45.0 bits (107), Expect = 1e-06
 Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 10/86 (11%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAA 74
          ++I  +   +    LK     +F++FG I E+   K   T  HKG A+L + +  SA  A
Sbjct: 16 LFIGQIPRNLDEKDLKP----LFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71

Query: 75 VEKMQG---FPFYDKPMRIQYAKTKS 97
             +      P  ++P++++ A ++S
Sbjct: 72 QSALHEQKTLPGMNRPIQVKPADSES 97

>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 = 37.3 bits (87), Expect = 6e-04
 Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 5/60 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           LF+  +P +     L+  F +F    E+ +++ +      G AF+ Y +   A  A  +L
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75

>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 = 45.9 bits (109), Expect = 1e-06
 Identities = 19/97 (19%), Positives = 42/97 (43%), Gaps = 7/97 (7%)

Query: 5   VANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQA 61
                 E      + +N +   V   QL+Q    +F+++G I     +   +T + +G  
Sbjct: 32  PTQMNPEPDVLRNLMVNYIPTTVDEVQLRQ----LFERYGPIESVKIVCDRETRQSRGYG 87

Query: 62  WLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           ++ F+  +SA  A+  + GF   +K +++  A +   
Sbjct: 88  FVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ 124

>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 = 44.0 bits (104), Expect = 5e-06
 Identities = 21/109 (19%), Positives = 38/109 (34%), Gaps = 6/109 (5%)

Query: 141 AGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKE 200
            G       L Q        + +   P    N L V  +P     + L+  F ++   + 
Sbjct: 13  YGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRN-LMVNYIPTTVDEVQLRQLFERYGPIES 71

Query: 201 VRMVEAKP-----GIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           V++V  +      G  FV++     A  A+  L    I  ++L +  A 
Sbjct: 72  VKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA 120

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 18/86 (20%), Positives = 32/86 (37%), Gaps = 7/86 (8%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI--LAFKTLKHKGQAWLVFKDVASAT 72
          N ++YI        +D +K+      +  G +L I          KG  ++VF  + SA 
Sbjct: 11 NRSVYIKGFPTDATLDDIKE----WLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSD 98
            VE   G  + +  + I +      
Sbjct: 67 KFVETP-GQKYKETDLLILFKDDYFA 91

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 42.8 bits (101), Expect = 8e-06
 Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 5/75 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQ 229
           ++++  P D T   ++ +         ++M         G  FV +     A   ++   
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TP 72

Query: 230 SLKIGQQQLLITYAK 244
             K  +  LLI +  
Sbjct: 73  GQKYKETDLLILFKD 87

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 20/96 (20%), Positives = 43/96 (44%), Gaps = 7/96 (7%)

Query: 6  ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAW 62
          + Q  + S +  +++ +L+ ++  + +K      F  FG I +   +    T K KG  +
Sbjct: 6  SGQKKDTSNHFHVFVGDLSPEITTEDIKA----AFAPFGRISDARVVKDMATGKSKGYGF 61

Query: 63 LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
          + F +   A  A+++M G     + +R  +A  K  
Sbjct: 62 VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPP 97

>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 = 42.3 bits (100), Expect = 1e-05
 Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           +FV ++  + T   ++  F+ F    + R+V+        G  FV + ++  A  A+Q +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77

Query: 229 QSLKIGQQQLLITYAKK 245
               +G +Q+   +A +
Sbjct: 78  GGQWLGGRQIRTNWATR 94

>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 = 45.6 bits (108), Expect = 1e-06
 Identities = 19/105 (18%), Positives = 35/105 (33%), Gaps = 8/105 (7%)

Query: 126 QHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTP 185
            H  +    GL P  +     T          G+        +   + + ++ +P+  T 
Sbjct: 4   SHHHHHHSSGLVPRGSHMASMT---GGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATE 60

Query: 186 MALQMFFSQFPGFKEVRMV---EAKP-GIAFVEYGDEMQATVAMQ 226
             +  FFS       V +    + +  G A VE+    +A  AM 
Sbjct: 61  NDIYNFFSPL-NPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMS 104

>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 = 44.5 bits (106), Expect = 1e-06
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 7/79 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQF--PGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQ 226
           L++ N+   TT   L             E++  E +      G A V  G E  +   M 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 227 SLQSLKIGQQQLLITYAKK 245
            L   ++  Q  ++T + K
Sbjct: 64  LLPKRELHGQNPVVTPSNK 82

>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 = 37.9 bits (89), Expect = 2e-04
 Identities = 14/87 (16%), Positives = 29/87 (33%), Gaps = 11/87 (12%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKH------KGQAWLVFKDVASA 71
          +YI NL      + L +         G   +IL  K  ++      KG A +     AS+
Sbjct: 4  LYIGNLTWWTTDEDLTE----AVHSLGVN-DILEIKFFENRANGQSKGFALVGVGSEASS 58

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKSD 98
             ++ +     + +   +  +     
Sbjct: 59 KKLMDLLPKRELHGQNPVVTPSNKLEH 85

>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 = 44.9 bits (107), Expect = 1e-06
 Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 7/87 (8%)

Query: 10  NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFKD 67
            E  P N +YI+NL   +   +L+     + K FG ++   IL   +   +G  +   + 
Sbjct: 21  QEQDPTN-LYISNLPLSMDEQELEN----MLKPFGQVISTRILRDSSGTSRGVGFARMES 75

Query: 68  VASATAAVEKMQGFPFYDKPMRIQYAK 94
                A +    G      P      +
Sbjct: 76  TEKCEAVIGHFNGKFIKTPPGVSAPTE 102

>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 = 44.5 bits (106), Expect = 2e-06
 Identities = 19/96 (19%), Positives = 36/96 (37%), Gaps = 10/96 (10%)

Query: 157 GGAKSVIPEAPAP--PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV-----EAKP- 208
           G        +  P  P    F+ N+P+D T  +++ FF        VR+        +  
Sbjct: 3   GSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLK 61

Query: 209 GIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           G  + E+ D      A+  L    +G +++ +  A 
Sbjct: 62  GFGYAEFEDLDSLLSALS-LNEESLGNRRIRVDVAD 96

>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 = 44.5 bits (105), Expect = 2e-06
 Identities = 17/89 (19%), Positives = 32/89 (35%), Gaps = 8/89 (8%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
               ++I +      +      L  + + FG I   L    L    +A++       A 
Sbjct: 13 ETRRVVHIMDFQRGKNLRYQ---LLQLVEPFGVISNHL---ILNKINEAFIEMATTEDAQ 66

Query: 73 AAVEKMQGFP--FYDKPMRIQYAKTKSDI 99
          AAV+     P   + KP+R+  ++    I
Sbjct: 67 AAVDYYTTTPALVFGKPVRVHLSQKYKRI 95

>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 = 20/84 (23%), Positives = 37/84 (44%), Gaps = 7/84 (8%)

Query: 16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASAT 72
            +++ +LN  V  + L+      FK F + L    +   +T   +G  ++ F     A 
Sbjct: 2  FNLFVGDLNVNVDDETLRN----AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 57

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTK 96
           A++ MQG     +P+RI +A   
Sbjct: 58 NAMDSMQGQDLNGRPLRINWAAKL 81

>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 = 42.5 bits (101), Expect = 5e-06
 Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 5/77 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           LFV ++  +     L+  F  FP +    ++         G  FV +  +  A  AM S+
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 229 QSLKIGQQQLLITYAKK 245
           Q   +  + L I +A K
Sbjct: 64  QGQDLNGRPLRINWAAK 80

>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 = 44.0 bits (104), Expect = 3e-06
 Identities = 15/84 (17%), Positives = 26/84 (30%), Gaps = 8/84 (9%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAA 74
           N + ++ L        LK       ++ G +     +  +   G   + F      T A
Sbjct: 15 ENRVVVSGLPPSGSWQDLKD----HMREAGDVC----YADVYRDGTGVVEFVRKEDMTYA 66

Query: 75 VEKMQGFPFYDKPMRIQYAKTKSD 98
          V K+    F        Y + K D
Sbjct: 67 VRKLDNTKFRSHEGETAYIRVKVD 90

>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 = 38.2 bits (89), Expect = 3e-04
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 8/85 (9%)

Query: 165 EAPAPPN----NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-KPGIAFVEYGDEM 219
            +  PP+    N + V  +P   +   L+    +  G  +V   +  + G   VE+  + 
Sbjct: 5   SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREA-G--DVCYADVYRDGTGVVEFVRKE 61

Query: 220 QATVAMQSLQSLKIGQQQLLITYAK 244
             T A++ L + K    +    Y +
Sbjct: 62  DMTYAVRKLDNTKFRSHEGETAYIR 86

>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 = 43.9 bits (104), Expect = 3e-06
 Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 5/74 (6%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV---EAKP-GIAF 212
           G + S      +   + + ++ +P+  T   +  FFS       V +    + +  G A 
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEAD 59

Query: 213 VEYGDEMQATVAMQ 226
           VE+     A  AM 
Sbjct: 60  VEFATHEDAVAAMA 73

>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 = 43.2 bits (102), Expect = 6e-06
 Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 6/75 (8%)

Query: 157 GGAKSVIPEAPAPPNN-ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV---EAKP-GIA 211
           G + S     P  P++  + V  +P       ++ FF        V ++     +  G  
Sbjct: 1   GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNG 59

Query: 212 FVEYGDEMQATVAMQ 226
            V++        A++
Sbjct: 60  LVKFLSPQDTFEALK 74

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 43.0 bits (102), Expect = 6e-06
 Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 5/74 (6%)

Query: 163 IPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGI----AFVEYGDE 218
           +PE    PN + FV  +        ++ FF+++   KEV+++  + G+     FV + ++
Sbjct: 2   LPEGKIMPNTV-FVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYND 60

Query: 219 MQATVAMQSLQSLK 232
           +     ++S  +  
Sbjct: 61  VDVQKIVESQINFH 74

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 16/85 (18%), Positives = 40/85 (47%), Gaps = 8/85 (9%)

Query: 16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFKDVASATA 73
          NT+++  ++ ++   +++      F ++G++ E  I+  +T   KG  ++ F +      
Sbjct: 10 NTVFVGGIDVRMDETEIRS----FFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65

Query: 74 AVEKMQGFPFYDKPMRIQYAKTKSD 98
           VE      F+ K +++  A  K +
Sbjct: 66 IVESQI--NFHGKKLKLGPAIRKQN 88

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 42.4 bits (100), Expect = 7e-06
 Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 10/63 (15%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP----------GIAFVEYGDEMQATV 223
           L+V N+P   T  A+  FF+       +      P            AF+E+    + T 
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 224 AMQ 226
           AM 
Sbjct: 69  AMA 71

>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 = 39.3 bits (92), Expect = 9e-05
 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTIL----EILAFKTLKHKGQAWLVFKDVASATA 73
          +Y+ N+   +  + +    +A  +  G        +LA +  + K  A+L F+ V   T 
Sbjct: 9  LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 74 AVEKMQGFPFYDKPMRI 90
          A+    G  F  + ++I
Sbjct: 69 AMA-FDGIIFQGQSLKI 84

>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 = 42.8 bits (101), Expect = 8e-06
 Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 158 GAKSVIPEAPAPPNN-ILFVQNVPHDTTPMALQMFFSQFPGFKE-VRMVEAKP----GIA 211
           G+      +P   N+  + ++ +P   +   +  FFS        + +         G A
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 212 FVEYGDEMQATVAMQ 226
           FV++  +  A  A++
Sbjct: 61  FVQFASQEIAEKALK 75

>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 = 42.7 bits (101), Expect = 9e-06
 Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 9/82 (10%)

Query: 154 PYPGGAKSVIPEAPAPPNNI----LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP- 208
              G +    P     P       +F   +     P  L+ FFS     ++VR++  +  
Sbjct: 4   GSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNS 63

Query: 209 ----GIAFVEYGDEMQATVAMQ 226
               GIA+VE+ +     +A+ 
Sbjct: 64  RRSKGIAYVEFCEIQSVPLAIG 85

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 16/89 (17%), Positives = 40/89 (44%), Gaps = 8/89 (8%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFK-TLKHKGQAWLVFKD 67
           E     T++   L  +++   L+      F   G + +  I++ + + + KG A++ F +
Sbjct: 21  EERDARTVFCMQLAARIRPRDLED----FFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 76

Query: 68  VASATAAVEKMQGFPFYDKPMRIQYAKTK 96
           + S   A+  + G      P+ +Q ++ +
Sbjct: 77  IQSVPLAIG-LTGQRLLGVPIIVQASQAE 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 = 42.6 bits (100), Expect = 1e-05
 Identities = 13/88 (14%), Positives = 28/88 (31%), Gaps = 8/88 (9%)

Query: 165 EAPAPPNNILFVQN--VPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQAT 222
           E  +     L V N  + +  +   L     +      + M   K   +F  Y    ++ 
Sbjct: 19  ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-PYSFARYRTTEESK 77

Query: 223 VAMQSLQSLKIGQQQ-----LLITYAKK 245
            A  +L   ++         L + + +K
Sbjct: 78  RAYVTLNGKEVVDDLGQKITLYLNFVEK 105

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 11/90 (12%), Positives = 30/90 (33%), Gaps = 14/90 (15%)

Query: 13  SPNNTIYINN--LNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
               ++ + N  L   V  +QL      V ++ G +  +       +K  ++  ++    
Sbjct: 23  YATQSLVVANGGLGNGVSRNQLLP----VLEKCGLVDAL---LMPPNKPYSFARYRTTEE 75

Query: 71  ATAAVEKMQGFPFYDK-----PMRIQYAKT 95
           +  A   + G    D       + + + + 
Sbjct: 76  SKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 10/65 (15%), Positives = 26/65 (40%), Gaps = 5/65 (7%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV---EAKP-GIAFVEYGDEMQA 221
           +     + + ++  P + T   +  F +       +R+V        G  FV++ +E + 
Sbjct: 5   SSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEV 63

Query: 222 TVAMQ 226
             A++
Sbjct: 64  KQALK 68

>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 = 42.5 bits (100), Expect = 1e-05
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 5/76 (6%)

Query: 156 PGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQF-PGFKEVRMV---EAKP-GI 210
           P G K     +P      ++++ +P +     +  FF +       + +      K  G 
Sbjct: 10  PSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE 69

Query: 211 AFVEYGDEMQATVAMQ 226
            FVE+ +E     A+ 
Sbjct: 70  GFVEFRNEADYKAALC 85

>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 = 41.3 bits (98), Expect = 2e-05
 Identities = 17/87 (19%), Positives = 38/87 (43%), Gaps = 8/87 (9%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFK-TLKHKGQAWLVFKDVA 69
          +   +IY+ N++     ++L+      F   G++    IL  K +   KG A++ F D  
Sbjct: 4  ADARSIYVGNVDYGATAEELEA----HFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 59

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTK 96
          S   ++  +    F  + +++   +T 
Sbjct: 60 SVRTSLA-LDESLFRGRQIKVIPKRTN 85

>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 = 40.6 bits (96), Expect = 3e-05
 Identities = 12/58 (20%), Positives = 24/58 (41%), Gaps = 5/58 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQ 226
           ++V NV +  T   L+  F        V ++  K      G A++E+ D+     ++ 
Sbjct: 9   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 18/123 (14%), Positives = 40/123 (32%), Gaps = 22/123 (17%)

Query: 4   EVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAF--KTLKHKGQ 60
           E + +         I++  + E  +   L+      F+Q+G I  I +     + K +G 
Sbjct: 93  EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD----YFEQYGKIEVIEIMTDRGSGKKRGF 148

Query: 61  AWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKG 120
           A++ F D  S    V + +          ++ A              + ++         
Sbjct: 149 AFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA--------------LSKQEMASASSSQ 193

Query: 121 KKR 123
           + R
Sbjct: 194 RGR 196

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 30/217 (13%), Positives = 66/217 (30%), Gaps = 76/217 (35%)

Query: 18  IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAA 74
           ++I  L+ +   + L+      F+Q+GT+ + +  +   T + +G  ++ +  V    AA
Sbjct: 16  LFIGGLSFETTDESLRS----HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71

Query: 75  VEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGM 134
           +   +      + +  + A              V RE  +R       +K          
Sbjct: 72  MN-ARPHKVDGRVVEPKRA--------------VSREDSQRPGAHLTVKK---------- 106

Query: 135 GLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQ 194
                                                  +FV  +  DT    L+ +F Q
Sbjct: 107 ---------------------------------------IFVGGIKEDTEEHHLRDYFEQ 127

Query: 195 FPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQ 226
           +   + + ++  +      G AFV + D       + 
Sbjct: 128 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164

>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 = 41.5 bits (97), Expect = 2e-05
 Identities = 14/95 (14%), Positives = 31/95 (32%), Gaps = 4/95 (4%)

Query: 154 PYPGGAKSVIPEAPAPPNNILFVQNVPHD-TTPMALQMFFSQFPGFKEVRMVEAKPGIAF 212
             P G      +       ++ + N+PH   +  A+      +   K   ++  K   AF
Sbjct: 8   KKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK-SQAF 66

Query: 213 VEYGDEMQATVAMQSLQS--LKIGQQQLLITYAKK 245
           +E      A   +       L    + + +  ++K
Sbjct: 67  IEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK 101

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 17/79 (21%), Positives = 28/79 (35%), Gaps = 8/79 (10%)

Query: 156 PGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQF----PGFKEVRMVEAKP--- 208
            G +  V          I+ ++ +P   T   +  FF Q      G + +  V       
Sbjct: 8   GGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRP 67

Query: 209 -GIAFVEYGDEMQATVAMQ 226
            G AFV +  E  A  A++
Sbjct: 68  TGDAFVLFACEEYAQNALR 86

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 4/77 (5%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
              I + NL E      LK     + ++        +  T    G   L F        
Sbjct: 27 KRYRITMKNLPEGCSWQDLKD----LARENSLETTFSSVNTRDFDGTGALEFPSEEILVE 82

Query: 74 AVEKMQGFPFYDKPMRI 90
          A+E++    F    + +
Sbjct: 83 ALERLNNIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 40.6 bits (95), Expect = 4e-05
 Identities = 9/78 (11%), Positives = 22/78 (28%), Gaps = 2/78 (2%)

Query: 154 PYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--PGIA 211
                 +             + ++N+P   +   L+    +         V  +   G  
Sbjct: 11  SSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTG 70

Query: 212 FVEYGDEMQATVAMQSLQ 229
            +E+  E     A++ L 
Sbjct: 71  ALEFPSEEILVEALERLN 88

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 8/95 (8%)

Query: 8  QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVF-KQFGTILE--ILAFKTLKHKGQAWLV 64
                P  ++++ +L   V    L +     F K + +     ++  +T   KG  ++ 
Sbjct: 2  SSGSSGPEYSLFVGDLTPDVDDGMLYE----FFVKVYPSCRGGKVVLDQTGVSKGYGFVK 57

Query: 65 FKDVASATAAVEKMQGFPFYD-KPMRIQYAKTKSD 98
          F D      A+ + QG      KP+R+  A  K+ 
Sbjct: 58 FTDELEQKRALTECQGAVGLGSKPVRLSVAIPKAS 92

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 174 LFVQNVPHDTTPMALQMFFSQ-FPGFKEVRMVEAKPGI----AFVEYGDEMQATVAMQSL 228
           LFV ++  D     L  FF + +P  +  ++V  + G+     FV++ DE++   A+   
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71

Query: 229 Q-SLKIGQQQLLITYAKK 245
           Q ++ +G + + ++ A  
Sbjct: 72  QGAVGLGSKPVRLSVAIP 89

>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 = 41.1 bits (96), Expect = 3e-05
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 7/77 (9%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFP---GFKEVRMVEAKP----G 209
            G+  ++         ++ ++ +P   +   +Q F S      G   V  +  +     G
Sbjct: 3   SGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSG 62

Query: 210 IAFVEYGDEMQATVAMQ 226
            AFVE   E    +A++
Sbjct: 63  EAFVELESEDDVKLALK 79

>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 = 41.0 bits (96), Expect = 5e-05
 Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 5/68 (7%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPG-FKEVRMVEAKP----GIAFVEYGDE 218
             A +  +  + ++ +P   T   +  FFS        + +         G AFV++  +
Sbjct: 35  NSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQ 94

Query: 219 MQATVAMQ 226
             A  A+ 
Sbjct: 95  ELAEKALG 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 = 40.5 bits (95), Expect = 6e-05
 Identities = 20/98 (20%), Positives = 40/98 (40%), Gaps = 8/98 (8%)

Query: 2   EPEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFK-TLKHK 58
              ++ +  +     ++Y+ N++       L+      F   G+I    IL  K +   K
Sbjct: 23  PQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEA----HFSSCGSINRITILCDKFSGHPK 78

Query: 59  GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTK 96
           G A++ F +  S  AAV  M    F  + +++   +T 
Sbjct: 79  GYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPKRTN 115

>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 = 39.3 bits (92), Expect = 2e-04
 Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 5/58 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQ 226
           ++V NV + +T   L+  FS       + ++  K      G A++E+ +      A+ 
Sbjct: 39  VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 39.5 bits (93), Expect = 7e-05
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 6/76 (7%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           ++V N+ +  T   ++  FSQF     V+++  +      G  FVE  +E   + A+  L
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIAKL 62

Query: 229 QSLKIGQQQLLITYAK 244
            +     + + +T A 
Sbjct: 63  DNTDFMGRTIRVTEAN 78

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 24/103 (23%), Positives = 41/103 (39%), Gaps = 19/103 (18%)

Query: 17  TIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASATA 73
            IY+ NL      +Q+K+    +F QFG +     I   +T K KG  ++  ++  S + 
Sbjct: 3   NIYVGNLVYSATSEQVKE----LFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSE 57

Query: 74  AVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRH 116
           A+ K+    F  + +R+  A  K              E    H
Sbjct: 58  AIAKLDNTDFMGRTIRVTEANPKK-----------SLEHHHHH 89

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 14/53 (26%), Positives = 18/53 (33%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQ 226
           +FV   P       L  +F  F     V M + K   A VE GD       + 
Sbjct: 11  VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS 63

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 40.6 bits (94), Expect = 1e-04
 Identities = 24/165 (14%), Positives = 49/165 (29%), Gaps = 14/165 (8%)

Query: 84  YDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGA 143
            DK ++ Q          K D  +VP E   +     +   D +   +A           
Sbjct: 31  RDKFLKEQI---------KLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEI 81

Query: 144 YGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRM 203
                 + + P     +          N  ++++  P D T   ++ +         ++M
Sbjct: 82  SEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM 141

Query: 204 VEAKP----GIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
                    G  FV +     A   +++    K  +  LLI +  
Sbjct: 142 RRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKD 185

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 38.6 bits (89), Expect = 2e-04
 Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 4/65 (6%)

Query: 33 KQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY 92
          K  L  + +++G +L ++     K  G A + F  V +A  AV+   G    D P++I +
Sbjct: 31 KDVLLRLLQKYGEVLNLVLSS--KKPGTAVVEFATVKAAELAVQNEVGLV--DNPLKISW 86

Query: 93 AKTKS 97
           + + 
Sbjct: 87 LEGQP 91

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 17/96 (17%), Positives = 33/96 (34%), Gaps = 7/96 (7%)

Query: 138 PAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFP- 196
            +     G+           G  S++         ++ ++ +P   +   +Q F S    
Sbjct: 11  SSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTI 70

Query: 197 --GFKEVRMVEAKP----GIAFVEYGDEMQATVAMQ 226
             G   V  +  +     G AFVE G E    +A++
Sbjct: 71  HDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK 106

>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 = 36.4 bits (85), Expect = 8e-04
 Identities = 16/59 (27%), Positives = 25/59 (42%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLK 232
           +FV     D T   L+ FFSQ+    +V + +     AFV + D+  A         +K
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIK 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	245
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
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	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
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	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	99.98
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.98
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.91
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.89
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.89
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.89
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.85
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.85
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.85
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.85
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.84
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.84
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.83
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.83
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.83
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.83
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.83
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.83
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.83
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.82
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.82
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.82
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.81
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.81
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.81
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.81
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.81
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.81
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.81
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.81
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.81
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.81
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.81
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.81
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.8
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.8
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.8
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.8
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.8
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.8
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.8
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.8
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.8
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.8
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.8
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.8
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.8
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.8
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.8
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.8
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.8
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.8
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.8
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.79
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.79
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.79
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.79
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.79
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.79
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.79
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.79
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.79
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.79
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.79
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.79
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.79
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.79
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.79
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.79
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.79
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.79
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.79
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.79
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.79
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.79
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.79
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.79
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.79
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.79
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.78
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.78
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.78
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.78
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.78
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.78
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.78
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.78
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.78
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.78
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.78
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.78
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.78
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.78
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.78
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.78
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.78
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.78
2div_A	99	TRNA selenocysteine associated protein; structural	99.78
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.78
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.78
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.78
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.77
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.77
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.77
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.77
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.77
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.77
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.77
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.77
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.77
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.77
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.77
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.77
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.77
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.77
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.77
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.77
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.77
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.77
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.77
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.77
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.77
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.77
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.77
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.77
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.77
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.77
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.77
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.77
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.76
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.76
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.76
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.76
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.76
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.76
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.76
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.76
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.76
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.76
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.76
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.76
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.76
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.76
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.76
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.76
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.76
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.76
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.76
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.76
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.76
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.76
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.76
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.76
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.76
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.76
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.76
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.76
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.76
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.76
2div_A	99	TRNA selenocysteine associated protein; structural	99.76
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.76
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.76
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.76
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.75
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.75
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.75
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.75
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.75
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.75
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.75
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.75
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.75
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.75
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.75
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.75
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.75
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.75
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.75
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.75
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.75
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.75
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.75
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.75
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.75
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.75
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.75
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.75
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.75
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.75
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.74
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.74
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.74
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.74
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.74
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.74
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.74
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.74
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.74
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.74
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.74
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.74
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.74
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.74
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.74
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.74
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.74
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.74
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.74
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.74
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.74
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.74
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.74
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.74
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.74
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.74
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.74
1x5p_A	97	Negative elongation factor E; structure genomics,	99.73
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.73
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.73
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.73
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.73
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.73
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.73
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.73
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.73
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.73
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.73
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.73
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.73
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.73
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.73
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.73
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.73
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.73
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.72
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.72
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.72
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.72
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.72
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.72
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.72
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.72
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.72
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.72
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.72
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.72
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.72
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.72
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.72
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.72
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.72
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.72
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.72
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.71
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.71
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.71
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.71
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.71
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.71
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.71
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.71
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.71
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.71
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.71
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.71
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.71
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.71
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.71
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.7
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.7
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.7
1x5p_A	97	Negative elongation factor E; structure genomics,	99.7
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.7
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.7
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.7
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.7
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.7
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.69
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.69
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.69
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.69
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.69
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.68
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.51
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.68
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.68
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.68
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.68
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.68
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.67
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.67
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.67
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.67
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.67
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.67
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.67
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.67
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.67
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.67
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.67
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.66
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.66
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.66
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.65
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.47
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.65
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.65
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.65
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.65
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.65
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.64
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.64
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.63
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.63
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.63
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.63
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.63
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.63
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.63
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.63
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.62
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.62
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.62
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.62
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.62
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.61
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.6
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.6
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.6
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.6
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.6
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.59
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.58
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.58
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.58
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.57
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.56
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.56
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.55
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.55
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.55
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.52
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.52
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.52
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.52
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.46
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.43
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.36
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.36
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.35
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.18
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.17
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.15
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.99
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.98
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.95
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.54
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.46
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.32
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.14
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.14
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.01
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.82
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.78
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.72
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.59
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.57
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.45
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.38
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.22
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.19
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.17
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.55
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.33
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.07
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	95.0
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	91.59
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	90.95

>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=1.1e-39  Score=264.63  Aligned_cols=238  Identities=50%  Similarity=0.810  Sum_probs=170.0

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      +..+..++++|||+|||.++++++|++.|+++|+.||.|.+|++.++++++|||||+|.+.++|.+|++.|||..+.|+.
T Consensus         2 ~~~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCC-------Ccc----------------ccCCC
Q 025973           88 MRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGL-------NPA----------------YAGAY  144 (245)
Q Consensus        88 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~----------------~~~~~  144 (245)
                      |+|.|+...........+.+.............................       ...                .....
T Consensus        82 l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  161 (282)
T 3pgw_A           82 MRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQP  161 (282)
T ss_pred             EEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCC
Confidence            9999998776544444443332222111111100000000000000000       000                00000


Q ss_pred             CCCCCCCCCCCCCCC-------------------CCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEec
Q 025973          145 GATPPLSQIPYPGGA-------------------KSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE  205 (245)
Q Consensus       145 ~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~  205 (245)
                      +.+.+....+.+...                   .........+++++|||+|||..+++++|+++|+.||.|.+|+++.
T Consensus       162 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~  241 (282)
T 3pgw_A          162 PYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP  241 (282)
T ss_pred             CCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEec
Confidence            000000000000000                   0001123345678899999999999999999999999999999999


Q ss_pred             CCCeEEEEEeCCHHHHHHHHHHhCCCeeC-CeEEEEEEecC
Q 025973          206 AKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITYAKK  245 (245)
Q Consensus       206 ~~~g~afv~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~ak~  245 (245)
                      +++|+|||+|.+.++|.+|+..|||..|+ |++|+|+||||
T Consensus       242 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~akk  282 (282)
T 3pgw_A          242 GRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK  282 (282)
T ss_pred             CCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEecC
Confidence            88899999999999999999999999999 99999999997

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=7.4e-37  Score=238.19  Aligned_cols=167  Identities=22%  Similarity=0.344  Sum_probs=143.3

Q ss_pred             ccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973            7 NQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus         7 ~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      +...+..|.++|||+|||.++++++    |+++|+.||.|.+|++.   .+++++|||||+|.+.++|.+|++.+|+..+
T Consensus         7 ~p~~p~~p~~tlfVgnLp~~~te~~----L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~   82 (213)
T 4f02_A            7 NPSAPSYPMASLYVGDLHPDVTEAM----LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI   82 (213)
T ss_dssp             --------CCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHH----HHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhc
Confidence            4455667889999999999999999    67999999999998765   3688999999999999999999999999999


Q ss_pred             CCceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCC
Q 025973           84 YDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVI  163 (245)
Q Consensus        84 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (245)
                      .|+.|++.++........                                                              
T Consensus        83 ~g~~i~~~~~~~~~~~~~--------------------------------------------------------------  100 (213)
T 4f02_A           83 KGKPVRIMWSQRDPSLRK--------------------------------------------------------------  100 (213)
T ss_dssp             TTEECEEEECCCCTHHHH--------------------------------------------------------------
T ss_pred             CCcccccccccccccccc--------------------------------------------------------------
Confidence            999999998765433111                                                              


Q ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEE
Q 025973          164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLI  240 (245)
Q Consensus       164 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v  240 (245)
                           ....+|||+|||..+++++|+++|+.||.|..+.++.++   +|||||+|.+.++|.+|++.|||..|+|++|.|
T Consensus       101 -----~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V  175 (213)
T 4f02_A          101 -----SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV  175 (213)
T ss_dssp             -----HCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             -----cccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEE
Confidence                 123569999999999999999999999999999998764   789999999999999999999999999999999


Q ss_pred             EEec
Q 025973          241 TYAK  244 (245)
Q Consensus       241 ~~ak  244 (245)
                      .||+
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=1.3e-35  Score=222.06  Aligned_cols=159  Identities=22%  Similarity=0.353  Sum_probs=141.9

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      ++|||+|||.++++++    |+++|+.||.|.+|.+..  ++.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus         1 R~l~V~nlp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~   76 (166)
T 3md3_A            1 RVLYVGNLDKAITEDI----LKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWA   76 (166)
T ss_dssp             CEEEEEEEETTCCHHH----HHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHH----HHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEc
Confidence            6899999999999999    679999999999987653  5678999999999999999999989999999999999997


Q ss_pred             cccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccE
Q 025973           94 KTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNI  173 (245)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (245)
                      .....                                                                   ....++.+
T Consensus        77 ~~~~~-------------------------------------------------------------------~~~~~~~~   89 (166)
T 3md3_A           77 FQSQQ-------------------------------------------------------------------SSSDDTFN   89 (166)
T ss_dssp             CCCCC-------------------------------------------------------------------CCCTTCEE
T ss_pred             CCCCC-------------------------------------------------------------------CCCCCCce
Confidence            54321                                                                   01124578


Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       174 l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      |||+|||..+++++|+++|+.||.|.++.++.++     +|+|||+|.+.++|.+|+..|||..++|++|.|.||++
T Consensus        90 l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A           90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             EEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            9999999999999999999999999999998763     68999999999999999999999999999999999986

>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=6.9e-35  Score=218.61  Aligned_cols=157  Identities=24%  Similarity=0.405  Sum_probs=142.3

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ++++|||+|||.++++++    |+++|+.||.|.+|.+.   .+|.++|||||+|.+.++|.+|++.|++..+.|+.|.|
T Consensus         2 ~~~~l~v~nlp~~~~~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v   77 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRE----LYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKV   77 (168)
T ss_dssp             CCSEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CccEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEE
Confidence            579999999999999999    77999999999998765   36789999999999999999999999999999999999


Q ss_pred             EEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           91 QYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP  170 (245)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (245)
                      .++.+...                                                                     ..+
T Consensus        78 ~~~~~~~~---------------------------------------------------------------------~~~   88 (168)
T 1b7f_A           78 SYARPGGE---------------------------------------------------------------------SIK   88 (168)
T ss_dssp             EECCCCSS---------------------------------------------------------------------TTT
T ss_pred             EecCCCcc---------------------------------------------------------------------cCC
Confidence            99764321                                                                     024


Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCC--eEEEEEEe
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQ--QQLLITYA  243 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~a  243 (245)
                      +.+|+|+|||..+++++|+++|+.||.|.++.++.++     +|+|||+|.+.++|.+|+..|||..+.|  ++|+|.||
T Consensus        89 ~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A           89 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            5679999999999999999999999999999998864     5899999999999999999999999987  99999997

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=1.3e-34  Score=216.75  Aligned_cols=157  Identities=20%  Similarity=0.414  Sum_probs=141.0

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ++++|||+|||.++++++    |+++|+.||.|.+|.+.+   +|.++|||||+|.+.++|.+|++.||+..+.|+.|.|
T Consensus         1 s~~~l~v~nlp~~~~~~~----l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v   76 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEE----FRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKV   76 (167)
T ss_dssp             CCSEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CcceEEEcCCCCCCCHHH----HHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEE
Confidence            468999999999999999    679999999999986553   7889999999999999999999999999999999999


Q ss_pred             EEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           91 QYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP  170 (245)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (245)
                      .++.+....                                                                     ..
T Consensus        77 ~~~~~~~~~---------------------------------------------------------------------~~   87 (167)
T 1fxl_A           77 SYARPSSAS---------------------------------------------------------------------IR   87 (167)
T ss_dssp             EECCCCCGG---------------------------------------------------------------------GT
T ss_pred             EecCCCccc---------------------------------------------------------------------CC
Confidence            998643220                                                                     13


Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeE--EEEEEe
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQ--LLITYA  243 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~--i~v~~a  243 (245)
                      ..+|+|+|||..+++++|+++|+.||.|..+.++.++     +|+|||+|.+.++|.+|+..|||..+.|+.  |+|.||
T Consensus        88 ~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A           88 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            4579999999999999999999999999999998764     689999999999999999999999999864  999987

>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=1.6e-34  Score=227.35  Aligned_cols=196  Identities=19%  Similarity=0.299  Sum_probs=150.6

Q ss_pred             CCCCCCCeEEEcCCCc-ccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           10 NEISPNNTIYINNLNE-KVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~-~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ...+++++|||+|||. ++++++    |+++|+.||.|.+|.+..+.  +|||||+|.+.++|.+|++.||+..+.|+.|
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~----L~~~F~~~G~i~~v~i~~~~--~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l  102 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQS----LFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPI  102 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHH----HHHHHHHHTCEEEEEECCTT--SCCEEEEESCHHHHHHHHHHHTTCBCSSSBC
T ss_pred             CCCCCCCEEEEeCCCcccCCHHH----HHHHHHhCCCeEEEEEEECC--CCEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            4467799999999999 999999    77999999999999888764  7999999999999999999999999999999


Q ss_pred             EEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           89 RIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPA  168 (245)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (245)
                      .|.++................ ..+...           .          .......            .+.........
T Consensus       103 ~v~~a~~~~~~~~~~~~~~~~-~~~~~~-----------~----------~~~~~~~------------~~~~~~~~~~~  148 (229)
T 2adc_A          103 RITLSKHQNVQLPREGQEDQG-LTKDYG-----------N----------SPLHRFK------------KPGSKNFQNIF  148 (229)
T ss_dssp             EEECCSCCCCCCCCSSSSTTT-TEEECT-----------T----------CSSCCCC------------STTSGGGTTCC
T ss_pred             EEEEecCccccCccccccccc-cccccc-----------c----------CcccccC------------CccccccccCC
Confidence            999987653321110000000 000000           0          0000000            00000001123


Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC-CeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFP-GFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g-~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~ak~  245 (245)
                      +++.+|||+|||..+++++|+++|+.|| .|.++.+++..+|+|||+|.+.++|.+|+..|||..+. |++|+|+||+.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            4678999999999999999999999999 99999998766799999999999999999999999999 99999999973

>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=9.2e-34  Score=220.94  Aligned_cols=170  Identities=21%  Similarity=0.325  Sum_probs=143.7

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .+.++|||+|||.++++++    |+++|+.||.|.+|.+..   ++.++|||||+|.+.++|.+|++.||+..+.|+.|.
T Consensus        26 ~~~~~l~V~nLp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~  101 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDT----IRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK  101 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHH----HHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCE
T ss_pred             CcCCEEEEECCCCCCCHHH----HHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEE
Confidence            3468999999999999999    779999999999997764   677899999999999999999999999999999999


Q ss_pred             EEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           90 IQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAP  169 (245)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (245)
                      |.++.........          .......                                                ..
T Consensus       102 v~~~~~~~~~~~~----------~~~~~~~------------------------------------------------~~  123 (216)
T 2qfj_A          102 VGRPSNIGQAQPI----------IDQLAEE------------------------------------------------AR  123 (216)
T ss_dssp             EECCSCCGGGHHH----------HHHHHHH------------------------------------------------HT
T ss_pred             EecCCCccccchh----------hhhhhcc------------------------------------------------cC
Confidence            9887654321110          0000000                                                02


Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+|||+|||..+++++|+++|+.||.|.++.++.++     +|+|||+|.+.++|.+|+..|||..|+|++|.|.||+
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~  203 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV  203 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEec
Confidence            45789999999999999999999999999999999863     6899999999999999999999999999999999986

>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=6.6e-34  Score=218.55  Aligned_cols=167  Identities=17%  Similarity=0.297  Sum_probs=141.7

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      ..+..+.++|||+|||.++++++    |+++|+.||.|.+|.+..   +|.++|||||+|.+.++|.+|+. +++..+.|
T Consensus         7 ~~~~~~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~-~~~~~~~g   81 (196)
T 1l3k_A            7 PKEPEQLRKLFIGGLSFETTDES----LRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDG   81 (196)
T ss_dssp             -CCCGGGGEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHh-cCCCEECC
Confidence            34566789999999999999999    779999999999986653   67899999999999999999999 49999999


Q ss_pred             ceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           86 KPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPE  165 (245)
Q Consensus        86 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (245)
                      +.|.|.++........                                                               .
T Consensus        82 ~~l~v~~~~~~~~~~~---------------------------------------------------------------~   98 (196)
T 1l3k_A           82 RVVEPKRAVSREDSQR---------------------------------------------------------------P   98 (196)
T ss_dssp             EECEEEECCC----------------------------------------------------------------------
T ss_pred             EEeeeecccCcccccc---------------------------------------------------------------c
Confidence            9999999765432100                                                               0


Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEE
Q 025973          166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLI  240 (245)
Q Consensus       166 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v  240 (245)
                      ....+..+|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.+.++|.+|+.. +|..|+|+.|.|
T Consensus        99 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v  177 (196)
T 1l3k_A           99 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEV  177 (196)
T ss_dssp             ----CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEE
T ss_pred             ccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEE
Confidence            011245789999999999999999999999999999999863     68999999999999999986 899999999999


Q ss_pred             EEec
Q 025973          241 TYAK  244 (245)
Q Consensus       241 ~~ak  244 (245)
                      .||.
T Consensus       178 ~~a~  181 (196)
T 1l3k_A          178 RKAL  181 (196)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9985

>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=4.9e-34  Score=219.75  Aligned_cols=192  Identities=20%  Similarity=0.333  Sum_probs=148.0

Q ss_pred             CCCeEEEcCCCc-ccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           14 PNNTIYINNLNE-KVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        14 ~~~~l~V~nLp~-~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      .+++|||+|||. ++++++    |+++|+.||.|.+|.+..+.  +|||||+|.+.++|.+|++.||+..+.|+.|.|.+
T Consensus         2 ~~~~l~v~nlp~~~~~~~~----l~~~F~~~G~i~~v~i~~~~--~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~   75 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQS----LFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL   75 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHH----HHHHHHTTCCCSEEECSTTC--SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEE
T ss_pred             CCcEEEEeCCCcccCCHHH----HHHHHHhcCCEEEEEEEeCC--CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEE
Confidence            368999999999 999999    77999999999999888754  78999999999999999999999999999999999


Q ss_pred             ccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 025973           93 AKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNN  172 (245)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  172 (245)
                      +................ ..+                         .+...   ..  .....   +.........++++
T Consensus        76 a~~~~~~~~~~~~~~~~-~~~-------------------------~~~~~---~~--~r~~~---~~~~~~~~~~~~~~  121 (198)
T 1qm9_A           76 SKHQNVQLPREGQEDQG-LTK-------------------------DYGNS---PL--HRFKK---PGSKNFQNIFPPSA  121 (198)
T ss_dssp             CCCCSCCCSSSSSSSSS-CEE-------------------------ESSCC---CT--TSSSS---CCCCCCSCCCCCCC
T ss_pred             ecCCCcCCCCcCCcccc-ccc-------------------------cccCC---ch--hhccC---ccccccccCCCCcc
Confidence            87654321110000000 000                         00000   00  00000   00000111234678


Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC-CeEEEEEEecC
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFP-GFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITYAKK  245 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g-~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~ak~  245 (245)
                      +|||+|||..+++++|+++|+.|| .|..+.++++.+|+|||+|.+.++|.+|+..|||..++ |++|+|.||+.
T Consensus       122 ~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          122 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             EEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence            999999999999999999999999 99999998877799999999999999999999999999 99999999973

>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=1.2e-33  Score=218.24  Aligned_cols=193  Identities=12%  Similarity=0.219  Sum_probs=142.5

Q ss_pred             CCCCeEEEcCCC-cccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           13 SPNNTIYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        13 ~~~~~l~V~nLp-~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      .++++|||+||| ..+++++    |+++|+.||.|.+|++.++  .+|||||+|.+.++|..|++.|||..+.|+.|+|.
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~----L~~~F~~~G~v~~v~i~~~--~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   75 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDR----VFNVFCLYGNVEKVKFMKS--KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVC   75 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHH----HHHHHTTTSCEEEEEECTT--STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCcccCCHHH----HHHHHHhcCCeEEEEEecC--CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            468999999999 8999999    7799999999999988765  47999999999999999999999999999999999


Q ss_pred             EccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 025973           92 YAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPN  171 (245)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (245)
                      +++.+.. ............ ...  ..                    +.   +.+.  .....   +.........+++
T Consensus        76 ~s~~~~~-~p~~~~~~~~~~-~~~--~~--------------------~~---~~~~--~r~~~---~~~~~~~~~~~p~  123 (205)
T 3tyt_A           76 VSKQPAI-MPGQSYGLEDGS-CSY--KD--------------------FS---ESRN--NRFST---PEQAAKNRIQHPS  123 (205)
T ss_dssp             ECSCSCC-CCCSCCBCTTSC-BSE--EE--------------------CT---TCTT--CSCSS---HHHHTTSCCCCCC
T ss_pred             EccCCcc-CCCcccccccCC-ccc--cc--------------------cC---CCcc--ccccC---cccccccccCCCc
Confidence            9875432 000000000000 000  00                    00   0000  00000   0000000122467


Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCe--eEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCe----EEEEEE
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGF--KEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQ----QLLITY  242 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v--~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~----~i~v~~  242 (245)
                      ++|||+|||..+|+++|+++|+.||.|  ..++++.++   +|+|||+|.+.++|..|+..|||..+.|+    ++.|.|
T Consensus       124 ~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~  203 (205)
T 3tyt_A          124 NVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKL  203 (205)
T ss_dssp             SEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEE
T ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEe
Confidence            889999999999999999999999999  899998863   59999999999999999999999999876    677776


Q ss_pred             e
Q 025973          243 A  243 (245)
Q Consensus       243 a  243 (245)
                      |
T Consensus       204 ~  204 (205)
T 3tyt_A          204 C  204 (205)
T ss_dssp             E
T ss_pred             c
Confidence            5

>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=1.6e-33  Score=212.47  Aligned_cols=158  Identities=18%  Similarity=0.399  Sum_probs=136.5

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CC--CeeeEEEEEecCHHHHHHHHHHHcCCccC---C
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TL--KHKGQAWLVFKDVASATAAVEKMQGFPFY---D   85 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~--~~kg~afV~F~~~~~A~~a~~~l~~~~~~---g   85 (245)
                      .+++|||+|||.++++++    |+++|+.||.|.+|.+.+   ++  .++|||||+|.+.++|.+|++.||+..+.   +
T Consensus         2 ~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~   77 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKD----LRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMH   77 (175)
T ss_dssp             CCEEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCS
T ss_pred             CceEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCc
Confidence            578999999999999999    779999999999986654   33  78999999999999999999999998776   5


Q ss_pred             ceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           86 KPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPE  165 (245)
Q Consensus        86 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (245)
                      +.+.+.++.....                                                                   
T Consensus        78 ~~~~~~~~~~~~~-------------------------------------------------------------------   90 (175)
T 3nmr_A           78 HPIQMKPADSEKN-------------------------------------------------------------------   90 (175)
T ss_dssp             SCCEEEECGGGCC-------------------------------------------------------------------
T ss_pred             cceEEcccccccc-------------------------------------------------------------------
Confidence            6777777543211                                                                   


Q ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeC---CeEE
Q 025973          166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIG---QQQL  238 (245)
Q Consensus       166 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~---g~~i  238 (245)
                       ......+|||+|||..+|+++|+++|+.||.|.++.++.++    +|+|||+|.+.++|.+|+..|||..+.   +++|
T Consensus        91 -~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l  169 (175)
T 3nmr_A           91 -NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPM  169 (175)
T ss_dssp             -SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCC
T ss_pred             -ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCe
Confidence             00245679999999999999999999999999999999863    689999999999999999999998776   4999


Q ss_pred             EEEEe
Q 025973          239 LITYA  243 (245)
Q Consensus       239 ~v~~a  243 (245)
                      .|.||
T Consensus       170 ~V~~a  174 (175)
T 3nmr_A          170 VVKFA  174 (175)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            99998

>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=8.8e-34  Score=212.41  Aligned_cols=155  Identities=21%  Similarity=0.354  Sum_probs=138.1

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ++++|||+|||.++++++    |+++|+.||.|.+|.+.+   +|.++|||||+|.+.++|.+|+..  +..+.|+.|.|
T Consensus         2 ~~~~l~v~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v   75 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDN----LREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDP   75 (167)
T ss_dssp             GGGEEEECSCCTTCCHHH----HHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCC
T ss_pred             CCcEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccc
Confidence            578999999999999999    679999999999998764   578999999999999999999994  67889999999


Q ss_pred             EEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           91 QYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP  170 (245)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (245)
                      .++.+....                                                                     .+
T Consensus        76 ~~~~~~~~~---------------------------------------------------------------------~~   86 (167)
T 2cjk_A           76 KRAIPRDEQ---------------------------------------------------------------------DK   86 (167)
T ss_dssp             EECCCHHHH---------------------------------------------------------------------HH
T ss_pred             ccccchhhc---------------------------------------------------------------------cC
Confidence            887543221                                                                     12


Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +.+|||+|||..+++++|+++|+.||.|.++.++.++     +|+|||+|.+.++|.+|++ ++|..++|++|.|.||+
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            3579999999999999999999999999999998763     6899999999999999998 89999999999999986

>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=5.2e-33  Score=209.21  Aligned_cols=154  Identities=22%  Similarity=0.419  Sum_probs=135.8

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhccc----C-------CeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCC
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQF----G-------TILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGF   81 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~----G-------~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~   81 (245)
                      +++++|||+|||.++++++    |+++|+.|    |       .|..+...   .++|||||+|.+.++|.+|+ .+|+.
T Consensus         2 r~~~~l~V~nLp~~~t~~~----l~~~F~~~g~~~g~~~~~~~~v~~~~~~---~~~g~afV~f~~~~~A~~A~-~~~~~   73 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEA----MMDFFNAQMRLGGLTQAPGNPVLAVQIN---QDKNFAFLEFRSVDETTQAM-AFDGI   73 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHH----HHHHHHHHHHHTTCCSSSSCSEEEEEEE---TTTTEEEEEESSHHHHHHHG-GGTTC
T ss_pred             CcccEEEEcCCCcccCHHH----HHHHHHHHhhhcccccCCCCceeeeEec---CCCCEEEEEeCCHHHHHHHH-HhCCc
Confidence            4679999999999999999    66888888    6       67777654   44799999999999999999 79999


Q ss_pred             ccCCceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCC
Q 025973           82 PFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKS  161 (245)
Q Consensus        82 ~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (245)
                      .+.|+.|.|.++.....                                                               
T Consensus        74 ~~~g~~i~v~~~~~~~~---------------------------------------------------------------   90 (172)
T 2g4b_A           74 IFQGQSLKIRRPHDYQP---------------------------------------------------------------   90 (172)
T ss_dssp             EETTEECEEECCSSCCC---------------------------------------------------------------
T ss_pred             EecCceeeecCCcccCC---------------------------------------------------------------
Confidence            99999999987543211                                                               


Q ss_pred             CCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCe
Q 025973          162 VIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQ  236 (245)
Q Consensus       162 ~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~  236 (245)
                            .....+|||+|||..+++++|+++|+.||.|..+.+..++     +|+|||+|.+.++|.+|+..|||..++|+
T Consensus        91 ------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  164 (172)
T 2g4b_A           91 ------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK  164 (172)
T ss_dssp             ------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTE
T ss_pred             ------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCe
Confidence                  0124669999999999999999999999999999999874     68999999999999999999999999999


Q ss_pred             EEEEEEe
Q 025973          237 QLLITYA  243 (245)
Q Consensus       237 ~i~v~~a  243 (245)
                      +|.|+||
T Consensus       165 ~l~V~~A  171 (172)
T 2g4b_A          165 KLLVQRA  171 (172)
T ss_dssp             ECEEEEC
T ss_pred             EEEEEeC
Confidence            9999998

>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=1.3e-32  Score=211.57  Aligned_cols=175  Identities=20%  Similarity=0.380  Sum_probs=138.9

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhccc----C-------CeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCC
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQF----G-------TILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGF   81 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~----G-------~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~   81 (245)
                      ..+++|||+|||.++++++    |+++|+.|    |       .|..+..   +.++|||||+|.+.++|.+|+ .||+.
T Consensus         2 ~~~~~l~V~nLp~~~te~~----l~~~F~~~g~i~g~~~~~~~~v~~~~~---~~~~g~afV~F~~~~~A~~Al-~l~g~   73 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEA----MMDFFNAQMRLGGLTQAPGNPVLAVQI---NQDKNFAFLEFRSVDETTQAM-AFDGI   73 (198)
T ss_dssp             --CCEEEEESCCTTCCHHH----HHHHHHHHHHHHTCCSSSSCSEEEEEE---ETTTTEEEEEESCSHHHHHHG-GGTTE
T ss_pred             CceeEEEEcCCCCCCCHHH----HHHHHHHHHhhcccccCCCCceEEeEe---cCCCCEEEEEeCCHHHHHHHH-HhcCC
Confidence            3579999999999999999    66999998    5       5666655   456899999999999999999 69999


Q ss_pred             ccCCceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCC
Q 025973           82 PFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKS  161 (245)
Q Consensus        82 ~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (245)
                      .+.|+.|.|.++............                                      ..       ...+    .
T Consensus        74 ~~~g~~i~v~~~~~~~~~~~~~~~--------------------------------------~~-------~~~~----~  104 (198)
T 2yh0_A           74 IFQGQSLKIRRPHDYQPLPGMSEN--------------------------------------PS-------VYVP----G  104 (198)
T ss_dssp             EETTEEEEEECCCCCCCCCCSSSC--------------------------------------SS-------CCCT----T
T ss_pred             EEcCceEEEeCCCCCCCCCCCcCC--------------------------------------Cc-------CCCC----C
Confidence            999999999987654221000000                                      00       0000    0


Q ss_pred             CCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCe
Q 025973          162 VIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQ  236 (245)
Q Consensus       162 ~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~  236 (245)
                      ........+..+|||+|||..+++++|+++|+.||.|..+.+..++     +|||||+|.++++|.+|+..|||..|+|+
T Consensus       105 ~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  184 (198)
T 2yh0_A          105 VVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK  184 (198)
T ss_dssp             SSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTE
T ss_pred             CccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            0011112456789999999999999999999999999999999874     68999999999999999999999999999


Q ss_pred             EEEEEEec
Q 025973          237 QLLITYAK  244 (245)
Q Consensus       237 ~i~v~~ak  244 (245)
                      +|.|.||+
T Consensus       185 ~l~v~~a~  192 (198)
T 2yh0_A          185 KLLVQRAS  192 (198)
T ss_dssp             ECEEEESC
T ss_pred             EEEEEECC
Confidence            99999986

>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=1.9e-33  Score=212.24  Aligned_cols=163  Identities=18%  Similarity=0.341  Sum_probs=135.3

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE--EEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~--i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ..+..+.++|||+|||.++++++|+    ++|+.||.+..  +....++.++|||||+|.+.++|.+|++ ||+..+.|+
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~----~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~   81 (175)
T 1fje_B            7 GSESTTPFNLFIGNLNPNKSVAELK----VAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGN   81 (175)
T ss_dssp             SSSCSSSEEEEEECCCTTSCHHHHH----HHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHH----HHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCe
Confidence            4567789999999999999999966    55555554433  3334567889999999999999999996 999999999


Q ss_pred             eEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           87 PMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEA  166 (245)
Q Consensus        87 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (245)
                      .|.|.++......                                                                   
T Consensus        82 ~l~v~~~~~~~~~-------------------------------------------------------------------   94 (175)
T 1fje_B           82 EIKLEKPKGRDSK-------------------------------------------------------------------   94 (175)
T ss_dssp             EEEEECCCCSSCS-------------------------------------------------------------------
T ss_pred             EEEEecCCCcccc-------------------------------------------------------------------
Confidence            9999998654210                                                                   


Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEec-CCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE-AKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~-~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+..+|||+|||..+++++|+++|+.||.|..+ ... ..+|+|||+|.+.++|.+|+..|||..|+|++|.|+||+
T Consensus        95 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  172 (175)
T 1fje_B           95 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG  172 (175)
T ss_dssp             TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECS
T ss_pred             ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecC
Confidence            01245789999999999999999999999998877 111 237999999999999999999999999999999999996

>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=1.6e-31  Score=216.78  Aligned_cols=163  Identities=18%  Similarity=0.256  Sum_probs=144.0

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .++.++|||+|||.++++++    |+++|+.||.|..|.+.   .+|.++|||||+|.+.++|.+|+..|+|..+.|+.|
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~----l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i  167 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQ----FEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL  167 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCCCEEEEcCCCCcCCHHH----HHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            34678999999999999999    67999999999988654   478899999999999999999999999999999999


Q ss_pred             EEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           89 RIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPA  168 (245)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (245)
                      .|.++.+.....                                                                  ..
T Consensus       168 ~v~~a~~~~~~~------------------------------------------------------------------~~  181 (284)
T 3smz_A          168 YVHWTDAGQLTP------------------------------------------------------------------AL  181 (284)
T ss_dssp             EEEECCGGGCCT------------------------------------------------------------------TT
T ss_pred             EEEECCCCCCCc------------------------------------------------------------------cc
Confidence            999986532100                                                                  01


Q ss_pred             CCccEEEEcCCCCCC-CHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDT-TPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~-t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ....+|||+|||..+ ++++|+++|+.||.|.++.+..+.    +|+|||+|.++++|.+|+..|||..|+|++|.|.||
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a  261 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC  261 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEe
Confidence            245779999999995 999999999999999999998863    689999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       262 ~  262 (284)
T 3smz_A          262 A  262 (284)
T ss_dssp             C
T ss_pred             c
Confidence            6

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.98  E-value=2.6e-31  Score=216.36  Aligned_cols=165  Identities=13%  Similarity=0.231  Sum_probs=140.1

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccC-CeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFG-TILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G-~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ..++|||+|||..+++++    |+++|+.|| .|..|.+..  .+.++|||||+|.+.++|.+|+..|||..+.|+.|.|
T Consensus       116 ~~~~l~v~nlp~~~t~~~----l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  191 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRN----IRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVT  191 (292)
T ss_dssp             CSCEEEEECCCTTCCHHH----HHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEECCCCCCCHHH----HHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            578999999999999999    779999999 999997764  4578999999999999999999999999999999999


Q ss_pred             EEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           91 QYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP  170 (245)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (245)
                      .++.+.......                                                              .....+
T Consensus       192 ~~a~~~~~~~~~--------------------------------------------------------------~~~~~~  209 (292)
T 2ghp_A          192 KVSNPLEKSKRT--------------------------------------------------------------DSATLE  209 (292)
T ss_dssp             EECCCC-----------------------------------------------------------------------CCT
T ss_pred             EECCCCcccccc--------------------------------------------------------------cccCCC
Confidence            998754331100                                                              001135


Q ss_pred             ccEEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEecCC------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          171 NNILFVQNVPHD-TTPMALQMFFSQFPGFKEVRMVEAK------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       171 ~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~v~l~~~~------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ..+|||+|||.. +++++|+++|+.||.|..|.++.+.      +|+|||+|.+.++|.+|+ .|||..|+|++|.|+||
T Consensus       210 ~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a  288 (292)
T 2ghp_A          210 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLA  288 (292)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEEC
T ss_pred             CceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEe
Confidence            678999999999 9999999999999999999998753      589999999999999999 99999999999999999


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus       289 ~~  290 (292)
T 2ghp_A          289 DK  290 (292)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.98  E-value=6.9e-31  Score=213.07  Aligned_cols=150  Identities=19%  Similarity=0.335  Sum_probs=137.3

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      ..++++|||+|||.++++++    |+++|+.|| |.+|.+   ++++|||||+|.+.++|.+|+..||+..+.|+.|.|.
T Consensus        19 ~~~~~~l~V~nLp~~~te~~----l~~~F~~~G-i~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   90 (284)
T 3smz_A           19 FRNRRKILIRGLPGDVTNQE----VHDLLSDYE-LKYCFV---DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQ   90 (284)
T ss_dssp             HHCCCEEEEECCCTTCCHHH----HHHHTTTSC-EEEEEE---ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHHcC-CEEEEE---ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEE
Confidence            34679999999999999999    679999999 988877   5668999999999999999999999999999999998


Q ss_pred             EccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 025973           92 YAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPN  171 (245)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (245)
                      ++.                                                                           .+
T Consensus        91 ~~~---------------------------------------------------------------------------~~   95 (284)
T 3smz_A           91 LQP---------------------------------------------------------------------------TD   95 (284)
T ss_dssp             ECC---------------------------------------------------------------------------CS
T ss_pred             ecC---------------------------------------------------------------------------CC
Confidence            731                                                                           34


Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+|||+|||..+++++|+++|+.||.|..+.++.++     +|+|||+|.+.++|..|+..|||..++|++|.|.||+
T Consensus        96 ~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           96 ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            579999999999999999999999999999988753     6899999999999999999999999999999999985

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.97  E-value=8.5e-31  Score=210.03  Aligned_cols=154  Identities=18%  Similarity=0.340  Sum_probs=137.6

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .....++++|||+|||.++|+++    |+++|+.||.|..|.+.+   ++|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus        16 ~~~~~~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~---~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l   88 (261)
T 3sde_A           16 EKTYTQRCRLFVGNLPTDITEED----FKRLFERYGEPSEVFINR---DRGFGFIRLESRTLAEIAKAELDGTILKSRPL   88 (261)
T ss_dssp             CCSSCGGGEEEEESCCTTCCHHH----HHHHTGGGCCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCEEEEECCCCCCCHHH----HHHHHHhcCCEEEEEEeC---CCcEEEEEECCHHHHHHHHHHcCCcEECCcee
Confidence            34456678999999999999999    669999999999998864   47999999999999999999999999999999


Q ss_pred             EEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           89 RIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPA  168 (245)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (245)
                      .|.++.                                                                          
T Consensus        89 ~v~~a~--------------------------------------------------------------------------   94 (261)
T 3sde_A           89 RIRFAT--------------------------------------------------------------------------   94 (261)
T ss_dssp             EEEECC--------------------------------------------------------------------------
T ss_pred             Eeeecc--------------------------------------------------------------------------
Confidence            999863                                                                          


Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhC-CCeeC---CeEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQ-SLKIG---QQQLLI  240 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~-g~~~~---g~~i~v  240 (245)
                       ++.+|||+|||..+|+++|+++|+.||.|.+|.++.+.    +|+|||+|.+.++|.+|+..|| |..+.   +++|.|
T Consensus        95 -~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 -HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             -CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             -cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence             23569999999999999999999999999999998763    6899999999999999999995 45554   999999


Q ss_pred             EEec
Q 025973          241 TYAK  244 (245)
Q Consensus       241 ~~ak  244 (245)
                      .+++
T Consensus       174 ~~~~  177 (261)
T 3sde_A          174 EPME  177 (261)
T ss_dssp             EECC
T ss_pred             eecc
Confidence            9985

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.97  E-value=3.1e-30  Score=210.06  Aligned_cols=154  Identities=16%  Similarity=0.213  Sum_probs=133.9

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCC-CCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKT-LKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~-~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ...+++++|||+|||.++++++    |+++|+.||.|.+|.+.++ ..++|||||+|.+.++|.+|++ +|+..+.|+.|
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i  110 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNK----VYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEI  110 (292)
T ss_dssp             ------CEEEEEEECTTCCHHH----HHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEE
Confidence            3466799999999999999999    7799999999999977652 2357999999999999999996 99999999999


Q ss_pred             EEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           89 RIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPA  168 (245)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (245)
                      .|.++                                                                           
T Consensus       111 ~v~~~---------------------------------------------------------------------------  115 (292)
T 2ghp_A          111 IVSHL---------------------------------------------------------------------------  115 (292)
T ss_dssp             EEEEC---------------------------------------------------------------------------
T ss_pred             EEEEC---------------------------------------------------------------------------
Confidence            99874                                                                           


Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFP-GFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g-~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                       ...+|||+|||..+++++|+++|+.|| .|..+.++.++    +|||||+|.+.++|..|+..|||..+.|++|.|.||
T Consensus       116 -~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 -TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             -CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             -CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence             235799999999999999999999999 99999998753    799999999999999999999999999999999997


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      .
T Consensus       195 ~  195 (292)
T 2ghp_A          195 N  195 (292)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.91  E-value=7.1e-24  Score=155.78  Aligned_cols=137  Identities=16%  Similarity=0.215  Sum_probs=111.8

Q ss_pred             CCCeeeEEEEEecCHHHHHHHHHHH-cCCccCCceEEEEEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhh
Q 025973           54 TLKHKGQAWLVFKDVASATAAVEKM-QGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQA  132 (245)
Q Consensus        54 ~~~~kg~afV~F~~~~~A~~a~~~l-~~~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (245)
                      ....+|+++|+|.+.++|.+|++.+ |+..+.| .+.+.++............                           
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~---------------------------   60 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHH---------------------------   60 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSS---------------------------
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccccc---------------------------
Confidence            3456899999999999999999999 9999999 9999887544321100000                           


Q ss_pred             cCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEE
Q 025973          133 GMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAF  212 (245)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~af  212 (245)
                                                ...........+.++|||+|||..+++++|+++|+.||.|.+|.++.+.+||||
T Consensus        61 --------------------------~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~af  114 (150)
T 2i2y_A           61 --------------------------HHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAF  114 (150)
T ss_dssp             --------------------------CCCCSCSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEE
T ss_pred             --------------------------ccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEE
Confidence                                      000001112235678999999999999999999999999999999998779999


Q ss_pred             EEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          213 VEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       213 v~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      |+|.+.++|..|+..|||..|+|++|+|.||+
T Consensus       115 V~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  146 (150)
T 2i2y_A          115 VEFEDPRDAADAVRELDGRTLCGCRVRVELSN  146 (150)
T ss_dssp             EEESSHHHHHHHHHHHSSSCSSSSCCEEEECC
T ss_pred             EEECCHHHHHHHHHHcCCCEECCeEEEEEEcC
Confidence            99999999999999999999999999999986

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.89  E-value=3e-23  Score=145.49  Aligned_cols=81  Identities=26%  Similarity=0.416  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      ..+++|||+|||.++++++    |+++|+.||.|.+|++.. .+.++|||||+|.+.++|.+|++.||+..+.|+.|+|.
T Consensus         3 ~~~~~lfV~nLp~~~te~~----L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~   78 (115)
T 4f25_A            3 LGSGNIFIKNLDKSIDNKA----LYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG   78 (115)
T ss_dssp             --CCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCEEEECCCCCCCCHHH----HHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3467899999999999999    779999999999987654 45579999999999999999999999999999999999


Q ss_pred             Eccccc
Q 025973           92 YAKTKS   97 (245)
Q Consensus        92 ~~~~~~   97 (245)
                      ++..+.
T Consensus        79 ~a~~~~   84 (115)
T 4f25_A           79 RFKSRK   84 (115)
T ss_dssp             ESSCCC
T ss_pred             ECCCcc
Confidence            987543

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.89  E-value=1.2e-22  Score=150.45  Aligned_cols=76  Identities=24%  Similarity=0.381  Sum_probs=71.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ....+|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|+|++|.|.||
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            356789999999999999999999999999999998863     689999999999999999999999999999999999


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       148 ~  148 (158)
T 2kn4_A          148 R  148 (158)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.89  E-value=8.8e-23  Score=144.89  Aligned_cols=99  Identities=29%  Similarity=0.509  Sum_probs=87.9

Q ss_pred             cccccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973            4 EVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus         4 ~~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      .......+.+++++|||+|||..+++++|++.|+++|+.||.|.+|.+.+++.++|||||+|.+.++|..|+..|||..+
T Consensus        18 ~~~s~~~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l   97 (127)
T 2a3j_A           18 DLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPF   97 (127)
T ss_dssp             ----CCCCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCC
T ss_pred             CcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEe
Confidence            34444566788999999999999999999999999999999999999988899999999999999999999999999999


Q ss_pred             CCceEEEEEccccchHhhh
Q 025973           84 YDKPMRIQYAKTKSDIIAK  102 (245)
Q Consensus        84 ~g~~i~v~~~~~~~~~~~~  102 (245)
                      .|+.|+|.|+..+......
T Consensus        98 ~gr~l~V~~a~~~~~~~~~  116 (127)
T 2a3j_A           98 QGNPLVITFSETPQSQVAE  116 (127)
T ss_dssp             TTSCCEEEECCCCCHHHHC
T ss_pred             CCCEEEEEEccCcchhccc
Confidence            9999999999988775543

>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=99.85  E-value=5e-21  Score=130.34  Aligned_cols=75  Identities=24%  Similarity=0.468  Sum_probs=70.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++|||+|||..+|+++|+++|+.||.|.++++++++     +|||||+|.++++|.+|++.|||..|+|++|+|.|||
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            45679999999999999999999999999999999864     6899999999999999999999999999999999996

>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=99.85  E-value=3.7e-21  Score=130.99  Aligned_cols=80  Identities=16%  Similarity=0.363  Sum_probs=73.3

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      -..+++|||+|||.++|+++    |+++|+.||.|.+|.+.   .+|.++|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus        16 ~~~gt~lfV~nLp~~~te~~----L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l   91 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDE----LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI   91 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            44578999999999999999    67999999999998654   468899999999999999999999999999999999


Q ss_pred             EEEEccc
Q 025973           89 RIQYAKT   95 (245)
Q Consensus        89 ~v~~~~~   95 (245)
                      +|.|+++
T Consensus        92 ~V~~AkP   98 (99)
T 4fxv_A           92 KVSYARP   98 (99)
T ss_dssp             EEEECCB
T ss_pred             EEEEeeC
Confidence            9999875

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.85  E-value=6.4e-21  Score=128.55  Aligned_cols=78  Identities=17%  Similarity=0.269  Sum_probs=72.2

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCe--eCCeEEEEEEec
Q 025973          167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLK--IGQQQLLITYAK  244 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~--~~g~~i~v~~ak  244 (245)
                      ..+++++|||+|||..+|+++|+++|++||.|.++.+++++ |+|||+|.+.++|..|+..||+..  +.|++|+|+||+
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~k-g~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~   95 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK-RQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST   95 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECS
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCC-CEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecc
Confidence            34578899999999999999999999999999999999875 999999999999999999999876  789999999997


Q ss_pred             C
Q 025973          245 K  245 (245)
Q Consensus       245 ~  245 (245)
                      .
T Consensus        96 ~   96 (100)
T 3r27_A           96 S   96 (100)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.85  E-value=3.3e-21  Score=130.97  Aligned_cols=91  Identities=68%  Similarity=1.089  Sum_probs=82.0

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .+.+++++|||+|||.++++++|++.|+++|+.||.|..|.+.+++.++|||||+|.+.++|.+|+..|||..+.|+.|+
T Consensus         3 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             ---CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            45678999999999999999998888889999999999999888888899999999999999999999999999999999


Q ss_pred             EEEccccchHh
Q 025973           90 IQYAKTKSDII  100 (245)
Q Consensus        90 v~~~~~~~~~~  100 (245)
                      |.++.+.....
T Consensus        83 v~~a~~~~~~~   93 (97)
T 1nu4_A           83 IQYAKTDSDII   93 (97)
T ss_dssp             EEECSSCCTHH
T ss_pred             EEEccCCCccc
Confidence            99998876543

>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=99.84  E-value=2.2e-20  Score=126.53  Aligned_cols=90  Identities=14%  Similarity=0.238  Sum_probs=80.1

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ++.+....++|||+|||.++++++|+..|+++|+.||.|.+|.+..+...+|||||+|.+.++|.+|++.|||..+.|+.
T Consensus         2 ss~~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~   81 (96)
T 2dgx_A            2 SSGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKK   81 (96)
T ss_dssp             CCCCCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            34556778999999999999999988778899999999999988765434899999999999999999999999999999


Q ss_pred             EEEEEccccc
Q 025973           88 MRIQYAKTKS   97 (245)
Q Consensus        88 i~v~~~~~~~   97 (245)
                      |+|.++.+..
T Consensus        82 l~V~~a~~~~   91 (96)
T 2dgx_A           82 ILVSLATGAS   91 (96)
T ss_dssp             EEEEECCCSS
T ss_pred             EEEEEcCCCC
Confidence            9999997654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.6e-20  Score=123.33  Aligned_cols=83  Identities=20%  Similarity=0.300  Sum_probs=75.6

Q ss_pred             CCCCCCCe-EEEcCCCcccChHHHHHHHHHhhccc-CCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           10 NEISPNNT-IYINNLNEKVKIDQLKQSLHAVFKQF-GTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        10 ~~~~~~~~-l~V~nLp~~~~~~~l~~~l~~~F~~~-G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      +..+|+.+ |||+|||.++++++|++.|+++|++| |.|.+|    ++   |+|||.|.+.++|.+|++.|||..+.|+.
T Consensus         3 ~~~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V----tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            3 SGSSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI----TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             SSCCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC----CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCCCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE----ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            34566777 99999999999999999999999999 599998    34   99999999999999999999999999999


Q ss_pred             EEEEEccccchH
Q 025973           88 MRIQYAKTKSDI   99 (245)
Q Consensus        88 i~v~~~~~~~~~   99 (245)
                      |+|.|++.+++.
T Consensus        76 i~v~~A~~~sd~   87 (96)
T 2diu_A           76 IIVSFTPKNREL   87 (96)
T ss_dssp             CEEESSCCSCCC
T ss_pred             EEEEecCCCcce
Confidence            999999887763

>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=99.83  E-value=9.6e-20  Score=124.03  Aligned_cols=76  Identities=20%  Similarity=0.360  Sum_probs=70.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHh--CCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL--QSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l--~g~~~~g~~i~v~~ak~  245 (245)
                      +++++|||+|||..+++++|+++|++||.|.+|.+++++ |||||+|.+.++|..|+..|  ++..+.|++|+|+||+.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~k-g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   90 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-NQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   90 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCC-CEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCc
Confidence            567899999999999999999999999999999999884 99999999999999999977  46789999999999973

>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=99.83  E-value=1.1e-20  Score=132.44  Aligned_cols=83  Identities=25%  Similarity=0.494  Sum_probs=76.9

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ++.++++|||+|||..+++++    |+++|+.||.|..|.+..++.++|||||+|.+.++|.+|+..|||..+.|+.|.|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   79 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEE----MYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVV   79 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            356789999999999999999    7799999999999998888888999999999999999999999999999999999


Q ss_pred             EEccccc
Q 025973           91 QYAKTKS   97 (245)
Q Consensus        91 ~~~~~~~   97 (245)
                      .++.+..
T Consensus        80 ~~a~~~~   86 (115)
T 3lqv_A           80 LYYNANR   86 (115)
T ss_dssp             EECCHHH
T ss_pred             EEecCCh
Confidence            9987543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.83  E-value=2.9e-20  Score=125.35  Aligned_cols=83  Identities=22%  Similarity=0.322  Sum_probs=72.9

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCc--cCC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFP--FYD   85 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~--~~g   85 (245)
                      +....+|+++|||+|||.++++++    |+++|++||.|.+|++.+   .||+|||+|.+.++|..|+..|++..  +.|
T Consensus        14 ~~~~~~ps~~l~V~NLp~~~te~~----L~~lF~~fG~V~~v~i~~---~kg~AFVef~~~~~A~~Av~~ln~~~~~i~G   86 (100)
T 3r27_A           14 DPHKTPASPVVHIRGLIDGVVEAD----LVEALQEFGPISYVVVMP---KKRQALVEFEDVLGACNAVNYAADNQIYIAG   86 (100)
T ss_dssp             ---CCCCCSEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCEEETT
T ss_pred             ccccCCCCcEEEEeCCCCCCCHHH----HHHHHhccCCEEEEEEEc---CCCEEEEEECCHHHHHHHHHHhcCCCceeCC
Confidence            445678899999999999999999    779999999999998875   46999999999999999999999876  779


Q ss_pred             ceEEEEEccccc
Q 025973           86 KPMRIQYAKTKS   97 (245)
Q Consensus        86 ~~i~v~~~~~~~   97 (245)
                      ++|.|.|++.+.
T Consensus        87 r~i~V~~S~~k~   98 (100)
T 3r27_A           87 HPAFVNYSTSQK   98 (100)
T ss_dssp             EEEEEEECSCSC
T ss_pred             cEEEEEeccccc
Confidence            999999997653

>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=99.83  E-value=3e-20  Score=126.46  Aligned_cols=76  Identities=11%  Similarity=0.165  Sum_probs=70.5

Q ss_pred             CCccEEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCC--eeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPH-DTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSL--KIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~-~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~--~~~g~~i~v~~ak~  245 (245)
                      .++++|||+|||. .+++++|+++|++||.|.+|.+++++ |||||+|.+.++|..|++.||+.  .|.|++|+|+||++
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k-g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   91 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI-NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   91 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS-SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC-CEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCC
Confidence            3678899999999 99999999999999999999999886 89999999999999999999864  59999999999973

>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=99.83  E-value=6e-20  Score=125.77  Aligned_cols=77  Identities=18%  Similarity=0.197  Sum_probs=70.5

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCC--eeCCeEEEEEEecC
Q 025973          168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSL--KIGQQQLLITYAKK  245 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~--~~~g~~i~v~~ak~  245 (245)
                      .+++++|||+|||..+++++|+++|++||.|.+|.+++++ |||||+|.+.++|..|+..|++.  .+.|++|+|+||+.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~k-g~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~   90 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK-RQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCC-CEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccC
Confidence            3567899999999999999999999999999999998875 99999999999999999988764  48999999999963

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=2.3e-20  Score=127.08  Aligned_cols=76  Identities=20%  Similarity=0.319  Sum_probs=70.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCC--CeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQS--LKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g--~~~~g~~i~v~~ak~  245 (245)
                      +++++|||+|||..+++++|+++|++||.|.+|.+++++ |||||+|.+.++|..|++.+++  ..|.|++|+|.||+.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~k-GfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~   91 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH   91 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCC-CEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCC
Confidence            356789999999999999999999999999999999985 9999999999999999998864  789999999999873

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.83  E-value=6.2e-20  Score=127.23  Aligned_cols=82  Identities=20%  Similarity=0.308  Sum_probs=74.6

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .++.++|||+|||.++++++    |+++|++||.|.+|.+.   .+++++|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus         3 ~~p~~~lfV~nL~~~~te~~----L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i   78 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETF----LKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNII   78 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHH----HHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCcEEEEECCCCCCCHHH----HHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            46789999999999999999    77999999999998654   468899999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 025973           89 RIQYAKTKS   97 (245)
Q Consensus        89 ~v~~~~~~~   97 (245)
                      +|.++....
T Consensus        79 ~V~~a~~~~   87 (110)
T 3s8s_A           79 HAQLDIKGQ   87 (110)
T ss_dssp             EEEECSTTH
T ss_pred             EEEECCCCc
Confidence            999986543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.82  E-value=9.4e-20  Score=126.32  Aligned_cols=77  Identities=13%  Similarity=0.131  Sum_probs=72.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ++.++|||+|||..+++++|+++|++||.|.+|.++.++     +|||||+|.+.++|..|++.|||..|.|++|.|.+|
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            456789999999999999999999999999999998764     689999999999999999999999999999999998


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      ++
T Consensus        84 ~~   85 (110)
T 3s8s_A           84 IK   85 (110)
T ss_dssp             ST
T ss_pred             CC
Confidence            63

>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=6.8e-20  Score=119.28  Aligned_cols=73  Identities=15%  Similarity=0.203  Sum_probs=69.2

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +.-|+|+||+..+|+++|+++|++||.|.++++... +|||||+|.++++|.+|++.||+..++|++|+|.+|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~-kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN-QGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCC-CcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            455999999999999999999999999999999886 4999999999999999999999999999999999984

>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=1.9e-19  Score=121.46  Aligned_cols=76  Identities=21%  Similarity=0.367  Sum_probs=71.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ++.++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.++++|.+|++.|||..|.|++|+|+||
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            466789999999999999999999999999999998863     589999999999999999999999999999999999


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      |
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            7

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.81  E-value=1.5e-19  Score=119.59  Aligned_cols=76  Identities=18%  Similarity=0.347  Sum_probs=71.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +++++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.++++|..|++.|||..++|++|+|+||
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            467889999999999999999999999999999998752     689999999999999999999999999999999999


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      |
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.81  E-value=1.1e-19  Score=127.18  Aligned_cols=74  Identities=19%  Similarity=0.357  Sum_probs=70.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +.+|||+|||..+++++|+++|+.||.|.+|+++.++   +|||||+|.++++|.+|++.|||..|+|++|.|.+|+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            4579999999999999999999999999999999864   6899999999999999999999999999999999986

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.81  E-value=9.5e-20  Score=122.69  Aligned_cols=73  Identities=27%  Similarity=0.491  Sum_probs=67.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCC--eeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCC----eeCCeEEEE
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPG--FKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSL----KIGQQQLLI  240 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~--v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~----~~~g~~i~v  240 (245)
                      ++|||+|||..+|+++|+++|++||.  +.+|++++++     +|||||+|.++++|.+|++.|||.    .++||+|.|
T Consensus        10 ~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V   89 (95)
T 2lkz_A           10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV   89 (95)
T ss_dssp             CEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEE
Confidence            57999999999999999999999995  6789998864     689999999999999999999996    488999999


Q ss_pred             EEec
Q 025973          241 TYAK  244 (245)
Q Consensus       241 ~~ak  244 (245)
                      +|||
T Consensus        90 ~~Ak   93 (95)
T 2lkz_A           90 DFAK   93 (95)
T ss_dssp             EECC
T ss_pred             EEcc
Confidence            9997

>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=99.81  E-value=1.4e-19  Score=126.33  Aligned_cols=77  Identities=19%  Similarity=0.317  Sum_probs=71.2

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCC--CeeCCeEEEEEEecC
Q 025973          168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQS--LKIGQQQLLITYAKK  245 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g--~~~~g~~i~v~~ak~  245 (245)
                      .+++++|||+|||..+++++|+++|++||.|.+|.+++++ |||||+|.+.++|..|+..+++  ..|.|++|+|+||+.
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~k-G~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  106 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH  106 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGG-TEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCC-CEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccC
Confidence            3567899999999999999999999999999999999885 9999999999999999998874  689999999999973

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.81  E-value=6.4e-19  Score=123.93  Aligned_cols=78  Identities=22%  Similarity=0.415  Sum_probs=72.0

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      ..++.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|++.|||..|+|++|+|.
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            34567889999999999999999999999999999998763     6899999999999999999999999999999999


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      |||
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            996

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.81  E-value=2.2e-19  Score=118.82  Aligned_cols=80  Identities=31%  Similarity=0.523  Sum_probs=73.3

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ...+.++|||+|||.++++++    |+++|+.||.|..|.+.   .++.++|||||+|.+.++|.+|++.|||..+.|+.
T Consensus         3 ~~~~~~~l~V~nl~~~~~~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   78 (85)
T 3mdf_A            3 MATTKRVLYVGGLAEEVDDKV----LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT   78 (85)
T ss_dssp             CCCCSSEEEEECCCTTCCHHH----HHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEECCCCCCCHHH----HHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            456789999999999999999    67999999999998764   46778999999999999999999999999999999


Q ss_pred             EEEEEcc
Q 025973           88 MRIQYAK   94 (245)
Q Consensus        88 i~v~~~~   94 (245)
                      |+|.+++
T Consensus        79 l~v~~ak   85 (85)
T 3mdf_A           79 IRVNLAK   85 (85)
T ss_dssp             CEEEECC
T ss_pred             EEEEEcC
Confidence            9999974

>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=99.81  E-value=3e-19  Score=123.88  Aligned_cols=85  Identities=21%  Similarity=0.383  Sum_probs=78.0

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .....+.++|||+|||.++++++    |+++|+.||.|..|.+..++.++|||||+|.+.++|.+|++.||+..+.|+.|
T Consensus        16 ~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   91 (109)
T 1x4a_A           16 GPAGNNDCRIYVGNLPPDIRTKD----IEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRL   91 (109)
T ss_dssp             CCCCCCSSEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            34466789999999999999999    77999999999999998888889999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 025973           89 RIQYAKTKS   97 (245)
Q Consensus        89 ~v~~~~~~~   97 (245)
                      +|.+++...
T Consensus        92 ~V~~a~~~~  100 (109)
T 1x4a_A           92 RVEFPRSGR  100 (109)
T ss_dssp             EEECCCCCC
T ss_pred             EEEEcccCC
Confidence            999987654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.81  E-value=2.1e-20  Score=125.25  Aligned_cols=80  Identities=16%  Similarity=0.334  Sum_probs=70.5

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccC-CeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHH-cCCccCCceEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFG-TILEILAFK---TLKHKGQAWLVFKDVASATAAVEKM-QGFPFYDKPMR   89 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G-~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l-~~~~~~g~~i~   89 (245)
                      +++|||+|||.++|+++    |+++|+.|| .|.+|++.+   +|.++|||||+|.+.++|.+|++.+ ++..+.|+.|+
T Consensus         1 S~~i~v~nLp~~~te~~----l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~   76 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDD----IRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVS   76 (91)
T ss_dssp             CCEEEEETCCSSCCHHH----HHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEE
Confidence            57899999999999999    669999999 798887654   6889999999999999999999977 45779999999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |.|+.++..
T Consensus        77 V~~a~~~~~   85 (91)
T 2lxi_A           77 MHYSDPKPK   85 (91)
T ss_dssp             EECCCSCCC
T ss_pred             EEEcCCCCC
Confidence            999977543

>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=2.8e-19  Score=123.69  Aligned_cols=86  Identities=24%  Similarity=0.481  Sum_probs=77.3

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ......+.++|||+|||..+++++    |+++|+.||.|..|.+.   .+|.++|||||+|.+.++|.+|++.|||..+.
T Consensus        19 ~~~~~~~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~   94 (108)
T 2jrs_A           19 LQKGSAGPMRLYVGSLHFNITEDM----LRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELA   94 (108)
T ss_dssp             SCCSCSSCEEEEEECCCSSCCHHH----HHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSS
T ss_pred             cccCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            345567789999999999999999    67999999999998665   46789999999999999999999999999999


Q ss_pred             CceEEEEEccccc
Q 025973           85 DKPMRIQYAKTKS   97 (245)
Q Consensus        85 g~~i~v~~~~~~~   97 (245)
                      |+.|+|.++.++.
T Consensus        95 g~~l~V~~a~~k~  107 (108)
T 2jrs_A           95 GRPMKVGHVTERT  107 (108)
T ss_dssp             SSCCEEECSCSSC
T ss_pred             CEEEEEEEcccCC
Confidence            9999999987654

>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=2.6e-19  Score=118.45  Aligned_cols=75  Identities=20%  Similarity=0.370  Sum_probs=71.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHh-CCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL-QSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l-~g~~~~g~~i~v~~ak  244 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..+.+.+++ |||||+|.+.++|..|+..| ||..+.|++|.|.|||
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~k-g~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ-QCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGG-TEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCC-CEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            456789999999999999999999999999999999875 89999999999999999999 9999999999999996

>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=1.8e-19  Score=119.77  Aligned_cols=81  Identities=22%  Similarity=0.390  Sum_probs=71.2

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..+.++|||+|||.++++++    |+++|+.||.|.+|.+.   .++.++|||||+|.+.++|.+|++.||+..+.|+.|
T Consensus         3 ~~~~~~l~v~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   78 (87)
T 3bs9_A            3 LGSHFHVFVGDLSPEITTAA----IAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI   78 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCceEEEEeCCCCCCCHHH----HHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            45688999999999999999    77999999999998665   367899999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      +|.++.++
T Consensus        79 ~v~~a~~k   86 (87)
T 3bs9_A           79 RTNWATRK   86 (87)
T ss_dssp             EEEEEC--
T ss_pred             EEEecCCC
Confidence            99998764

>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=99.81  E-value=2.3e-19  Score=122.87  Aligned_cols=87  Identities=21%  Similarity=0.273  Sum_probs=75.4

Q ss_pred             ccccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCC--c
Q 025973            5 VANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGF--P   82 (245)
Q Consensus         5 ~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~--~   82 (245)
                      ........+++++|||+|||.++++++    |+++|++||.|..|.+.++   ||||||+|.+.++|.+|++.|++.  .
T Consensus         5 ~~~~~~~~~p~~~l~V~nLp~~~te~~----L~~~F~~fG~V~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~   77 (104)
T 1wex_A            5 SSGSHHKVSVSPVVHVRGLCESVVEAD----LVEALEKFGTICYVMMMPF---KRQALVEFENIDSAKECVTFAADVPVY   77 (104)
T ss_dssp             CCCSCCCCCCCSEEEEESCCSSCCHHH----HHHHHTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCB
T ss_pred             CCCCCCcCCCCCEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEECC---CCEEEEEECCHHHHHHHHHHhccCCce
Confidence            344455678899999999999999999    7799999999999988753   799999999999999999988764  5


Q ss_pred             cCCceEEEEEccccch
Q 025973           83 FYDKPMRIQYAKTKSD   98 (245)
Q Consensus        83 ~~g~~i~v~~~~~~~~   98 (245)
                      +.|+.|.|.|+..+..
T Consensus        78 i~Gr~l~V~~a~~~~~   93 (104)
T 1wex_A           78 IAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             SSSSBCEEEECSSSSC
T ss_pred             ECCEEEEEEEccCccc
Confidence            8999999999976544

>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=1.9e-19  Score=124.23  Aligned_cols=77  Identities=16%  Similarity=0.241  Sum_probs=70.2

Q ss_pred             CCCccEEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCC--CeeCCeEEEEEEec
Q 025973          168 APPNNILFVQNVPHD-TTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQS--LKIGQQQLLITYAK  244 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g--~~~~g~~i~v~~ak  244 (245)
                      ..++++|||+|||.. +++++|+++|++||.|.+|.+++.+ |||||+|.+.++|..|+..||+  ..|.|++|+|.||+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~k-g~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~  100 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK-SQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE  100 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT-TEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCC-CEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECc
Confidence            346789999999998 9999999999999999999998775 9999999999999999998865  56899999999997


Q ss_pred             C
Q 025973          245 K  245 (245)
Q Consensus       245 ~  245 (245)
                      +
T Consensus       101 ~  101 (112)
T 1x4f_A          101 K  101 (112)
T ss_dssp             S
T ss_pred             c
Confidence            4

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=4.7e-19  Score=119.70  Aligned_cols=76  Identities=22%  Similarity=0.298  Sum_probs=71.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +++++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.++++|.+|+..|||..|.|++|.|.||
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP   92 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            467889999999999999999999999999999998753     589999999999999999999999999999999999


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        93 ~   93 (95)
T 2cqc_A           93 S   93 (95)
T ss_dssp             S
T ss_pred             C
Confidence            7

>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=2.6e-19  Score=121.29  Aligned_cols=81  Identities=19%  Similarity=0.433  Sum_probs=74.7

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      |+++|||+|||.++++++    |+++|+.||.|..|.+..   +|.++|||||+|.+.++|.+|++.|||..+.|+.|+|
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   76 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQ----ILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC   76 (96)
T ss_dssp             CCSEEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCcEEEEECCCCCCCHHH----HHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            578999999999999999    779999999999998764   4788999999999999999999999999999999999


Q ss_pred             EEccccch
Q 025973           91 QYAKTKSD   98 (245)
Q Consensus        91 ~~~~~~~~   98 (245)
                      .++.+...
T Consensus        77 ~~a~~~~~   84 (96)
T 2x1f_A           77 GYSSNSDI   84 (96)
T ss_dssp             EECSCSSG
T ss_pred             EEcCCCCC
Confidence            99987654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.80  E-value=1.7e-19  Score=117.34  Aligned_cols=76  Identities=12%  Similarity=0.182  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      ...+.-|||+||++.+|+++    |+++|.+||+|.++++..   ++|||||+|.+.++|.+|++.||+..+.|++|+|.
T Consensus         4 ~~~~~wL~VgNL~~~~te~~----L~~lF~q~G~V~~~~l~~---~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~   76 (89)
T 2wbr_A            4 AWGSSWLLLKNLTAQIDGPT----LRTLCMQHGPLVSFHPYL---NQGIALCKYTTREEANKAQMALNNCVLANTTIFAE   76 (89)
T ss_dssp             CCCCCEEEEECCCTTCCCHH----HHHHHHHHSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCccceEEEeCCCccCCHHH----HHHHHHhhCCEEEEEEcC---CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            45688999999999999999    779999999999998764   58999999999999999999999999999999999


Q ss_pred             Ecc
Q 025973           92 YAK   94 (245)
Q Consensus        92 ~~~   94 (245)
                      ++.
T Consensus        77 ~A~   79 (89)
T 2wbr_A           77 SPS   79 (89)
T ss_dssp             CCC
T ss_pred             ECC
Confidence            984

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1e-19  Score=123.87  Aligned_cols=82  Identities=22%  Similarity=0.299  Sum_probs=72.9

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcC--CccCCce
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQG--FPFYDKP   87 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~--~~~~g~~   87 (245)
                      ..+.+.++|||+|||.++++++    |+++|++||.|.+|++.++   ||||||+|.+.++|.+|++.|++  ..+.|++
T Consensus        11 ~~~~~~~~LfV~nLp~~vte~d----L~~lF~~fG~V~~v~i~~~---kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~   83 (105)
T 1sjq_A           11 GSGVPSRVIHIRKLPIDVTEGE----VISLGLPFGKVTNLLMLKG---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQP   83 (105)
T ss_dssp             -CCCCCCEEEECSCCTTSCHHH----HHHHHHHHCCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTSCCEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEcC---CCEEEEEECCHHHHHHHHHHhccCCceECCEE
Confidence            3467889999999999999999    6799999999999988764   79999999999999999998864  7899999


Q ss_pred             EEEEEccccch
Q 025973           88 MRIQYAKTKSD   98 (245)
Q Consensus        88 i~v~~~~~~~~   98 (245)
                      |.|.+++.+..
T Consensus        84 l~V~~A~~~~~   94 (105)
T 1sjq_A           84 IYIQFSNHKEL   94 (105)
T ss_dssp             CCBCCCSSSSC
T ss_pred             EEEEEcCCCCC
Confidence            99999976544

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.80  E-value=4.7e-19  Score=117.73  Aligned_cols=77  Identities=22%  Similarity=0.380  Sum_probs=70.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +++.+|||+|||..+++++|+++|+.||.|.++.++.++     +|||||+|.+.++|..|+..|||..+.|++|+|.||
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            356789999999999999999999999999999998864     689999999999999999999999999999999999


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus        84 ~~   85 (87)
T 3bs9_A           84 TR   85 (87)
T ss_dssp             C-
T ss_pred             CC
Confidence            73

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.80  E-value=4e-20  Score=123.90  Aligned_cols=74  Identities=30%  Similarity=0.424  Sum_probs=67.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhC-CCeeCCeEEEEEEe
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFP-GFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQ-SLKIGQQQLLITYA  243 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g-~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~-g~~~~g~~i~v~~a  243 (245)
                      +++|||+|||..+|+++|+++|+.|| .|.+|++++++     +|||||+|.++++|.+|++.++ +..++|++|.|.||
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 79999998763     6999999999999999999874 57899999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        81 ~   81 (91)
T 2lxi_A           81 D   81 (91)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=8.5e-19  Score=120.28  Aligned_cols=76  Identities=24%  Similarity=0.387  Sum_probs=71.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.++   +|||||+|.+.++|.+|+..|||..|.|++|+|.||+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   91 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECC
Confidence            456789999999999999999999999999999999863   6899999999999999999999999999999999986

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=3.1e-19  Score=120.39  Aligned_cols=83  Identities=23%  Similarity=0.452  Sum_probs=75.3

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      +....++.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++.||+..+.
T Consensus         9 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~   84 (94)
T 2e5h_A            9 SGGLAPSKSTVYVSNLPFSLTNND----LYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLF   84 (94)
T ss_dssp             CCSCCCCTTSEEEESCCTTSCHHH----HHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEET
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHH----HHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeC
Confidence            445577889999999999999999    779999999999997765   4678899999999999999999999999999


Q ss_pred             CceEEEEEcc
Q 025973           85 DKPMRIQYAK   94 (245)
Q Consensus        85 g~~i~v~~~~   94 (245)
                      |+.|+|.+++
T Consensus        85 g~~l~v~~ak   94 (94)
T 2e5h_A           85 GRVIKASIAI   94 (94)
T ss_dssp             TEEEEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999974

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.80  E-value=4.1e-19  Score=116.92  Aligned_cols=78  Identities=26%  Similarity=0.458  Sum_probs=71.8

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      +.+|||+|||.++++++    |+++|+.||.|.+|.+.   .++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus         1 t~~l~V~nlp~~~t~~~----l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   76 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDET----LRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN   76 (83)
T ss_dssp             CEEEEEECCCTTCCHHH----HHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CeEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            46899999999999999    67999999999998655   468899999999999999999999999999999999999


Q ss_pred             Ecccc
Q 025973           92 YAKTK   96 (245)
Q Consensus        92 ~~~~~   96 (245)
                      ++.++
T Consensus        77 ~a~~~   81 (83)
T 3md1_A           77 WAAKL   81 (83)
T ss_dssp             ECCCC
T ss_pred             ecCcC
Confidence            98765

>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=4e-19  Score=121.00  Aligned_cols=85  Identities=21%  Similarity=0.311  Sum_probs=76.9

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ....+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+..||+..+.|+
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   78 (99)
T 1whw_A            3 SGSSGSGRLFVRNLSYTSSEED----LEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGR   78 (99)
T ss_dssp             CCCCSCEEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            3456789999999999999999    779999999999997764   677899999999999999999999999999999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|+|.++.++..
T Consensus        79 ~l~V~~a~~~~~   90 (99)
T 1whw_A           79 MLHVLPSTIKKE   90 (99)
T ss_dssp             EEEEEECCCCST
T ss_pred             EEEEEEcCCCcc
Confidence            999999987654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.3e-19  Score=120.48  Aligned_cols=85  Identities=20%  Similarity=0.366  Sum_probs=76.6

Q ss_pred             ccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973            7 NQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus         7 ~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      ....+..++++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+..||+..+
T Consensus         7 ~~~~~~~~~~~l~v~nlp~~~t~~~----l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   82 (95)
T 2cqc_A            7 GNRANPDPNCCLGVFGLSLYTTERD----LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL   82 (95)
T ss_dssp             CCCCSCCGGGCEEEESCCSSCCHHH----HHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             CCCCCCCCCCEEEEECCCCCCCHHH----HHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEE
Confidence            4456678899999999999999999    779999999999987653   578899999999999999999999999999


Q ss_pred             CCceEEEEEccc
Q 025973           84 YDKPMRIQYAKT   95 (245)
Q Consensus        84 ~g~~i~v~~~~~   95 (245)
                      .|+.|+|.+++.
T Consensus        83 ~g~~l~v~~a~~   94 (95)
T 2cqc_A           83 DGRRIRVSGPSS   94 (95)
T ss_dssp             TTEEEEEECCSC
T ss_pred             CCEEEEEEecCC
Confidence            999999999864

>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=4.5e-19  Score=121.66  Aligned_cols=89  Identities=25%  Similarity=0.389  Sum_probs=78.9

Q ss_pred             cccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            6 ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ........+.++|||+|||.++++++    |+++|+.||.|..|.+.. ++.++|||||+|.+.++|.+|+..||+..+.
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~   81 (103)
T 2d9p_A            6 SGDRITRYQVVNLYVKNLDDGIDDER----LRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVA   81 (103)
T ss_dssp             CCCCCCCSSCCCEEEECCCTTCCHHH----HHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSS
T ss_pred             CCCccCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            34455567899999999999999999    779999999999986554 6788999999999999999999999999999


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |+.|.|.++.++..
T Consensus        82 g~~l~V~~a~~~~~   95 (103)
T 2d9p_A           82 TKPLYVALAQRKEE   95 (103)
T ss_dssp             SSBCEEEECSSCCC
T ss_pred             CcEEEEEEeccccc
Confidence            99999999987654

>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=1.7e-18  Score=118.80  Aligned_cols=76  Identities=21%  Similarity=0.359  Sum_probs=71.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.++   +|||||+|.+.++|..|+..|||..|.|++|.|.||+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   91 (103)
T 2cq3_A           13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   91 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            456789999999999999999999999999999999864   6899999999999999999999999999999999986

>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=120.28  Aligned_cols=86  Identities=22%  Similarity=0.426  Sum_probs=77.4

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      +..+..+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++ ||+..+.
T Consensus         3 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~   77 (99)
T 2dgs_A            3 SGSSGSKSNKIFVGGIPHNCGETE----LREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIM   77 (99)
T ss_dssp             CCCCCSSCCEEEEESCCSSCCHHH----HHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSS
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEEC
Confidence            445677889999999999999999    779999999999997765   57789999999999999999999 9999999


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |+.|+|.++.++..
T Consensus        78 g~~l~V~~a~~~~~   91 (99)
T 2dgs_A           78 GKKVEVKRAEPRDS   91 (99)
T ss_dssp             SCBCEEEECCCCCC
T ss_pred             CeEEEEEECCCCcc
Confidence            99999999976644

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.80  E-value=7.2e-19  Score=115.75  Aligned_cols=74  Identities=26%  Similarity=0.382  Sum_probs=70.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .+|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.++++|..|+..|||..++|++|+|.||++
T Consensus         2 ~~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            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            579999999999999999999999999999998763     68999999999999999999999999999999999974

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=6e-19  Score=119.21  Aligned_cols=83  Identities=30%  Similarity=0.561  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .++.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++.||+..+.|+.|
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~----l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   77 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDM----LRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPM   77 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHH----HHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCcEEEEeCCCCCCCHHH----HHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Confidence            45789999999999999999    679999999999987665   47789999999999999999999999999999999


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      +|.++.++..
T Consensus        78 ~V~~a~~~~~   87 (95)
T 2dnz_A           78 RVGHVTERLD   87 (95)
T ss_dssp             EEEESSCCCC
T ss_pred             EEEEcccccC
Confidence            9999976644

>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=8.8e-19  Score=118.86  Aligned_cols=75  Identities=23%  Similarity=0.432  Sum_probs=71.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC--CeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG--QQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~--g~~i~v~~ak  244 (245)
                      +++++|||+|||..+++++|+++|+.||.|..+.+..+ +|||||+|.+.++|..|+..|||..+.  |++|.|.||+
T Consensus        15 ~~~~~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           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECC
Confidence            46678999999999999999999999999999999887 589999999999999999999999999  9999999996

>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=99.80  E-value=6.7e-19  Score=119.90  Aligned_cols=76  Identities=25%  Similarity=0.411  Sum_probs=71.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      ++.++|||+|||..+++++|+++|+.||.|..|.+.+++ |||||+|.+.++|..|+..|||..|.|++|.|.||+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~k-g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   88 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   88 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT-TEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCC-CEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCC
Confidence            466789999999999999999999999999999999875 8999999999999999999999999999999999973

>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=99.80  E-value=5.8e-19  Score=120.15  Aligned_cols=84  Identities=25%  Similarity=0.328  Sum_probs=74.0

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHc--CCccCC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQ--GFPFYD   85 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~--~~~~~g   85 (245)
                      .....+++++|||+|||.++++++    |+++|++||.|..|.+.++   ||||||+|.+.++|.+|++.|+  +..+.|
T Consensus         8 ~~~~~~p~~~l~V~nLp~~~te~~----L~~~F~~fG~v~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G   80 (101)
T 2cq1_A            8 DKMDGAPSRVLHIRKLPGEVTETE----VIALGLPFGKVTNILMLKG---KNQAFLELATEEAAITMVNYYSAVTPHLRN   80 (101)
T ss_dssp             CCCCSSCCSEEEEESCCTTCCHHH----HHHTTTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCccCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEECC---CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            345567899999999999999999    6799999999999988764   7999999999999999999875  577999


Q ss_pred             ceEEEEEccccch
Q 025973           86 KPMRIQYAKTKSD   98 (245)
Q Consensus        86 ~~i~v~~~~~~~~   98 (245)
                      +.|.|.|+..+..
T Consensus        81 r~l~V~~a~~~~~   93 (101)
T 2cq1_A           81 QPIYIQYSNHKEL   93 (101)
T ss_dssp             EECEEEECSCSSC
T ss_pred             cEEEEEEcCcccC
Confidence            9999999976544

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=7e-19  Score=120.03  Aligned_cols=84  Identities=19%  Similarity=0.360  Sum_probs=75.7

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      .+..+.++|||+|||.++++++    |+++|+.||.|..|.+..  ++.++|||||+|.+.++|.+|++.||+..+.|+.
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   87 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEE----LEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENI   87 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHH----HHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHH----HHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            4466789999999999999999    779999999999986553  6788999999999999999999999999999999


Q ss_pred             EEEEEccccc
Q 025973           88 MRIQYAKTKS   97 (245)
Q Consensus        88 i~v~~~~~~~   97 (245)
                      |+|.++.++.
T Consensus        88 l~v~~a~~~~   97 (100)
T 2do4_A           88 IKVAISNSGP   97 (100)
T ss_dssp             EEEEECCCCS
T ss_pred             EEEEECCCCC
Confidence            9999987654

>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=99.79  E-value=5.8e-19  Score=121.55  Aligned_cols=87  Identities=28%  Similarity=0.420  Sum_probs=78.3

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ...+..+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+..||+..+.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~   83 (105)
T 1x5u_A            8 PISERNQDATVYVGGLDEKVSEPL----LWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY   83 (105)
T ss_dssp             CCCCCCTTTEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCS
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeEC
Confidence            445567889999999999999999    779999999999997765   6778999999999999999999999999999


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |+.|+|.++.+...
T Consensus        84 g~~l~v~~a~~~~~   97 (105)
T 1x5u_A           84 GKPIRVNKASAHNK   97 (105)
T ss_dssp             SCBCEEEETTTTSC
T ss_pred             CeEEEEEECCCCCc
Confidence            99999999876543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.5e-19  Score=122.01  Aligned_cols=88  Identities=23%  Similarity=0.439  Sum_probs=78.5

Q ss_pred             ccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973            7 NQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus         7 ~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      .......+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++.||+..+
T Consensus         4 ~~~~~~~~~~~l~v~nLp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   79 (102)
T 1x5s_A            4 GSSGMASDEGKLFVGGLSFDTNEQS----LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSV   79 (102)
T ss_dssp             SCCCCCCCCSEEEEESCCTTCCHHH----HHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCT
T ss_pred             CCCCCCCCCCEEEEECCCCCCCHHH----HHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEE
Confidence            3455677899999999999999999    679999999999987765   567899999999999999999999999999


Q ss_pred             CCceEEEEEccccch
Q 025973           84 YDKPMRIQYAKTKSD   98 (245)
Q Consensus        84 ~g~~i~v~~~~~~~~   98 (245)
                      .|+.|+|.++.+...
T Consensus        80 ~g~~l~v~~a~~~~~   94 (102)
T 1x5s_A           80 DGRQIRVDQAGKSSD   94 (102)
T ss_dssp             TSCCCEEEEEECCCC
T ss_pred             CCeEEEEEECCCCCC
Confidence            999999999876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=1e-18  Score=119.91  Aligned_cols=77  Identities=23%  Similarity=0.380  Sum_probs=72.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|.|++|+|.||
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   92 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEC
Confidence            467889999999999999999999999999999998864     689999999999999999999999999999999998


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus        93 ~~   94 (103)
T 2cq0_A           93 KP   94 (103)
T ss_dssp             SC
T ss_pred             CC
Confidence            63

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=1.4e-18  Score=118.58  Aligned_cols=76  Identities=24%  Similarity=0.448  Sum_probs=71.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..+.++.++    +|||||+|.+.++|..|+..|||..|.|++|+|.||+
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   94 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISN   94 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            456789999999999999999999999999999999865    5899999999999999999999999999999999986

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=4.8e-19  Score=122.76  Aligned_cols=78  Identities=21%  Similarity=0.345  Sum_probs=72.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ....++|||+|||..+++++|+++|+.||.|..+.+..++   +|||||+|.+.++|.+|+..|||..|+|++|.|.+|+
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  105 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT  105 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            3466789999999999999999999999999999998763   6899999999999999999999999999999999997


Q ss_pred             C
Q 025973          245 K  245 (245)
Q Consensus       245 ~  245 (245)
                      .
T Consensus       106 ~  106 (109)
T 2err_A          106 A  106 (109)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=5.2e-19  Score=121.35  Aligned_cols=88  Identities=20%  Similarity=0.299  Sum_probs=77.6

Q ss_pred             ccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            7 NQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         7 ~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      ....+..+.++|||+|||..+++++    |+++|+.||.|..|.+.. .+.++|||||+|.+.++|.+|+..||+..+.|
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   82 (103)
T 2cqi_A            7 GMMEDDGQPRTLYVGNLSRDVTEVL----ILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILG   82 (103)
T ss_dssp             CCCCCSCCCCEEEEESCCTTCCHHH----HHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCCCCCEEEEeCCCccCCHHH----HHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCC
Confidence            3455677899999999999999999    779999999999997765 34468999999999999999999999999999


Q ss_pred             ceEEEEEccccch
Q 025973           86 KPMRIQYAKTKSD   98 (245)
Q Consensus        86 ~~i~v~~~~~~~~   98 (245)
                      +.|+|.++.+...
T Consensus        83 ~~l~V~~a~~~~~   95 (103)
T 2cqi_A           83 KEVKVNWATTPSS   95 (103)
T ss_dssp             EEEEEEECCCTTC
T ss_pred             CeEEEEECCCCcc
Confidence            9999999977543

>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=3e-19  Score=122.34  Aligned_cols=88  Identities=28%  Similarity=0.449  Sum_probs=78.6

Q ss_pred             ccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973            7 NQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus         7 ~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      .+.....+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++.||+..+
T Consensus         4 ~~~~~~~~~~~l~V~nLp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   79 (102)
T 2cqb_A            4 GSSGMATTKRVLYVGGLAEEVDDKV----LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL   79 (102)
T ss_dssp             CSSCSCCCCSCEEEESCCSSCCHHH----HHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEE
T ss_pred             CcCCcCCCCCEEEEeCCCCCCCHHH----HHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            3455677899999999999999999    779999999999987764   477899999999999999999999999999


Q ss_pred             CCceEEEEEccccch
Q 025973           84 YDKPMRIQYAKTKSD   98 (245)
Q Consensus        84 ~g~~i~v~~~~~~~~   98 (245)
                      .|+.|+|.++.+...
T Consensus        80 ~g~~l~V~~a~~~~~   94 (102)
T 2cqb_A           80 FGRTIRVNLAKPMRI   94 (102)
T ss_dssp             TTEEEEEEECCCCCC
T ss_pred             CCcEEEEEeCCCCCC
Confidence            999999999876543

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.79  E-value=8.3e-19  Score=118.77  Aligned_cols=76  Identities=21%  Similarity=0.416  Sum_probs=71.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      |+++|||+|||..+++++|+++|+.||.|.++.++.++     +|||||+|.+.++|..|+..|||..++|++|.|.||+
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            35789999999999999999999999999999998763     6899999999999999999999999999999999996


Q ss_pred             C
Q 025973          245 K  245 (245)
Q Consensus       245 ~  245 (245)
                      .
T Consensus        81 ~   81 (96)
T 2x1f_A           81 N   81 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=4.7e-19  Score=121.57  Aligned_cols=87  Identities=24%  Similarity=0.400  Sum_probs=77.9

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      +.++..+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+..||+..+.
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~   81 (103)
T 2dnm_A            6 SGPDVDGMITLKVDNLTYRTSPDS----LRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELD   81 (103)
T ss_dssp             CSSCCSCCCEEEEESCCTTCCHHH----HHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBT
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            445667789999999999999999    679999999999997764   4778999999999999999999999999999


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |+.|.|.++.....
T Consensus        82 g~~l~V~~a~~~~~   95 (103)
T 2dnm_A           82 GRELRVQVARYGRR   95 (103)
T ss_dssp             TBCCEEEECSSCCS
T ss_pred             CcEEEEEECCcCCC
Confidence            99999999876543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.79  E-value=2e-19  Score=122.66  Aligned_cols=83  Identities=16%  Similarity=0.181  Sum_probs=74.3

Q ss_pred             CCCCCeEEEcCCCc------ccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCc
Q 025973           12 ISPNNTIYINNLNE------KVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFP   82 (245)
Q Consensus        12 ~~~~~~l~V~nLp~------~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~   82 (245)
                      ...+++|||+|||.      ++++++    |+++|++||.|.+|.+.   .+|+++|||||+|.+.++|.+|++.|||..
T Consensus         3 ~~~~~~vfV~nLp~v~~~~~~~~~~~----L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~   78 (100)
T 3ns6_A            3 LGSDQYIVVNGAPVIPSAKVPVLKKA----LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKR   78 (100)
T ss_dssp             SCGGGEEEEESCCCCBGGGHHHHHHH----HHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCB
T ss_pred             CCcCcEEEEeCCCcCChHHHHHHHHH----HHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcc
Confidence            34578999999999      999999    77999999999998765   368899999999999999999999999999


Q ss_pred             cCC-ceEEEEEccccch
Q 025973           83 FYD-KPMRIQYAKTKSD   98 (245)
Q Consensus        83 ~~g-~~i~v~~~~~~~~   98 (245)
                      +.| +.|+|.++.+...
T Consensus        79 ~~g~r~l~V~~a~~~~~   95 (100)
T 3ns6_A           79 LDLKHRLFLYTMKDVER   95 (100)
T ss_dssp             SSSSCBCEEEESHHHHH
T ss_pred             cCCCeEEEEEECchhhh
Confidence            999 9999999876543

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=8.4e-19  Score=118.72  Aligned_cols=75  Identities=24%  Similarity=0.257  Sum_probs=71.1

Q ss_pred             CccEEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          170 PNNILFVQNVPHDTTPMALQ----MFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~----~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ..++|||+|||..+++++|+    ++|+.||.|.+|.++.++  +|||||+|.+.++|..|+..|||..|.|++|+|.+|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   87 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   87 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            55789999999999999999    999999999999999764  689999999999999999999999999999999999


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        88 ~   88 (96)
T 2dgx_A           88 T   88 (96)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.79  E-value=6.1e-19  Score=118.44  Aligned_cols=83  Identities=20%  Similarity=0.246  Sum_probs=75.5

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ...+.++|||+|||.++++++    |+++|+.||.|..|.+.. ++.++|||||+|.+.++|.+|+..||+..+.|+.|+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~----l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~   79 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKM----LKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREID   79 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHH----HHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            456789999999999999999    679999999999986654 778999999999999999999999999999999999


Q ss_pred             EEEccccc
Q 025973           90 IQYAKTKS   97 (245)
Q Consensus        90 v~~~~~~~   97 (245)
                      |.++.+..
T Consensus        80 v~~a~~~~   87 (92)
T 2dgv_A           80 VRIDRNAS   87 (92)
T ss_dssp             CEECSCCS
T ss_pred             EEEcCCCC
Confidence            99987654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.79  E-value=1.1e-18  Score=118.89  Aligned_cols=76  Identities=21%  Similarity=0.354  Sum_probs=71.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKE--------VRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQ  235 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~--------v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g  235 (245)
                      ++..+|||+|||..+++++|+++|+.||.|..        +.++.++     +|||||+|.+.++|..|++.|||..+.|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            46678999999999999999999999999999        9998763     6899999999999999999999999999


Q ss_pred             eEEEEEEec
Q 025973          236 QQLLITYAK  244 (245)
Q Consensus       236 ~~i~v~~ak  244 (245)
                      ++|+|.+|+
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999996

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=1.1e-18  Score=120.62  Aligned_cols=87  Identities=17%  Similarity=0.326  Sum_probs=77.9

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC----CCCeeeEEEEEecCHHHHHHHHHHH-cCCc
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK----TLKHKGQAWLVFKDVASATAAVEKM-QGFP   82 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~----~~~~kg~afV~F~~~~~A~~a~~~l-~~~~   82 (245)
                      ...+..+.++|||+|||..+++++    |+++|+.||.|..|.+..    ++.++|||||+|.+.++|.+|+..| |+..
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~   83 (107)
T 2cph_A            8 QVPKKQTTSKILVRNIPFQANQRE----IRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTH   83 (107)
T ss_dssp             SSCCSSCCCCEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCB
T ss_pred             ccccCCCCCEEEEeCCCCcCCHHH----HHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCe
Confidence            345567899999999999999999    779999999999997753    5778999999999999999999999 9999


Q ss_pred             cCCceEEEEEccccch
Q 025973           83 FYDKPMRIQYAKTKSD   98 (245)
Q Consensus        83 ~~g~~i~v~~~~~~~~   98 (245)
                      +.|+.|+|.++.++..
T Consensus        84 ~~g~~l~v~~a~~~~~   99 (107)
T 2cph_A           84 LYGRRLVLEWADSEVT   99 (107)
T ss_dssp             SSSCBCEEEECCCCCC
T ss_pred             ECCCEEEEEeCCCCCC
Confidence            9999999999977644

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.79  E-value=9.3e-19  Score=119.20  Aligned_cols=83  Identities=36%  Similarity=0.557  Sum_probs=74.5

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE--------EEec---CCCCeeeEEEEEecCHHHHHHHHH
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--------ILAF---KTLKHKGQAWLVFKDVASATAAVE   76 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~--------i~~~---~~~~~kg~afV~F~~~~~A~~a~~   76 (245)
                      ......+.++|||+|||.++++++    |+++|+.||.|.+        |.+.   .+|.++|||||+|.+.++|.+|++
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~   81 (99)
T 2la6_A            6 HHHSHSDNNTIFVQGLGENVTIES----VADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAID   81 (99)
T ss_dssp             SCCSCCCCSEEEEECCCSSCCHHH----HHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHH
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHH----HHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHH
Confidence            345677899999999999999999    7799999999988        7554   468899999999999999999999


Q ss_pred             HHcCCccCCceEEEEEcc
Q 025973           77 KMQGFPFYDKPMRIQYAK   94 (245)
Q Consensus        77 ~l~~~~~~g~~i~v~~~~   94 (245)
                      .|||..+.|+.|+|.+++
T Consensus        82 ~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           82 WFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             HHTTCBSSSSBCEEEECC
T ss_pred             HhCCCEeCCcEEEEEecC
Confidence            999999999999999874

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=7e-19  Score=120.70  Aligned_cols=87  Identities=26%  Similarity=0.461  Sum_probs=77.8

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ......+.++|||+|||.++++++    |+++|+.||.|..|.+.   .++.++|||||+|.+.++|.+|+..||+..+.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~   83 (103)
T 2cq0_A            8 PNRRADDNATIRVTNLSEDTRETD----LQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYD   83 (103)
T ss_dssp             SCCCCSSSEEEEEESCCTTCCHHH----HHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEET
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeC
Confidence            344567799999999999999999    77999999999998665   36789999999999999999999999999999


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |+.|+|.++.++..
T Consensus        84 g~~l~v~~a~~~~~   97 (103)
T 2cq0_A           84 HLILNVEWAKPSTN   97 (103)
T ss_dssp             TEECEEEESSCCCC
T ss_pred             CcEEEEEECCCCCC
Confidence            99999999876543

>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=99.79  E-value=7.6e-19  Score=118.70  Aligned_cols=76  Identities=14%  Similarity=0.242  Sum_probs=71.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.+..++    +|||||+|.++++|.+|+..|||..|.|++|.|.||+
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            466889999999999999999999999999999999864    6899999999999999999999999999999999997

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.79  E-value=1.9e-18  Score=120.90  Aligned_cols=77  Identities=21%  Similarity=0.374  Sum_probs=72.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ....+|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|+..|||..|.|++|.|.||
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   92 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            466789999999999999999999999999999999874     689999999999999999999999999999999999


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus        93 ~~   94 (115)
T 2dgo_A           93 TR   94 (115)
T ss_dssp             SC
T ss_pred             cC
Confidence            63

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=1.2e-18  Score=117.75  Aligned_cols=77  Identities=16%  Similarity=0.326  Sum_probs=71.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +++++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.+.++|..|+..|||..|.|++|+|.||
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            356789999999999999999999999999999999863     689999999999999999999999999999999998


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus        83 ~~   84 (95)
T 2dnz_A           83 TE   84 (95)
T ss_dssp             SC
T ss_pred             cc
Confidence            63

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.79  E-value=1.2e-18  Score=122.03  Aligned_cols=77  Identities=23%  Similarity=0.452  Sum_probs=71.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ++.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|+..|||..|.|++|+|.||
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            456789999999999999999999999999999998864     589999999999999999999999999999999998


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus       103 ~~  104 (115)
T 2cpz_A          103 RS  104 (115)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.79  E-value=1.3e-18  Score=119.69  Aligned_cols=76  Identities=18%  Similarity=0.267  Sum_probs=71.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|+..|||..|.|++|.|.||
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   92 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   92 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            466789999999999999999999999999999998864     689999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        93 ~   93 (105)
T 1x5u_A           93 S   93 (105)
T ss_dssp             T
T ss_pred             C
Confidence            6

>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=99.79  E-value=2.2e-18  Score=119.42  Aligned_cols=76  Identities=18%  Similarity=0.397  Sum_probs=71.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.+..+.  +|||||+|.+.++|..|++.||+..|.|++|.|.||+
T Consensus        20 ~~~~~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           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   97 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcc
Confidence            456789999999999999999999999999999998754  6899999999999999999999999999999999986

>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=99.79  E-value=1.3e-18  Score=118.43  Aligned_cols=77  Identities=19%  Similarity=0.242  Sum_probs=71.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|.|++|.|.+|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            356789999999999999999999999999999998764     689999999999999999999999999999999998


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus        86 ~~   87 (99)
T 1whw_A           86 TI   87 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.79  E-value=1.4e-18  Score=119.60  Aligned_cols=85  Identities=20%  Similarity=0.369  Sum_probs=75.9

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC--
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD--   85 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g--   85 (245)
                      ....+.++|||+|||.++++++    |+++|+.||.|..|.+.  +++.++|||||+|.+.++|.+|++.||+..+.|  
T Consensus        10 ~~~~~~~~l~v~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~   85 (105)
T 2dnh_A           10 SRGGRDRKLFVGMLNKQQSEED----VLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGA   85 (105)
T ss_dssp             CSCCCCCEEEEESCCTTCCHHH----HHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCC
Confidence            3456789999999999999999    77999999999998655  367889999999999999999999999999998  


Q ss_pred             -ceEEEEEccccch
Q 025973           86 -KPMRIQYAKTKSD   98 (245)
Q Consensus        86 -~~i~v~~~~~~~~   98 (245)
                       +.|+|.++.....
T Consensus        86 ~~~l~V~~a~~~~~   99 (105)
T 2dnh_A           86 SSSLVVKFADTDKE   99 (105)
T ss_dssp             SSCCEEEESCSSCC
T ss_pred             CccEEEEECccCcc
Confidence             9999999977654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=9.1e-19  Score=120.76  Aligned_cols=82  Identities=18%  Similarity=0.369  Sum_probs=74.3

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ...++++|||+|||.++++++    |+++|+.||.|..|.+.   .++.++|||||+|.+.++|.+|+..|||..+.|+.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   94 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEED----IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP   94 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSB
T ss_pred             CCCCCCEEEEeCCCCCCCHHH----HHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcE
Confidence            345678999999999999999    77999999999998765   35889999999999999999999999999999999


Q ss_pred             EEEEEcccc
Q 025973           88 MRIQYAKTK   96 (245)
Q Consensus        88 i~v~~~~~~   96 (245)
                      |+|.++.++
T Consensus        95 l~V~~a~~~  103 (106)
T 1p27_B           95 ISVDWCFVR  103 (106)
T ss_dssp             CEEEESEES
T ss_pred             EEEEeecCC
Confidence            999998765

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=1.6e-18  Score=119.68  Aligned_cols=77  Identities=23%  Similarity=0.463  Sum_probs=71.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC------CeEEEEEeCCHHHHHHHHHHh-CCCeeCCeEEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK------PGIAFVEYGDEMQATVAMQSL-QSLKIGQQQLLIT  241 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~------~g~afv~f~~~~~A~~A~~~l-~g~~~~g~~i~v~  241 (245)
                      .++++|||+|||..+++++|+++|+.||.|..|.++.+.      +|||||+|.+.++|.+|+..| ||..|.|++|.|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~   92 (107)
T 2cph_A           13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   92 (107)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEE
Confidence            456789999999999999999999999999999998872      699999999999999999999 9999999999999


Q ss_pred             EecC
Q 025973          242 YAKK  245 (245)
Q Consensus       242 ~ak~  245 (245)
                      ||+.
T Consensus        93 ~a~~   96 (107)
T 2cph_A           93 WADS   96 (107)
T ss_dssp             ECCC
T ss_pred             eCCC
Confidence            9963

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.79  E-value=2.2e-18  Score=118.57  Aligned_cols=76  Identities=20%  Similarity=0.364  Sum_probs=71.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCC---eEEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQ---QQLLIT  241 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g---~~i~v~  241 (245)
                      +++++|||+|||..+++++|+++|+.||.|..|.++.++    +|||||+|.+.++|.+|+..|||..+.|   ++|.|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            457889999999999999999999999999999999874    5899999999999999999999999997   999999


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      ||+
T Consensus        93 ~a~   95 (105)
T 2dnh_A           93 FAD   95 (105)
T ss_dssp             ESC
T ss_pred             ECc
Confidence            996

>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=99.78  E-value=5.4e-19  Score=123.27  Aligned_cols=83  Identities=22%  Similarity=0.293  Sum_probs=73.8

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcC--CccCCc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQG--FPFYDK   86 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~--~~~~g~   86 (245)
                      ....+++++|||+|||.++++++    |+++|++||.|.+|.+.++   ||||||+|.+.++|.+|++.|++  ..+.|+
T Consensus        25 ~~~~~ps~~LfVgNLp~~vte~d----L~~lF~~fG~V~~v~i~~~---kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr   97 (119)
T 2ad9_A           25 RSAGVPSRVIHIRKLPIDVTEGE----VISLGLPFGKVTNLLMLKG---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ   97 (119)
T ss_dssp             TSCSSCCSEEEEESCCTTCCHHH----HHHHHTTTSCCCEEEEEGG---GTEEEEECSCHHHHHHHHHHHHHHCCCBTTB
T ss_pred             cccCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhccCCceECCe
Confidence            34567899999999999999999    6799999999999988754   79999999999999999998874  689999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      +|.|.+++.+..
T Consensus        98 ~l~V~~a~~k~~  109 (119)
T 2ad9_A           98 PIYIQFSNHKEL  109 (119)
T ss_dssp             CCEEEECSSSSC
T ss_pred             EEEEEEccCCCC
Confidence            999999976544

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.78  E-value=1.9e-19  Score=123.09  Aligned_cols=76  Identities=20%  Similarity=0.368  Sum_probs=70.4

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEccc
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKT   95 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~~   95 (245)
                      ++|||+|||.++++++    |+++|+.||.|..|.+..+  ++|||||+|.+.++|.+|++.||+..+.|+.|+|.++.+
T Consensus         1 ~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   74 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGE----LERAFSYYGPLRTVWIARN--PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTG   74 (101)
T ss_dssp             CEEEEECCCSSCSHHH----HHHHHHHHCCCSEEEEESS--SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSS
T ss_pred             CEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEeeC--CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccC
Confidence            5899999999999999    6799999999999988766  789999999999999999999999999999999999876


Q ss_pred             cc
Q 025973           96 KS   97 (245)
Q Consensus        96 ~~   97 (245)
                      ..
T Consensus        75 ~~   76 (101)
T 2hvz_A           75 MP   76 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.78  E-value=4.8e-19  Score=120.46  Aligned_cols=81  Identities=20%  Similarity=0.310  Sum_probs=72.0

Q ss_pred             CCCCCCeEEEcCCCc-ccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCC--ccCCce
Q 025973           11 EISPNNTIYINNLNE-KVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGF--PFYDKP   87 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~-~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~--~~~g~~   87 (245)
                      ...++++|||+|||. ++++++    |+++|++||.|.+|++.++   +|||||+|.+.++|..|++.||+.  .+.|++
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~d----L~~lF~~fG~V~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~   83 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQ----LLQLVEPFGVISNHLILNK---INEAFIEMATTEDAQAAVDYYTTTPALVFGKP   83 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHH----HHTTTGGGSCEEEEEECSS---SSCEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCcCCHHH----HHHHHHhcCCEEEEEEEcC---CCEEEEEECCHHHHHHHHHHHcCCCceECCcE
Confidence            456899999999999 999999    7799999999999988754   589999999999999999999864  489999


Q ss_pred             EEEEEccccch
Q 025973           88 MRIQYAKTKSD   98 (245)
Q Consensus        88 i~v~~~~~~~~   98 (245)
                      |.|.++.....
T Consensus        84 l~V~~a~~~~~   94 (102)
T 1x4d_A           84 VRVHLSQKYKR   94 (102)
T ss_dssp             CEEEEECCCTT
T ss_pred             EEEEECCCCCC
Confidence            99999976443

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=4.9e-19  Score=120.36  Aligned_cols=82  Identities=22%  Similarity=0.368  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC------CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK------TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~------~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .++++|||+|||.++++++    |+++|+.||.|..|.+..      ++.++|||||+|.+.++|.+|+..||+..+.|+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   78 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEET----LKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGH   78 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            5689999999999999999    679999999999987663      447899999999999999999999999999999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|.|.++.+...
T Consensus        79 ~l~V~~a~~~~~   90 (98)
T 2cpf_A           79 KLEVRISERATK   90 (98)
T ss_dssp             ECEEECSSCSSC
T ss_pred             EEEEEEccCCCC
Confidence            999999876543

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.5e-18  Score=119.02  Aligned_cols=87  Identities=22%  Similarity=0.351  Sum_probs=77.2

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCC-CCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKT-LKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~-~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ......+.++|||+|||.++++++    |+++|+.||.|..|.+..+ +.++|||||+|.+.++|.+|+..||+..+.|+
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   83 (103)
T 2cq3_A            8 NSESKSTPKRLHVSNIPFRFRDPD----LRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGR   83 (103)
T ss_dssp             CSCCSCCCCEEEEESCCTTCCHHH----HHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            445677889999999999999999    7799999999999877643 34789999999999999999999999999999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|+|.++.++..
T Consensus        84 ~l~v~~a~~~~~   95 (103)
T 2cq3_A           84 KIEVNNATARVM   95 (103)
T ss_dssp             ECEEEECCSSCC
T ss_pred             EEEEEEcccCCC
Confidence            999999977644

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.78  E-value=1.4e-18  Score=121.67  Aligned_cols=87  Identities=24%  Similarity=0.405  Sum_probs=78.0

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ...+..+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++.||+..+.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~   83 (115)
T 2dgo_A            8 QKKDTSNHFHVFVGDLSPEITTED----IKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG   83 (115)
T ss_dssp             SCCCSTTCEEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEET
T ss_pred             CCCCCCCCcEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            445677899999999999999999    779999999999986653   6788999999999999999999999999999


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |+.|+|.++..+..
T Consensus        84 g~~l~V~~a~~~~~   97 (115)
T 2dgo_A           84 GRQIRTNWATRKPP   97 (115)
T ss_dssp             TEECEEEESSCCCC
T ss_pred             CEEEEEEEccCCCC
Confidence            99999999976644

>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=99.78  E-value=6.9e-19  Score=122.30  Aligned_cols=75  Identities=24%  Similarity=0.356  Sum_probs=70.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .+++|||+|||..+++++|+++|+.||.|..|.+.+.+ |||||+|.+.++|..|+..|||..|.|++|.|+||+.
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-ITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSS-SCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCC-CEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            46789999999999999999999999999999998765 8999999999999999999999999999999999963

>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=99.78  E-value=2.2e-18  Score=116.79  Aligned_cols=75  Identities=13%  Similarity=0.267  Sum_probs=70.1

Q ss_pred             CCCccEEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          168 APPNNILFVQNVPH-DTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       168 ~~~~~~l~v~nl~~-~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .+++++|||+|||. .+++++|+++|+.||.|..+.+.   +|||||+|.+.++|..|+..|||..++|++|.|+||+.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC---SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCC
Confidence            35678899999998 99999999999999999999984   59999999999999999999999999999999999973

>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=1.3e-18  Score=120.92  Aligned_cols=86  Identities=21%  Similarity=0.382  Sum_probs=77.5

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHc------
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQ------   79 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~------   79 (245)
                      ..+..+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+..||      
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~   84 (111)
T 1x4h_A            9 PSDVTEGKTVFIRNLSFDSEEEA----LGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGG   84 (111)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTC
T ss_pred             CCcCCCCCEEEEECCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccC
Confidence            45567799999999999999999    779999999999998774   57789999999999999999999999      


Q ss_pred             CCccCCceEEEEEccccch
Q 025973           80 GFPFYDKPMRIQYAKTKSD   98 (245)
Q Consensus        80 ~~~~~g~~i~v~~~~~~~~   98 (245)
                      +..+.|+.|+|.++.++..
T Consensus        85 ~~~~~g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           85 GLKLDGRQLKVDLAVTRDE  103 (111)
T ss_dssp             CEESSSCEEEEECCCCCCC
T ss_pred             CcEEcCEEEEEEECCCCcc
Confidence            9999999999999976644

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.2e-18  Score=119.27  Aligned_cols=77  Identities=26%  Similarity=0.413  Sum_probs=72.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.++++|..|+..|||..|.|++|+|.||
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   89 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            456789999999999999999999999999999998863     689999999999999999999999999999999999


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus        90 ~~   91 (102)
T 1x5s_A           90 GK   91 (102)
T ss_dssp             EC
T ss_pred             CC
Confidence            74

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.78  E-value=1.8e-18  Score=119.64  Aligned_cols=77  Identities=16%  Similarity=0.318  Sum_probs=71.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ++.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|++.|||..|.|++|+|.+|
T Consensus        24 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a  103 (108)
T 2jrs_A           24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV  103 (108)
T ss_dssp             SSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            456789999999999999999999999999999998753     689999999999999999999999999999999998


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus       104 ~~  105 (108)
T 2jrs_A          104 TE  105 (108)
T ss_dssp             CS
T ss_pred             cc
Confidence            73

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.9e-18  Score=115.56  Aligned_cols=74  Identities=22%  Similarity=0.370  Sum_probs=69.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..+.+.   +|||||+|.+.++|..|+..|||..+.|++|+|.||+.
T Consensus         6 ~~~~~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            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKN   79 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCC
Confidence            466789999999999999999999999999999998   58999999999999999999999999999999999863

>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=99.78  E-value=9.5e-19  Score=122.50  Aligned_cols=86  Identities=24%  Similarity=0.404  Sum_probs=76.3

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      ..+..+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++.||+..+.|
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   94 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQD----LLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM   94 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHH----HHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECC
Confidence            34456789999999999999999    679999999998876543   67899999999999999999999999999999


Q ss_pred             ceEEEEEccccch
Q 025973           86 KPMRIQYAKTKSD   98 (245)
Q Consensus        86 ~~i~v~~~~~~~~   98 (245)
                      +.|+|.++.++..
T Consensus        95 ~~l~V~~a~~~~~  107 (115)
T 2cpz_A           95 KRLKVQLKRSKND  107 (115)
T ss_dssp             EECEEECCCCSCC
T ss_pred             EEEEEEEcCCCCc
Confidence            9999999876644

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.2e-18  Score=119.23  Aligned_cols=76  Identities=18%  Similarity=0.347  Sum_probs=71.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|.|++|.|.||
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            456789999999999999999999999999999998762     689999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        90 ~   90 (102)
T 2cqb_A           90 K   90 (102)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.5e-18  Score=119.00  Aligned_cols=76  Identities=22%  Similarity=0.333  Sum_probs=71.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|.|++|.|.||
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            356789999999999999999999999999999998763     689999999999999999999999999999999999


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        91 ~   91 (103)
T 2dnm_A           91 R   91 (103)
T ss_dssp             S
T ss_pred             C
Confidence            7

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.78  E-value=9.5e-19  Score=118.21  Aligned_cols=82  Identities=22%  Similarity=0.432  Sum_probs=73.7

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ....+.++|||+|||..+++++    |+++|+.||.|..|.+..  ++.++|||||+|.+.++|.+|++.||+..+.|+.
T Consensus        11 ~~~~~~~~l~v~nlp~~~~~~~----l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (95)
T 2ywk_A           11 AQEEADRTVFVGNLEARVREEI----LYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRP   86 (95)
T ss_dssp             -CTTGGGEEEEECCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHH----HHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCE
Confidence            4466789999999999999999    779999999999986653  5788999999999999999999999999999999


Q ss_pred             EEEEEccc
Q 025973           88 MRIQYAKT   95 (245)
Q Consensus        88 i~v~~~~~   95 (245)
                      |+|.+++.
T Consensus        87 l~V~~a~~   94 (95)
T 2ywk_A           87 INVSGPSS   94 (95)
T ss_dssp             CEEECCCC
T ss_pred             EEEEEcCC
Confidence            99999753

>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=99.78  E-value=8.4e-19  Score=122.85  Aligned_cols=84  Identities=32%  Similarity=0.483  Sum_probs=75.5

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      +..+.++|||+|||.++++++    |+++|+.||.|..|.+..  ++.++|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l   78 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKM----LKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAI   78 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHH----HHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            345679999999999999999    679999999999886654  67889999999999999999999999999999999


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      .|.+++....
T Consensus        79 ~V~~a~~~~~   88 (116)
T 2fy1_A           79 KVEQAKKPSF   88 (116)
T ss_dssp             EEEECCCSSC
T ss_pred             EEEECCCCCC
Confidence            9999976543

>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=2.1e-19  Score=122.90  Aligned_cols=76  Identities=24%  Similarity=0.414  Sum_probs=71.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      +.+++|||+|||..+++++|+++|+.||.|.++.+...+ |||||+|.+.++|..|+..|||..++|++|+|.||+.
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~-g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK-GCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTT-TEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCC-CEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            356789999999999999999999999999999998665 9999999999999999999999999999999999973

>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=1.5e-18  Score=119.90  Aligned_cols=73  Identities=32%  Similarity=0.530  Sum_probs=69.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++++|||+|||..+++++|+++|+.||.|..+.+.   +|||||+|.+.++|..|+..|||..|+|++|.|.||+
T Consensus        29 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  101 (108)
T 2jvo_A           29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK  101 (108)
T ss_dssp             CSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            466789999999999999999999999999999998   5999999999999999999999999999999999986

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=3.3e-18  Score=116.44  Aligned_cols=75  Identities=24%  Similarity=0.438  Sum_probs=70.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|+. ||+..|.|++|.|.||
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            456789999999999999999999999999999998763     6899999999999999998 9999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        87 ~   87 (99)
T 2dgs_A           87 E   87 (99)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=7.3e-19  Score=119.72  Aligned_cols=85  Identities=16%  Similarity=0.339  Sum_probs=75.8

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeE-EEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL-EILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~-~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      ++....++++|||+|||.++++++    |+++|+.||.|. .|.+.   .++.++|||||+|.+.++|.+|++.||+..+
T Consensus         2 ss~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~   77 (99)
T 2div_A            2 SSGSSGMAASLWMGDLEPYMDENF----ISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPL   77 (99)
T ss_dssp             CCCCCSSSSEEEECSCCTTCCHHH----HHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEE
T ss_pred             CCCCCCCccEEEEeCCCCCCCHHH----HHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCcc
Confidence            345567899999999999999999    679999999998 87654   3678999999999999999999999999999


Q ss_pred             CCce----EEEEEcccc
Q 025973           84 YDKP----MRIQYAKTK   96 (245)
Q Consensus        84 ~g~~----i~v~~~~~~   96 (245)
                      .|+.    |+|.|+.+.
T Consensus        78 ~g~~~~~~l~v~~a~~~   94 (99)
T 2div_A           78 PGATPAKRFKLNYATYS   94 (99)
T ss_dssp             SSCSSCEECCEEETTCC
T ss_pred             CCCCcceeEEEeecCCC
Confidence            9999    999998764

>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=1.6e-18  Score=119.76  Aligned_cols=82  Identities=24%  Similarity=0.441  Sum_probs=74.2

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .....++++|||+|||..+++++    |+++|+.||.|..|.+.  .++.++|||||+|.+.++|.+|++.||+..+.|+
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   98 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDAD----IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR   98 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            45667899999999999999999    67999999999987654  4788899999999999999999999999999999


Q ss_pred             eEEEEEcc
Q 025973           87 PMRIQYAK   94 (245)
Q Consensus        87 ~i~v~~~~   94 (245)
                      .|+|.++.
T Consensus        99 ~l~V~~a~  106 (107)
T 3ulh_A           99 PMNIQLVT  106 (107)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEeC
Confidence            99999975

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=3e-18  Score=117.50  Aligned_cols=76  Identities=20%  Similarity=0.305  Sum_probs=71.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC---CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA---KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~---~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.+   .+|||||+|.+.++|..|+..|||..|.|++|.|.||+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ   91 (103)
T ss_dssp             SSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEec
Confidence            35678999999999999999999999999999999975   26899999999999999999999999999999999986

>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=99.78  E-value=2.2e-18  Score=116.87  Aligned_cols=82  Identities=27%  Similarity=0.539  Sum_probs=74.3

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC--Cc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY--DK   86 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~--g~   86 (245)
                      .....+.++|||+|||.++++++    |+++|+.||.|..|.+...   +|||||+|.+.++|.+|++.||+..+.  |+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~v~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~   83 (97)
T 1why_A           11 YGKANPTTRLWVGGLGPNTSLAA----LAREFDRFGSIRTIDHVKG---DSFAYIQYESLDAAQAACAKMRGFPLGGPDR   83 (97)
T ss_dssp             CCCCCCCSCEEEECCCSSCCHHH----HHHHHHTTSCEEEEEECSS---SCCEEEEESSHHHHHHHHHHHTTCBCSSSSC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEeCC---CCEEEEEECCHHHHHHHHHHHCCCEeCCCCc
Confidence            34567789999999999999999    7799999999999988754   789999999999999999999999999  99


Q ss_pred             eEEEEEccccc
Q 025973           87 PMRIQYAKTKS   97 (245)
Q Consensus        87 ~i~v~~~~~~~   97 (245)
                      .|+|.++.++.
T Consensus        84 ~l~V~~a~~~~   94 (97)
T 1why_A           84 RLRVDFAKSGP   94 (97)
T ss_dssp             BCEEEECCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999997753

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.77  E-value=1.3e-19  Score=130.31  Aligned_cols=75  Identities=24%  Similarity=0.388  Sum_probs=70.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ++++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|+..|||..|.|++|+|.||+
T Consensus        46 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~  125 (135)
T 2lea_A           46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR  125 (135)
T ss_dssp             GCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45679999999999999999999999999999998753     6899999999999999999999999999999999997

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=7.3e-19  Score=121.81  Aligned_cols=86  Identities=22%  Similarity=0.356  Sum_probs=76.3

Q ss_pred             ccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            7 NQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         7 ~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      .......+.++|||+|||.++++++    |+++|+.||.|..|.+.. .+.++|||||+|.+.++|.+|+..|||..+.|
T Consensus        21 ~~~~~~~~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g   96 (109)
T 2err_A           21 MNTENKSQPKRLHVSNIPFRFRDPD----LRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEG   96 (109)
T ss_dssp             -CCSCTTCCCEEEEESCCTTCCHHH----HHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETT
T ss_pred             CCccCCCCCCEEEEECCCCcCCHHH----HHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3455677889999999999999999    779999999999987764 34578999999999999999999999999999


Q ss_pred             ceEEEEEcccc
Q 025973           86 KPMRIQYAKTK   96 (245)
Q Consensus        86 ~~i~v~~~~~~   96 (245)
                      +.|+|.++.++
T Consensus        97 ~~l~V~~a~~~  107 (109)
T 2err_A           97 RKIEVNNATAR  107 (109)
T ss_dssp             EECEEEECCCS
T ss_pred             EEEEEEECCCC
Confidence            99999998765

>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=99.77  E-value=1.6e-18  Score=120.31  Aligned_cols=84  Identities=19%  Similarity=0.305  Sum_probs=75.5

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ....++++|||+|||..+++++    |+++|+.||.|..|.+..   +|.++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   96 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDE----IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ   96 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHH----HHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            3456678999999999999999    779999999999997763   678899999999999999999999999999999


Q ss_pred             eEEEEEccccc
Q 025973           87 PMRIQYAKTKS   97 (245)
Q Consensus        87 ~i~v~~~~~~~   97 (245)
                      .|+|.++.++.
T Consensus        97 ~l~V~~a~~~~  107 (110)
T 1oo0_B           97 TIQVDWCFVKG  107 (110)
T ss_dssp             ECEEEESEESS
T ss_pred             EEEEEEcccCC
Confidence            99999987653

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.77  E-value=1.4e-18  Score=123.21  Aligned_cols=77  Identities=16%  Similarity=0.328  Sum_probs=70.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEecC--CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQ----MFFSQFPGFKEVRMVEA--KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~----~~f~~~g~v~~v~l~~~--~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      +++++|||+|||..+++++|+    ++|+.||.|.+|.+..+  .+|||||+|.+.++|..|+..|||..|.|++|+|.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~  106 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF  106 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEE
Confidence            457789999999999999876    79999999999988763  379999999999999999999999999999999999


Q ss_pred             ecC
Q 025973          243 AKK  245 (245)
Q Consensus       243 ak~  245 (245)
                      |+.
T Consensus       107 a~~  109 (127)
T 2a3j_A          107 SET  109 (127)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            973

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.77  E-value=2e-18  Score=115.89  Aligned_cols=77  Identities=17%  Similarity=0.229  Sum_probs=71.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..+.+..+.   +|||||+|.+.++|..|+..|||..|.|++|.|.||+.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   85 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRN   85 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            356789999999999999999999999999999998742   68999999999999999999999999999999999863

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=2e-18  Score=118.19  Aligned_cols=87  Identities=21%  Similarity=0.283  Sum_probs=78.3

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ......+.++|||+|||.++++++    |+++|+.|+.|..+....++.++|||||+|.+.++|.+|+..||+..+.|+.
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 2fc8_A            8 PNARSQPSKTLFVKGLSEDTTEET----LKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNK   83 (102)
T ss_dssp             TSSSSCCCSSEEEECCCTTCCHHH----HHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCCEEEEeCCCCccCHHH----HHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            445677899999999999999999    6699999987777777778999999999999999999999999999999999


Q ss_pred             EEEEEccccch
Q 025973           88 MRIQYAKTKSD   98 (245)
Q Consensus        88 i~v~~~~~~~~   98 (245)
                      |+|.+++++..
T Consensus        84 l~V~~a~~~~~   94 (102)
T 2fc8_A           84 VTLDWAKPKGE   94 (102)
T ss_dssp             CEEEECCCCCS
T ss_pred             EEEEEecCCCC
Confidence            99999987654

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.77  E-value=1.5e-18  Score=119.64  Aligned_cols=87  Identities=24%  Similarity=0.421  Sum_probs=77.2

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCcc-
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPF-   83 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~-   83 (245)
                      ......+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+..||+..+ 
T Consensus         6 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~   81 (106)
T 2dgp_A            6 SGMKDHDAIKLFIGQIPRNLDEKD----LKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTL   81 (106)
T ss_dssp             CSCCCTTCEEEEEESCCTTCCHHH----HHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCccc
Confidence            345567789999999999999999    679999999999998775   577899999999999999999999999887 


Q ss_pred             --CCceEEEEEccccch
Q 025973           84 --YDKPMRIQYAKTKSD   98 (245)
Q Consensus        84 --~g~~i~v~~~~~~~~   98 (245)
                        .|+.|+|.++.....
T Consensus        82 ~~~g~~l~v~~a~~~~~   98 (106)
T 2dgp_A           82 PGMNRPIQVKPADSESR   98 (106)
T ss_dssp             TTCSSCCEEEECCCCSC
T ss_pred             CCCCceEEEEECCcccc
Confidence              889999999876543

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.77  E-value=1.2e-18  Score=124.31  Aligned_cols=85  Identities=22%  Similarity=0.410  Sum_probs=76.7

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      ..+..++++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+..||+..+.|
T Consensus        40 ~~~~~~~~~l~V~nLp~~~te~~----L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g  115 (129)
T 2kxn_B           40 RANPDPNCCLGVFGLSLYTTERD----LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG  115 (129)
T ss_dssp             SSCCCCSSCBCEETCTTSCCHHH----HHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            34567899999999999999999    779999999999987764   57889999999999999999999999999999


Q ss_pred             ceEEEEEccccc
Q 025973           86 KPMRIQYAKTKS   97 (245)
Q Consensus        86 ~~i~v~~~~~~~   97 (245)
                      +.|.|.++.++.
T Consensus       116 ~~l~V~~a~~~~  127 (129)
T 2kxn_B          116 RRIRVDFSITKR  127 (129)
T ss_dssp             SCCEESCCSSSS
T ss_pred             EEEEEEEecCCC
Confidence            999999987653

>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=99.77  E-value=2.5e-18  Score=116.57  Aligned_cols=81  Identities=17%  Similarity=0.280  Sum_probs=71.2

Q ss_pred             ccCCCCCCCCeEEEcCCCc-ccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            7 NQGNEISPNNTIYINNLNE-KVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         7 ~~~~~~~~~~~l~V~nLp~-~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      ......+++++|||+|||. ++++++    |+++|+.||.|..|.+.     +|||||+|.+.++|.+|+..|||..+.|
T Consensus        14 ~~~~~~~~~~~l~V~nLp~~~~t~~~----L~~~F~~~G~v~~v~i~-----~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (97)
T 2xnq_A           14 LVPRGSHMKSRLFIGNLPLKNVSKED----LFRIFSPYGHIMQINIK-----NAFGFIQFDNPQSVRDAIEXESQEMNFG   84 (97)
T ss_dssp             -----CCTTCEEEEESCCSSCCCHHH----HHHHHGGGSCEEEEEEC-----SSEEEEEESSHHHHHHHHHHHTTSEETT
T ss_pred             cccCCCCCCCEEEEeCCCcccCCHHH----HHHHHHhcCCEEEEEEe-----CCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3445677899999999998 999999    77999999999999884     6899999999999999999999999999


Q ss_pred             ceEEEEEcccc
Q 025973           86 KPMRIQYAKTK   96 (245)
Q Consensus        86 ~~i~v~~~~~~   96 (245)
                      +.|+|.+++..
T Consensus        85 ~~l~V~~a~~~   95 (97)
T 2xnq_A           85 KKLILEVSSSN   95 (97)
T ss_dssp             EECEEEECCCC
T ss_pred             EEEEEEecCCC
Confidence            99999998764

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.5e-18  Score=116.00  Aligned_cols=80  Identities=20%  Similarity=0.385  Sum_probs=73.1

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ....+.++|||+|||.++++++    |+++|+.||.|..|.+.     +|||||+|.+.++|.+|+..||+..+.|+.|+
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   73 (90)
T 2dnq_A            3 SGSSGMVKLFIGNLPREATEQE----IRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNIN   73 (90)
T ss_dssp             SCSSCCEEEEEESCCSSCCHHH----HHHHHHTSSCEEEEEEE-----TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHhcCCccCCcEEE
Confidence            3467889999999999999999    77999999999999876     58999999999999999999999999999999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |.++.++..
T Consensus        74 v~~a~~~~~   82 (90)
T 2dnq_A           74 VEASKNKSK   82 (90)
T ss_dssp             EECSSCCCC
T ss_pred             EEECCCCCC
Confidence            999876644

>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=5.1e-18  Score=117.36  Aligned_cols=73  Identities=15%  Similarity=0.171  Sum_probs=70.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCC-----eEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQ-----QQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g-----~~i~v~~ak  244 (245)
                      ...+|||+|||..+++++|+++|+.||.|..|.++.+  |||||+|.+.++|..|++.|||..|.|     ++|.|.+|+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~   91 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   91 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCC
Confidence            4678999999999999999999999999999999987  899999999999999999999999999     999999986

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.77  E-value=2.2e-18  Score=114.45  Aligned_cols=81  Identities=16%  Similarity=0.323  Sum_probs=70.8

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ......+.++|||+|||.++++++    |+++|+.||.|..|.+.   .++.++|||||+|.+.++|.+|++ +++..+.
T Consensus         4 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~   78 (87)
T 3s7r_A            4 ASKNEEDAGKMFVGGLSWDTSKKD----LKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLD   78 (87)
T ss_dssp             ---CCSCTTEEEEECCCTTCCHHH----HHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEET
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEEC
Confidence            345567889999999999999999    67999999999998665   368899999999999999999997 6888899


Q ss_pred             CceEEEEEc
Q 025973           85 DKPMRIQYA   93 (245)
Q Consensus        85 g~~i~v~~~   93 (245)
                      |+.|.|.+|
T Consensus        79 g~~i~v~~A   87 (87)
T 3s7r_A           79 GRVIDPKKA   87 (87)
T ss_dssp             TEEEEEEEC
T ss_pred             CEEEEEEeC
Confidence            999999875

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.77  E-value=1.2e-18  Score=117.31  Aligned_cols=80  Identities=16%  Similarity=0.347  Sum_probs=69.4

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCC--eEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCC----c
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGT--ILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGF----P   82 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~--v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~----~   82 (245)
                      ...=.+|||+|||+.+|+++    |+++|++||.  |.+|++.   .+|.+||||||+|.+.++|.+|++.||+.    .
T Consensus         6 ~~~m~tlfV~nL~~~~tee~----L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~   81 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDS----IMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLK   81 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHH----HHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEE
T ss_pred             CCccCEEEEeCCCCcCCHHH----HHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCce
Confidence            44557899999999999999    7799999996  4466554   46889999999999999999999999996    4


Q ss_pred             cCCceEEEEEccc
Q 025973           83 FYDKPMRIQYAKT   95 (245)
Q Consensus        83 ~~g~~i~v~~~~~   95 (245)
                      +.|+.|.|.||+.
T Consensus        82 i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           82 IDGKTIGVDFAKS   94 (95)
T ss_dssp             ETTEEEEEEECCC
T ss_pred             ECCEEEEEEEccC
Confidence            7899999999864

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.77  E-value=4.4e-18  Score=117.48  Aligned_cols=76  Identities=18%  Similarity=0.289  Sum_probs=71.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++.+|||+|||..+++++|+++|+.||.|..|.++.++    +|||||+|.+.++|.+|+..|||..|.|++|.|+||+
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            467889999999999999999999999999999999763    6899999999999999999999999999999999985

>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=99.77  E-value=2.1e-18  Score=119.50  Aligned_cols=76  Identities=22%  Similarity=0.370  Sum_probs=71.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      +..++|||+|||..+++++|+++|+.||.|..|.++.++ |||||+|.+.++|..|+..|||..|.|++|.|.||+.
T Consensus        23 ~~~~~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           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   98 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCC-CEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCC
Confidence            356789999999999999999999999999999999884 9999999999999999999999999999999999873

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=7.1e-18  Score=117.79  Aligned_cols=76  Identities=17%  Similarity=0.214  Sum_probs=71.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++++|||+|||..+++++|+++|+.||.|.+|.++.++    +|||||+|.+.++|..|+..|||..|.|++|.|.||+
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   92 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDE   92 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcc
Confidence            456789999999999999999999999999999999864    5899999999999999999999999999999999986

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.6e-18  Score=117.39  Aligned_cols=75  Identities=16%  Similarity=0.304  Sum_probs=70.6

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEV-RMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v-~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ++++|||+|||..+++++|+++|+.||.|..+ .++.++     +|||||+|.++++|..|+..|||..|.|++|.|.||
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            56789999999999999999999999999998 888762     689999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        84 ~   84 (96)
T 1x5t_A           84 F   84 (96)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=99.77  E-value=3.2e-18  Score=118.78  Aligned_cols=76  Identities=24%  Similarity=0.349  Sum_probs=71.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.+.++|..|+..|||..|.|++|.|.||
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            466889999999999999999999999999999998764     689999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       104 ~  104 (110)
T 1oo0_B          104 F  104 (110)
T ss_dssp             E
T ss_pred             c
Confidence            5

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=6e-19  Score=119.44  Aligned_cols=82  Identities=30%  Similarity=0.521  Sum_probs=74.0

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE-EecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i-~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .++++|||+|||.++++++    |+++|+.||.|..| .+..   ++.++|||||+|.+.++|.+|+..||+..+.|+.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   78 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKL----LYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPI   78 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHH----HHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            5689999999999999999    77999999999877 6554   67789999999999999999999999999999999


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      +|.++.++..
T Consensus        79 ~v~~a~~~~~   88 (96)
T 1x5t_A           79 TVSYAFKKDS   88 (96)
T ss_dssp             EEEESCCCCC
T ss_pred             EEEEecccCC
Confidence            9999976543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=2.7e-18  Score=118.36  Aligned_cols=76  Identities=22%  Similarity=0.347  Sum_probs=71.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|+|++|.|.||
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            356789999999999999999999999999999998764     589999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       101 ~  101 (106)
T 1p27_B          101 F  101 (106)
T ss_dssp             E
T ss_pred             c
Confidence            6

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.5e-18  Score=118.67  Aligned_cols=85  Identities=18%  Similarity=0.254  Sum_probs=74.8

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ..+...+.++|||+|||.++++++    |+++|+.||.|. +....++.++|||||+|.+.++|.+|+..||+..+.|+.
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~g~v~-~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   82 (101)
T 2fc9_A            8 NSTWSGESKTLVLSNLSYSATEET----LQEVFEKATFIK-VPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRA   82 (101)
T ss_dssp             CCCCSCCCSEEEEESCCTTCCHHH----HHHHCSSCSEEE-CCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEE
T ss_pred             CccCCCCCCEEEEeCCCCCCCHHH----HHHHHHhCCEEE-EEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeE
Confidence            445567899999999999999999    679999999984 333367889999999999999999999999999999999


Q ss_pred             EEEEEccccc
Q 025973           88 MRIQYAKTKS   97 (245)
Q Consensus        88 i~v~~~~~~~   97 (245)
                      |+|.++.++.
T Consensus        83 l~v~~a~~~~   92 (101)
T 2fc9_A           83 IRLELQGPRG   92 (101)
T ss_dssp             EEEEECSSCC
T ss_pred             EEEEEcCCCC
Confidence            9999987654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.77  E-value=2.9e-18  Score=121.05  Aligned_cols=72  Identities=25%  Similarity=0.297  Sum_probs=68.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeE-EEEEeCCHHHHHHHHHHhCCCeeCC--eEEEEEEec
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGI-AFVEYGDEMQATVAMQSLQSLKIGQ--QQLLITYAK  244 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~-afv~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~ak  244 (245)
                      .|||+||+..+|+++|+++|+.||.|.+|.++...+|+ |||+|.+.++|..|++.|||..|.|  ++|+|+|||
T Consensus        30 ~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak  104 (130)
T 3zzy_A           30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  104 (130)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECS
T ss_pred             EEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecC
Confidence            46799999999999999999999999999998776787 9999999999999999999999988  999999997

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.77  E-value=3e-18  Score=127.63  Aligned_cols=76  Identities=24%  Similarity=0.349  Sum_probs=71.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++++|||+|||..+++++|..+|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|.|++|.|.||
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  149 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  149 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356789999999999999999999999999999999863     699999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       150 ~  150 (165)
T 1rk8_A          150 F  150 (165)
T ss_dssp             E
T ss_pred             c
Confidence            5

>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=99.77  E-value=2.6e-18  Score=118.07  Aligned_cols=83  Identities=22%  Similarity=0.326  Sum_probs=74.3

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCC----CCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKT----LKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~----~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      .+..+.++|||+|||.++++++    |+++|+.|| |..|.+..+    +.++|||||+|.+.++|.+|+ .||+..+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g   83 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEES----IKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN   83 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHH----HHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETT
T ss_pred             CCCCCCCEEEEeCCCCcCCHHH----HHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCC
Confidence            3456789999999999999999    679999999 999987753    788999999999999999999 799999999


Q ss_pred             ceEEEEEccccch
Q 025973           86 KPMRIQYAKTKSD   98 (245)
Q Consensus        86 ~~i~v~~~~~~~~   98 (245)
                      +.|.|.++.++..
T Consensus        84 ~~l~V~~a~~~~~   96 (104)
T 1wi8_A           84 KRIRVDVADQAQD   96 (104)
T ss_dssp             EECEEEECCCCCC
T ss_pred             cEEEEEEccCCCC
Confidence            9999999977544

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=2.6e-18  Score=116.77  Aligned_cols=76  Identities=28%  Similarity=0.415  Sum_probs=70.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      ++++|||+|||..+++++|+++|+.||.|..|.+..++        +|||||+|.+.++|..|+..|||..|.|++|.|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            56779999999999999999999999999999998632        4899999999999999999999999999999999


Q ss_pred             EecC
Q 025973          242 YAKK  245 (245)
Q Consensus       242 ~ak~  245 (245)
                      ||+.
T Consensus        84 ~a~~   87 (98)
T 2cpf_A           84 ISER   87 (98)
T ss_dssp             CSSC
T ss_pred             EccC
Confidence            9863

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.77  E-value=1.7e-18  Score=123.44  Aligned_cols=76  Identities=22%  Similarity=0.326  Sum_probs=71.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|+..|||..|.|++|.|.||
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a  123 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS  123 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            466789999999999999999999999999999998753     689999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       124 ~  124 (129)
T 2kxn_B          124 I  124 (129)
T ss_dssp             S
T ss_pred             c
Confidence            6

>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=99.77  E-value=3.6e-19  Score=119.06  Aligned_cols=79  Identities=20%  Similarity=0.202  Sum_probs=66.0

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccC--CeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFG--TILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G--~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      .+|||+|||.++++++    |+++|+.||  .|.+|.+.   .+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|
T Consensus         2 ~~l~V~nL~~~~t~~~----l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V   77 (90)
T 3p5t_L            2 IALYIGNLTWWTTDED----LTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVV   77 (90)
T ss_dssp             --CEEESCCTTCCHHH----HHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEE
T ss_pred             eEEEEeCCCCCCCHHH----HHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEE
Confidence            5799999999999999    669999999  88887544   37899999999999999999999999999999999999


Q ss_pred             EEccccch
Q 025973           91 QYAKTKSD   98 (245)
Q Consensus        91 ~~~~~~~~   98 (245)
                      .++.+...
T Consensus        78 ~~~~~~~~   85 (90)
T 3p5t_L           78 TPSNKLEH   85 (90)
T ss_dssp             CCC-----
T ss_pred             EECCCCcc
Confidence            99876543

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=1.6e-18  Score=120.54  Aligned_cols=84  Identities=13%  Similarity=0.281  Sum_probs=74.8

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHH---HhhcccCCeEEEEecCCC------CeeeEEEEEecCHHHHHHHHHHHcC
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLH---AVFKQFGTILEILAFKTL------KHKGQAWLVFKDVASATAAVEKMQG   80 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~---~~F~~~G~v~~i~~~~~~------~~kg~afV~F~~~~~A~~a~~~l~~   80 (245)
                      ......++|||+|||.++++++    |.   ++|++||.|..|.+.++.      .++|||||+|.+.++|.+|++.||+
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~----l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng   85 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPE----VLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNN   85 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHH----HHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTT
T ss_pred             ccccCCCEEEEECCCCCCCHHH----HHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCC
Confidence            3456689999999999999999    77   999999999998776532      4669999999999999999999999


Q ss_pred             CccCCceEEEEEccccc
Q 025973           81 FPFYDKPMRIQYAKTKS   97 (245)
Q Consensus        81 ~~~~g~~i~v~~~~~~~   97 (245)
                      ..+.|+.|+|.++.++.
T Consensus        86 ~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           86 VVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             EEETTEEEEEESCCCCS
T ss_pred             CEECCEEEEEEeccccc
Confidence            99999999999998764

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=4.6e-18  Score=118.78  Aligned_cols=84  Identities=23%  Similarity=0.378  Sum_probs=75.2

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .....++++|||+|||.++++++    |+++|+.||.|..|.+.  +++.++|||||+|.+.++|.+|+..||+..+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~~~~~----l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   84 (114)
T 2do0_A            9 LQAGRLGSTVFVANLDYKVGWKK----LKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDR   84 (114)
T ss_dssp             CCCCCCCSCEEEESCCTTCCHHH----HHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCC
Confidence            34566789999999999999999    67999999999987654  4678899999999999999999999999999999


Q ss_pred             eEEEEEcccc
Q 025973           87 PMRIQYAKTK   96 (245)
Q Consensus        87 ~i~v~~~~~~   96 (245)
                      .|.|.++...
T Consensus        85 ~l~v~~a~~~   94 (114)
T 2do0_A           85 PMHVKMDERA   94 (114)
T ss_dssp             ECEEEECSCC
T ss_pred             EEEEEEcccC
Confidence            9999998653

>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=99.76  E-value=2.8e-18  Score=132.07  Aligned_cols=76  Identities=20%  Similarity=0.287  Sum_probs=72.8

Q ss_pred             CCccEEEEcCCC-CCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVP-HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~-~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +++++|||+||| ..+++++|+++|+.||.|.+|+++++++|||||+|.++++|..|++.|||..+.|++|+|.||+
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 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            356789999999 8999999999999999999999999888999999999999999999999999999999999986

>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=99.76  E-value=2.5e-18  Score=119.53  Aligned_cols=76  Identities=17%  Similarity=0.300  Sum_probs=70.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHH---HHhccCCCeeEEEEecCC--------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeE
Q 025973          169 PPNNILFVQNVPHDTTPMALQ---MFFSQFPGFKEVRMVEAK--------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQ  237 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~---~~f~~~g~v~~v~l~~~~--------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~  237 (245)
                      ...++|||+|||..+++++|+   ++|+.||.|..|.++.++        +|||||+|.++++|.+|+..|||..|.|++
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            346789999999999999999   999999999999998754        389999999999999999999999999999


Q ss_pred             EEEEEec
Q 025973          238 LLITYAK  244 (245)
Q Consensus       238 i~v~~ak  244 (245)
                      |+|.||+
T Consensus        93 l~V~~a~   99 (111)
T 2cpi_A           93 LKASLGT   99 (111)
T ss_dssp             EEEESCC
T ss_pred             EEEEecc
Confidence            9999986

>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=99.76  E-value=4.8e-18  Score=113.02  Aligned_cols=74  Identities=19%  Similarity=0.280  Sum_probs=69.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC------CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA------KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~------~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++|||+|||..+++++|+++|+.||.|..+.++.+      .+|+|||+|.+.++|..|+..|||..++|++|.|++|+
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   83 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL   83 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECC
Confidence            467999999999999999999999999999999874      36899999999999999999999999999999999986

>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=99.76  E-value=1e-18  Score=120.52  Aligned_cols=82  Identities=15%  Similarity=0.237  Sum_probs=72.7

Q ss_pred             CCCCCCCeEEEcCCCcc-cChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcC--CccCCc
Q 025973           10 NEISPNNTIYINNLNEK-VKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQG--FPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~-~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~--~~~~g~   86 (245)
                      .+..++++|||+|||.+ +++++    |+++|++||.|.+|++.+   +||||||+|.+.++|..|++.|++  ..+.|+
T Consensus        20 ~~~~p~~~l~V~NLp~~~~te~~----L~~lF~~fG~V~~v~i~~---~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr   92 (112)
T 1x4f_A           20 QKQELGRVIHLSNLPHSGYSDSA----VLKLAEPYGKIKNYILMR---MKSQAFIEMETREDAMAMVDHCLKKALWFQGR   92 (112)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHH----HHTTTTTTSCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSS
T ss_pred             ccCCCCCEEEEeCCCCccCCHHH----HHHHHHhcCCEEEEEEec---CCCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            45778999999999998 99999    779999999999998864   479999999999999999998864  568999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|+|.++..+..
T Consensus        93 ~l~V~~a~~~~~  104 (112)
T 1x4f_A           93 CVKVDLSEKYKK  104 (112)
T ss_dssp             CCEEEEECSCSS
T ss_pred             EEEEEECccccc
Confidence            999999876544

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.76  E-value=2e-18  Score=119.39  Aligned_cols=75  Identities=11%  Similarity=0.105  Sum_probs=69.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEec-CCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFP-GFKEVRMVE-AKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g-~v~~v~l~~-~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+|||+|||..+++++|+++|+.|| .|..+.+.. ..+|||||+|.+.++|..|++.|||..|.|++|+|.+|+
T Consensus        27 ~~~~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           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDD  103 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            456899999999999999999999999 899999864 347999999999999999999999999999999999986

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=7.1e-18  Score=113.20  Aligned_cols=73  Identities=19%  Similarity=0.288  Sum_probs=69.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..+.+.+   +||||+|.+.++|..|+..|||..|.|++|.|.||+
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~---~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   80 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK---DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLST   80 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS---SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC---CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            4667899999999999999999999999999999973   599999999999999999999999999999999986

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=6.6e-18  Score=117.40  Aligned_cols=76  Identities=26%  Similarity=0.391  Sum_probs=71.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhC------CCeeCCeE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQ------SLKIGQQQ  237 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~------g~~~~g~~  237 (245)
                      .++++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|+..||      |..|.|++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            356789999999999999999999999999999999763     6899999999999999999999      99999999


Q ss_pred             EEEEEec
Q 025973          238 LLITYAK  244 (245)
Q Consensus       238 i~v~~ak  244 (245)
                      |.|.||+
T Consensus        93 l~v~~a~   99 (111)
T 1x4h_A           93 LKVDLAV   99 (111)
T ss_dssp             EEEECCC
T ss_pred             EEEEECC
Confidence            9999986

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.76  E-value=1.8e-18  Score=121.57  Aligned_cols=81  Identities=25%  Similarity=0.383  Sum_probs=73.1

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .+..+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++.||+..+.|+
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  110 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTD----LASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTK  110 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHH----HHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            3456689999999999999999    779999999999997764   578899999999999999999999999999999


Q ss_pred             eEEEEEcc
Q 025973           87 PMRIQYAK   94 (245)
Q Consensus        87 ~i~v~~~~   94 (245)
                      .|+|.+++
T Consensus       111 ~l~V~~ak  118 (118)
T 2khc_A          111 RLKVQLKK  118 (118)
T ss_dssp             ECCEEEC-
T ss_pred             EEEEEecC
Confidence            99999874

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.4e-18  Score=118.88  Aligned_cols=82  Identities=21%  Similarity=0.385  Sum_probs=73.4

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      .+....++|||+|||.++++++    |+++|+.||.|.+|.+..  .|.++|||||+|.+.++|.+|+. +++..+.|+.
T Consensus         6 ~~~~~~~~lfV~~Lp~~~te~~----L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~   80 (103)
T 1s79_A            6 KNDVKNRSVYIKGFPTDATLDD----IKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETD   80 (103)
T ss_dssp             SSCSGGGCEEEECCCTTCCHHH----HHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTT
T ss_pred             cccCCCCEEEEECCCCCCCHHH----HHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEE
Confidence            4456779999999999999999    669999999999987664  47789999999999999999999 8999999999


Q ss_pred             EEEEEcccc
Q 025973           88 MRIQYAKTK   96 (245)
Q Consensus        88 i~v~~~~~~   96 (245)
                      |.|.++...
T Consensus        81 l~V~~~~~~   89 (103)
T 1s79_A           81 LLILFKDDY   89 (103)
T ss_dssp             CEEEEHHHH
T ss_pred             EEEEEchHH
Confidence            999987553

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=1.8e-18  Score=118.90  Aligned_cols=86  Identities=21%  Similarity=0.295  Sum_probs=76.5

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcc-cCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCc-cC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQ-FGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFP-FY   84 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~-~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~-~~   84 (245)
                      ..+..+.++|||+|||.++++++    |+++|+. ||.|..|.+..  ++.++|||||+|.+.++|.+|++.||+.. +.
T Consensus         3 ~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~   78 (104)
T 2dhg_A            3 SGSSGPEYSLFVGDLTPDVDDGM----LYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLG   78 (104)
T ss_dssp             CCCSSCCCCEEEECCCTTCCHHH----HHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSS
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHH----HHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccC
Confidence            34567889999999999999999    7799999 99999886543  78899999999999999999999999999 99


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |+.|+|.++.++..
T Consensus        79 g~~l~v~~a~~~~~   92 (104)
T 2dhg_A           79 SKPVRLSVAIPKAS   92 (104)
T ss_dssp             SSCCCCCBCCCCCS
T ss_pred             CEeEEEEEccCCCc
Confidence            99999999876543

>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=99.76  E-value=1.7e-18  Score=119.46  Aligned_cols=76  Identities=14%  Similarity=0.187  Sum_probs=69.9

Q ss_pred             CCccEEEE--cCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCee-----CCeEEEEE
Q 025973          169 PPNNILFV--QNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI-----GQQQLLIT  241 (245)
Q Consensus       169 ~~~~~l~v--~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~-----~g~~i~v~  241 (245)
                      .++++|||  +||+..+++++|+++|++||.|.+|.+..++ |||||+|.+.++|..|++.|||..+     .|++|.|.
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~r-gfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~  101 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-PYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN  101 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC-SCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCC-CEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEE
Confidence            35678999  6699999999999999999999999988774 9999999999999999999999988     69999999


Q ss_pred             EecC
Q 025973          242 YAKK  245 (245)
Q Consensus       242 ~ak~  245 (245)
                      ||+.
T Consensus       102 ~a~~  105 (114)
T 2cq2_A          102 FVEK  105 (114)
T ss_dssp             EESC
T ss_pred             eccc
Confidence            9974

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.76  E-value=9.9e-19  Score=119.23  Aligned_cols=75  Identities=20%  Similarity=0.307  Sum_probs=70.5

Q ss_pred             CccEEEEcCCCC------CCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCC-eE
Q 025973          170 PNNILFVQNVPH------DTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQ-QQ  237 (245)
Q Consensus       170 ~~~~l~v~nl~~------~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g-~~  237 (245)
                      .+++|||+|||.      .+++++|+++|+.||.|.+|.++.++     +|||||+|.++++|.+|+..|||..|.| ++
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            467899999999      99999999999999999999998754     6999999999999999999999999999 99


Q ss_pred             EEEEEec
Q 025973          238 LLITYAK  244 (245)
Q Consensus       238 i~v~~ak  244 (245)
                      |+|.+|+
T Consensus        85 l~V~~a~   91 (100)
T 3ns6_A           85 LFLYTMK   91 (100)
T ss_dssp             CEEEESH
T ss_pred             EEEEECc
Confidence            9999985

>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=99.76  E-value=2.5e-18  Score=116.80  Aligned_cols=76  Identities=22%  Similarity=0.328  Sum_probs=68.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +..++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.++++|.+|++.|||..|.|++|+|.+|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            456789999999999999999999999999766666532     699999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        93 ~   93 (98)
T 2cqp_A           93 S   93 (98)
T ss_dssp             S
T ss_pred             C
Confidence            6

>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=99.76  E-value=2.4e-18  Score=114.46  Aligned_cols=80  Identities=20%  Similarity=0.274  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCC---CC-eeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKT---LK-HKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~---~~-~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ...++|||+|||.++++++    |+++|+.||.|..|.+..+   +. ++|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus         2 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   77 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDH----IMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI   77 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEE
Confidence            3568999999999999999    6799999999999877643   23 78999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      +|.++.+.
T Consensus        78 ~v~~a~~~   85 (88)
T 4a8x_A           78 TATAVLAP   85 (88)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCC
Confidence            99998654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.76  E-value=1.9e-18  Score=118.90  Aligned_cols=81  Identities=21%  Similarity=0.323  Sum_probs=72.7

Q ss_pred             CCCCCeEEEcCCCccc------ChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973           12 ISPNNTIYINNLNEKV------KIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~------~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ...+++|||+|||..+      ++++    |+++|+.||.|..|.+.+ +|.++|||||+|.+.++|.+|+..|||..+.
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~----l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~   87 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNV----IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD   87 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHH----HHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECS
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHH----HHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccC
Confidence            4457899999999999      6788    779999999999997764 7889999999999999999999999999999


Q ss_pred             Cc-eEEEEEcccc
Q 025973           85 DK-PMRIQYAKTK   96 (245)
Q Consensus        85 g~-~i~v~~~~~~   96 (245)
                      |+ .|+|.++...
T Consensus        88 g~~~l~V~~a~~~  100 (105)
T 2nlw_A           88 KQHTFRVNLFTDF  100 (105)
T ss_dssp             TTCEEEEECSCCC
T ss_pred             CCceEEEEEcchH
Confidence            98 9999998653

>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=1.1e-17  Score=113.87  Aligned_cols=74  Identities=23%  Similarity=0.359  Sum_probs=69.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccC--CCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQF--PGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~--g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .++++|||+|||..+++++|+++|+.|  |.|..+.+.   +|||||+|.+.++|..|+..|||..|.|++|.|.||+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   88 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   88 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe---CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCC
Confidence            467889999999999999999999999  999998875   48999999999999999999999999999999999873

>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=99.76  E-value=2.4e-18  Score=113.78  Aligned_cols=80  Identities=21%  Similarity=0.377  Sum_probs=72.4

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHH-cCCccCCc
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKM-QGFPFYDK   86 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l-~~~~~~g~   86 (245)
                      ......+.++|||+|||.++++++    |+++|+.||.|..|.+.+   ++|||||+|.+.++|.+|+..| ++..+.|+
T Consensus         5 ~~~~~~~~~~l~V~~l~~~~t~~~----l~~~f~~~G~i~~~~~~~---~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~   77 (85)
T 2ytc_A            5 SSGEDKTITTLYVGGLGDTITETD----LRNHFYQFGEIRTITVVQ---RQQCAFIQFATRQAAEVAAEKSFNKLIVNGR   77 (85)
T ss_dssp             CCCSCSSCCCEEEECCTTTSCHHH----HHHHHHTTSCEEEEEEEG---GGTEEEEEESSHHHHHHHHHTTTTTCEETTE
T ss_pred             CCCCCCCccEEEEcCCCCCCCHHH----HHHHHHhCCCEeEEEEEC---CCCEEEEEECCHHHHHHHHHHhcCCeeECCC
Confidence            445567789999999999999999    679999999999998875   4799999999999999999998 99999999


Q ss_pred             eEEEEEcc
Q 025973           87 PMRIQYAK   94 (245)
Q Consensus        87 ~i~v~~~~   94 (245)
                      .|+|.|++
T Consensus        78 ~l~v~~ak   85 (85)
T 2ytc_A           78 RLNVKWGR   85 (85)
T ss_dssp             ECCEEECC
T ss_pred             EEEEEecC
Confidence            99999974

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=6.1e-18  Score=117.95  Aligned_cols=77  Identities=26%  Similarity=0.314  Sum_probs=71.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCee--------EEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFK--------EVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQ  235 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~--------~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g  235 (245)
                      ..+++|||+|||..+++++|+++|+.||.|.        .|.++.++     +|||||+|.+.++|..|+..|||..|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   92 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCC
Confidence            4567899999999999999999999999998        68988763     6899999999999999999999999999


Q ss_pred             eEEEEEEecC
Q 025973          236 QQLLITYAKK  245 (245)
Q Consensus       236 ~~i~v~~ak~  245 (245)
                      ++|+|.||+.
T Consensus        93 ~~l~V~~a~~  102 (113)
T 2cpe_A           93 SKLKVSLARK  102 (113)
T ss_dssp             EECEEECSSC
T ss_pred             CEEEEEECCC
Confidence            9999999873

>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=99.76  E-value=2.6e-18  Score=116.95  Aligned_cols=84  Identities=17%  Similarity=0.420  Sum_probs=75.6

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ......+.++|||+|||.++++++    |+++|+.||.|..|.+.++   +|||||+|.+.++|.+|++.||+..+.|+.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~~~~~---kg~afV~f~~~~~a~~a~~~l~g~~~~g~~   80 (99)
T 2cpj_A            8 GEKTFTQRSRLFVGNLPPDITEEE----MRKLFEKYGKAGEVFIHKD---KGFGFIRLETRTLAEIAKVELDNMPLRGKQ   80 (99)
T ss_dssp             CSCCCCCTTEEEEESCCTTCCHHH----HHHHTSTTCCCSEEEEETT---TTEEEEECSSSHHHHHHHHHHTTCCBTTBC
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHH----HHHHHhhcCCeEEEEEecC---CCEEEEEECCHHHHHHHHHHhCCCEeCCce
Confidence            445567889999999999999999    7799999999999988754   699999999999999999999999999999


Q ss_pred             EEEEEccccch
Q 025973           88 MRIQYAKTKSD   98 (245)
Q Consensus        88 i~v~~~~~~~~   98 (245)
                      |+|.++.++..
T Consensus        81 l~v~~a~~~~~   91 (99)
T 2cpj_A           81 LRVRFACHSAS   91 (99)
T ss_dssp             CEEEESSCCSC
T ss_pred             EEEEEcCCCCC
Confidence            99999977544

>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=99.76  E-value=5.5e-18  Score=118.56  Aligned_cols=76  Identities=24%  Similarity=0.481  Sum_probs=71.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++++|||+|||..+++++|+++|+.||.|..|.++.+.  +|||||+|.+.++|..|+..|||..+.|+.|.|.||+
T Consensus         6 ~~~~~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            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            356789999999999999999999999999999998754  6899999999999999999999999999999999986

>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=99.76  E-value=4.1e-18  Score=119.32  Aligned_cols=76  Identities=20%  Similarity=0.370  Sum_probs=71.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      ..++|||+|||..+++++|+++|+.||.|..|.+..++    +|||||+|.+.++|..|+..|||..|.|++|.|.||+.
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   85 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK   85 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            45689999999999999999999999999999999864    68999999999999999999999999999999999973

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.76  E-value=1.7e-18  Score=119.80  Aligned_cols=82  Identities=13%  Similarity=0.134  Sum_probs=71.8

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccC-CeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFG-TILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G-~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..+...++|||+|||.++++++    |+++|+.|| .|..+.+.. +.++|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus        23 ~~p~~~~~l~VgnLp~~~te~d----L~~~F~~~G~~v~~v~i~~-~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i   97 (111)
T 2jvr_A           23 KLPAKRYRITMKNLPEGCSWQD----LKDLARENSLETTFSSVNT-RDFDGTGALEFPSEEILVEALERLNNIEFRGSVI   97 (111)
T ss_dssp             --CCCCEEEEEECSSCCCCHHH----HHHHHHHHTCCCSEEECSS-CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHH----HHHHHHHhCCeeEEEEEEc-CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            3466788999999999999999    669999999 898887753 3578999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      .|.++...
T Consensus        98 ~V~~a~~~  105 (111)
T 2jvr_A           98 TVERDDNP  105 (111)
T ss_dssp             EEEESCC-
T ss_pred             EEEECCCC
Confidence            99998654

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.76  E-value=1.6e-18  Score=118.29  Aligned_cols=83  Identities=19%  Similarity=0.301  Sum_probs=69.5

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC----CCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK----TLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~----~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      ........++|||+|||.++++++    |+++|+.|| |.+|.+..    +|+++|||||+|.+.++|.+|+ .|||..+
T Consensus        12 ~~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~   85 (100)
T 2j76_E           12 SRLPKSPPYTAFLGNLPYDVTEES----IKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESL   85 (100)
T ss_dssp             --------CEEEESCCSSCCSSSH----HHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCB
T ss_pred             CcCCCCCCcEEEEeCCCCCCCHHH----HHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEE
Confidence            334566789999999999999999    679999999 99997764    5778999999999999999999 7999999


Q ss_pred             CCceEEEEEcccc
Q 025973           84 YDKPMRIQYAKTK   96 (245)
Q Consensus        84 ~g~~i~v~~~~~~   96 (245)
                      .|+.|+|.++.++
T Consensus        86 ~g~~l~V~~a~~~   98 (100)
T 2j76_E           86 GNRRIRVDVADQA   98 (100)
T ss_dssp             TTBCCCCEECCCS
T ss_pred             CCeEEEEEeccCC
Confidence            9999999998764

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.76  E-value=1.2e-17  Score=114.44  Aligned_cols=74  Identities=23%  Similarity=0.472  Sum_probs=69.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.++|||+|||..+++++|+++|+.|| |..|.++.++     +|||||+|.+.++|..|+ .|||..|.|++|.|.||
T Consensus        13 ~~~~~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 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEe
Confidence            3567899999999999999999999997 9999999864     689999999999999999 89999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        91 ~   91 (103)
T 2dng_A           91 E   91 (103)
T ss_dssp             C
T ss_pred             c
Confidence            6

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.76  E-value=1e-18  Score=114.52  Aligned_cols=72  Identities=24%  Similarity=0.413  Sum_probs=65.6

Q ss_pred             CCeEEEcCCCccc------ChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc-
Q 025973           15 NNTIYINNLNEKV------KIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK-   86 (245)
Q Consensus        15 ~~~l~V~nLp~~~------~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~-   86 (245)
                      +++|||+|||..+      ++++    |+++|+.||.|.+|.+.+ +|+++|||||+|.+.++|.+|+..|||..+.|+ 
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~----l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~   76 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNV----IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   76 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHH----HHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHH----HHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCce
Confidence            4799999999999      6688    779999999999997764 788999999999999999999999999999999 


Q ss_pred             eEEE
Q 025973           87 PMRI   90 (245)
Q Consensus        87 ~i~v   90 (245)
                      .|+|
T Consensus        77 ~l~V   80 (81)
T 2krb_A           77 TFRV   80 (81)
T ss_dssp             CCCC
T ss_pred             eEEe
Confidence            8876

>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=99.76  E-value=4.7e-18  Score=117.17  Aligned_cols=76  Identities=21%  Similarity=0.354  Sum_probs=71.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCee---CCeEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKI---GQQQLLI  240 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~---~g~~i~v  240 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..+   .|++|.|
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v   90 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQV   90 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEE
Confidence            466789999999999999999999999999999998863     68999999999999999999999987   8999999


Q ss_pred             EEec
Q 025973          241 TYAK  244 (245)
Q Consensus       241 ~~ak  244 (245)
                      .||+
T Consensus        91 ~~a~   94 (106)
T 2dgp_A           91 KPAD   94 (106)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9986

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=3e-18  Score=119.58  Aligned_cols=85  Identities=35%  Similarity=0.530  Sum_probs=75.8

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeE--------EEEec---CCCCeeeEEEEEecCHHHHHHHHHHH
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--------EILAF---KTLKHKGQAWLVFKDVASATAAVEKM   78 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~--------~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l   78 (245)
                      .+..+.++|||+|||.++++++    |+++|+.||.|.        .|.+.   .++.++|||||+|.+.++|.+|++.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l   85 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDD----LADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWF   85 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHH----HHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHH
T ss_pred             ccCCCCCEEEEcCCCCCCCHHH----HHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHc
Confidence            4567789999999999999999    679999999998        46555   46788999999999999999999999


Q ss_pred             cCCccCCceEEEEEccccch
Q 025973           79 QGFPFYDKPMRIQYAKTKSD   98 (245)
Q Consensus        79 ~~~~~~g~~i~v~~~~~~~~   98 (245)
                      |+..+.|+.|+|.++..+..
T Consensus        86 ~g~~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           86 DGKDFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTCEETTEECEEECSSCCCC
T ss_pred             CCCccCCCEEEEEECCCCCC
Confidence            99999999999999877654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=5.2e-18  Score=115.03  Aligned_cols=76  Identities=25%  Similarity=0.411  Sum_probs=68.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      ..+++|||+|||..+++++|+++|+.||.|. +.++.++ +|||||+|.+.++|..|+..|||..|.|++|.|.+|+.
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   93 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ   93 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            3467899999999999999999999999996 5555443 79999999999999999999999999999999999863

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1e-18  Score=120.07  Aligned_cols=82  Identities=20%  Similarity=0.425  Sum_probs=74.2

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .+.++|||+|||..+++++    |+++|+.||.|..|.+.   .+|.++|||||+|.+.++|.+|++.|||..+.|+.|+
T Consensus         6 ~~~~~l~V~nlp~~~~~~~----l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQ----LKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR   81 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHH----HHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBE
T ss_pred             CCccEEEEeCCCCcCCHHH----HHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            4568999999999999999    77999999999888655   4688899999999999999999999999999999999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |.++.+...
T Consensus        82 v~~a~~~~~   90 (104)
T 1p1t_A           82 VDNAASEKN   90 (104)
T ss_dssp             EEETTCTTH
T ss_pred             EEeCCCccc
Confidence            999877654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.76  E-value=1.9e-17  Score=119.70  Aligned_cols=77  Identities=21%  Similarity=0.378  Sum_probs=71.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ...++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|+..|||..|.|++|+|.||
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  119 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            456789999999999999999999999999999998763     689999999999999999999999999999999998


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus       120 ~~  121 (139)
T 1u6f_A          120 AS  121 (139)
T ss_dssp             SC
T ss_pred             CC
Confidence            63

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3.5e-18  Score=116.29  Aligned_cols=76  Identities=14%  Similarity=0.266  Sum_probs=71.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCee-EEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeE----E
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFK-EVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQ----L  238 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~-~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~----i  238 (245)
                      .++++|||+|||..+++++|+++|+.||.|. .+.++.++     +|||||+|.+.++|..|+..|||..+.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            3567899999999999999999999999999 99999864     589999999999999999999999999999    9


Q ss_pred             EEEEec
Q 025973          239 LITYAK  244 (245)
Q Consensus       239 ~v~~ak  244 (245)
                      +|.||+
T Consensus        87 ~v~~a~   92 (99)
T 2div_A           87 KLNYAT   92 (99)
T ss_dssp             CEEETT
T ss_pred             EEeecC
Confidence            999986

>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=99.76  E-value=5.4e-18  Score=113.04  Aligned_cols=73  Identities=19%  Similarity=0.339  Sum_probs=69.2

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.+.++|.+|+ .+||..|.|++|.|.+|+
T Consensus         6 ~~~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            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            4689999999999999999999999999999998764     789999999999999999 899999999999999986

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.2e-17  Score=117.10  Aligned_cols=76  Identities=22%  Similarity=0.346  Sum_probs=70.6

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      ..+.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|+..+|+ .|.|++|.|.|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            3466889999999999999999999999999999999863     68999999999999999999998 89999999999


Q ss_pred             ec
Q 025973          243 AK  244 (245)
Q Consensus       243 ak  244 (245)
                      |+
T Consensus        93 a~   94 (116)
T 2cqd_A           93 AY   94 (116)
T ss_dssp             ST
T ss_pred             cc
Confidence            85

>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=99.76  E-value=1.3e-17  Score=115.71  Aligned_cols=73  Identities=23%  Similarity=0.341  Sum_probs=68.7

Q ss_pred             CCccEEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHD-TTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..+++|||+|||.. +++++|+++|+.||.|..|.+   .+|||||+|.+.++|..|+..|||..|.|++|.|.||+
T Consensus        25 ~~~~~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           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAG   98 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            35578999999999 999999999999999999998   35899999999999999999999999999999999996

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.2e-17  Score=114.74  Aligned_cols=74  Identities=24%  Similarity=0.447  Sum_probs=69.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      .+..+|||+|||..+++++|+++|+.|| |..|.++.++      +|||||+|.+.++|.+|+ .|||..|.|++|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            3567899999999999999999999999 9999998753      689999999999999999 8999999999999999


Q ss_pred             ec
Q 025973          243 AK  244 (245)
Q Consensus       243 ak  244 (245)
                      |+
T Consensus        91 a~   92 (104)
T 1wi8_A           91 AD   92 (104)
T ss_dssp             CC
T ss_pred             cc
Confidence            86

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.75  E-value=2e-18  Score=116.80  Aligned_cols=82  Identities=20%  Similarity=0.366  Sum_probs=70.5

Q ss_pred             cCCCCCCCCeEEEcCCCc-ccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973            8 QGNEISPNNTIYINNLNE-KVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~-~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .....+++++|||+|||. .+++++    |+++|+.||.|..|.+.     +|||||+|.+.++|.+|+..||+..+.|+
T Consensus         3 ~~~~~~~~~~l~V~nlp~~~~t~~~----l~~~F~~~G~v~~v~i~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~   73 (96)
T 2kvi_A            3 EMHNIPPKSRLFIGNLPLKNVSKED----LFRIFSPYGHIMQINIK-----NAFGFIQFDNPQSVRDAIECESQEMNFGK   73 (96)
T ss_dssp             ------CCEEEEEESSTTSCCCHHH----HHHHHTTTCCCCEEEEE-----TTEEEEEESCHHHHHHHHHHHTCSSCBTT
T ss_pred             ccccCCCCCEEEEeCCCcccCCHHH----HHHHHHhcCCEEEEEEe-----CCEEEEEECCHHHHHHHHHHcCCCeeCCc
Confidence            345577899999999998 999999    77999999999999874     68999999999999999999999999999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|+|.++.....
T Consensus        74 ~l~V~~a~~~~~   85 (96)
T 2kvi_A           74 KLILEVSSSNAR   85 (96)
T ss_dssp             TBCEEEEECCCC
T ss_pred             EEEEEEcCcCCC
Confidence            999999876543

>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=99.75  E-value=3.6e-18  Score=115.80  Aligned_cols=77  Identities=26%  Similarity=0.443  Sum_probs=71.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEecC--CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQ----MFFSQFPGFKEVRMVEA--KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~----~~f~~~g~v~~v~l~~~--~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      +++++|||+|||..+++++|+    ++|+.||.|..|.+...  .+|||||+|.+.++|..|+..|||..++|++|.|+|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   85 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   85 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            467889999999999999999    99999999999998752  258999999999999999999999999999999999


Q ss_pred             ecC
Q 025973          243 AKK  245 (245)
Q Consensus       243 ak~  245 (245)
                      |+.
T Consensus        86 a~~   88 (97)
T 1nu4_A           86 AKT   88 (97)
T ss_dssp             CSS
T ss_pred             ccC
Confidence            963

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.75  E-value=1.6e-18  Score=117.30  Aligned_cols=82  Identities=26%  Similarity=0.358  Sum_probs=74.2

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ....+.++|||+|||..+++++    |+++|+.||.|..+  ..++.++|||||+|.+.++|.+|+..||+..+.|+.|.
T Consensus        11 ~~~~~~~~l~V~nL~~~~t~~~----l~~~F~~~g~v~~~--~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   84 (96)
T 1fjc_A           11 KKVRAARTLLAKNLSFNITEDE----LKEVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVS   84 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHH----HHHHHCSEEEECCE--EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHH----HHHHHhhCCcEEEe--CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            4456789999999999999999    67999999998777  56788999999999999999999999999999999999


Q ss_pred             EEEccccc
Q 025973           90 IQYAKTKS   97 (245)
Q Consensus        90 v~~~~~~~   97 (245)
                      |.++.++.
T Consensus        85 v~~a~~~~   92 (96)
T 1fjc_A           85 LYYTGEKG   92 (96)
T ss_dssp             EEECSSSC
T ss_pred             EEEcCCCC
Confidence            99987653

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=7.2e-18  Score=112.70  Aligned_cols=74  Identities=23%  Similarity=0.306  Sum_probs=69.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..+.+++   +||||+|.+.++|..|+..|||..+.|++|.|.||+.
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~---~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   80 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK---DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTK   80 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS---SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC---CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCC
Confidence            3567899999999999999999999999999999984   5999999999999999999999999999999999863

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.75  E-value=6.1e-18  Score=115.97  Aligned_cols=84  Identities=25%  Similarity=0.394  Sum_probs=74.1

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      ..+..+.++|||+|||.++++++    |+++|+.|| |..|.+..   ++.++|||||+|.+.++|.+|+ .||+..+.|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g   82 (103)
T 2dng_A            9 ELPTEPPYTAYVGNLPFNTVQGD----IDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGD   82 (103)
T ss_dssp             CCCSSSCEEEEEESCCTTCCHHH----HHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETT
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHH----HHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECC
Confidence            34566789999999999999999    679999997 98886653   5789999999999999999999 799999999


Q ss_pred             ceEEEEEccccch
Q 025973           86 KPMRIQYAKTKSD   98 (245)
Q Consensus        86 ~~i~v~~~~~~~~   98 (245)
                      +.|+|.++.+...
T Consensus        83 ~~l~V~~a~~~~~   95 (103)
T 2dng_A           83 RSLRVDIAEGRKQ   95 (103)
T ss_dssp             EECEEEECCCCCC
T ss_pred             eEEEEEEecCCCC
Confidence            9999999876543

>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=99.75  E-value=9.3e-19  Score=117.06  Aligned_cols=73  Identities=22%  Similarity=0.279  Sum_probs=66.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFP--GFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g--~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+|||+|||..+++++|+++|+.||  .|.++.++.++     +|||||+|.+.++|.+|++.|||..|.|++|+|.+|+
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            3599999999999999999999999  99999998864     6899999999999999999999999999999999885

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.75  E-value=5.9e-18  Score=120.36  Aligned_cols=85  Identities=18%  Similarity=0.339  Sum_probs=75.9

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ....++++|||+|||..+++++    |.++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++.||+..+.|+
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   92 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEED----IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   92 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            3456688999999999999999    669999999999997653   678899999999999999999999999999999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|.|.++..+..
T Consensus        93 ~l~v~~a~~~~~  104 (126)
T 3ex7_B           93 PISVDWCFVRGP  104 (126)
T ss_dssp             BCEEEESEESSS
T ss_pred             EEEEEEecCCCC
Confidence            999999876543

>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=99.75  E-value=7e-18  Score=115.67  Aligned_cols=73  Identities=26%  Similarity=0.447  Sum_probs=68.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++++|||+|||..+++++|+++|+.||.|..|.++   ++||||+|.+.++|.+|+..|||..|.|++|.|.||+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   81 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK   81 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcC
Confidence            356789999999999999999999999999999987   4799999999999999999999999999999999986

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=9.8e-19  Score=115.66  Aligned_cols=79  Identities=20%  Similarity=0.250  Sum_probs=71.3

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..++++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++.|||..+.|+.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~----l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~   77 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQD----LVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   77 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHH----HHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CCCCcEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEE
Confidence            46789999999999999999    779999999999987654   57789999999999999999999999999999999


Q ss_pred             EEEEcc
Q 025973           89 RIQYAK   94 (245)
Q Consensus        89 ~v~~~~   94 (245)
                      ++.++.
T Consensus        78 ~~~~~~   83 (85)
T 1x4e_A           78 KQSGPS   83 (85)
T ss_dssp             CSSCCC
T ss_pred             eecCCC
Confidence            887653

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=5.7e-18  Score=118.31  Aligned_cols=74  Identities=20%  Similarity=0.430  Sum_probs=69.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+ .|||..|.|++|.|.||+
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            45689999999999999999999999999999998653     689999999999999999 899999999999999985

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.75  E-value=7.3e-18  Score=121.96  Aligned_cols=85  Identities=21%  Similarity=0.395  Sum_probs=76.1

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .+..+.++|||+|||.++++++    |+++|+.||.|.+|.+.   .++.++|||||+|.+.++|.+|++.||+..+.|+
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  112 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQ----LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNK  112 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHH----HHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            4456689999999999999999    67999999999998665   3678899999999999999999999999999999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|+|.++.....
T Consensus       113 ~l~v~~a~~~~~  124 (139)
T 1u6f_A          113 RLKVALAASGHQ  124 (139)
T ss_dssp             EEEEEESSCCCC
T ss_pred             EEEEEECCCCCC
Confidence            999999976544

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.75  E-value=6.5e-18  Score=119.79  Aligned_cols=85  Identities=24%  Similarity=0.394  Sum_probs=75.9

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .....++++|||+|||.++++++    |+++|+.||.|..|.+..  +|.++|||||+|.+.++|.+|+..||+..+.|+
T Consensus        29 ~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  104 (124)
T 2kt5_A           29 GEGVETGAKLLVSNLDFGVSDAD----IQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGR  104 (124)
T ss_dssp             CCCCSSCEEEEEESCCSSCCHHH----HHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            34567789999999999999999    679999999999886654  677899999999999999999999999999999


Q ss_pred             eEEEEEccccc
Q 025973           87 PMRIQYAKTKS   97 (245)
Q Consensus        87 ~i~v~~~~~~~   97 (245)
                      .|+|.++....
T Consensus       105 ~l~V~~a~~~~  115 (124)
T 2kt5_A          105 PMDIQLVASQI  115 (124)
T ss_dssp             EEEEEEECCTT
T ss_pred             EEEEEEeCCCC
Confidence            99999987643

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.2e-18  Score=117.09  Aligned_cols=74  Identities=18%  Similarity=0.286  Sum_probs=69.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+|||+|||..+|+++|+++|+.||.|.+|.++.++    +|||||+|.++++|..|+. ++|..|.|++|.|.+++
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            45789999999999999999999999999999999853    7999999999999999999 89999999999999874

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=8.3e-18  Score=114.23  Aligned_cols=84  Identities=19%  Similarity=0.233  Sum_probs=73.7

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE---EEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~---i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      .......++|||+|||.++++++    |+++|+.||.|..   +....++.++|||||+|.+.++|.+|++.||+..+.|
T Consensus         9 ~~~~~~~~~l~v~nLp~~~t~~~----l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   84 (98)
T 2cqp_A            9 SSGKPGPTIIKVQNMPFTVSIDE----ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS   84 (98)
T ss_dssp             CCCCCSSEEEEEESCCTTCCHHH----HHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            34456679999999999999999    6699999999864   3445678899999999999999999999999999999


Q ss_pred             ceEEEEEcccc
Q 025973           86 KPMRIQYAKTK   96 (245)
Q Consensus        86 ~~i~v~~~~~~   96 (245)
                      +.|+|.++...
T Consensus        85 ~~l~V~~a~~~   95 (98)
T 2cqp_A           85 RKVKLVLGSGP   95 (98)
T ss_dssp             EECEEEESSCS
T ss_pred             eEEEEEEcCCC
Confidence            99999998653

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.75  E-value=6.3e-18  Score=120.22  Aligned_cols=76  Identities=22%  Similarity=0.347  Sum_probs=71.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++.+|||+|||..+++++|.++|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|.|++|.|.||
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            356789999999999999999999999999999998764     789999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       100 ~  100 (126)
T 3ex7_B          100 F  100 (126)
T ss_dssp             E
T ss_pred             c
Confidence            5

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.75  E-value=2.1e-18  Score=117.90  Aligned_cols=73  Identities=23%  Similarity=0.350  Sum_probs=69.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ++|||+|||..+++++|+++|+.||.|..+.++.+.+|||||+|.+.++|..|+..|||..+.|++|.|.||+
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 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELST   73 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEcc
Confidence            3699999999999999999999999999999998866999999999999999999999999999999999986

>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=99.75  E-value=4.2e-18  Score=118.00  Aligned_cols=81  Identities=23%  Similarity=0.408  Sum_probs=74.1

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      .....++|||+|||.++++++    |+.+|+.||.|..|.+..+   +|||||+|.+.++|.+|+..||+..+.|+.|+|
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~----l~~~F~~~G~i~~v~i~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   93 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQL----MRQTFSPFGQIMEIRVFPE---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKC   93 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHH----HHHHHHHHSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEeCC---CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            456789999999999999999    6799999999999988765   799999999999999999999999999999999


Q ss_pred             EEccccch
Q 025973           91 QYAKTKSD   98 (245)
Q Consensus        91 ~~~~~~~~   98 (245)
                      .|+++...
T Consensus        94 ~~a~~~~~  101 (109)
T 1x4g_A           94 YWGKESPD  101 (109)
T ss_dssp             ECCCCCCS
T ss_pred             EecCCCCC
Confidence            99977644

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.75  E-value=4.8e-18  Score=114.96  Aligned_cols=73  Identities=16%  Similarity=0.351  Sum_probs=68.7

Q ss_pred             CCccEEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPH-DTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~-~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +++++|||+|||. .+++++|+++|+.||.|..+.+.   +|||||+|.+.++|..|+..|||..+.|++|.|.||+
T Consensus         8 ~~~~~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            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSS   81 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE---TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcC
Confidence            4678899999998 99999999999999999999985   5899999999999999999999999999999999986

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=7.1e-18  Score=118.19  Aligned_cols=84  Identities=19%  Similarity=0.245  Sum_probs=75.3

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ...+..+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+..+++ .+.
T Consensus        10 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~   84 (116)
T 2cqd_A           10 GSQKDTTFTKIFVGGLPYHTTDAS----LRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IID   84 (116)
T ss_dssp             CCCCSCSSSEEEEECCCSSCCHHH----HHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EET
T ss_pred             CCcCCCCCCEEEEeCCCCCCCHHH----HHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCC
Confidence            445567789999999999999999    679999999999997765   477899999999999999999999998 899


Q ss_pred             CceEEEEEcccc
Q 025973           85 DKPMRIQYAKTK   96 (245)
Q Consensus        85 g~~i~v~~~~~~   96 (245)
                      |+.|+|.++...
T Consensus        85 g~~l~V~~a~~~   96 (116)
T 2cqd_A           85 GRKANVNLAYLG   96 (116)
T ss_dssp             TEECEEEESTTT
T ss_pred             CEEEEEEEcccC
Confidence            999999998654

>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=99.75  E-value=3.2e-18  Score=118.92  Aligned_cols=78  Identities=18%  Similarity=0.235  Sum_probs=71.2

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      ...+++|||+|||.++++++    |+++|+.||.|..|.+.+   ++|||||+|.+.++|.+|+..|||..+.|+.|.|.
T Consensus         7 ~~~~~~l~V~nLp~~~te~~----L~~~F~~~G~i~~v~i~~---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   79 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAE----IQETFSRFGSLGRVLLPE---GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCS---SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEeC---CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            44578999999999999999    779999999999998874   56899999999999999999999999999999999


Q ss_pred             Ecccc
Q 025973           92 YAKTK   96 (245)
Q Consensus        92 ~~~~~   96 (245)
                      |+...
T Consensus        80 ~a~~~   84 (111)
T 1whx_A           80 WAPIG   84 (111)
T ss_dssp             EEETT
T ss_pred             ECCCC
Confidence            98653

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=7.3e-18  Score=110.69  Aligned_cols=72  Identities=13%  Similarity=0.227  Sum_probs=64.3

Q ss_pred             CCccE-EEEcCCCCCCCHHH----HHHHhccCC-CeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          169 PPNNI-LFVQNVPHDTTPMA----LQMFFSQFP-GFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       169 ~~~~~-l~v~nl~~~~t~~~----l~~~f~~~g-~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      +++.+ |||+|||..+++++    |+++|++|| +|.+|.     .|+|||.|.+.++|.+|++.|||+.+.||+|+|+|
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt-----gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~   80 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT-----GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSF   80 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC-----TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEES
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe-----cCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEe
Confidence            34555 99999999999988    558999994 999882     29999999999999999999999999999999999


Q ss_pred             ecC
Q 025973          243 AKK  245 (245)
Q Consensus       243 ak~  245 (245)
                      |+.
T Consensus        81 A~~   83 (96)
T 2diu_A           81 TPK   83 (96)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            973

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.75  E-value=1.6e-17  Score=120.28  Aligned_cols=75  Identities=17%  Similarity=0.338  Sum_probs=69.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.++++|.+|+..|||..|.|++|+|.||
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            466789999999999999999999999999999998762     699999999999999999999999999999999987

>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=99.75  E-value=2e-18  Score=117.73  Aligned_cols=75  Identities=24%  Similarity=0.448  Sum_probs=68.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      ...++|||+|||..+++++|+++|+.|| |.+|.++.++      +|||||+|.+.++|..|+ .|||..|+|+.|.|.+
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEe
Confidence            4567899999999999999999999999 9999998764      689999999999999999 8999999999999999


Q ss_pred             ecC
Q 025973          243 AKK  245 (245)
Q Consensus       243 ak~  245 (245)
                      |+.
T Consensus        95 a~~   97 (100)
T 2j76_E           95 ADQ   97 (100)
T ss_dssp             CCC
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=99.75  E-value=2.9e-18  Score=120.02  Aligned_cols=84  Identities=27%  Similarity=0.513  Sum_probs=74.2

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCe----EEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTI----LEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v----~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      .+..++++|||+|||.++++++    |+++|+.||.|    ..+... ++.++|||||+|.+.++|.+|+..||+..+.|
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~----l~~~f~~~G~v~~~~~~~~~~-~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   94 (115)
T 2cpx_A           20 NPGEPNKVLYLKNLSPRVTERD----LVSLFARFQEKKGPPIQFRMM-TGRMRGQAFITFPNKEIAWQALHLVNGYKLYG   94 (115)
T ss_dssp             CCCSCCSEEEEECCCTTCCHHH----HHHHTHHHHHSSSSCCEEEEE-CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHHHhCCccceEEEEEcC-CCccceEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            3456789999999999999999    66999999998    455444 78899999999999999999999999999999


Q ss_pred             ceEEEEEccccch
Q 025973           86 KPMRIQYAKTKSD   98 (245)
Q Consensus        86 ~~i~v~~~~~~~~   98 (245)
                      +.|+|.++.+...
T Consensus        95 ~~l~v~~a~~~~~  107 (115)
T 2cpx_A           95 KILVIEFGKNKKQ  107 (115)
T ss_dssp             CBCEEEECCCCSC
T ss_pred             cEEEEEEccCCCC
Confidence            9999999977644

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.75  E-value=2.6e-18  Score=116.07  Aligned_cols=76  Identities=21%  Similarity=0.312  Sum_probs=68.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ++.++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.++++|.+|++.|||..|.|++|+|.+|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            355789999999999999999999999999777766532     689999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
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=99.74  E-value=8.1e-18  Score=112.45  Aligned_cols=80  Identities=18%  Similarity=0.329  Sum_probs=72.9

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .....+.++|||+|||.++++++    |+++|+.||.|..|.+.+     +||||+|.+.++|.+|+..||+..+.|+.|
T Consensus         3 ~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~~~~~~-----~~afV~f~~~~~a~~A~~~l~g~~~~g~~l   73 (90)
T 2dnp_A            3 SGSSGNTWKIFVGNVSAACTSQE----LRSLFERRGRVIECDVVK-----DYAFVHMEKEADAKAAIAQLNGKEVKGKRI   73 (90)
T ss_dssp             CCSSCCSCCEEEESCCTTCCHHH----HHHHHHHHSCEEEEEECS-----SCEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHcCCCEEEEEEEC-----CEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            44567889999999999999999    679999999999998873     599999999999999999999999999999


Q ss_pred             EEEEccccc
Q 025973           89 RIQYAKTKS   97 (245)
Q Consensus        89 ~v~~~~~~~   97 (245)
                      +|.++.+..
T Consensus        74 ~v~~a~~~~   82 (90)
T 2dnp_A           74 NVELSTKGQ   82 (90)
T ss_dssp             EEEESCCCC
T ss_pred             EEEECCCCC
Confidence            999987653

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.74  E-value=4.6e-18  Score=117.50  Aligned_cols=80  Identities=24%  Similarity=0.515  Sum_probs=71.8

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ....+.++|||+|||.++++++    |+++|+.||.|..|.+.     +|||||+|.+.++|.+|+..|||..+.|+.|.
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~----L~~~F~~~G~i~~v~i~-----kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   96 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESE----LNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE   96 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHH----HHHHHTTTSCCCEEEEE-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCEEEEECCCCCCCHHH----HHHHHHhcCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            4466789999999999999999    77999999999999876     68999999999999999999999999999999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |.++.....
T Consensus        97 V~~a~~~~~  105 (108)
T 2jvo_A           97 VVYSKLPAK  105 (108)
T ss_dssp             EESCSCCC-
T ss_pred             EEEecCCCC
Confidence            999876543

>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=6.8e-18  Score=117.87  Aligned_cols=89  Identities=11%  Similarity=0.070  Sum_probs=76.0

Q ss_pred             cccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCe-EEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCc
Q 025973            6 ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTI-LEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFP   82 (245)
Q Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v-~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~   82 (245)
                      ........+.++|||+|||.++++++    |+++|+.||.| ..|.+.  +++.++|||||+|.+.++|.+|++. |+..
T Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~   80 (114)
T 2cpy_A            6 SGEGDVNSAKVCAHITNIPFSITKMD----VLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKK   80 (114)
T ss_dssp             CCCCSCCSCCCEEEEESCCTTSCHHH----HHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEE
T ss_pred             CCCCCCCCCccEEEEeCcCCcCCHHH----HHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCc
Confidence            33445567789999999999999999    77999999999 555443  4788999999999999999999995 9999


Q ss_pred             cCCceEEEEEccccchH
Q 025973           83 FYDKPMRIQYAKTKSDI   99 (245)
Q Consensus        83 ~~g~~i~v~~~~~~~~~   99 (245)
                      |.|+.|.|.++..+...
T Consensus        81 ~~gr~i~v~~a~~~~~~   97 (114)
T 2cpy_A           81 LNGREAFVHVVTLEDMR   97 (114)
T ss_dssp             ETTEEEEEEEECHHHHH
T ss_pred             cCCeEEEEEECCHHHHH
Confidence            99999999999776543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.3e-17  Score=113.48  Aligned_cols=87  Identities=16%  Similarity=0.332  Sum_probs=75.8

Q ss_pred             ccccccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhccc--CCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcC
Q 025973            3 PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQF--GTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQG   80 (245)
Q Consensus         3 p~~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~--G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~   80 (245)
                      |+.........+.++|||+|||..+++++    |+++|+.|  |.|..|.+.     +|||||+|.+.++|.+|+..||+
T Consensus         3 p~~~~~~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~g~g~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g   73 (99)
T 2cpd_A            3 SGSSGDEDTMSSVKILYVRNLMLSTSEEM----IEKEFNNIKPGAVERVKKI-----RDYAFVHFSNREDAVEAMKALNG   73 (99)
T ss_dssp             CCCCCCCSCSSCCCEEEEESCCTTCCHHH----HHHHHHTTSTTCEEEEEEC-----SSEEEEEESSHHHHHHHHHHHSS
T ss_pred             CcccccccccCCcCEEEEeCCCCCCCHHH----HHHHHHhcCCcceEEEEEe-----CCeEEEEeCCHHHHHHHHHHhCC
Confidence            34444555677889999999999999999    67999999  999998765     57999999999999999999999


Q ss_pred             CccCCceEEEEEccccch
Q 025973           81 FPFYDKPMRIQYAKTKSD   98 (245)
Q Consensus        81 ~~~~g~~i~v~~~~~~~~   98 (245)
                      ..+.|+.|+|.++.++..
T Consensus        74 ~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpd_A           74 KVLDGSPIEVTLAKPVDK   91 (99)
T ss_dssp             EEETTEEEEEECCCCCCC
T ss_pred             CEeCCcEEEEEECCCCCC
Confidence            999999999999976543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.74  E-value=8.4e-18  Score=121.72  Aligned_cols=81  Identities=31%  Similarity=0.528  Sum_probs=73.1

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      .....+.++|||+|||..+++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++.||+..+.|
T Consensus        57 ~~~~~~~~~l~v~nlp~~~~~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  132 (140)
T 2ku7_A           57 GGSATTKRVLYVGGLAEEVDDKV----LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG  132 (140)
T ss_dssp             CSSCSSCCEEEEECCCTTCCHHH----HHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETT
T ss_pred             CCCCCCCcEEEEEeCCCCCCHHH----HHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            34566799999999999999999    779999999999997764   57889999999999999999999999999999


Q ss_pred             ceEEEEEc
Q 025973           86 KPMRIQYA   93 (245)
Q Consensus        86 ~~i~v~~~   93 (245)
                      +.|+|.+|
T Consensus       133 ~~l~v~~A  140 (140)
T 2ku7_A          133 RTIRVNLA  140 (140)
T ss_dssp             EEEEEEC-
T ss_pred             EEEEEEeC
Confidence            99999875

>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=99.74  E-value=2.1e-17  Score=115.41  Aligned_cols=83  Identities=14%  Similarity=0.332  Sum_probs=73.8

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCcc----
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPF----   83 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~----   83 (245)
                      .+..+.++|||+|||.++++++    |+++|+.||.|..|.+..  ++.++|||||+|.+.++|.+|+..|||..+    
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~   95 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQE----LENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPP   95 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHH----HHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCT
T ss_pred             ccCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCc
Confidence            4456789999999999999999    779999999999986553  678899999999999999999999999999    


Q ss_pred             ----CCceEEEEEcccc
Q 025973           84 ----YDKPMRIQYAKTK   96 (245)
Q Consensus        84 ----~g~~i~v~~~~~~   96 (245)
                          .++.|.|.|+.+.
T Consensus        96 ~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           96 GVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             TSCCCSSCBEEEECCCS
T ss_pred             cccCCCCceeEEccCCC
Confidence                5788999998754

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.74  E-value=5.8e-18  Score=112.88  Aligned_cols=78  Identities=19%  Similarity=0.359  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ..++|||+|||.++++++    |+++|+.||.|..|.+.   .++.++|||||+|.+.++|.+|+ .||+..+.|+.|+|
T Consensus         5 ~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V   79 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEE----LEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKV   79 (89)
T ss_dssp             HHTEEEEESCCTTCCHHH----HHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEE
T ss_pred             cCCEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEE
Confidence            358999999999999999    67999999999998654   36788999999999999999999 79999999999999


Q ss_pred             EEcccc
Q 025973           91 QYAKTK   96 (245)
Q Consensus        91 ~~~~~~   96 (245)
                      .++++.
T Consensus        80 ~~a~~~   85 (89)
T 3ucg_A           80 IPKRTN   85 (89)
T ss_dssp             EETTTT
T ss_pred             EEccCC
Confidence            998754

>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=99.74  E-value=1.6e-17  Score=110.23  Aligned_cols=74  Identities=15%  Similarity=0.283  Sum_probs=68.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.+.++|.+|+. +++..+.|++|.|.+|
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            456789999999999999999999999999999998764     6899999999999999996 5888999999999987

>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=99.74  E-value=1.2e-17  Score=115.40  Aligned_cols=82  Identities=16%  Similarity=0.225  Sum_probs=73.7

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC---
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD---   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g---   85 (245)
                      .......++|||+|||.++++++    |+++|+.||.|..|.+..+    |||||+|.+.++|.+|++.||+..+.|   
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~~i~~~----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~   80 (108)
T 1x4c_A            9 PPSRRSENRVVVSGLPPSGSWQD----LKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEG   80 (108)
T ss_dssp             CCCCSCCCEEEEESCCSSCCHHH----HHHHHGGGSCEEEEEEETT----TEEEEEESSHHHHHHHHHHSSSEEEECTTS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEeEEEEecC----CEEEEEECCHHHHHHHHHHHCcCCccCCcC
Confidence            34456689999999999999999    6699999999999988766    899999999999999999999999999   


Q ss_pred             --ceEEEEEccccch
Q 025973           86 --KPMRIQYAKTKSD   98 (245)
Q Consensus        86 --~~i~v~~~~~~~~   98 (245)
                        +.|+|.++.++..
T Consensus        81 ~~~~i~V~~a~~~~~   95 (108)
T 1x4c_A           81 ETAYIRVKVDGPRSP   95 (108)
T ss_dssp             CEEEEEEEESSCCSC
T ss_pred             cceEEEEEeCCCCCC
Confidence              9999999987543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.74  E-value=6.2e-18  Score=124.40  Aligned_cols=81  Identities=17%  Similarity=0.208  Sum_probs=72.5

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccC--CeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFG--TILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G--~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..++|||+|||.++++++    |+++|+.||  .|.+|.+.   .+|.++|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus        54 ~~~~lfVgnLp~~~te~~----L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l  129 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQ----LIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV  129 (156)
T ss_dssp             --CEEEEECCCTTCCHHH----HHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEe
Confidence            468999999999999999    679999999  89988654   478999999999999999999999999999999999


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      .|.++.++..
T Consensus       130 ~V~~a~~~~~  139 (156)
T 3n9u_C          130 DVRPATRQNL  139 (156)
T ss_dssp             EEEECCHHHH
T ss_pred             EEEEcCCCcc
Confidence            9999976543

>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=99.74  E-value=3e-18  Score=115.71  Aligned_cols=81  Identities=20%  Similarity=0.221  Sum_probs=69.2

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE---EecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i---~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ...++.++|||+|||.++++++    |+++|+.||.|..+   ....++.++|||||+|.+.++|.+|++.||+..+.|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr   85 (95)
T 2ek1_A           10 SGKPGPTVIKVQNMPFTVSIDE----ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSR   85 (95)
T ss_dssp             -----CEEEEEECCCTTCCHHH----HHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCc
Confidence            3455679999999999999999    66999999998654   3445788999999999999999999999999999999


Q ss_pred             eEEEEEcc
Q 025973           87 PMRIQYAK   94 (245)
Q Consensus        87 ~i~v~~~~   94 (245)
                      .|+|.++.
T Consensus        86 ~l~v~~a~   93 (95)
T 2ek1_A           86 KVKLSGPS   93 (95)
T ss_dssp             ECEEECCC
T ss_pred             EEEEEecc
Confidence            99999875

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.74  E-value=2.4e-18  Score=117.54  Aligned_cols=78  Identities=23%  Similarity=0.460  Sum_probs=71.2

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ....+++|||+|||.++++++    |+++|+.||.|.+|.+.   +++|||||+|.+.++|.+|+..|||..+.|+.|+|
T Consensus        23 ~~~~~~~l~V~nlp~~~~~~~----l~~~f~~~G~i~~~~~~---~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   95 (101)
T 2la4_A           23 APPRVTTAYIGNIPHFATEAD----LIPLFQNFGFILDFKHY---PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRT   95 (101)
T ss_dssp             SCSSCCEEEEESCCTTCCHHH----HHHHHHTTSCCSEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCC
T ss_pred             CCCCCCEEEEcCCCcccCHHH----HHHHHHhCCCEEEEEEe---cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345679999999999999999    67999999999999876   35799999999999999999999999999999999


Q ss_pred             EEccc
Q 025973           91 QYAKT   95 (245)
Q Consensus        91 ~~~~~   95 (245)
                      .|+++
T Consensus        96 ~~a~~  100 (101)
T 2la4_A           96 GWGKE  100 (101)
T ss_dssp             CBCCC
T ss_pred             EeccC
Confidence            99865

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=3.2e-18  Score=116.05  Aligned_cols=82  Identities=20%  Similarity=0.385  Sum_probs=71.4

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .+.+..++|||+|||.++++++    |+++|+.||.|. +.+. ++.++|||||+|.+.++|.+|++.||+..+.|+.|+
T Consensus        14 ~~~~~~~~l~V~nL~~~~t~~~----l~~~F~~~G~v~-~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (97)
T 2e5j_A           14 EGAPLAADVYVGNLPRDARVSD----LKRALRELGSVP-LRLT-WQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLR   87 (97)
T ss_dssp             SSSCCCCEEEEECCCTTCCHHH----HHHHHHHTTCCC-SEEE-EETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCEEEEeCCCCcCcHHH----HHHHHHhcCCEE-EEEE-cCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            4456689999999999999999    669999999985 3333 346789999999999999999999999999999999


Q ss_pred             EEEccccc
Q 025973           90 IQYAKTKS   97 (245)
Q Consensus        90 v~~~~~~~   97 (245)
                      |.++.++.
T Consensus        88 V~~a~~~~   95 (97)
T 2e5j_A           88 VALARQQR   95 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99987653

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.2e-17  Score=112.00  Aligned_cols=82  Identities=18%  Similarity=0.357  Sum_probs=73.8

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      +.....+.++|||+|||.++++++    |+++|+.||.|..|.+.+     +||||+|.+.++|.+|+..||+..+.|+.
T Consensus         3 ~~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~v~~~~-----~~afV~f~~~~~a~~A~~~l~g~~~~g~~   73 (92)
T 2dgt_A            3 SGSSGKASTKLHVGNISPTCTNQE----LRAKFEEYGPVIECDIVK-----DYAFVHMERAEDAVEAIRGLDNTEFQGKR   73 (92)
T ss_dssp             CSCCCCSSEEEEEESCCSSCCHHH----HHHHHHTTSCCCEEEECS-----SEEEEEESCHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEC-----CEEEEEECCHHHHHHHHHHhCCCeeCCcE
Confidence            345577889999999999999999    679999999999998873     59999999999999999999999999999


Q ss_pred             EEEEEccccch
Q 025973           88 MRIQYAKTKSD   98 (245)
Q Consensus        88 i~v~~~~~~~~   98 (245)
                      |+|.++.++..
T Consensus        74 l~V~~a~~~~~   84 (92)
T 2dgt_A           74 MHVQLSTSRLR   84 (92)
T ss_dssp             EEEEESSCCCS
T ss_pred             EEEEEccCCCC
Confidence            99999976544

>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=3e-18  Score=117.92  Aligned_cols=86  Identities=13%  Similarity=0.300  Sum_probs=76.3

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ......+.++|||+|||..+++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+.. |+..+.
T Consensus         9 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~   83 (105)
T 2dh8_A            9 NNSGADEIGKLFVGGLDWSTTQET----LRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLD   83 (105)
T ss_dssp             CCCCSSSSSEECCBSCCTTCCHHH----HHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEET
T ss_pred             CcCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeEC
Confidence            344567889999999999999999    679999999999986654   678899999999999999999997 999999


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |+.|.|.++.++..
T Consensus        84 g~~l~V~~a~~~~~   97 (105)
T 2dh8_A           84 GRNIDPKPCTPRGM   97 (105)
T ss_dssp             TEEEBCCCSCCSSC
T ss_pred             CEEEEEEEccCCCC
Confidence            99999999876654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=6.2e-18  Score=116.12  Aligned_cols=76  Identities=25%  Similarity=0.448  Sum_probs=71.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhcc-CCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCe-eCCeEEEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQ-FPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLK-IGQQQLLITY  242 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~-~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~-~~g~~i~v~~  242 (245)
                      .++.+|||+|||..+++++|+++|+. ||.|..|.++.++    +|||||+|.+.++|..|+..|||.. |.|++|.|.+
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~   86 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSV   86 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEE
Confidence            35678999999999999999999999 9999999999863    6899999999999999999999999 9999999999


Q ss_pred             ec
Q 025973          243 AK  244 (245)
Q Consensus       243 ak  244 (245)
                      |+
T Consensus        87 a~   88 (104)
T 2dhg_A           87 AI   88 (104)
T ss_dssp             CC
T ss_pred             cc
Confidence            85

>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=4.2e-18  Score=120.20  Aligned_cols=80  Identities=35%  Similarity=0.539  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeE-EEEEecCHHHHHHHHHHHcCCccCC--ceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQ-AWLVFKDVASATAAVEKMQGFPFYD--KPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~-afV~F~~~~~A~~a~~~l~~~~~~g--~~i~   89 (245)
                      ..-..|||+||++.+++++    |+++|++||.|.+|++...  .+|+ |||+|.+.++|.+|++.|||..|.|  ++|+
T Consensus        26 s~VL~I~V~NL~~~vte~~----L~~lFs~yG~V~~V~i~~~--~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~Lr   99 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDV----LHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR   99 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHH----HHHHHTTSSCEEEEEEEEE--TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEE
T ss_pred             CceEEEEECCCCCCCCHHH----HHHHHhCcCCEEEEEEEcC--CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEE
Confidence            3445667999999999999    7799999999999977642  3577 9999999999999999999999998  8999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |+|+++...
T Consensus       100 I~~ak~~~l  108 (130)
T 3zzy_A          100 IDFSKLTSL  108 (130)
T ss_dssp             EEECSCSSC
T ss_pred             EEecCCCce
Confidence            999987754

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.74  E-value=5.7e-17  Score=113.95  Aligned_cols=75  Identities=25%  Similarity=0.259  Sum_probs=67.7

Q ss_pred             CCccE--EEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeE-EEEEeCCHHHHHHHHHHhCCCeeCC--eEEEEEEe
Q 025973          169 PPNNI--LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGI-AFVEYGDEMQATVAMQSLQSLKIGQ--QQLLITYA  243 (245)
Q Consensus       169 ~~~~~--l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~-afv~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~a  243 (245)
                      +++++  |||+||+..+++++|+++|+.||.|.+|.++.. .|+ |||+|.+.++|..|++.|||..|.|  ++|+|.||
T Consensus        21 ~ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           21 GGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             CCCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             CCCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            34555  579999999999999999999999999999764 586 9999999999999999999999987  69999999


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      |
T Consensus       100 k  100 (124)
T 2e5i_A          100 R  100 (124)
T ss_dssp             S
T ss_pred             c
Confidence            7

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.74  E-value=6.5e-18  Score=116.97  Aligned_cols=84  Identities=20%  Similarity=0.320  Sum_probs=70.0

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      .....+.++|||+|||.++++++    |+++|+.||.|.+|.+..   +|.++|||||+|.+.++|.+|+..+ +..+.|
T Consensus        19 ~~~~~~~~~lfV~nLp~~~te~~----L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g   93 (109)
T 2rs2_A           19 SHMGSSGCKMFIGGLSWQTTQEG----LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDS   93 (109)
T ss_dssp             -------CCEEEESCCTTCCHHH----HHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETT
T ss_pred             cccCCCCCEEEEeCCCCCCCHHH----HHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCC
Confidence            34466789999999999999999    779999999999997765   4788999999999999999999965 589999


Q ss_pred             ceEEEEEccccc
Q 025973           86 KPMRIQYAKTKS   97 (245)
Q Consensus        86 ~~i~v~~~~~~~   97 (245)
                      +.|.|.++.++.
T Consensus        94 ~~l~V~~a~~~~  105 (109)
T 2rs2_A           94 KTIDPKVAFPRR  105 (109)
T ss_dssp             EEEEEEECCCCC
T ss_pred             EEEEEEEccCCC
Confidence            999999987654

>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=99.74  E-value=1.2e-17  Score=114.48  Aligned_cols=80  Identities=24%  Similarity=0.441  Sum_probs=72.6

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ....+.++|||+|||.++++++    |+++|+.||.|..|.+.     ++||||+|.+.++|.+|++.||+..+.|+.|.
T Consensus         6 ~~~~~~~~l~V~nl~~~~t~~~----l~~~F~~~G~i~~v~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   76 (103)
T 2dgu_A            6 SGMAKVKVLFVRNLANTVTEEI----LEKAFSQFGKLERVKKL-----KDYAFIHFDERDGAVKAMEEMNGKDLEGENIE   76 (103)
T ss_dssp             CCCCCCCCEEEECCCTTCCHHH----HHHHHHHHSCEEEEEEC-----SSCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEE-----CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEE
Confidence            4456789999999999999999    77999999999999876     46999999999999999999999999999999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |.++.+...
T Consensus        77 v~~a~~~~~   85 (103)
T 2dgu_A           77 IVFAKPPDQ   85 (103)
T ss_dssp             EEECCCCCC
T ss_pred             EEEcCCCcc
Confidence            999976544

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1e-17  Score=112.17  Aligned_cols=83  Identities=10%  Similarity=0.095  Sum_probs=73.6

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .......++|||+|||.++++++    |+++|+.| .|..|.+.  .+|.++|||||+|.+.++|.+|+. ||+..+.|+
T Consensus         4 ~~~~~~~~~l~v~nLp~~~t~~~----l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr   77 (91)
T 2dgw_A            4 GSSGTTCHTVKLRGAPFNVTEKN----VMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGR   77 (91)
T ss_dssp             CCCCCCCCEEEEECCCSSCCHHH----HHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTE
T ss_pred             CCCCCCccEEEEECCCCCCCHHH----HHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCc
Confidence            34566789999999999999999    66999999 88887655  468889999999999999999999 999999999


Q ss_pred             eEEEEEccccc
Q 025973           87 PMRIQYAKTKS   97 (245)
Q Consensus        87 ~i~v~~~~~~~   97 (245)
                      .|.|.++..+.
T Consensus        78 ~i~v~~a~~~~   88 (91)
T 2dgw_A           78 YIEVFREKSGP   88 (91)
T ss_dssp             EEEEEEESSCC
T ss_pred             EEEEEECCcCC
Confidence            99999987653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.74  E-value=1.3e-17  Score=122.67  Aligned_cols=75  Identities=16%  Similarity=0.153  Sum_probs=69.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFP--GFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g--~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      ...+|||+|||..+++++|+++|+.||  .|..|+++.++     +|||||+|.+.++|.+|+..|||..|+|++|.|.+
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            456899999999999999999999999  99999998764     68999999999999999999999999999999999


Q ss_pred             ec
Q 025973          243 AK  244 (245)
Q Consensus       243 ak  244 (245)
                      |+
T Consensus       134 a~  135 (156)
T 3n9u_C          134 AT  135 (156)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.74  E-value=9.3e-17  Score=113.80  Aligned_cols=76  Identities=18%  Similarity=0.275  Sum_probs=71.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++++|||+|||..+++++|+++|+.||.|..|.+..++    +|||||+|.+.++|..|+..|||..|.|++|+|.||.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  112 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  112 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeC
Confidence            466789999999999999999999999999999998863    6899999999999999999999999999999999986

>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=99.74  E-value=6.2e-18  Score=116.11  Aligned_cols=75  Identities=28%  Similarity=0.406  Sum_probs=70.6

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +.++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.+.++|..|+..|||..|.|++|.|.||+
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            45679999999999999999999999999999998764     6899999999999999999999999999999999986

>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=1.7e-17  Score=113.93  Aligned_cols=83  Identities=11%  Similarity=0.129  Sum_probs=73.3

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE-EEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE-ILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~-i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      ..+....++|||+|||.++++++    |+++|+.||.|.. |.+.  .+|+++|||||+|.+.++|.+|+.. |+..+.|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~te~~----l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~g   83 (104)
T 1wg5_A            9 SPDTANDGFVRLRGLPFGCSKEE----IVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGH   83 (104)
T ss_dssp             CSSCSCCCEEEEESCCTTCCHHH----HHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCC
Confidence            34566789999999999999999    6799999999987 6544  4788999999999999999999996 9999999


Q ss_pred             ceEEEEEcccc
Q 025973           86 KPMRIQYAKTK   96 (245)
Q Consensus        86 ~~i~v~~~~~~   96 (245)
                      +.|.|.++..+
T Consensus        84 r~i~v~~~~~~   94 (104)
T 1wg5_A           84 RYIEIFKSSRA   94 (104)
T ss_dssp             SCCEEEEECTT
T ss_pred             cEEEEEECCHH
Confidence            99999987654

>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=99.74  E-value=1.5e-17  Score=121.93  Aligned_cols=82  Identities=18%  Similarity=0.375  Sum_probs=74.9

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .....+.++|||+|||.++++++    |+++|+.||.|.+|.+..+  ++|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus        67 ~~~~~~~~~l~V~nl~~~~t~~~----l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  140 (150)
T 2i2y_A           67 RDSCPLDCKVYVGNLGNNGNKTE----LERAFGYYGPLRSVWVARN--PPGFAFVEFEDPRDAADAVRELDGRTLCGCRV  140 (150)
T ss_dssp             SSSSTTSCEEEEESCCSCCSCHH----HHHHHHHHSCEEEEEECSS--SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCC
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHH----HHHHHHhhCCEEEEEEeeC--CCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            34466789999999999999999    7799999999999988865  58999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      +|.++.++
T Consensus       141 ~v~~a~~~  148 (150)
T 2i2y_A          141 RVELSNGE  148 (150)
T ss_dssp             EEEECCCC
T ss_pred             EEEEcCCC
Confidence            99998765

>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=9.7e-18  Score=115.36  Aligned_cols=76  Identities=21%  Similarity=0.309  Sum_probs=70.7

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      ....++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.++++|..|+.. |+..|.|++|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            3466789999999999999999999999999999999874     58999999999999999998 99999999999999


Q ss_pred             ec
Q 025973          243 AK  244 (245)
Q Consensus       243 ak  244 (245)
                      |+
T Consensus        92 a~   93 (105)
T 2dh8_A           92 CT   93 (105)
T ss_dssp             SC
T ss_pred             cc
Confidence            86

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=4.8e-17  Score=110.21  Aligned_cols=73  Identities=29%  Similarity=0.372  Sum_probs=67.7

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++++|||+||  .+++++|+++|+.||.|..|.+... +|||||+|.+.++|.+|+..|||..|.|++|.|.||+
T Consensus        13 ~~~~~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           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP-RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   85 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCS
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCC-CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECC
Confidence            35678999996  8999999999999999999999755 4999999999999999999999999999999999986

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.73  E-value=2.2e-18  Score=123.38  Aligned_cols=83  Identities=18%  Similarity=0.378  Sum_probs=73.3

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE--EEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCC----
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGF----   81 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~--i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~----   81 (245)
                      ...++++|||+|||.++++++    |+++|+.||.|..  |++.   .+|+++|||||+|.+. +|.+|+..||+.    
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~----L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~   93 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDS----ILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPL   93 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHH----HHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHH----HHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCc
Confidence            356789999999999999999    6799999999965  6544   3788999999999999 999999999999    


Q ss_pred             ccCCceEEEEEccccch
Q 025973           82 PFYDKPMRIQYAKTKSD   98 (245)
Q Consensus        82 ~~~g~~i~v~~~~~~~~   98 (245)
                      .+.|+.|.|.++.+...
T Consensus        94 ~~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           94 TIDGKTINVEFAKGSKR  110 (131)
T ss_dssp             CGGGCCCCCEECCCSCC
T ss_pred             cCCCEEEEEEECCCCCC
Confidence            99999999999976543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2.1e-18  Score=114.05  Aligned_cols=76  Identities=16%  Similarity=0.226  Sum_probs=70.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +++++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.++++|..|+..|||..+.|+.|+++++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            356789999999999999999999999999999998863     689999999999999999999999999999999887


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.73  E-value=3e-18  Score=124.60  Aligned_cols=84  Identities=27%  Similarity=0.504  Sum_probs=75.6

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE--------EEecCCCCeeeEEEEEecCHHHHHHHHHHHcCC
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--------ILAFKTLKHKGQAWLVFKDVASATAAVEKMQGF   81 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~--------i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~   81 (245)
                      .+..++++|||+|||.++++++    |+.+|+.||.|..        |.+..++.++|||||+|.+.++|.+|+..|||.
T Consensus        40 ~~~~~~~~l~V~nLp~~~te~~----L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~  115 (143)
T 3egn_A           40 EPGEPNCRIYVKNLAKHVQEKD----LKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGY  115 (143)
T ss_dssp             CCCSCCSEEEEEEECTTCCHHH----HHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCC
Confidence            4467889999999999999999    6699999998865        555678899999999999999999999999999


Q ss_pred             ccCCceEEEEEccccc
Q 025973           82 PFYDKPMRIQYAKTKS   97 (245)
Q Consensus        82 ~~~g~~i~v~~~~~~~   97 (245)
                      .+.|+.|.|.++....
T Consensus       116 ~~~g~~l~V~~a~~~~  131 (143)
T 3egn_A          116 VLFGKPMVVQFARSAR  131 (143)
T ss_dssp             EETTEECEEEECCCSC
T ss_pred             EeCCcEEEEEECCCCC
Confidence            9999999999997653

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=3.5e-17  Score=109.56  Aligned_cols=75  Identities=16%  Similarity=0.303  Sum_probs=69.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ....+|||+|||..+++++|+++|+.| .|..|.++.+.    +|+|||+|.+.++|..|+. |||..|+|+.|.|.+|+
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEES
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECC
Confidence            356789999999999999999999999 99999998763    6899999999999999999 99999999999999986


Q ss_pred             C
Q 025973          245 K  245 (245)
Q Consensus       245 ~  245 (245)
                      .
T Consensus        86 ~   86 (91)
T 2dgw_A           86 S   86 (91)
T ss_dssp             S
T ss_pred             c
Confidence            3

>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=1.1e-17  Score=115.91  Aligned_cols=83  Identities=16%  Similarity=0.391  Sum_probs=73.7

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCC-eEEEEec-C---CCCeeeEEEEEecCHHHHHHHHHHHc--CCccC
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGT-ILEILAF-K---TLKHKGQAWLVFKDVASATAAVEKMQ--GFPFY   84 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~-v~~i~~~-~---~~~~kg~afV~F~~~~~A~~a~~~l~--~~~~~   84 (245)
                      ..+.++|||+|||.++++++    |+++|+.||. |..|.+. .   ++.++|||||+|.+.++|.+|+..||  +..+.
T Consensus         5 s~~~~~l~V~nLp~~~t~~~----l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~   80 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREE----ILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLW   80 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHH----HHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBT
T ss_pred             ccCCCEEEEeCCCCcCCHHH----HHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceec
Confidence            45689999999999999999    6699999998 9998776 2   46789999999999999999999996  58999


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |+.|+|.++.++..
T Consensus        81 g~~l~V~~a~~~~~   94 (109)
T 2dis_A           81 GHQIAVDWAEPEID   94 (109)
T ss_dssp             TBCCEEEESCSSCS
T ss_pred             CCeEEEEEcCCCCC
Confidence            99999999977644

>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=99.73  E-value=2.9e-17  Score=121.15  Aligned_cols=76  Identities=24%  Similarity=0.314  Sum_probs=71.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.++++|..|+..||+..|.|++|.|.||
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            356789999999999999999999999999999998864     589999999999999999999999999999999999


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       117 ~  117 (156)
T 1h2v_Z          117 A  117 (156)
T ss_dssp             S
T ss_pred             C
Confidence            6

>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=99.73  E-value=1.9e-17  Score=122.07  Aligned_cols=84  Identities=19%  Similarity=0.274  Sum_probs=75.5

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ...+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+..||+..|.|+.
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  110 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQ----IYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI  110 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            345789999999999999999    679999999999987653   5778999999999999999999999999999999


Q ss_pred             EEEEEccccch
Q 025973           88 MRIQYAKTKSD   98 (245)
Q Consensus        88 i~v~~~~~~~~   98 (245)
                      |+|.++.+...
T Consensus       111 l~V~~a~~~~~  121 (156)
T 1h2v_Z          111 IRTDWDAGFKE  121 (156)
T ss_dssp             CEEEEESCCCT
T ss_pred             EEEEECCCCCC
Confidence            99999976543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2.3e-17  Score=111.62  Aligned_cols=75  Identities=17%  Similarity=0.258  Sum_probs=69.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEE-EecCC-CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVR-MVEAK-PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~-l~~~~-~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++|||+|||..+++++|+.+|+.||.|..++ ++.++ .+.|||+|.+.++|..|+..|||..|.|++|.|.||+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   90 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIP   90 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            456799999999999999999999999999994 77764 5679999999999999999999999999999999986

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.73  E-value=4.4e-18  Score=109.75  Aligned_cols=72  Identities=18%  Similarity=0.379  Sum_probs=66.1

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      +|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++ +|+..+.|+.|.|.+|
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 KIFVGGLSVNTTVED----VKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHH----HHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHH----HHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            589999999999999    669999999999987654   67889999999999999999998 9999999999999875

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.5e-17  Score=116.46  Aligned_cols=74  Identities=18%  Similarity=0.310  Sum_probs=69.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+.. |+..|.|++|.|.+|+
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            45789999999999999999999999999999999863     68999999999999999997 9999999999999986

>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=99.73  E-value=1.8e-17  Score=122.57  Aligned_cols=83  Identities=23%  Similarity=0.438  Sum_probs=75.5

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      .....++|||+|||.++++++    |+++|+.||.|..|.+..   +|.++|||||+|.+.++|.+|+..|||..+.|+.
T Consensus        66 ~~~~~~~l~v~nl~~~~~~~~----l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  141 (158)
T 2kn4_A           66 DVEGMTSLKVDNLTYRTSPDT----LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRE  141 (158)
T ss_dssp             CCCBCCEEEEESCCTTCCHHH----HHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSE
T ss_pred             CCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            345689999999999999999    679999999999997764   6789999999999999999999999999999999


Q ss_pred             EEEEEccccc
Q 025973           88 MRIQYAKTKS   97 (245)
Q Consensus        88 i~v~~~~~~~   97 (245)
                      |+|.++.+..
T Consensus       142 l~v~~a~~~~  151 (158)
T 2kn4_A          142 LRVQMARYGR  151 (158)
T ss_dssp             EEEEEECCSS
T ss_pred             EEEEECCCCC
Confidence            9999987653

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.73  E-value=1.1e-17  Score=114.99  Aligned_cols=75  Identities=21%  Similarity=0.349  Sum_probs=68.9

Q ss_pred             CccEEEEcCCCCCC------CHHHHHHHhccCCCeeEEEEecC---CCeEEEEEeCCHHHHHHHHHHhCCCeeCCe-EEE
Q 025973          170 PNNILFVQNVPHDT------TPMALQMFFSQFPGFKEVRMVEA---KPGIAFVEYGDEMQATVAMQSLQSLKIGQQ-QLL  239 (245)
Q Consensus       170 ~~~~l~v~nl~~~~------t~~~l~~~f~~~g~v~~v~l~~~---~~g~afv~f~~~~~A~~A~~~l~g~~~~g~-~i~  239 (245)
                      .+++|||+|||..+      |+++|+.+|+.||.|..|.+++.   .+|||||+|.+.++|..|+..|||..|.|+ +|+
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~   93 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   93 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEE
Confidence            45789999999999      78999999999999999998842   269999999999999999999999999998 999


Q ss_pred             EEEec
Q 025973          240 ITYAK  244 (245)
Q Consensus       240 v~~ak  244 (245)
                      |.+|.
T Consensus        94 V~~a~   98 (105)
T 2nlw_A           94 VNLFT   98 (105)
T ss_dssp             EECSC
T ss_pred             EEEcc
Confidence            99985

>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=1.1e-17  Score=118.67  Aligned_cols=84  Identities=14%  Similarity=0.174  Sum_probs=73.9

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE---EEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~---i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ......++|||+|||.++++++    |+++|+.||.|..   +....+|.++|||||+|.+.++|.+|+. ||+..|.|+
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~----l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr   94 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKH----VIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNR   94 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHH----HHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTS
T ss_pred             CCCCCCcEEEEeCCCCCCCHHH----HHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCc
Confidence            3455679999999999999999    6799999999854   4455689999999999999999999999 999999999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|.|.++..+..
T Consensus        95 ~i~V~~a~~~~~  106 (124)
T 1wel_A           95 FIQVHPITKKGM  106 (124)
T ss_dssp             CBEEEEECHHHH
T ss_pred             EEEEEECCHHHH
Confidence            999999876543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=4.2e-17  Score=111.34  Aligned_cols=73  Identities=19%  Similarity=0.261  Sum_probs=66.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC----CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA----KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~----~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++++|||+|||..+++++|+++|+.||.|   .++.+    .+|||||+|.++++|..|+..|||..|.|++|+|.||+
T Consensus        13 ~~~~~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           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQG   89 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcC
Confidence            467889999999999999999999999987   34443    26899999999999999999999999999999999986

>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=1.9e-17  Score=114.66  Aligned_cols=75  Identities=19%  Similarity=0.299  Sum_probs=67.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ...++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+..+ +..|+|++|.|.+|
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVA  101 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEc
Confidence            355779999999999999999999999999999998864     689999999999999999976 69999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       102 ~  102 (109)
T 2rs2_A          102 F  102 (109)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.73  E-value=3.3e-17  Score=112.27  Aligned_cols=84  Identities=17%  Similarity=0.239  Sum_probs=73.6

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      .....+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+.  ++..+.|
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g   82 (103)
T 2cqg_A            9 KRAVQKTSDLIVLGLPWKTTEQD----LKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDG   82 (103)
T ss_dssp             SCCCCCCCCEEEESCCSSCCHHH----HHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETT
T ss_pred             CCccCCCCEEEEEcCCCcCCHHH----HHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCC
Confidence            34566789999999999999999    779999999999986653   58899999999999999999999  4778999


Q ss_pred             ceEEEEEccccch
Q 025973           86 KPMRIQYAKTKSD   98 (245)
Q Consensus        86 ~~i~v~~~~~~~~   98 (245)
                      +.|.|.++.++..
T Consensus        83 ~~l~v~~a~~~~~   95 (103)
T 2cqg_A           83 RWCDCKLPNSKQS   95 (103)
T ss_dssp             EEEEEECCCTTCC
T ss_pred             eEEEEEecCCCCc
Confidence            9999999876544

>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=99.73  E-value=1.1e-17  Score=116.94  Aligned_cols=80  Identities=18%  Similarity=0.402  Sum_probs=72.3

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ..++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+ .||+..|.|+.|.|
T Consensus        24 ~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   98 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRD----LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIV   98 (114)
T ss_dssp             HHTEEEEESCCTTCCHHH----HHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEE
Confidence            357999999999999999    679999999999997764   4778999999999999999999 79999999999999


Q ss_pred             EEccccch
Q 025973           91 QYAKTKSD   98 (245)
Q Consensus        91 ~~~~~~~~   98 (245)
                      .++..+..
T Consensus        99 ~~a~~~~~  106 (114)
T 2cq4_A           99 QASQAEKN  106 (114)
T ss_dssp             EEHHHHHH
T ss_pred             EecCCCcc
Confidence            99876544

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.72  E-value=6.7e-18  Score=108.88  Aligned_cols=70  Identities=20%  Similarity=0.310  Sum_probs=66.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.++++|.+|++ +||..++|++|.|.+|
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            38999999999999999999999999999998764     6899999999999999998 9999999999999987

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1e-17  Score=112.71  Aligned_cols=73  Identities=22%  Similarity=0.351  Sum_probs=66.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCC-CeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPG-FKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQS-LKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~-v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g-~~~~g~~i~v~~ak  244 (245)
                      +.++|||+|||..+++++|+++|+.||. |..+.+. . +|||||+|.+.++|..|+..||| ..+.|++|+|.||+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-~-~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~   81 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-K-SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSV   81 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-E-TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-C-CCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEcc
Confidence            4567999999999999999999999999 6555553 3 58999999999999999999999 99999999999986

>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=99.72  E-value=1.8e-17  Score=110.30  Aligned_cols=74  Identities=18%  Similarity=0.275  Sum_probs=68.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .+.+|||+|||..+++++|+++|+.| .|.++.+... +|||||+|.++++|..|+..|||..+.|++|+|.||+.
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-DLKYCYVDRN-KRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEGG-GTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeCC-CcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            45679999999999999999999999 9999988643 59999999999999999999999999999999999863

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.72  E-value=8.5e-18  Score=120.33  Aligned_cols=75  Identities=23%  Similarity=0.399  Sum_probs=69.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeE--EEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCC----eeCCeE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKE--VRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSL----KIGQQQ  237 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~--v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~----~~~g~~  237 (245)
                      .++++|||+|||..+|+++|+++|+.||.|..  |+++.++     +|||||+|.+. +|..|+..|||.    .+.|++
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            45678999999999999999999999999966  9998865     79999999999 999999999999    999999


Q ss_pred             EEEEEec
Q 025973          238 LLITYAK  244 (245)
Q Consensus       238 i~v~~ak  244 (245)
                      |.|.||+
T Consensus       100 l~V~~a~  106 (131)
T 2m2b_A          100 INVEFAK  106 (131)
T ss_dssp             CCCEECC
T ss_pred             EEEEECC
Confidence            9999986

>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=99.72  E-value=1.4e-17  Score=121.91  Aligned_cols=82  Identities=35%  Similarity=0.519  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC--ceEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD--KPMR   89 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g--~~i~   89 (245)
                      +....+|||+||++.+++++    |+++|++||.|.+|++.. ..++|||||+|.+.++|.+|++.|||..|.|  +.|+
T Consensus        43 ps~vl~l~VgNL~~~vted~----L~~~Fs~fG~V~~V~i~~-k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~  117 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDV----LHQIFSKFGTVLKIITFT-KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR  117 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHH----HHHHHHHHSCEEEEEEEE-SSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEE
T ss_pred             CCceEEEEEeCcCCCCCHHH----HHHHHHhcCCEEEEEEEe-CCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEE
Confidence            33456689999999999999    779999999999998753 2357899999999999999999999999976  9999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |.|++++..
T Consensus       118 V~~Ak~~~l  126 (164)
T 1sjr_A          118 IDFSKLTSL  126 (164)
T ss_dssp             EEECSSSSC
T ss_pred             EEEecCCcc
Confidence            999987654

>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=99.72  E-value=2.6e-17  Score=120.49  Aligned_cols=73  Identities=25%  Similarity=0.250  Sum_probs=67.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-CeEEEEEeCCHHHHHHHHHHhCCCeeCC--eEEEEEEec
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-PGIAFVEYGDEMQATVAMQSLQSLKIGQ--QQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-~g~afv~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~ak  244 (245)
                      ..|||+||+..+|+++|+++|++||.|.+|.+...+ +|||||+|.+.++|..|++.|||..|.|  ++|+|+|||
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            458899999999999999999999999999997654 6899999999999999999999999965  999999997

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.72  E-value=2.9e-17  Score=122.22  Aligned_cols=84  Identities=19%  Similarity=0.319  Sum_probs=74.5

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ...++++|||+|||..+++++    |+.+|+.||.|..|.+.   .+|.++|||||+|.+.++|.+|+..|||..|.|+.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~----L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  143 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDE----IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT  143 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHH----HHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            345678999999999999999    77999999999998665   47889999999999999999999999999999999


Q ss_pred             EEEEEccccch
Q 025973           88 MRIQYAKTKSD   98 (245)
Q Consensus        88 i~v~~~~~~~~   98 (245)
                      |.|.|+..+..
T Consensus       144 l~V~~a~~~~~  154 (165)
T 1rk8_A          144 IQVDWCFVKGP  154 (165)
T ss_dssp             CEEEESEECC-
T ss_pred             EEEEEecCCCC
Confidence            99999876544

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.72  E-value=5.9e-18  Score=121.65  Aligned_cols=86  Identities=22%  Similarity=0.410  Sum_probs=76.5

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      ..+..+.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+..||+..+.|
T Consensus        41 ~~~~~~~~~l~V~nLp~~~te~~----L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g  116 (135)
T 2lea_A           41 PPDVEGMTSLKVDNLTYRTSPDT----LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG  116 (135)
T ss_dssp             CSSGGGCCCEEEECCCSSCHHHH----HHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            34455688999999999999999    679999999999987764   67889999999999999999999999999999


Q ss_pred             ceEEEEEccccch
Q 025973           86 KPMRIQYAKTKSD   98 (245)
Q Consensus        86 ~~i~v~~~~~~~~   98 (245)
                      +.|+|.++++...
T Consensus       117 ~~l~V~~a~~~~~  129 (135)
T 2lea_A          117 RELRVQMARYGRP  129 (135)
T ss_dssp             SCCEEEECCCCCC
T ss_pred             EEEEEEECCCCCC
Confidence            9999999876543

>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=99.72  E-value=1.3e-16  Score=111.33  Aligned_cols=76  Identities=14%  Similarity=0.300  Sum_probs=70.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCee--------CCe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKI--------GQQ  236 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~--------~g~  236 (245)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.++    +|||||+|.+.++|..|+..|||..|        .++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~  102 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE  102 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCC
Confidence            356789999999999999999999999999999999863    58999999999999999999999999        688


Q ss_pred             EEEEEEec
Q 025973          237 QLLITYAK  244 (245)
Q Consensus       237 ~i~v~~ak  244 (245)
                      +|.|.||+
T Consensus       103 ~l~v~~a~  110 (114)
T 1x5o_A          103 PLLCKFSG  110 (114)
T ss_dssp             CBEEEECC
T ss_pred             ceeEEccC
Confidence            89999986

>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=99.72  E-value=1.4e-17  Score=141.82  Aligned_cols=75  Identities=31%  Similarity=0.425  Sum_probs=70.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +.++|||+|||..+|+++|..+|+.||.|..|.|+.++     +|||||+|.+.++|..|+..|||..|.|++|.|.||+
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            55789999999999999999999999999999998763     7999999999999999999999999999999999986

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.3e-17  Score=115.33  Aligned_cols=76  Identities=25%  Similarity=0.455  Sum_probs=69.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCe----eEEEEecCC-CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGF----KEVRMVEAK-PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v----~~v~l~~~~-~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++++|||+|||..+++++|+++|+.||.|    ..+.+..++ +|||||+|.+.++|..|+..|||..|.|++|.|.||
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            466889999999999999999999999998    566666443 699999999999999999999999999999999999


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       103 ~  103 (115)
T 2cpx_A          103 K  103 (115)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=2.6e-17  Score=114.86  Aligned_cols=75  Identities=17%  Similarity=0.286  Sum_probs=69.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCe-eEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGF-KEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v-~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+..+|||+|||..+++++|+++|+.||.| ..|.++.++    +|||||+|.+.++|..|+.. |+..|.|+.|.|.+|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVV   91 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEEC
Confidence            356789999999999999999999999999 889988753    78999999999999999986 999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        92 ~   92 (114)
T 2cpy_A           92 T   92 (114)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=7.1e-18  Score=113.44  Aligned_cols=80  Identities=26%  Similarity=0.364  Sum_probs=70.1

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCC-eEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcC-CccCCceE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGT-ILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQG-FPFYDKPM   88 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~-v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~-~~~~g~~i   88 (245)
                      ...+.++|||+|||.++++++    |+++|+.||. |..+.+    .++|||||+|.+.++|.+|++.||+ ..+.|+.|
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~vv~~~~~----~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l   75 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADD----LRQLFGDRKLPLAGQVL----LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIM   75 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHH----HHHHHHHTTCCCSSCEE----EETTEEEECCSCHHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHH----HHHHHHHcCCceEEEEE----cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEE
Confidence            456789999999999999999    6799999999 555544    3578999999999999999999999 99999999


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      +|.++.++..
T Consensus        76 ~v~~a~~~~~   85 (93)
T 2cqh_A           76 EVDYSVSKKL   85 (93)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEccCccc
Confidence            9999976543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.72  E-value=2.4e-17  Score=115.74  Aligned_cols=75  Identities=17%  Similarity=0.277  Sum_probs=69.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPG---FKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~---v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      ....+|||+|||..+|+++|+++|+.||.   |..|.++.++    +|||||+|.+.++|.+|+. +||..|+|+.|.|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEE
Confidence            35678999999999999999999999999   8899988764    6899999999999999999 99999999999999


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      +|+
T Consensus        94 ~a~   96 (118)
T 2db1_A           94 KSH   96 (118)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            985

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.7e-17  Score=113.41  Aligned_cols=83  Identities=11%  Similarity=0.129  Sum_probs=71.8

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .......++|||+|||+++++++    |+++|+.||.+ +|.+.  ++++++|||||+|.+.++|.+|++ +|+..+.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~te~~----l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr   82 (102)
T 1wez_A            9 SFQSTTGHCVHMRGLPYRATEND----IYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHR   82 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHH----HHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCc
Confidence            34567789999999999999999    66999999965 66443  478899999999999999999996 799999999


Q ss_pred             eEEEEEccccc
Q 025973           87 PMRIQYAKTKS   97 (245)
Q Consensus        87 ~i~v~~~~~~~   97 (245)
                      .|.|.++....
T Consensus        83 ~i~V~~~~~~~   93 (102)
T 1wez_A           83 YVELFLNSTAG   93 (102)
T ss_dssp             CCEEEEECCCC
T ss_pred             EEEEEECCCCC
Confidence            99999876543

>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=99.72  E-value=1.9e-17  Score=114.90  Aligned_cols=77  Identities=27%  Similarity=0.417  Sum_probs=70.3

Q ss_pred             CCCCCCeEEEcCCCcc-cChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           11 EISPNNTIYINNLNEK-VKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~-~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      +..++++|||+|||.+ +++++    |+++|+.||.|..|.+     ++|||||+|.+.++|.+|+..||+..+.|+.|+
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~----l~~~F~~~G~v~~v~i-----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   93 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSD----VETIFSKYGRVAGCSV-----HKGYAFVQYSNERHARAAVLGENGRVLAGQTLD   93 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHH----HHHHHGGGSCCSEEEE-----ETTEEEEECSSSHHHHHHHHHHTTCEETTEECC
T ss_pred             CCCCCcEEEEeCCCcccCCHHH----HHHHHHhCCCeEEEEE-----eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            3445699999999999 99999    7799999999999987     579999999999999999999999999999999


Q ss_pred             EEEcccc
Q 025973           90 IQYAKTK   96 (245)
Q Consensus        90 v~~~~~~   96 (245)
                      |.++...
T Consensus        94 V~~a~~~  100 (110)
T 1wf1_A           94 INMAGEP  100 (110)
T ss_dssp             EEESCCC
T ss_pred             EEECCCC
Confidence            9998754

>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=2.7e-18  Score=114.80  Aligned_cols=78  Identities=24%  Similarity=0.471  Sum_probs=68.2

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      ++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.+ |.+|+..|||..+.|+.|+|.+
T Consensus         2 ~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~   76 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQ----VKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTE   76 (90)
T ss_dssp             EEEEEEEECTTSSHHH----HTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEE
T ss_pred             cEEEECCCCCCCCHHH----HHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEE
Confidence            6899999999999999    669999999999987764   4788999999999999 9999999999999999999999


Q ss_pred             ccccch
Q 025973           93 AKTKSD   98 (245)
Q Consensus        93 ~~~~~~   98 (245)
                      +.+...
T Consensus        77 a~~~~~   82 (90)
T 2ki2_A           77 ANPKKS   82 (90)
T ss_dssp             C-----
T ss_pred             cCCCCC
Confidence            876544

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=6.1e-18  Score=109.61  Aligned_cols=73  Identities=22%  Similarity=0.391  Sum_probs=66.7

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      ++|||+|||.++++++    |+++|++||.|..|.+..   ++.++|||||+|.+.++|.+|++.++ ..+.|+.|.|.+
T Consensus         1 ~~l~v~nlp~~~t~~~----l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~   75 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEG----LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKV   75 (77)
T ss_dssp             CCEEEESCCSSCCSHH----HHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEE
T ss_pred             CEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEe
Confidence            5799999999999999    669999999998886654   57889999999999999999999888 999999999988


Q ss_pred             c
Q 025973           93 A   93 (245)
Q Consensus        93 ~   93 (245)
                      +
T Consensus        76 a   76 (77)
T 1uaw_A           76 A   76 (77)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=99.72  E-value=6.4e-17  Score=111.00  Aligned_cols=76  Identities=17%  Similarity=0.305  Sum_probs=68.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKE-VRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~-v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ....+|||+|||..+++++|+++|+.||.|.. |.++.+.    +|||||+|.++++|.+|+.. |+..++|+.|.|.+|
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEEC
Confidence            35678999999999999999999999999987 8887653    68999999999999999997 999999999999988


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      .+
T Consensus        92 ~~   93 (104)
T 1wg5_A           92 SR   93 (104)
T ss_dssp             CT
T ss_pred             CH
Confidence            63

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.71  E-value=5.2e-17  Score=114.14  Aligned_cols=79  Identities=27%  Similarity=0.407  Sum_probs=68.9

Q ss_pred             CCCCe--EEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeE-EEEEecCHHHHHHHHHHHcCCccCC--ce
Q 025973           13 SPNNT--IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQ-AWLVFKDVASATAAVEKMQGFPFYD--KP   87 (245)
Q Consensus        13 ~~~~~--l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~-afV~F~~~~~A~~a~~~l~~~~~~g--~~   87 (245)
                      +++++  |||+||+..+++++    |+++|++||.|.+|++...   .|| |||+|.+.++|..|++.|||..|.|  +.
T Consensus        21 ~ps~vl~l~V~NL~~~vt~~~----L~~~Fs~yG~V~~v~i~~~---~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~   93 (124)
T 2e5i_A           21 GGNKVLLLSIQNPLYPITVDV----LYTVCNPVGKVQRIVIFKR---NGIQAMVEFESVLCAQKAKAALNGADIYAGCCT   93 (124)
T ss_dssp             CCCSEEEEEEESCCSCCCHHH----HHHHHTTTSCEEEEEEEES---SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSE
T ss_pred             CCCcEEEEEEcCcCCCCCHHH----HHHHHHhcCCEEEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeE
Confidence            44555  57999999999999    7799999999999977642   385 9999999999999999999999987  69


Q ss_pred             EEEEEccccch
Q 025973           88 MRIQYAKTKSD   98 (245)
Q Consensus        88 i~v~~~~~~~~   98 (245)
                      |+|.++++...
T Consensus        94 l~V~~Ak~~~l  104 (124)
T 2e5i_A           94 LKIEYARPTRL  104 (124)
T ss_dssp             EEEECCSCSCC
T ss_pred             EEEEEecCCcc
Confidence            99999987764

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=4.9e-17  Score=109.92  Aligned_cols=84  Identities=13%  Similarity=0.256  Sum_probs=72.1

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEE-ecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEIL-AFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~-~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      +.+.....++|||+|||.++++++    |+++|+.||.|..|+ +..+. ..+.|||+|.+.++|.+|+..|||..+.|+
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~~~~i~~~~-~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~   82 (96)
T 2e44_A            8 SVPKRQRIRKLQIRNIPPHLQWEV----LDSLLVQYGVVESCEQVNTDS-ETAVVNVTYSSKDQARQALDKLNGFQLENF   82 (96)
T ss_dssp             CCCCCCSCCCEEEEEECSSSCHHH----HHHHHHHHSCEEEEEEECCSS-SSEEEEEEESSHHHHHHHHHHHTTCBCSSC
T ss_pred             CCCCCCCCCEEEEEcCCCCCCHHH----HHHHHHhcCCeEEEEEeecCC-CCCEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            334455689999999999999999    679999999999994 55432 234499999999999999999999999999


Q ss_pred             eEEEEEcccc
Q 025973           87 PMRIQYAKTK   96 (245)
Q Consensus        87 ~i~v~~~~~~   96 (245)
                      .|+|.++.++
T Consensus        83 ~l~V~~a~~~   92 (96)
T 2e44_A           83 TLKVAYIPDE   92 (96)
T ss_dssp             BCEEEECCCC
T ss_pred             EEEEEEcCcc
Confidence            9999999775

>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=99.71  E-value=2.4e-17  Score=113.76  Aligned_cols=80  Identities=13%  Similarity=0.220  Sum_probs=70.5

Q ss_pred             CCCCCCeEEE--cCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCcc-----
Q 025973           11 EISPNNTIYI--NNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPF-----   83 (245)
Q Consensus        11 ~~~~~~~l~V--~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~-----   83 (245)
                      ...++++|||  +||+.++++++    |+++|++||.|..|.+..   .+|||||+|.+.++|.+|++.|||..+     
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~----L~~~F~~fG~v~~v~i~~---~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg   93 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQ----LLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKRAYVTLNGKEVVDDLG   93 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHH----HHHHHHHHSCEEEEECCT---TCSCEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             CCCCCCEEEEECCCCCCCCCHHH----HHHHHHhcCCeEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCEEccccC
Confidence            3567899999  77999999999    779999999999998764   379999999999999999999999987     


Q ss_pred             CCceEEEEEccccc
Q 025973           84 YDKPMRIQYAKTKS   97 (245)
Q Consensus        84 ~g~~i~v~~~~~~~   97 (245)
                      .|+.|.|.|+....
T Consensus        94 ~g~~l~v~~a~~~p  107 (114)
T 2cq2_A           94 QKITLYLNFVEKVQ  107 (114)
T ss_dssp             CEEECEEEEESCCC
T ss_pred             CCcEEEEEecccCc
Confidence            58899999986543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.71  E-value=1.5e-17  Score=116.81  Aligned_cols=83  Identities=7%  Similarity=0.127  Sum_probs=72.5

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCC---eEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGT---ILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~---v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ......++|||+|||.++++++    |+++|+.||.   |..|++.  ++|+++|||||+|.+.++|.+|++ +|+..+.
T Consensus        12 ~~~~~~~~l~V~nLp~~~te~~----l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~   86 (118)
T 2db1_A           12 PEGGEGYVVKLRGLPWSCSIED----VQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMG   86 (118)
T ss_dssp             SCBCCCCEEEEESCCTTCCHHH----HHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEET
T ss_pred             CCCCCCcEEEEeCCCCCCCHHH----HHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeEC
Confidence            3456689999999999999999    6799999998   6666443  468899999999999999999999 9999999


Q ss_pred             CceEEEEEccccc
Q 025973           85 DKPMRIQYAKTKS   97 (245)
Q Consensus        85 g~~i~v~~~~~~~   97 (245)
                      |+.|.|.++..+.
T Consensus        87 gr~i~V~~a~~~~   99 (118)
T 2db1_A           87 HRYIEVFKSHRTE   99 (118)
T ss_dssp             TEEEEEEEECHHH
T ss_pred             CeEEEEEECCHHH
Confidence            9999999986554

>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=1.1e-17  Score=119.82  Aligned_cols=85  Identities=7%  Similarity=0.105  Sum_probs=73.4

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCC---eEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGT---ILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~---v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      .++....++|||+|||+++|+++    |+++|+.||.   |..|.+.  +.|+++|||||+|.+.++|.+|++ +|+..+
T Consensus        38 ~~~~~~~~~lfVgnLp~~~te~d----L~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l  112 (136)
T 2hgl_A           38 GPEGGEGFVVKLRGLPWSCSVED----VQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESM  112 (136)
T ss_dssp             CSSCCTTCEEEEESCCTTCCHHH----HHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEES
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEE
Confidence            34566789999999999999999    6799999998   6665443  458899999999999999999999 999999


Q ss_pred             CCceEEEEEccccch
Q 025973           84 YDKPMRIQYAKTKSD   98 (245)
Q Consensus        84 ~g~~i~v~~~~~~~~   98 (245)
                      .|+.|.|.++..+..
T Consensus       113 ~gr~i~V~~a~~~e~  127 (136)
T 2hgl_A          113 GHRYIEVFKSHRTEM  127 (136)
T ss_dssp             SSSEEEEEECCHHHH
T ss_pred             CCEEEEEEECChHHH
Confidence            999999999865443

>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=99.71  E-value=1.3e-16  Score=109.32  Aligned_cols=74  Identities=22%  Similarity=0.258  Sum_probs=67.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+.  ++..|.|++|.|.||
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a   90 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLP   90 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEec
Confidence            355679999999999999999999999999999998864     5899999999999999998  478999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        91 ~   91 (103)
T 2cqg_A           91 N   91 (103)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.71  E-value=7.2e-17  Score=107.46  Aligned_cols=72  Identities=25%  Similarity=0.327  Sum_probs=63.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCee--CCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI--GQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~--~g~~i~v~~ak  244 (245)
                      ++..+|||+|||..+|+++|+++|+.||.|.++.++.+.+|||||+|.++++|..    ++|..+  .|++|.|.+|+
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~   82 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAE   82 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcC
Confidence            4567899999999999999999999999999999998878999999999999883    566554  59999999986

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.71  E-value=3.2e-17  Score=116.17  Aligned_cols=74  Identities=16%  Similarity=0.323  Sum_probs=69.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+ .|||..|.|++|.|.||+
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            35689999999999999999999999999999998753     689999999999999999 799999999999999986

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=8.7e-17  Score=109.94  Aligned_cols=73  Identities=27%  Similarity=0.489  Sum_probs=64.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++++|||+|||..+++++|+++|+.|+   .+.++.++     +|||||+|.++++|..|+..|||..|.|++|.|.||
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA   89 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            4567899999999999999999999885   44555442     689999999999999999999999999999999999


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        90 ~   90 (102)
T 2fc8_A           90 K   90 (102)
T ss_dssp             C
T ss_pred             c
Confidence            7

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.71  E-value=1.1e-17  Score=109.50  Aligned_cols=69  Identities=23%  Similarity=0.389  Sum_probs=63.6

Q ss_pred             cEEEEcCCCCCC------CHHHHHHHhccCCCeeEEEEecC---CCeEEEEEeCCHHHHHHHHHHhCCCeeCCe-EEEE
Q 025973          172 NILFVQNVPHDT------TPMALQMFFSQFPGFKEVRMVEA---KPGIAFVEYGDEMQATVAMQSLQSLKIGQQ-QLLI  240 (245)
Q Consensus       172 ~~l~v~nl~~~~------t~~~l~~~f~~~g~v~~v~l~~~---~~g~afv~f~~~~~A~~A~~~l~g~~~~g~-~i~v  240 (245)
                      ++|||+|||..+      ++++|+++|+.||.|..+.+.+.   .+|||||+|.++++|..|+..|||..|.|+ +|+|
T Consensus         2 ~~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            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            579999999999      78999999999999999998852   269999999999999999999999999999 8876

>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=99.71  E-value=3.7e-17  Score=113.21  Aligned_cols=76  Identities=22%  Similarity=0.346  Sum_probs=69.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEe-cC-----CCeEEEEEeCCHHHHHHHHHHhC--CCeeCCeEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPG-FKEVRMV-EA-----KPGIAFVEYGDEMQATVAMQSLQ--SLKIGQQQLL  239 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~-v~~v~l~-~~-----~~g~afv~f~~~~~A~~A~~~l~--g~~~~g~~i~  239 (245)
                      .++++|||+|||..+++++|+++|+.||. |.++.++ .+     .+|||||+|.++++|..|+..||  +..+.|++|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            35678999999999999999999999998 9999998 32     26999999999999999999996  5999999999


Q ss_pred             EEEec
Q 025973          240 ITYAK  244 (245)
Q Consensus       240 v~~ak  244 (245)
                      |.||+
T Consensus        86 V~~a~   90 (109)
T 2dis_A           86 VDWAE   90 (109)
T ss_dssp             EEESC
T ss_pred             EEEcC
Confidence            99996

>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=3.6e-18  Score=116.69  Aligned_cols=82  Identities=15%  Similarity=0.341  Sum_probs=71.2

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE--EecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI--LAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i--~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ...+.++|||+|||.++++++    |+++|+.||.|..+  ....++.++|||||+|.+.++|.+|++ ||+..+.|+.|
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l   87 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAE----LKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEI   87 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHH----HHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHH----HHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEE
Confidence            345689999999999999999    66999999988762  223467889999999999999999999 99999999999


Q ss_pred             EEEEccccc
Q 025973           89 RIQYAKTKS   97 (245)
Q Consensus        89 ~v~~~~~~~   97 (245)
                      +|.++.++.
T Consensus        88 ~V~~a~~~~   96 (101)
T 1fj7_A           88 KLEKPKGRD   96 (101)
T ss_dssp             EEECCSCCC
T ss_pred             EEEEcCCCC
Confidence            999987654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=7e-17  Score=111.37  Aligned_cols=73  Identities=14%  Similarity=0.221  Sum_probs=67.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+|||+|||..+++++|+++|+.| .|..|.++.++    +|||||+|.++++|.+|+ .+|+..|+|+.|.|..|+
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-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            45689999999999999999999999 89999998754    799999999999999999 599999999999998875

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=1.4e-17  Score=107.87  Aligned_cols=70  Identities=20%  Similarity=0.347  Sum_probs=66.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +|||+|||..+++++|+++|+.||.|..+.++.++     +|+|||+|.++++|..|+..++ ..+.|++|.|.+|
T Consensus         2 ~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            59999999999999999999999999999998864     6899999999999999999998 9999999999997

>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=2.3e-17  Score=116.93  Aligned_cols=75  Identities=15%  Similarity=0.296  Sum_probs=66.1

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEec-C---C-CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE-A---K-PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~-~---~-~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ....+|||+|||..+++++|+++|+.||.|..+.++. .   + +|||||+|.+.++|..|+. +||..|+|+.|.|.+|
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            3557899999999999999999999999997633333 2   1 6999999999999999999 9999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus       102 ~  102 (124)
T 1wel_A          102 T  102 (124)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.70  E-value=3.4e-17  Score=116.08  Aligned_cols=79  Identities=24%  Similarity=0.370  Sum_probs=71.6

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ..++|||+|||.++++++    |+++|+.||.|.+|.+.   .++.++|||||+|.+.++|.+|+ .||+..+.|+.|+|
T Consensus        35 ~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V  109 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQD----LEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKV  109 (124)
T ss_dssp             HHTEEEEEEECTTCCHHH----HHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEE
Confidence            368999999999999999    67999999999998665   47889999999999999999999 69999999999999


Q ss_pred             EEccccc
Q 025973           91 QYAKTKS   97 (245)
Q Consensus        91 ~~~~~~~   97 (245)
                      .+++...
T Consensus       110 ~~a~~~~  116 (124)
T 2jwn_A          110 LPKRTNM  116 (124)
T ss_dssp             EESSCCC
T ss_pred             EECCCCC
Confidence            9987543

>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=99.70  E-value=3e-17  Score=109.20  Aligned_cols=78  Identities=18%  Similarity=0.318  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      ...++|||+|||.++++++    |+++|++| .|..|.+.   +++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~-~v~~~~i~---~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   74 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQE----VHDLLKDY-DLKYCYVD---RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL   74 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHH----HHHHTCSS-CCCCEEEE---GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHhhC-CeEEEEEe---CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEE
Confidence            4578999999999999999    67999999 89888774   6789999999999999999999999999999999999


Q ss_pred             ccccch
Q 025973           93 AKTKSD   98 (245)
Q Consensus        93 ~~~~~~   98 (245)
                      +.....
T Consensus        75 a~~~~~   80 (88)
T 1wg1_A           75 QPTDAL   80 (88)
T ss_dssp             CCCCCC
T ss_pred             cCCCce
Confidence            876543

>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=99.70  E-value=7.3e-18  Score=112.67  Aligned_cols=72  Identities=24%  Similarity=0.369  Sum_probs=67.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ++|||+|||..+++++|+++|+.||.|.++.++.++     +|||||+|.+.+ |..|+..|||..++|++|+|.+|.
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-VSEAIAKLDNTDFMGRTIRVTEAN   78 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC-
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcC
Confidence            469999999999999999999999999999998753     689999999999 999999999999999999999986

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=9.2e-17  Score=108.80  Aligned_cols=80  Identities=19%  Similarity=0.358  Sum_probs=71.3

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ....++++|||+||  ++++++    |+++|+.||.|..|.+.   .++|||||+|.+.++|.+|+..||+..+.|+.|+
T Consensus        10 ~~~~~~~~l~V~n~--~~t~~~----l~~~F~~~G~i~~v~i~---~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   80 (97)
T 1x5p_A           10 RAPRKGNTLYVYGE--DMTPTL----LRGAFSPFGNIIDLSMD---PPRNCAFVTYEKMESADQAVAELNGTQVESVQLK   80 (97)
T ss_dssp             CCCCCCSEEEEECS--SCCHHH----HHHHHTTTSCEEEEEEE---TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEE
T ss_pred             CCCCCCCEEEEcCC--CCCHHH----HHHHHhhCCCEEEEEec---CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            44567899999996  899999    77999999999999874   5679999999999999999999999999999999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |.++.++..
T Consensus        81 v~~a~~~~~   89 (97)
T 1x5p_A           81 VNIARKQPM   89 (97)
T ss_dssp             EECCSSCCC
T ss_pred             EEECCCCCC
Confidence            999876543

>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=99.70  E-value=1e-16  Score=109.54  Aligned_cols=74  Identities=18%  Similarity=0.246  Sum_probs=67.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ....+|||+|||..+|+++|+++|+.||.+ .|.++.++    +|||||+|.++++|.+|+. +|+..|+|+.|.|.+|.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            355789999999999999999999999954 89988764    6899999999999999995 79999999999999875

>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=99.70  E-value=4.9e-17  Score=116.54  Aligned_cols=75  Identities=19%  Similarity=0.294  Sum_probs=69.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPG---FKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~---v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      ....+|||+|||..+|+++|+++|+.||.   |..|.++.++    +|||||+|.+.++|.+|+. +||..|+|+.|.|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVF  120 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            35678999999999999999999999999   8889998764    6899999999999999999 99999999999999


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      +|+
T Consensus       121 ~a~  123 (136)
T 2hgl_A          121 KSH  123 (136)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            985

>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=114.00  Aligned_cols=85  Identities=12%  Similarity=0.092  Sum_probs=73.9

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCC---eEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGT---ILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~---v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      ..+....++|||+|||.++++++    |+++|+.||.   |..|.+..  .|+++|||||+|.+.++|.+|+. +|+..+
T Consensus         5 ~~~~~~~~~l~V~nLp~~~te~~----l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~   79 (107)
T 2lmi_A            5 EEEVDDVFLIRAQGLPWSCTMED----VLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYM   79 (107)
T ss_dssp             CCCCSSCCEEEEECCCSSCCSHH----HHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCS
T ss_pred             cCCCCCccEEEEeCCCCCCCHHH----HHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCccee
Confidence            34466789999999999999999    6699999988   77776553  57889999999999999999999 999999


Q ss_pred             CCceEEEEEccccch
Q 025973           84 YDKPMRIQYAKTKSD   98 (245)
Q Consensus        84 ~g~~i~v~~~~~~~~   98 (245)
                      .|+.|.|.++.....
T Consensus        80 ~gr~i~V~~a~~~~~   94 (107)
T 2lmi_A           80 GQRYVEVYEINNEDV   94 (107)
T ss_dssp             SSSCCCCEECCHHHH
T ss_pred             CCeEEEEEECCHHHH
Confidence            999999999876543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=3.3e-17  Score=114.76  Aligned_cols=80  Identities=14%  Similarity=0.343  Sum_probs=72.2

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      +.++|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|
T Consensus        26 ~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V  100 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEES----LRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEP  100 (116)
T ss_dssp             HHTEEEEECCTTCCCHHH----HHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEE
Confidence            368999999999999999    679999999999887664   578899999999999999999996 999999999999


Q ss_pred             EEccccch
Q 025973           91 QYAKTKSD   98 (245)
Q Consensus        91 ~~~~~~~~   98 (245)
                      .++.++..
T Consensus       101 ~~a~~~~~  108 (116)
T 1x4b_A          101 KRAVAREE  108 (116)
T ss_dssp             ECCSSCCC
T ss_pred             EECCCCcc
Confidence            99977654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.69  E-value=4.8e-17  Score=110.00  Aligned_cols=75  Identities=20%  Similarity=0.335  Sum_probs=67.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC-CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~-~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.++|||+|||..+++++|+++|+.||.|..+ ...+ .+|||||+|.+.++|..|+..|||..+.|++|.|.||+
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   89 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcC
Confidence            456889999999999999999999999998777 2222 26999999999999999999999999999999999985

>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=99.69  E-value=1.3e-16  Score=106.27  Aligned_cols=80  Identities=18%  Similarity=0.363  Sum_probs=62.3

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCcc--CCc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPF--YDK   86 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~--~g~   86 (245)
                      .....+.++|||+|||.++++++    |+++|++||.|.+|.+..+  ++|||||+|.+.++|.+    +++..+  .|+
T Consensus         5 ~~~~~~~~~l~V~~Lp~~~te~~----L~~~F~~~G~i~~v~i~~~--srGfaFV~F~~~~~A~~----~~~~~~~~~g~   74 (89)
T 3d2w_A            5 HHHHHHGSKVFVGRCTEDMTAEE----LQQFFCQYGEVVDVFIPKP--FRAFAFVTFADDKVAQS----LCGEDLIIKGI   74 (89)
T ss_dssp             ------CCEEEEESCCTTCCHHH----HHHHHTTTSCEEEEECCSS--CCSEEEEEESCHHHHHH----HTTCEEEETTE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHhccCCEEEEEEeeC--CCCEEEEEECCHHHHHH----HcCCCcccCCE
Confidence            44567889999999999999999    7799999999999988864  78999999999999983    566554  489


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|.|.++.++..
T Consensus        75 ~v~v~~a~~k~~   86 (89)
T 3d2w_A           75 SVHISNAEPKHN   86 (89)
T ss_dssp             EEEEEECC----
T ss_pred             EEEEEEcCCCCc
Confidence            999999876543

>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=106.70  Aligned_cols=72  Identities=19%  Similarity=0.281  Sum_probs=65.4

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      +|||+|||.++++++    |+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|++ +++..+.|+.|.|.++
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 KIFVGGLSPDTPEEK----IREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHH----HHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            599999999999999    669999999999987654   57889999999999999999999 5999999999999875

>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=1.6e-16  Score=123.16  Aligned_cols=76  Identities=21%  Similarity=0.275  Sum_probs=70.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.++|||+|||..+|+++|+++|+.||.|.+|++++++     +|||||+|.+.++|..|+..+|+..+.|+.|++.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            356789999999999999999999999999999999864     689999999999999999999999999999999987


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      .
T Consensus        93 ~   93 (213)
T 4f02_A           93 Q   93 (213)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.69  E-value=8.5e-17  Score=116.89  Aligned_cols=76  Identities=20%  Similarity=0.451  Sum_probs=67.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEecC--CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEE
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKE--------VRMVEA--KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQL  238 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~--------v~l~~~--~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i  238 (245)
                      .++++|||+|||..+|+++|+.+|+.||.|..        +.+...  .+|||||+|.+.++|..|+..|||..|.|++|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            35678999999999999999999999998865        444432  27999999999999999999999999999999


Q ss_pred             EEEEec
Q 025973          239 LITYAK  244 (245)
Q Consensus       239 ~v~~ak  244 (245)
                      .|.||+
T Consensus       123 ~V~~a~  128 (143)
T 3egn_A          123 VVQFAR  128 (143)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            999996

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.68  E-value=1.1e-16  Score=120.21  Aligned_cols=84  Identities=23%  Similarity=0.372  Sum_probs=75.5

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ....++++|||+|||..+++++    |.++|+.||.|..|.+..  ++.++|||||+|.+.++|.+|++.||+..+.|+.
T Consensus        83 ~~~~~~~~l~V~nLp~~~te~~----L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~  158 (177)
T 2f3j_A           83 EGVETGAKLLVSNLDFGVSDAD----IQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRP  158 (177)
T ss_dssp             SSCTTCEEEEEECCCSCCCHHH----HHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEE
Confidence            3456789999999999999999    669999999999987664  5788999999999999999999999999999999


Q ss_pred             EEEEEccccc
Q 025973           88 MRIQYAKTKS   97 (245)
Q Consensus        88 i~v~~~~~~~   97 (245)
                      |+|.++....
T Consensus       159 l~V~~a~~~~  168 (177)
T 2f3j_A          159 MDIQLVASQI  168 (177)
T ss_dssp             CEEEEESSGG
T ss_pred             EEEEEecCCC
Confidence            9999987653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.51  E-value=2.4e-18  Score=120.65  Aligned_cols=84  Identities=37%  Similarity=0.583  Sum_probs=75.0

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE--------EEecC---CCCeeeEEEEEecCHHHHHHHHHHHc
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--------ILAFK---TLKHKGQAWLVFKDVASATAAVEKMQ   79 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~--------i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~   79 (245)
                      +..+.++|||+|||.++++++    |+++|+.||.|..        |.+..   ++.++|||||+|.+.++|.+|+..||
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~   78 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIES----VADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD   78 (116)
Confidence            456789999999999999999    6699999999987        65543   57889999999999999999999999


Q ss_pred             CCccCCceEEEEEccccch
Q 025973           80 GFPFYDKPMRIQYAKTKSD   98 (245)
Q Consensus        80 ~~~~~g~~i~v~~~~~~~~   98 (245)
                      +..+.|+.|+|.++.++..
T Consensus        79 g~~~~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           79 GKEFSGNPIKVSFATRRAD   97 (116)
Confidence            9999999999999877654

>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=99.68  E-value=8.1e-17  Score=112.52  Aligned_cols=73  Identities=15%  Similarity=0.193  Sum_probs=66.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeE-----EEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQ-----LLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~-----i~v~~ak  244 (245)
                      ...+|||+|||..+++++|+++|+.||.|..|.++.+  |||||+|.+.++|..|+..|||..|.|++     |+|..++
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~   92 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   92 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCC
Confidence            4567999999999999999999999999999999877  89999999999999999999999999998     6666553

>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=99.68  E-value=8.8e-17  Score=125.67  Aligned_cols=75  Identities=21%  Similarity=0.266  Sum_probs=69.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFP--GFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g--~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      ..++|||+||+..+|+++|+++|+.||  .|.+|.|+.++     +|||||+|.+.++|.+|+..|||..|.|++|+|.|
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            456799999999999999999999999  99999999874     68999999999999999999999999999999999


Q ss_pred             ec
Q 025973          243 AK  244 (245)
Q Consensus       243 ak  244 (245)
                      |+
T Consensus       147 a~  148 (229)
T 3q2s_C          147 VN  148 (229)
T ss_dssp             CC
T ss_pred             CC
Confidence            86

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=5.5e-17  Score=111.89  Aligned_cols=78  Identities=6%  Similarity=0.145  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      ..++|||+|||.++++++    |+++|+.| .|..|.+.  ++|+++|||||+|.+.++|.+|+. +|+..+.|+.|.|.
T Consensus        15 ~~~~v~V~nLp~~~te~d----l~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   88 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMEND----VRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVS   88 (109)
T ss_dssp             HHHEEEEECCCSSCCHHH----HHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHHH-TTTEEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEE
Confidence            357999999999999999    66999999 78888665  367889999999999999999995 99999999999998


Q ss_pred             Eccccc
Q 025973           92 YAKTKS   97 (245)
Q Consensus        92 ~~~~~~   97 (245)
                      .+....
T Consensus        89 ~a~~~~   94 (109)
T 2dnn_A           89 PATERQ   94 (109)
T ss_dssp             ECCHHH
T ss_pred             ECCccc
Confidence            886543

>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=99.68  E-value=1.6e-16  Score=111.03  Aligned_cols=75  Identities=16%  Similarity=0.263  Sum_probs=65.3

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce-----
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP-----   87 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~-----   87 (245)
                      ...++|||+|||.++++++    |.++|+.||.|..|.+..+    |||||+|.+.++|.+|++.||+..|.|+.     
T Consensus        14 r~~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~~~i~~~----g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~   85 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQD----LKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   85 (115)
T ss_dssp             ---CCEEEEECCSSCCTTH----HHHHHGGGSCEEEEEECTT----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEecC----CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEE
Confidence            4679999999999999999    6699999999999988765    89999999999999999999999999998     


Q ss_pred             EEEEEccc
Q 025973           88 MRIQYAKT   95 (245)
Q Consensus        88 i~v~~~~~   95 (245)
                      |+|..+.+
T Consensus        86 i~v~~~~~   93 (115)
T 3beg_B           86 IRVKVDGP   93 (115)
T ss_dssp             CEEEECC-
T ss_pred             EEeccCCC
Confidence            66666544

>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=99.68  E-value=6.3e-17  Score=126.52  Aligned_cols=81  Identities=20%  Similarity=0.176  Sum_probs=72.3

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccC--CeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFG--TILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G--~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..++|||+|||.++++++    |+++|+.||  .|.+|.+.   .+++++|||||+|.+.++|.+|++.||+..|.|+.|
T Consensus        67 ~~~~lfVgnL~~~~te~~----L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l  142 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDED----LTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNP  142 (229)
T ss_dssp             --CEEEEESCCTTCCHHH----HHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCC
T ss_pred             CccEEEEeCCCCCCCHHH----HHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEe
Confidence            567899999999999999    669999999  89988654   378899999999999999999999999999999999


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      +|.++.....
T Consensus       143 ~V~~a~~~~~  152 (229)
T 3q2s_C          143 VVTPVNKQFL  152 (229)
T ss_dssp             EEEECCHHHH
T ss_pred             EEEECCCCcc
Confidence            9999976543

>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=99.67  E-value=2.3e-16  Score=104.62  Aligned_cols=71  Identities=27%  Similarity=0.368  Sum_probs=66.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccC----C-------CeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQF----P-------GFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQL  238 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~----g-------~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i  238 (245)
                      +.++|||+|||..+++++|+++|+.|    |       .|.++.+..++ |||||+|.++++|..|+ .|||..+.|++|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~k-g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   82 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK-NFAFLEFRSVDETTQAM-AFDGIIFQGQSL   82 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSS-SEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCC-cEEEEEcCCHHHHHHHH-hcCCCEECCeEE
Confidence            56789999999999999999999999    8       89999998875 99999999999999999 999999999999


Q ss_pred             EEEE
Q 025973          239 LITY  242 (245)
Q Consensus       239 ~v~~  242 (245)
                      +|+.
T Consensus        83 ~V~r   86 (87)
T 2hzc_A           83 KIRR   86 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9974

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=1.8e-16  Score=106.77  Aligned_cols=79  Identities=18%  Similarity=0.236  Sum_probs=68.5

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .....++|||+|||.++++++    |+++|+.||.|.+|...+ ++.   ||||+|.+.++|.+|+. ||+..+.|+.|.
T Consensus         4 ~~~~~~~l~V~nl~~~~t~~~----l~~~F~~~G~v~~v~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~   75 (94)
T 2e5g_A            4 GSSGLRSVFVSGFPRGVDSAQ----LSEYFLAFGPVASVVMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLR   75 (94)
T ss_dssp             CCTTCCEEEEECCCTTCCHHH----HHHHGGGTSCEEEEEECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECC
T ss_pred             ccCCCCEEEEECCCCCCCHHH----HHHHHHhcCCeEEEEEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEE
Confidence            355678999999999999999    679999999999984433 332   99999999999999999 999999999999


Q ss_pred             EEEccccc
Q 025973           90 IQYAKTKS   97 (245)
Q Consensus        90 v~~~~~~~   97 (245)
                      |.++..+.
T Consensus        76 V~~a~~~~   83 (94)
T 2e5g_A           76 VRPREQKE   83 (94)
T ss_dssp             CBCSCCSC
T ss_pred             EEECCcCC
Confidence            99876543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.67  E-value=2.3e-16  Score=118.44  Aligned_cols=76  Identities=18%  Similarity=0.275  Sum_probs=71.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++++|||+|||..+++++|+++|+.||.|..|.++.++    +|||||+|.+.++|..|+..|||..|.|++|.|.||.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            467899999999999999999999999999999998753    6899999999999999999999999999999999985

>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=99.67  E-value=3.4e-17  Score=105.54  Aligned_cols=70  Identities=19%  Similarity=0.359  Sum_probs=65.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.++++|..|+. +++..+.|++|.|.+|
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            48999999999999999999999999999998753     6899999999999999998 5899999999999987

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1e-16  Score=112.80  Aligned_cols=81  Identities=16%  Similarity=0.177  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCe----EEEE--ecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTI----LEIL--AFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v----~~i~--~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ...++|||+|||+++++++    |+++|+.||.|    ..|+  ...+|+++|||||+|.+.++|.+|++. |+..+.|+
T Consensus        21 ~~~~~v~V~nLp~~~te~d----l~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR   95 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEE----VVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKR   95 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHH----HHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSC
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCe
Confidence            5578999999999999999    66999999975    3443  336889999999999999999999995 99999999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|.|..+..+..
T Consensus        96 ~i~V~~a~~~e~  107 (123)
T 2dha_A           96 YIELFRSTAAEV  107 (123)
T ss_dssp             EECCEEECHHHH
T ss_pred             EEEEEECCHHHH
Confidence            999988765443

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.67  E-value=5.8e-16  Score=106.04  Aligned_cols=76  Identities=12%  Similarity=0.179  Sum_probs=67.8

Q ss_pred             CCccEEEEcCCCC-----CCCHHHHHHHhccCCCeeEEEEecCC------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeE
Q 025973          169 PPNNILFVQNVPH-----DTTPMALQMFFSQFPGFKEVRMVEAK------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQ  237 (245)
Q Consensus       169 ~~~~~l~v~nl~~-----~~t~~~l~~~f~~~g~v~~v~l~~~~------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~  237 (245)
                      .++++|+|+||..     ..++++|++.|++||.|.+|.++.++      +|+|||+|.++++|.+|+..|||..|.|++
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4678999999963     23789999999999999999998642      699999999999999999999999999999


Q ss_pred             EEEEEec
Q 025973          238 LLITYAK  244 (245)
Q Consensus       238 i~v~~ak  244 (245)
                      |.|.||.
T Consensus        86 i~v~~a~   92 (105)
T 2pe8_A           86 VKACFYN   92 (105)
T ss_dssp             CEEEECC
T ss_pred             EEEEEcC
Confidence            9999985

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.67  E-value=4.2e-17  Score=111.35  Aligned_cols=73  Identities=16%  Similarity=0.244  Sum_probs=65.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC-----CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-----KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~-----~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +..+|||+|||..+++++|+++|+.||.|.. .++.+     .+|||||+|.+.++|..|++ |||..|.|++|.|.+|+
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcC
Confidence            4678999999999999999999999998866 33332     26899999999999999998 99999999999999986

>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=99.67  E-value=1e-16  Score=113.12  Aligned_cols=81  Identities=12%  Similarity=0.133  Sum_probs=70.1

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeE--EEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~--~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      .+....++|||+|||+++++++    |+++|+.| .|.  .|.+.  ++|+++|||||+|.+.++|.+|++ +++..+.|
T Consensus        37 ~~~~~~~~lfVgnLp~~~te~d----L~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~g  110 (126)
T 2hgm_A           37 ADSANDGFVRLRGLPFGCTKEE----IVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGH  110 (126)
T ss_dssp             TCSSSCCEEEEECCCTTCCHHH----HHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECC
Confidence            4456789999999999999999    67999999 566  77655  358899999999999999999999 58899999


Q ss_pred             ceEEEEEcccc
Q 025973           86 KPMRIQYAKTK   96 (245)
Q Consensus        86 ~~i~v~~~~~~   96 (245)
                      +.|.|..+..+
T Consensus       111 R~I~V~~a~~~  121 (126)
T 2hgm_A          111 RYIEVFKSSQE  121 (126)
T ss_dssp             BCCCCEEECHH
T ss_pred             EEEEEEECCHH
Confidence            99999887644

>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=99.67  E-value=1.4e-16  Score=105.63  Aligned_cols=73  Identities=21%  Similarity=0.428  Sum_probs=66.1

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhccc----C-------CeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcC
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQF----G-------TILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQG   80 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~----G-------~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~   80 (245)
                      ..+.++|||+|||.++++++    |+++|+.|    |       .|.++.+.++   +|||||+|.+.++|.+|+ .||+
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~----l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~---kg~afV~f~~~~~a~~A~-~l~g   74 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEA----MMDFFNAQMRLGGLTQAPGNPVLAVQINQD---KNFAFLEFRSVDETTQAM-AFDG   74 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHH----HHHHHHHHHHHTTCCSSSSCSEEEEEECSS---SSEEEEEESSHHHHHHHG-GGTT
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHHHhhhcccccCCCCcceEEEecCC---CcEEEEEcCCHHHHHHHH-hcCC
Confidence            45679999999999999999    66999999    8       8999988754   799999999999999999 8999


Q ss_pred             CccCCceEEEEE
Q 025973           81 FPFYDKPMRIQY   92 (245)
Q Consensus        81 ~~~~g~~i~v~~   92 (245)
                      ..+.|+.|+|..
T Consensus        75 ~~~~g~~l~V~r   86 (87)
T 2hzc_A           75 IIFQGQSLKIRR   86 (87)
T ss_dssp             CEETTEECEEEC
T ss_pred             CEECCeEEEEeC
Confidence            999999999874

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.67  E-value=5.1e-16  Score=115.14  Aligned_cols=81  Identities=25%  Similarity=0.446  Sum_probs=74.0

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ....+.++|||+|||..+++++    |+++|+.||.|..+.+.   .+|.++|+|||+|.+.++|.+|+..|||..+.|+
T Consensus        82 ~~~~~~~~l~v~nl~~~~t~~~----l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  157 (166)
T 3md3_A           82 SSSDDTFNLFVGDLNVNVDDET----LRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR  157 (166)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHH----HHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCceEEECCCCCCCCHHH----HHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCc
Confidence            3456789999999999999999    67999999999998665   4688999999999999999999999999999999


Q ss_pred             eEEEEEcc
Q 025973           87 PMRIQYAK   94 (245)
Q Consensus        87 ~i~v~~~~   94 (245)
                      .|+|.|++
T Consensus       158 ~i~v~~a~  165 (166)
T 3md3_A          158 PLRINWAA  165 (166)
T ss_dssp             ECEEEESC
T ss_pred             EEEEEecC
Confidence            99999985

>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=99.67  E-value=6.9e-17  Score=111.44  Aligned_cols=74  Identities=18%  Similarity=0.217  Sum_probs=68.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPG---FKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~---v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      ...+|||+|||..+|+++|+++|+.||.   |..|.++.++    +|||||+|.+.++|..|+. +|+..++|+.|.|.+
T Consensus        10 ~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (107)
T 2lmi_A           10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYE   88 (107)
T ss_dssp             SCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEE
Confidence            5678999999999999999999999888   8999998764    6899999999999999999 999999999999999


Q ss_pred             ec
Q 025973          243 AK  244 (245)
Q Consensus       243 ak  244 (245)
                      |+
T Consensus        89 a~   90 (107)
T 2lmi_A           89 IN   90 (107)
T ss_dssp             CC
T ss_pred             CC
Confidence            85

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=3.7e-16  Score=105.15  Aligned_cols=74  Identities=22%  Similarity=0.281  Sum_probs=64.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+|||+|||..+++++|+.+|+.||.|.+|.+.+....||||+|.+.++|..|+. |||..|+|++|.|.+|+
T Consensus         7 ~~~~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            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            456899999999999999999999999999883322221199999999999999999 99999999999999875

>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=99.66  E-value=2.2e-16  Score=123.73  Aligned_cols=77  Identities=29%  Similarity=0.422  Sum_probs=73.4

Q ss_pred             CCCccEEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          168 APPNNILFVQNVPH-DTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       168 ~~~~~~l~v~nl~~-~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++++|||+|||. .+++++|+++|+.||.|.+|.++.+++|||||+|.+.++|..|++.|||..|.|++|.|.||+
T Consensus        31 ~~~~~~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           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK  108 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            35678999999999 999999999999999999999999988999999999999999999999999999999999986

>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=4.5e-17  Score=111.41  Aligned_cols=81  Identities=19%  Similarity=0.357  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ..+.++|||+|||.++++++    |+++|+.||.|..|.+..  +|.++|||||+|.+.++|.+|+.  ++..+.|+.|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~   79 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETE----IRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLK   79 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEE
Confidence            34578999999999999999    779999999999986554  77899999999999999999999  99999999999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |.++..+..
T Consensus        80 v~~a~~~~~   88 (102)
T 2xs2_A           80 LGPAIRKQN   88 (102)
T ss_dssp             EEEEEECC-
T ss_pred             EEECCcCcc
Confidence            999876543

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.66  E-value=7.4e-16  Score=114.39  Aligned_cols=74  Identities=24%  Similarity=0.483  Sum_probs=70.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +++|||+|||..+++++|+++|+.||.|.++.++.++     +|+|||+|.++++|..|+..|||..+.|++|.|.+++
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            5689999999999999999999999999999999865     4899999999999999999999999999999999985

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=8.1e-18  Score=117.90  Aligned_cols=76  Identities=21%  Similarity=0.354  Sum_probs=70.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKE--------VRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQ  235 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~--------v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g  235 (245)
                      .++++|||+|||..+++++|+++|+.||.|..        |.++.++     +|||||+|.+.++|..|+..|||..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            35678999999999999999999999999988        8888763     6899999999999999999999999999


Q ss_pred             eEEEEEEec
Q 025973          236 QQLLITYAK  244 (245)
Q Consensus       236 ~~i~v~~ak  244 (245)
                      ++|.|.||+
T Consensus        85 ~~l~V~~a~   93 (116)
T 2lcw_A           85 NPIKVSFAT   93 (116)
Confidence            999999986

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.65  E-value=6.6e-16  Score=114.91  Aligned_cols=75  Identities=27%  Similarity=0.491  Sum_probs=70.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ++++|||+|||..+++++|+++|+.||.|.++.++.++     +|||||+|.++++|..|+..|||..+.|++|.|.|++
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            45789999999999999999999999999999998764     5899999999999999999999999999999999986

>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=99.65  E-value=2e-16  Score=105.15  Aligned_cols=73  Identities=26%  Similarity=0.317  Sum_probs=63.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ++++|||+|||..+++++|+++|+.||.|..+.++.+.+|||||+|.+.++|..|..  .+..+.|++|.|.+|+
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecC
Confidence            457899999999999999999999999999999998878999999999999975422  1244589999999986

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.65  E-value=3e-16  Score=122.30  Aligned_cols=76  Identities=21%  Similarity=0.395  Sum_probs=71.1

Q ss_pred             CCCccEEEEcCCCCCC---------CHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCee-----
Q 025973          168 APPNNILFVQNVPHDT---------TPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI-----  233 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~---------t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~-----  233 (245)
                      ...+++|||+||+..+         ++++|+.+|+.||.|.+|+++.++ |||||+|.+.++|..|++.|||..|     
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~k-G~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK-NCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGG-TEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCC-CEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            3467889999999888         799999999999999999999875 9999999999999999999999999     


Q ss_pred             -------CCeEEEEEEec
Q 025973          234 -------GQQQLLITYAK  244 (245)
Q Consensus       234 -------~g~~i~v~~ak  244 (245)
                             .|+.|.|.||+
T Consensus       210 ~e~~~~~~gr~L~V~wA~  227 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWAN  227 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC
T ss_pred             ccccccCCCCEEEEEEcc
Confidence                   89999999997

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.65  E-value=9e-16  Score=105.10  Aligned_cols=81  Identities=16%  Similarity=0.241  Sum_probs=69.2

Q ss_pred             CCCCCeEEEcCCCc-----ccChHHHHHHHHHhhcccCCeEEEEecCC----CCeeeEEEEEecCHHHHHHHHHHHcCCc
Q 025973           12 ISPNNTIYINNLNE-----KVKIDQLKQSLHAVFKQFGTILEILAFKT----LKHKGQAWLVFKDVASATAAVEKMQGFP   82 (245)
Q Consensus        12 ~~~~~~l~V~nLp~-----~~~~~~l~~~l~~~F~~~G~v~~i~~~~~----~~~kg~afV~F~~~~~A~~a~~~l~~~~   82 (245)
                      ..++++|+|+||..     +.++++    |++.|++||.|.+|.+.++    +.++|+|||+|.+.++|.+|+..|||..
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~d----l~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~   80 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVE----TKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRY   80 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHH----HHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHH----HHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCE
Confidence            45789999999973     224556    7799999999999977642    5789999999999999999999999999


Q ss_pred             cCCceEEEEEcccc
Q 025973           83 FYDKPMRIQYAKTK   96 (245)
Q Consensus        83 ~~g~~i~v~~~~~~   96 (245)
                      |.|+.|.|.++...
T Consensus        81 ~~Gr~i~v~~a~~~   94 (105)
T 2pe8_A           81 FGGRVVKACFYNLD   94 (105)
T ss_dssp             ETTEECEEEECCHH
T ss_pred             ECCcEEEEEEcCHH
Confidence            99999999998653

>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=99.65  E-value=4.3e-16  Score=116.85  Aligned_cols=80  Identities=26%  Similarity=0.362  Sum_probs=73.6

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ...+.++|||+|||.++++++    |+++|+.||.|..+  ..++.++|||||+|.+.++|.+|+..|||..+.|+.|+|
T Consensus        95 ~~~~~~~l~v~nlp~~~t~~~----l~~~F~~~g~v~~~--~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  168 (175)
T 1fje_B           95 KVRAARTLLAKNLSFNITEDE----LKEVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL  168 (175)
T ss_dssp             TTGGGGEEEEESCCSSCCHHH----HHHHCTTCSEEEEE--CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEE
T ss_pred             ccccCCEEEEeCCCCCCCHHH----HHHHHHhcCeEEEe--cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            345679999999999999999    67999999999887  678889999999999999999999999999999999999


Q ss_pred             EEcccc
Q 025973           91 QYAKTK   96 (245)
Q Consensus        91 ~~~~~~   96 (245)
                      .|+.++
T Consensus       169 ~~a~~k  174 (175)
T 1fje_B          169 YYTGEK  174 (175)
T ss_dssp             EECSSC
T ss_pred             EecCCC
Confidence            999765

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.64  E-value=2.6e-16  Score=107.57  Aligned_cols=73  Identities=18%  Similarity=0.396  Sum_probs=68.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++|||+|||..+++++|+++|+.||.|..+.++.++    +|||||+|.+.++|..|+.  ++..++|++|.|.+|.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            45789999999999999999999999999999999864    6899999999999999998  9999999999999874

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.64  E-value=8.7e-17  Score=115.58  Aligned_cols=82  Identities=12%  Similarity=0.134  Sum_probs=69.5

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .....++|||+|||+++++++    |+++|+.|| |.+|.+.  ++++++|||||+|.+.++|.+|+ .+|+..+.|+.|
T Consensus        42 ~~~~~~~lfV~nLp~~~te~d----L~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i  115 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATEND----IYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYI  115 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHH----HHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHH----HHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEE
Confidence            345678999999999999999    669999999 5577655  35788999999999999999999 589999999999


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      .|..+.....
T Consensus       116 ~V~~a~~~~~  125 (139)
T 2hgn_A          116 ELFLNSTTGA  125 (139)
T ss_dssp             CCEECCCSCC
T ss_pred             EEEECCCCCC
Confidence            9998876543

>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=99.63  E-value=3.6e-15  Score=103.63  Aligned_cols=76  Identities=18%  Similarity=0.293  Sum_probs=66.2

Q ss_pred             CCccEEEEcCCCCCCC-----------HHHHHHHhccCCCeeEEEEec-CCCeEEEEEeCCHHHHHHHHHHhCCCeeCCe
Q 025973          169 PPNNILFVQNVPHDTT-----------PMALQMFFSQFPGFKEVRMVE-AKPGIAFVEYGDEMQATVAMQSLQSLKIGQQ  236 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t-----------~~~l~~~f~~~g~v~~v~l~~-~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~  236 (245)
                      .++++|+|+||.....           +++|+++|++||.|..|.+.. ..+|||||+|.+.++|..|+..|||..|.|+
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   92 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR   92 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            4678999999954432           689999999999999996642 2379999999999999999999999999999


Q ss_pred             EEEEEEec
Q 025973          237 QLLITYAK  244 (245)
Q Consensus       237 ~i~v~~ak  244 (245)
                      +|.|.||+
T Consensus        93 ~l~v~~a~  100 (112)
T 2dit_A           93 QITAQAWD  100 (112)
T ss_dssp             ECEEEECC
T ss_pred             EEEEEEeC
Confidence            99999985

>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=99.63  E-value=1.1e-15  Score=114.13  Aligned_cols=80  Identities=21%  Similarity=0.357  Sum_probs=72.2

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      .....++|||+|||.++++++    |+++|+.||.|..|.+.   .+|.++|||||+|.+.++|.+|++.|||..+.|+.
T Consensus        90 ~~~~~~~l~v~nlp~~~t~~~----l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  165 (172)
T 2g4b_A           90 PLPGAHKLFIGGLPNYLNDDQ----VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK  165 (172)
T ss_dssp             CCTTTTCEEEECCCTTCCHHH----HHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEEcCCCcCCHHH----HHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeE
Confidence            345579999999999999999    77999999999988654   36788999999999999999999999999999999


Q ss_pred             EEEEEcc
Q 025973           88 MRIQYAK   94 (245)
Q Consensus        88 i~v~~~~   94 (245)
                      |.|.+|.
T Consensus       166 l~V~~As  172 (172)
T 2g4b_A          166 LLVQRAS  172 (172)
T ss_dssp             CEEEECC
T ss_pred             EEEEeCC
Confidence            9999873

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.63  E-value=5.1e-16  Score=118.81  Aligned_cols=74  Identities=30%  Similarity=0.443  Sum_probs=71.4

Q ss_pred             ccEEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPH-DTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~-~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +++|||+|||. .+++++|+++|+.||.|.+|.++.+++|||||+|.++++|..|+..|||..+.|++|.|.||+
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            56899999999 999999999999999999999999988999999999999999999999999999999999986

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.63  E-value=5.3e-16  Score=109.44  Aligned_cols=73  Identities=18%  Similarity=0.313  Sum_probs=66.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCee--EEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFK--EVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~--~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ...+|||+|||..+|+++|+++|+.| .|.  .|.++.++    +|||||+|.++++|.+|+. +++..|+|+.|.|.+|
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~a  118 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKS  118 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            45789999999999999999999999 666  89998764    7999999999999999998 5789999999999987


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      .
T Consensus       119 ~  119 (126)
T 2hgm_A          119 S  119 (126)
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=99.63  E-value=8.5e-16  Score=107.16  Aligned_cols=76  Identities=20%  Similarity=0.325  Sum_probs=62.9

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---C---CCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---T---LKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~---~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      .....++|||+|||.++++++    |+++|++||.|. +.+..   +   |+++|||||+|.+.++|.+|++.|++  +.
T Consensus         4 ~~~~~~~lfVgnLp~~~te~~----L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~   76 (114)
T 2dnl_A            4 GSSGSRKVFVGGLPPDIDEDE----ITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--ED   76 (114)
T ss_dssp             SSSCCCCEEEECCCTTCCHHH----HHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ET
T ss_pred             CCCCCCEEEEcCCCCCCCHHH----HHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cC
Confidence            345689999999999999999    679999999998 55443   2   67899999999999999999998843  56


Q ss_pred             CceEEEEEc
Q 025973           85 DKPMRIQYA   93 (245)
Q Consensus        85 g~~i~v~~~   93 (245)
                      |+.+.+..+
T Consensus        77 G~~~~~~~~   85 (114)
T 2dnl_A           77 GKLYLCVSS   85 (114)
T ss_dssp             TEEEEEECC
T ss_pred             CcEEEeccC
Confidence            666666544

>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=99.63  E-value=1.6e-16  Score=114.25  Aligned_cols=73  Identities=19%  Similarity=0.246  Sum_probs=67.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+|||+|||..+|+++|+++|+.|| |..|.|+.++    +|||||+|.++++|.+|+ .+|+..|+|+.|.|.+|.
T Consensus        45 ~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           45 TGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECC
Confidence            456799999999999999999999999 6799998764    789999999999999999 789999999999999875

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.63  E-value=1.8e-15  Score=117.22  Aligned_cols=82  Identities=27%  Similarity=0.411  Sum_probs=74.2

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ...++|||+|||.++++++    |+++|+.||.|..|.+..   +|.++|||||+|.+.++|.+|++.||+..+.|+.|.
T Consensus       123 ~~~~~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          123 RAFNRIYVASVHQDLSDDD----IKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLR  198 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHH----HHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCE
T ss_pred             CCCcEEEEeCCCCcCCHHH----HHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEE
Confidence            4568999999999999999    679999999999986653   678899999999999999999999999999999999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |.++.+...
T Consensus       199 V~~a~~~~~  207 (216)
T 2qfj_A          199 VGKAVTPPM  207 (216)
T ss_dssp             EEECSSCSS
T ss_pred             EEEecCCCC
Confidence            999876543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=4.5e-16  Score=109.54  Aligned_cols=74  Identities=20%  Similarity=0.266  Sum_probs=66.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCe----eEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGF----KEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v----~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      ...+|||+|||..+|+++|+++|+.||.|    ..|.|+.++    +|||||+|.+.++|.+|+.. |+..++|+.|.|.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~  100 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELF  100 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEE
Confidence            45789999999999999999999999975    688888653    69999999999999999985 9999999999998


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      .|.
T Consensus       101 ~a~  103 (123)
T 2dha_A          101 RST  103 (123)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            874

>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=99.62  E-value=2.8e-16  Score=104.43  Aligned_cols=78  Identities=18%  Similarity=0.361  Sum_probs=65.3

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      .++++|||+|||.++++++    |+++|+.||.|.+|.+..+  ++|||||+|.+.++|.+|...  ...+.|+.|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~   74 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDE----LREFFSQYGDVMDVFIPKP--FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISN   74 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHH----HHHHSTTTSCCCEEECCSS--CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHH----HHHHHHHcCCeeEEEEecC--CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEe
Confidence            4679999999999999999    6799999999999988754  689999999999999764331  3445799999999


Q ss_pred             ccccch
Q 025973           93 AKTKSD   98 (245)
Q Consensus        93 ~~~~~~   98 (245)
                      +.++..
T Consensus        75 a~~~~~   80 (88)
T 1wf0_A           75 AEPKHN   80 (88)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            876544

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.62  E-value=1.2e-15  Score=118.98  Aligned_cols=81  Identities=22%  Similarity=0.319  Sum_probs=70.1

Q ss_pred             CCCCCCeEEEcCCCccc---------ChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCC
Q 025973           11 EISPNNTIYINNLNEKV---------KIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGF   81 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~---------~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~   81 (245)
                      ....+++|||+|||..+         ++++    |+.+|++||.|.+|.+..   ++|||||.|.+.++|..|++.|+|.
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~----L~~~F~~fG~I~~v~v~~---~kG~AFV~F~~~~~Ae~A~~am~g~  202 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESR----IRFVFSRLGDIDRIRYVE---SKNCGFVKFKYQANAEFAKEAMSNQ  202 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHH----HHHHHHTTSCEEEEEEEG---GGTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHH----HHHHHHccCCEEEEEEEC---CCCEEEEEeCCHHHHHHHHHHhCCC
Confidence            35678999999999998         6888    779999999999998874   5799999999999999999999999


Q ss_pred             cc------------CCceEEEEEccccch
Q 025973           82 PF------------YDKPMRIQYAKTKSD   98 (245)
Q Consensus        82 ~~------------~g~~i~v~~~~~~~~   98 (245)
                      .+            .|+.|.|.|+.....
T Consensus       203 ~l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          203 TLLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             EEeccccccccccCCCCEEEEEEccCCCC
Confidence            99            899999999987654

>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=99.62  E-value=1.3e-15  Score=129.71  Aligned_cols=82  Identities=15%  Similarity=0.287  Sum_probs=74.2

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..+.++|||+|||..+++++    |..+|+.||.|..|.+.   .++.++|||||+|.+.++|.+|+..|||..|.|+.|
T Consensus        99 ~~~~~~lfV~nL~~~~te~~----L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i  174 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESK----LRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV  174 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEE
Confidence            44578999999999999999    67999999999998765   367889999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 025973           89 RIQYAKTKS   97 (245)
Q Consensus        89 ~v~~~~~~~   97 (245)
                      .|.++....
T Consensus       175 ~V~~a~~~~  183 (437)
T 3pgw_S          175 LVDVERGRT  183 (437)
T ss_pred             EEEEeCCCC
Confidence            999997643

>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=99.62  E-value=2.5e-15  Score=112.46  Aligned_cols=79  Identities=22%  Similarity=0.394  Sum_probs=70.3

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccC---Cc
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFY---DK   86 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~---g~   86 (245)
                      ..+.++|||+|||.++++++    |+++|+.||.|..|.+.  .+|.++|||||+|.+.++|.+|++.|||..+.   |+
T Consensus        92 ~~~~~~l~v~nl~~~~t~~~----l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~  167 (175)
T 3nmr_A           92 AVEDRKLFIGMISKKCTEND----IRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSS  167 (175)
T ss_dssp             CGGGSEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSS
T ss_pred             cCCCCeEEEcCCCCcCCHHH----HHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCC
Confidence            44678999999999999999    67999999999998655  36788999999999999999999999998776   48


Q ss_pred             eEEEEEcc
Q 025973           87 PMRIQYAK   94 (245)
Q Consensus        87 ~i~v~~~~   94 (245)
                      .|.|.|+.
T Consensus       168 ~l~V~~ad  175 (175)
T 3nmr_A          168 PMVVKFAD  175 (175)
T ss_dssp             CCEEEECC
T ss_pred             CeEEEecC
Confidence            99999973

>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=99.62  E-value=3.4e-15  Score=120.47  Aligned_cols=77  Identities=27%  Similarity=0.447  Sum_probs=71.1

Q ss_pred             CCCccEEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          168 APPNNILFVQNVPHDTTPMALQ----MFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~----~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      ..++++|||+|||..+++++|+    ++|+.||.|..|++..+.  +|||||+|.+.++|..|+..|||..|.|+.|+|.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   85 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   85 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            3567899999999999999976    899999999999988743  6999999999999999999999999999999999


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      ||+
T Consensus        86 ~a~   88 (282)
T 3pgw_A           86 YAK   88 (282)
T ss_pred             Eec
Confidence            986

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.61  E-value=2e-15  Score=115.35  Aligned_cols=82  Identities=21%  Similarity=0.337  Sum_probs=74.5

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..+.++|||+|||..+++++    |+++|+.||.|..|.+.   .+|.++|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~----l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  186 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQ----VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL  186 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHH----HHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            36789999999999999999    77999999999998655   377889999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 025973           89 RIQYAKTKS   97 (245)
Q Consensus        89 ~v~~~~~~~   97 (245)
                      .|.++.+..
T Consensus       187 ~v~~a~~~~  195 (198)
T 2yh0_A          187 LVQRASVGA  195 (198)
T ss_dssp             EEEESCCCC
T ss_pred             EEEECCCCC
Confidence            999987653

>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=99.60  E-value=3.7e-15  Score=102.08  Aligned_cols=76  Identities=21%  Similarity=0.343  Sum_probs=66.7

Q ss_pred             CCccEEEEcCC--CCCC--------CHHHHHHHhccCCCeeEEEEecCC-------CeEEEEEeCCHHHHHHHHHHhCCC
Q 025973          169 PPNNILFVQNV--PHDT--------TPMALQMFFSQFPGFKEVRMVEAK-------PGIAFVEYGDEMQATVAMQSLQSL  231 (245)
Q Consensus       169 ~~~~~l~v~nl--~~~~--------t~~~l~~~f~~~g~v~~v~l~~~~-------~g~afv~f~~~~~A~~A~~~l~g~  231 (245)
                      .|+++|.+.|+  |..+        .+++|++.|++||.|.+|.++.++       +|+|||+|.++++|.+|+..|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            46789999999  3333        347999999999999999998752       699999999999999999999999


Q ss_pred             eeCCeEEEEEEec
Q 025973          232 KIGQQQLLITYAK  244 (245)
Q Consensus       232 ~~~g~~i~v~~ak  244 (245)
                      .|+||+|.|.|+.
T Consensus        83 ~f~GR~i~v~~~~   95 (105)
T 3v4m_A           83 KFANRVVVTKYCD   95 (105)
T ss_dssp             EETTEECEEEEEC
T ss_pred             EeCCCEEEEEEeC
Confidence            9999999999973

>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=99.60  E-value=3e-15  Score=104.03  Aligned_cols=88  Identities=18%  Similarity=0.318  Sum_probs=71.9

Q ss_pred             CCCCCCCCeEEEcCCCcccC--h-----HHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCC
Q 025973            9 GNEISPNNTIYINNLNEKVK--I-----DQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGF   81 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~--~-----~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~   81 (245)
                      ...+.++++|+|.||.....  +     +++.+.|+++|++||.|..|.+. +..++|||||+|.+.++|.+|+..|||.
T Consensus         9 ~~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~-~~~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A            9 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLF-DRHPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEE-TTCTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEe-cCCCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            34677899999999943322  1     22444488999999999998663 4457899999999999999999999999


Q ss_pred             ccCCceEEEEEccccc
Q 025973           82 PFYDKPMRIQYAKTKS   97 (245)
Q Consensus        82 ~~~g~~i~v~~~~~~~   97 (245)
                      .+.|+.|+|.++.+..
T Consensus        88 ~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           88 WFGGRQITAQAWDGTT  103 (112)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCcEEEEEEeCCCC
Confidence            9999999999987654

>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=99.60  E-value=1.1e-15  Score=113.57  Aligned_cols=78  Identities=17%  Similarity=0.395  Sum_probs=71.5

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      +.++|||+|||.++++++    |+++|+.||.|..|.+..   +|.++|||||+|.+.++|.+|++ +++..+.|+.|.|
T Consensus        86 ~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V  160 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKE----FEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEI  160 (167)
T ss_dssp             HCEEEEEEEECTTCCHHH----HHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEE
T ss_pred             CCCeEEECCCCCCCCHHH----HHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEE
Confidence            467999999999999999    679999999999987664   57889999999999999999999 8999999999999


Q ss_pred             EEcccc
Q 025973           91 QYAKTK   96 (245)
Q Consensus        91 ~~~~~~   96 (245)
                      .++.++
T Consensus       161 ~~a~pk  166 (167)
T 2cjk_A          161 KRAEPR  166 (167)
T ss_dssp             EECCCC
T ss_pred             eecCCC
Confidence            999765

>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=99.60  E-value=6.1e-15  Score=100.97  Aligned_cols=84  Identities=14%  Similarity=0.330  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCC--CcccCh----HHHHHHHHHhhcccCCeEEEEecCC-----CCeeeEEEEEecCHHHHHHHHHHHcCC
Q 025973           13 SPNNTIYINNL--NEKVKI----DQLKQSLHAVFKQFGTILEILAFKT-----LKHKGQAWLVFKDVASATAAVEKMQGF   81 (245)
Q Consensus        13 ~~~~~l~V~nL--p~~~~~----~~l~~~l~~~F~~~G~v~~i~~~~~-----~~~kg~afV~F~~~~~A~~a~~~l~~~   81 (245)
                      .|++.|.+.|+  |.+..+    ++|.+-|++.|++||.|.+|.+.++     +.++|+|||+|.+.++|.+|+..|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            57899999998  334432    3466668899999999999988764     256899999999999999999999999


Q ss_pred             ccCCceEEEEEcccc
Q 025973           82 PFYDKPMRIQYAKTK   96 (245)
Q Consensus        82 ~~~g~~i~v~~~~~~   96 (245)
                      .|.||.|+|.++...
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999997654

>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=99.60  E-value=3.9e-15  Score=113.55  Aligned_cols=82  Identities=21%  Similarity=0.315  Sum_probs=69.9

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..+.++|||+|||.++++++    |+++|+.||.|..|.+..   +|.++|||||+|.+.++|.+|+.. ++..+.|+.|
T Consensus       101 ~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i  175 (196)
T 1l3k_A          101 HLTVKKIFVGGIKEDTEEHH----LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNC  175 (196)
T ss_dssp             --CCSEEEEECCTTTCCHHH----HHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEEC
T ss_pred             CCCcceEEEeCCCCCCCHHH----HHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEE
Confidence            34568999999999999999    679999999999986653   678999999999999999999995 8999999999


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      .|.++.++..
T Consensus       176 ~v~~a~~k~~  185 (196)
T 1l3k_A          176 EVRKALSKQE  185 (196)
T ss_dssp             EEEECC----
T ss_pred             EEEecCChhH
Confidence            9999987765

>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=99.59  E-value=7.9e-15  Score=117.07  Aligned_cols=75  Identities=24%  Similarity=0.382  Sum_probs=70.9

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..+++|||+|||..+|+++|+++|+.||.|..|.+.+++ |||||+|.+.++|..|+..+||..+.|++|.|.||.
T Consensus        20 ~~~~~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           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR-GFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT   94 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTT-TEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCC-cEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecc
Confidence            456789999999999999999999999999999998875 999999999999999999999999999999999985

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.58  E-value=5.1e-15  Score=112.71  Aligned_cols=77  Identities=22%  Similarity=0.420  Sum_probs=68.2

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      .++|||+|||.++++++    |+.+|+.||.|..|++.+  ++.++|||||+|.+.++|.+|+..+ +..+.|+.|.|.+
T Consensus       109 ~~~l~V~nLp~~~t~~~----L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~  183 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDD----IKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILF  183 (193)
T ss_dssp             HTEEEEECCCTTCCHHH----HHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEE
T ss_pred             cCEEEecCCCCcCCHHH----HHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEE
Confidence            48999999999999999    679999999999987654  5788999999999999999999855 5589999999998


Q ss_pred             cccc
Q 025973           93 AKTK   96 (245)
Q Consensus        93 ~~~~   96 (245)
                      ...-
T Consensus       184 ~~~y  187 (193)
T 2voo_A          184 KDDY  187 (193)
T ss_dssp             TTTC
T ss_pred             hHHH
Confidence            7643

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.58  E-value=9.5e-15  Score=111.20  Aligned_cols=75  Identities=17%  Similarity=0.287  Sum_probs=67.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      ..++|||+|||..+++++|+.+|+.||.|..|.+..+.    +|||||+|.+.++|..|+..+ +..+.|++|.|.+++.
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            34789999999999999999999999999999998753    699999999999999999865 5699999999999863

>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=2.1e-15  Score=104.70  Aligned_cols=76  Identities=13%  Similarity=0.145  Sum_probs=64.9

Q ss_pred             CeEEEcCC----CcccChHHHHHHHHHhhcccCCeEEEE---ecCCCCeeeEEEEEecC----HHH----HHHHHH--HH
Q 025973           16 NTIYINNL----NEKVKIDQLKQSLHAVFKQFGTILEIL---AFKTLKHKGQAWLVFKD----VAS----ATAAVE--KM   78 (245)
Q Consensus        16 ~~l~V~nL----p~~~~~~~l~~~l~~~F~~~G~v~~i~---~~~~~~~kg~afV~F~~----~~~----A~~a~~--~l   78 (245)
                      ++|||+||    |+.+++++    |..+|+.||.|.++.   +..||.++|||||+|.+    +++    |.+|+.  .+
T Consensus         3 ~kI~VgnL~~~~~~~tte~~----Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~l   78 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDIS----IKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHES   78 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHH----HHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTT
T ss_pred             cEEEEeCCCCCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhh
Confidence            68999999    99999999    669999999998863   44589999999999996    333    888988  78


Q ss_pred             cCCccCCceEEEEEccc
Q 025973           79 QGFPFYDKPMRIQYAKT   95 (245)
Q Consensus        79 ~~~~~~g~~i~v~~~~~   95 (245)
                      ||..+.|+.|+|.+-..
T Consensus        79 ng~~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           79 SGCFIMGFKFEVILNKH   95 (136)
T ss_dssp             TCEEETTEEEEEEECCT
T ss_pred             cCCeecCcEEEEEECcc
Confidence            99999999999998543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.57  E-value=4.6e-15  Score=102.96  Aligned_cols=73  Identities=10%  Similarity=0.154  Sum_probs=64.5

Q ss_pred             cEEEEcCC----CCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCC----HHH----HHHHHH--HhCCCe
Q 025973          172 NILFVQNV----PHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGD----EMQ----ATVAMQ--SLQSLK  232 (245)
Q Consensus       172 ~~l~v~nl----~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~----~~~----A~~A~~--~l~g~~  232 (245)
                      ..|||+||    |..+++++|+++|+.||.|.++.++.|+     +|||||+|.+    +++    |.+|+.  .+||..
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            45999999    9999999999999999999999999986     7999999996    433    788888  789999


Q ss_pred             eCCeEEEEEEec
Q 025973          233 IGQQQLLITYAK  244 (245)
Q Consensus       233 ~~g~~i~v~~ak  244 (245)
                      |+|++|+|.+-+
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            999999998753

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=9.7e-15  Score=101.75  Aligned_cols=69  Identities=17%  Similarity=0.259  Sum_probs=57.6

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      .+++|||+|||..+++++|+++|+.||.|. +.++.++        +|||||+|.++++|..|++.|+  .+.|+.|.+.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            456799999999999999999999999999 7776532        6899999999999999999983  2455555444

>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=99.56  E-value=2.1e-14  Score=99.48  Aligned_cols=85  Identities=18%  Similarity=0.253  Sum_probs=74.3

Q ss_pred             CCCCCCeEEEcCCCcccC------hHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973           11 EISPNNTIYINNLNEKVK------IDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~------~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ++.++++|.+.|+=....      .++|++-|++.|++||.|.+|.+.++. .+|+|||+|.+.++|.+|++.|||..|.
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 QPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS-AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC-TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC-CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            457899999999865443      578888899999999999999887653 5899999999999999999999999999


Q ss_pred             CceEEEEEcccc
Q 025973           85 DKPMRIQYAKTK   96 (245)
Q Consensus        85 g~~i~v~~~~~~   96 (245)
                      |+.|+|.|+...
T Consensus        82 GR~i~v~~~~~~   93 (114)
T 3s6e_A           82 GKMITAAYVPLP   93 (114)
T ss_dssp             TEECEEEEECHH
T ss_pred             CEEEEEEEEcHH
Confidence            999999998644

>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=99.55  E-value=2.6e-14  Score=99.70  Aligned_cols=75  Identities=15%  Similarity=0.190  Sum_probs=66.6

Q ss_pred             CccEEEEcCCCC-----CCCHHHHHHHhccCCCeeEEEEecCC---------CeEEEEEeCCHHHHHHHHHHhCCCeeCC
Q 025973          170 PNNILFVQNVPH-----DTTPMALQMFFSQFPGFKEVRMVEAK---------PGIAFVEYGDEMQATVAMQSLQSLKIGQ  235 (245)
Q Consensus       170 ~~~~l~v~nl~~-----~~t~~~l~~~f~~~g~v~~v~l~~~~---------~g~afv~f~~~~~A~~A~~~l~g~~~~g  235 (245)
                      ++++|+++|+-.     .-.+++|++.|++||.|.+|.++.++         +|++||+|.++++|.+|+..|||..|+|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            678999999942     23479999999999999999998753         3899999999999999999999999999


Q ss_pred             eEEEEEEec
Q 025973          236 QQLLITYAK  244 (245)
Q Consensus       236 ~~i~v~~ak  244 (245)
                      |+|.|.|+.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999973

>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=99.55  E-value=1.9e-14  Score=100.40  Aligned_cols=83  Identities=11%  Similarity=0.232  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCcccC-hHHHHHHHHHhhcccCCeEEEEecC-------CCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973           13 SPNNTIYINNLNEKVK-IDQLKQSLHAVFKQFGTILEILAFK-------TLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~-~~~l~~~l~~~F~~~G~v~~i~~~~-------~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      +++++|+|+|+-.... .++|.+-|++.|++||.|.+|.+.+       +++++|++||+|.+.++|.+|+..|||..|.
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            4789999999943211 2346666889999999999987654       2457899999999999999999999999999


Q ss_pred             CceEEEEEccc
Q 025973           85 DKPMRIQYAKT   95 (245)
Q Consensus        85 g~~i~v~~~~~   95 (245)
                      ||.|+|.|+..
T Consensus        98 GR~i~v~~~~~  108 (118)
T 3ue2_A           98 GRKVVAEVYDQ  108 (118)
T ss_dssp             TEECEEEEECH
T ss_pred             CcEEEEEEcCh
Confidence            99999999865

>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=99.55  E-value=5.1e-14  Score=97.56  Aligned_cols=75  Identities=11%  Similarity=0.112  Sum_probs=66.1

Q ss_pred             CccEEEEcCCCCCC----------CHHHHHHHhccCCCeeEEEEecCC-CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEE
Q 025973          170 PNNILFVQNVPHDT----------TPMALQMFFSQFPGFKEVRMVEAK-PGIAFVEYGDEMQATVAMQSLQSLKIGQQQL  238 (245)
Q Consensus       170 ~~~~l~v~nl~~~~----------t~~~l~~~f~~~g~v~~v~l~~~~-~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i  238 (245)
                      ++++|.+.|+-..-          .+++|++.|++||.|.+|.+.++. +|+|||+|.+.++|.+|+..|||..|+|+.|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i   85 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMI   85 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            67889999994221          246889999999999999998764 7999999999999999999999999999999


Q ss_pred             EEEEec
Q 025973          239 LITYAK  244 (245)
Q Consensus       239 ~v~~ak  244 (245)
                      .|.|+.
T Consensus        86 ~v~~~~   91 (114)
T 3s6e_A           86 TAAYVP   91 (114)
T ss_dssp             EEEEEC
T ss_pred             EEEEEc
Confidence            999974

>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=99.52  E-value=1.1e-14  Score=99.53  Aligned_cols=74  Identities=15%  Similarity=0.284  Sum_probs=63.0

Q ss_pred             EcCCCcccChHHHH-------HHHHHhh-cccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           20 INNLNEKVKIDQLK-------QSLHAVF-KQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        20 V~nLp~~~~~~~l~-------~~l~~~F-~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      +.|||..+++++|+       +.|+..| ++||.|.+|.+.+  +++++|||||.|.+.++|.+|+..|||..+.|+.|+
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            56778888888765       3345666 9999999998775  457899999999999999999999999999999999


Q ss_pred             EEEc
Q 025973           90 IQYA   93 (245)
Q Consensus        90 v~~~   93 (245)
                      |.|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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=99.52  E-value=4.4e-14  Score=96.56  Aligned_cols=65  Identities=14%  Similarity=0.256  Sum_probs=56.0

Q ss_pred             CCCCCCHHHHHHHh------------ccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          179 VPHDTTPMALQMFF------------SQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       179 l~~~~t~~~l~~~f------------~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      |+..+++++|+++|            ++||.|.+|.++.++    +|+|||+|.++++|.+|+..|||..|.|++|+|.|
T Consensus        23 l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~  102 (104)
T 1jmt_A           23 LRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL  102 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             cccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEE
Confidence            33344566665555            999999999999864    79999999999999999999999999999999999


Q ss_pred             e
Q 025973          243 A  243 (245)
Q Consensus       243 a  243 (245)
                      +
T Consensus       103 s  103 (104)
T 1jmt_A          103 S  103 (104)
T ss_dssp             C
T ss_pred             c
Confidence            7

>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=99.52  E-value=3.9e-14  Score=116.11  Aligned_cols=76  Identities=16%  Similarity=0.166  Sum_probs=67.1

Q ss_pred             CCccEEEEcCC--CCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC---Ce--EEEEE
Q 025973          169 PPNNILFVQNV--PHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG---QQ--QLLIT  241 (245)
Q Consensus       169 ~~~~~l~v~nl--~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~---g~--~i~v~  241 (245)
                      .++.+|||+|+  +..+|+++|+++|++||.|.+|.+.++ +|||||+|.+.++|.+|++.|||..+.   |+  +|.|.
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~-kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~   94 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN   94 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTT-CSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEE
Confidence            46788999995  689999999999999999999988776 499999999999999999999998872   44  68889


Q ss_pred             EecC
Q 025973          242 YAKK  245 (245)
Q Consensus       242 ~ak~  245 (245)
                      |+++
T Consensus        95 ~~~~   98 (345)
T 3tht_A           95 FVEK   98 (345)
T ss_dssp             ECSS
T ss_pred             Eeec
Confidence            8853

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=1.4e-13  Score=93.03  Aligned_cols=72  Identities=18%  Similarity=0.207  Sum_probs=61.8

Q ss_pred             ccEEEEcCCC-------CCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          171 NNILFVQNVP-------HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       171 ~~~l~v~nl~-------~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+.|.|.-..       ..+++++|+++|++||.|.+|.++...+|||||+|.+.++|..|+..++  .+.|++|+|.||
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~~a   87 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKISWL   87 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEECS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEEEc
Confidence            4456666543       4589999999999999999999987668999999999999999999755  467999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      +
T Consensus        88 ~   88 (100)
T 2d9o_A           88 E   88 (100)
T ss_dssp             S
T ss_pred             c
Confidence            6

>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=99.46  E-value=1.4e-13  Score=112.76  Aligned_cols=77  Identities=14%  Similarity=0.263  Sum_probs=67.3

Q ss_pred             CCCCCCeEEEcC--CCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC---C
Q 025973           11 EISPNNTIYINN--LNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY---D   85 (245)
Q Consensus        11 ~~~~~~~l~V~n--Lp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~---g   85 (245)
                      ...|+++|||+|  |+..+++++    |+++|++||.|.+|++..   +||||||+|.+.++|.+|++.|||..+.   |
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~----L~~~F~~~G~V~~v~~~~---~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g   86 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQ----LLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKRAYVTLNGKEVVDDLG   86 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHH----HHHHHHTTSCEEEEECCT---TCSEEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHH----HHHHHHhcCCeEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCccccccC
Confidence            367899999999  578999999    779999999999998764   4799999999999999999999998773   4


Q ss_pred             c--eEEEEEcc
Q 025973           86 K--PMRIQYAK   94 (245)
Q Consensus        86 ~--~i~v~~~~   94 (245)
                      +  .+.|.|+.
T Consensus        87 ~~~~ly~~~~~   97 (345)
T 3tht_A           87 QKITLYLNFVE   97 (345)
T ss_dssp             CEEECEEEECS
T ss_pred             CceEEEEEEee
Confidence            5  67888874

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.43  E-value=1.2e-12  Score=88.49  Aligned_cols=78  Identities=19%  Similarity=0.293  Sum_probs=65.2

Q ss_pred             CCCCCeEEEcCCC-------cccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973           12 ISPNNTIYINNLN-------EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus        12 ~~~~~~l~V~nLp-------~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ....++|.|.-..       ..+++++    |+++|++||.|.+|.+.  ++++|||||+|.+.++|..|++.++  .+.
T Consensus         7 ~~~~~~~~v~w~~~~~~~~~~~~te~~----L~~~F~~~G~V~~v~i~--~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~   78 (100)
T 2d9o_A            7 GQGTPKLKLKWKCKKEDESKGGYSKDV----LLRLLQKYGEVLNLVLS--SKKPGTAVVEFATVKAAELAVQNEV--GLV   78 (100)
T ss_dssp             CCSSCEEEEECCCCSSCSCCCSCCHHH----HHHHHHTTSCEEEEEEE--SSSSSEEEEEESCHHHHHHHHHTCC--BCS
T ss_pred             CCccceEEEeeeccCccCcCCCCCHHH----HHHHHHhcCCEEEEEEc--cCCCCEEEEEECCHHHHHHHHHhcC--CCC
Confidence            4456788887665       4589999    77999999999999887  4678999999999999999999744  467


Q ss_pred             CceEEEEEccccc
Q 025973           85 DKPMRIQYAKTKS   97 (245)
Q Consensus        85 g~~i~v~~~~~~~   97 (245)
                      |+.|+|.|+....
T Consensus        79 g~~l~V~~a~~~~   91 (100)
T 2d9o_A           79 DNPLKISWLEGQP   91 (100)
T ss_dssp             SSBCEEECSSCCC
T ss_pred             CCeEEEEEccCCC
Confidence            9999999987654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.36  E-value=4.2e-12  Score=82.57  Aligned_cols=73  Identities=16%  Similarity=0.214  Sum_probs=62.7

Q ss_pred             CCCccEEEEcCCC----CCCCH----HHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEE
Q 025973          168 APPNNILFVQNVP----HDTTP----MALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLL  239 (245)
Q Consensus       168 ~~~~~~l~v~nl~----~~~t~----~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~  239 (245)
                      .||..+|+|.-.+    ...-.    .+|.+.|++||.|..++++.++   +||+|.+.++|.+|+. |||..++||.|+
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~---~fVtF~d~~sAlaAi~-mnG~~v~Gr~Lk   79 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK---MWVTFLEGSSALNVLS-LNGKELLNRTIT   79 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS---EEEEESSHHHHHHGGG-GTTCEETTEEEE
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC---EEEEECChHHHHHHHh-cCCeEeCCeEEE
Confidence            3566778888765    23333    6789999999999999999875   8999999999999998 999999999999


Q ss_pred             EEEec
Q 025973          240 ITYAK  244 (245)
Q Consensus       240 v~~ak  244 (245)
                      |++++
T Consensus        80 V~lkt   84 (91)
T 2dnr_A           80 IALKS   84 (91)
T ss_dssp             EEECC
T ss_pred             EEeCC
Confidence            99986

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=5.8e-12  Score=87.34  Aligned_cols=76  Identities=13%  Similarity=0.156  Sum_probs=68.1

Q ss_pred             CCCCccEEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCC-HHHHHHHHHHhC--CCeeCCeEEEEEE
Q 025973          167 PAPPNNILFVQNVPHD-TTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGD-EMQATVAMQSLQ--SLKIGQQQLLITY  242 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~-~~~A~~A~~~l~--g~~~~g~~i~v~~  242 (245)
                      ..+++.+|+|+||+.. +++++|+++|+.||.|.+|.+..+.. .|||+|.+ +++|..|+..+|  +..|.|..+.+..
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~-tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK-EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS-EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC-EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            3467899999999999 99999999999999999999999985 89999999 899999999995  6888898888765


Q ss_pred             e
Q 025973          243 A  243 (245)
Q Consensus       243 a  243 (245)
                      .
T Consensus        93 L   93 (121)
T 1owx_A           93 L   93 (121)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.35  E-value=5.9e-12  Score=81.90  Aligned_cols=79  Identities=19%  Similarity=0.331  Sum_probs=69.7

Q ss_pred             CCCCCCeEEEcCCC----cccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           11 EISPNNTIYINNLN----EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        11 ~~~~~~~l~V~nLp----~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      -.+|..+|+|.-.|    ....+++|...|.+.|++||.|..+++..+     .+||+|.+.++|.+|++ |||..+.|+
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 SGSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-----KMWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             CCCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-----SEEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-----CEEEEECChHHHHHHHh-cCCeEeCCe
Confidence            36788999999887    356788888889999999999999988864     39999999999999999 999999999


Q ss_pred             eEEEEEccc
Q 025973           87 PMRIQYAKT   95 (245)
Q Consensus        87 ~i~v~~~~~   95 (245)
                      .|+|.++.+
T Consensus        77 ~LkV~lkt~   85 (91)
T 2dnr_A           77 TITIALKSP   85 (91)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEeCCC
Confidence            999999765

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.18  E-value=1.9e-10  Score=79.71  Aligned_cols=83  Identities=13%  Similarity=0.166  Sum_probs=71.3

Q ss_pred             CCCCCCCCeEEEcCCCcc-cChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecC-HHHHHHHHHHHc--CCccC
Q 025973            9 GNEISPNNTIYINNLNEK-VKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKD-VASATAAVEKMQ--GFPFY   84 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~-~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~-~~~A~~a~~~l~--~~~~~   84 (245)
                      +-..++++.|||+||+.+ +++++    |.++|+.||.|..|.+.+..   -.|||.|.+ .++|..|+..||  +..|.
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sred----Lke~F~~~G~V~~Vd~~~g~---~tgfVrf~~~~~~A~~av~~ln~~~~~i~   84 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCRED----LHILFSNHGEIKWIDFVRGA---KEGIILFKEKAKEALGKAKDANNGNLQLR   84 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHH----HHHHTCSSCCEEEEECCTTC---SEEEEEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             cccccCCeEEEEecCCCCcCCHHH----HHHHHHhcCCEEEEEEecCC---CEEEEEECCChHHHHHHHHHhhcCCcEEe
Confidence            345778999999999999 99999    66999999999999887654   369999999 899999999995  68899


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |..+++.......+
T Consensus        85 g~~~~~evL~GeeE   98 (121)
T 1owx_A           85 NKEVTWEVLEGEVE   98 (121)
T ss_dssp             SSSEEEEECCHHHH
T ss_pred             CcEEEEEECCCHHH
Confidence            99999988765544

>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=99.17  E-value=4.1e-11  Score=78.27  Aligned_cols=79  Identities=16%  Similarity=0.241  Sum_probs=68.8

Q ss_pred             CCCCCCCCeEEEcCCCc-----ccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCcc
Q 025973            9 GNEISPNNTIYINNLNE-----KVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPF   83 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~-----~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~   83 (245)
                      ....+|..+|+|.-++.     .+.+++|...|.+.|+.||.|..+++..+.     +||+|.+.++|.+|++ |||..+
T Consensus         9 ~~~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-----~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A            9 SFQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-----MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-----EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             eecCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-----EEEEEcChHHHHHHHh-cCCeee
Confidence            44578899999998874     467777887799999999999999887652     9999999999999999 999999


Q ss_pred             CCceEEEEEc
Q 025973           84 YDKPMRIQYA   93 (245)
Q Consensus        84 ~g~~i~v~~~   93 (245)
                      .||.|+|.+-
T Consensus        83 ~Gr~L~V~~k   92 (95)
T 1ufw_A           83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             CCeEEEEecc
Confidence            9999999874

>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=99.15  E-value=1.1e-10  Score=76.24  Aligned_cols=71  Identities=15%  Similarity=0.267  Sum_probs=61.4

Q ss_pred             CCCccEEEEcCCCCC-----CCH----HHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEE
Q 025973          168 APPNNILFVQNVPHD-----TTP----MALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQL  238 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~-----~t~----~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i  238 (245)
                      .||..+|+|.-++..     ...    .+|.+.|+.||.|..++++.++   +||+|.+.++|.+|+. |||..++||.|
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~---~fVtF~d~~sAl~AI~-ldG~~v~Gr~L   87 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---MLVTFADSHSALSVLD-VDGMKVKGRAV   87 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---EEEECSCSHHHHHHHH-GGGSEETTEEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc---EEEEEcChHHHHHHHh-cCCeeeCCeEE
Confidence            467778999887633     222    5689999999999999999875   9999999999999998 99999999999


Q ss_pred             EEEE
Q 025973          239 LITY  242 (245)
Q Consensus       239 ~v~~  242 (245)
                      +|.+
T Consensus        88 ~V~~   91 (95)
T 1ufw_A           88 KISG   91 (95)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            9986

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.99  E-value=2.3e-09  Score=71.35  Aligned_cols=70  Identities=10%  Similarity=0.169  Sum_probs=66.2

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccC-----CCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQF-----PGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~-----g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      .++|-+-|||+.++...|+.+..++     |.+..|.|.++- +-|+|+|.+...|.+|.-.|+|..|.|++|++.
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH-~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF-NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT-TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC-CceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            4679999999999999999999999     999999999997 689999999999999999999999999999986

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.98  E-value=3.9e-09  Score=81.88  Aligned_cols=84  Identities=12%  Similarity=0.215  Sum_probs=65.9

Q ss_pred             CCCCeEEEcCCC-cccChHHHHHHHHHhhcccCCeEEEEecC-------CCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973           13 SPNNTIYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAFK-------TLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus        13 ~~~~~l~V~nLp-~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-------~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      .+...+.+.|+- ..-.++++.+.|++.|++||.|.+|.+.+       +++++|++||+|.+.++|.+|+..|||..+.
T Consensus       122 ~~s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~  201 (222)
T 3dxb_A          122 MESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA  201 (222)
T ss_dssp             CBCSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSS
T ss_pred             cccccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceEC
Confidence            344555555554 23333445556889999999999986642       4478999999999999999999999999999


Q ss_pred             CceEEEEEcccc
Q 025973           85 DKPMRIQYAKTK   96 (245)
Q Consensus        85 g~~i~v~~~~~~   96 (245)
                      ||.|.+.|+...
T Consensus       202 gr~i~~~~~~~~  213 (222)
T 3dxb_A          202 GRKVVAEVYDQE  213 (222)
T ss_dssp             SSBCEEEECCHH
T ss_pred             CeEEEEEEcCHH
Confidence            999999998643

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.95  E-value=3.2e-09  Score=82.40  Aligned_cols=73  Identities=14%  Similarity=0.171  Sum_probs=61.8

Q ss_pred             ccEEEEcCCC-----CCCCHHHHHHHhccCCCeeEEEEecC---------CCeEEEEEeCCHHHHHHHHHHhCCCeeCCe
Q 025973          171 NNILFVQNVP-----HDTTPMALQMFFSQFPGFKEVRMVEA---------KPGIAFVEYGDEMQATVAMQSLQSLKIGQQ  236 (245)
Q Consensus       171 ~~~l~v~nl~-----~~~t~~~l~~~f~~~g~v~~v~l~~~---------~~g~afv~f~~~~~A~~A~~~l~g~~~~g~  236 (245)
                      ..++.+.|+-     ..-.+++|...|+.||.|.++.++.+         .+|++||+|.+.++|.+|++.|||..|.||
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            3456666662     34467899999999999999999742         158999999999999999999999999999


Q ss_pred             EEEEEEe
Q 025973          237 QLLITYA  243 (245)
Q Consensus       237 ~i~v~~a  243 (245)
                      .|.+.|+
T Consensus       204 ~i~~~~~  210 (222)
T 3dxb_A          204 KVVAEVY  210 (222)
T ss_dssp             BCEEEEC
T ss_pred             EEEEEEc
Confidence            9999986

>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=98.54  E-value=1.5e-07  Score=62.56  Aligned_cols=77  Identities=18%  Similarity=0.321  Sum_probs=67.6

Q ss_pred             CeEEEcCCCccc-ChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEcc
Q 025973           16 NTIYINNLNEKV-KIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAK   94 (245)
Q Consensus        16 ~~l~V~nLp~~~-~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~   94 (245)
                      ++|+|.||+.++ ..+++++.++.+|..|+++......++-   +-.-|.|.+.++|.+|-..||+..|.|+.|+|.|+.
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF---RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq   82 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF---KRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT---TEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc---eEEEEEeCChHHHHHHHHHhccceecCceeEEEecC
Confidence            579999999988 7788888899999999988887666554   246899999999999999999999999999999987


Q ss_pred             c
Q 025973           95 T   95 (245)
Q Consensus        95 ~   95 (245)
                      +
T Consensus        83 ~   83 (104)
T 1wey_A           83 T   83 (104)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.46  E-value=7.5e-07  Score=59.38  Aligned_cols=76  Identities=20%  Similarity=0.238  Sum_probs=64.8

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhccc-----CCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQF-----GTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~-----G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      .....++|-+-|||..+++..|    +.+.+.+     |.+..|.+..+-   +-|+|+|.+...|-+|.-.|+|..|.|
T Consensus        17 ~~~~~rtiaL~~ipDtvndarI----r~lve~~~~i~~g~i~KI~L~pDH---~GAivef~d~~~AgKasLaL~G~ef~g   89 (117)
T 2l9w_A           17 SKELETLICLFPLSDKVSPSLI----CQFLQEEIHINEKDIRKILLVSDF---NGAIIIFRDSKFAAKMLMILNGSQFQG   89 (117)
T ss_dssp             TTTTTSCEEEECCCTTCCHHHH----HHHHHHHTCCCTTTCSEEEEETTT---TEEEEECSCHHHHHHHHHHHSSEEETT
T ss_pred             CccCCcEEEEecCCCCCCHHHH----HHHHhhhhccCccceeEEEEecCC---CceEEEEccchhhHHHHhhcCCeeecC
Confidence            3445789999999999999994    4777777     989888777653   679999999999999999999999999


Q ss_pred             ceEEEEEc
Q 025973           86 KPMRIQYA   93 (245)
Q Consensus        86 ~~i~v~~~   93 (245)
                      ++|+|.-.
T Consensus        90 r~Lr~gTv   97 (117)
T 2l9w_A           90 KVIRSGTI   97 (117)
T ss_dssp             EEEEEECH
T ss_pred             eEEEecCH
Confidence            99999764

>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=98.32  E-value=1.7e-06  Score=57.50  Aligned_cols=72  Identities=10%  Similarity=0.154  Sum_probs=61.7

Q ss_pred             cEEEEcCCCCCC-C----HHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          172 NILFVQNVPHDT-T----PMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~-t----~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ++|+|.||+..+ .    .+.++++|..|+.+......++-+ -..|.|.++++|.+|...||+..|.|++|+|-||+
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            459999998544 1    367899999999988888777753 57899999999999999999999999999999874

>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=98.14  E-value=1.1e-05  Score=52.72  Aligned_cols=64  Identities=16%  Similarity=0.223  Sum_probs=51.9

Q ss_pred             cccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHc
Q 025973            6 ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQ   79 (245)
Q Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~   79 (245)
                      .+.+..+...+.++| ++|..+.-.|    |.++|+.||.|.--++..|     .|||.|.+.+.|..|+..+.
T Consensus         7 ~g~d~~p~r~HVf~l-~FP~ewKt~D----I~~lFs~fggv~I~WidDT-----sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A            7 GGPDLQPKRDHVLHV-TFPKEWKTSD----LYQLFSAFGNIQISWIDDT-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSCCCCCCCSEEEE-ECCTTCCHHH----HHHHHTTTCSCCCEEEETT-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCeEEEE-eCChhhhhHH----HHHHhhccCCEEEEEEcCC-----eEEEEecCHHHHHHHHHhcc
Confidence            345556667788888 9999999999    7799999997754455443     79999999999999999764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.14  E-value=3.4e-05  Score=50.99  Aligned_cols=73  Identities=16%  Similarity=0.181  Sum_probs=58.7

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcc----c-CCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQ----F-GTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~----~-G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ....++|.|.|||++++++.    |.-+|+.    - |.|..|....     +.|+|.|.+.+.|+..++ -....++|.
T Consensus         5 ~~~~~~I~V~~lPp~~~~e~----L~LYFEn~rrsGGG~V~~v~~~~-----~~AvItF~d~~va~rVL~-k~~H~L~~~   74 (104)
T 2dhx_A            5 SSGGVAVEVRGLPPAVPDEL----LTLYFENRRRSGGGPVLSWQRLG-----CGGVLTFREPADAERVLA-QADHELHGA   74 (104)
T ss_dssp             CCCCCEEEEESCCTTSCHHH----HHHHHHCTTTTCCCCEEEEEEET-----TEEEEEESSHHHHHHHHT-CSCCBSSSS
T ss_pred             ccCccEEEEECCCCCCChhH----heEEEeCCCcCCCceeeEEEEcC-----CcEEEEEcChHHHHHHhc-CCcceecCe
Confidence            34678999999999999887    5567765    2 5888886654     579999999999999988 347888999


Q ss_pred             eEEEEEcc
Q 025973           87 PMRIQYAK   94 (245)
Q Consensus        87 ~i~v~~~~   94 (245)
                      .|.|....
T Consensus        75 ~LsV~P~~   82 (104)
T 2dhx_A           75 QLSLRPAP   82 (104)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEcCC
Confidence            99997643

>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=4.5e-05  Score=49.75  Aligned_cols=62  Identities=10%  Similarity=0.192  Sum_probs=56.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-------CeEEEEEeCCHHHHHHHHHHhCCCeeC
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-------PGIAFVEYGDEMQATVAMQSLQSLKIG  234 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-------~g~afv~f~~~~~A~~A~~~l~g~~~~  234 (245)
                      .|.|++||+.+|++++.+.++.+..+.+..+++++       ..-|+|.|.+.+++..-.+.++|+.|.
T Consensus         3 KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            3 KVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             EEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             EEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            58999999999999999999999999888888764       357999999999999999999998885

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.82  E-value=0.0003  Score=46.47  Aligned_cols=69  Identities=10%  Similarity=0.110  Sum_probs=58.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccC-----CCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQF-----PGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~-----g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      ...+|.|.|||..+.++.|.-+|++-     |.|..+...+   +-|+|+|.++..|+++|.. ..+.|.+.+|.|..
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P   80 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRP   80 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEc
Confidence            46789999999999999999999862     5689888876   5799999999999999973 36788888888753

>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=97.78  E-value=0.00012  Score=47.80  Aligned_cols=75  Identities=17%  Similarity=0.309  Sum_probs=55.4

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-----CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc----
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-----TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK----   86 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-----~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~----   86 (245)
                      ++|-|++||+.+|+++    +.+..+.+..+.......     .....+.|||.|.+.+++......++|..|.+.    
T Consensus         2 ~KvVIRrLPP~Lteee----F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~   77 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQ----LQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQE   77 (91)
T ss_dssp             CEEEEEEECTTCCHHH----HHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCE
T ss_pred             cEEEEeCCCCCCCHHH----HHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCE
Confidence            5799999999999999    557667777665544332     112336799999999999999999999888632    


Q ss_pred             -eEEEEEcc
Q 025973           87 -PMRIQYAK   94 (245)
Q Consensus        87 -~i~v~~~~   94 (245)
                       .-.|++|.
T Consensus        78 ~~a~VE~AP   86 (91)
T 1uw4_A           78 YPAIVEFAP   86 (91)
T ss_dssp             EECEEEECS
T ss_pred             eeeEEEEcC
Confidence             33455553

>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=97.72  E-value=2.9e-05  Score=50.82  Aligned_cols=56  Identities=18%  Similarity=0.281  Sum_probs=46.6

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHc
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQ   79 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~   79 (245)
                      ..+.++| ++|..+.-.|    |.++|+.||.|.--++..|     .|||.|.+.+.|..|+..+.
T Consensus         5 R~HV~~l-~FP~ewKt~D----i~~lFs~fggv~I~WidDT-----sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            5 SDHVLHV-TFPKEWKTSD----LYQLFSAFGNIQISWIDDT-----SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEEE-ECCTTCCHHH----HHHHTTTSEEEEEEEEETT-----EEEEEEEEECHHHHHHHHHT
T ss_pred             CCeEEEE-eCChhhhhHH----HHHHHhccCCEEEEEEcCC-----eEEEEecCHHHHHHHHHhcc
Confidence            4566777 9999999999    7799999997754455544     79999999999999999765

>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=97.59  E-value=0.00031  Score=47.93  Aligned_cols=76  Identities=13%  Similarity=0.135  Sum_probs=60.6

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC-ceEEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD-KPMRI   90 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g-~~i~v   90 (245)
                      ....+-|-|-+.|+.....     +.+.|++||.|.+.....   ..++-.|.|.+..+|.+|+. .||..+.| ..|-|
T Consensus        21 ~~~~~wVtVFGFp~~~~~~-----VL~~F~~~G~Iv~~~~~~---~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV   91 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQASASY-----ILLQFAQYGNILKHVMSN---TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGV   91 (119)
T ss_dssp             CGGGGEEEEECCCGGGHHH-----HHHHHHTTSCEEEEEECS---SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEE
T ss_pred             CCCCCEEEEECCCHHHHHH-----HHHHHHhhCcEEEeccCC---CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEE
Confidence            4447889999999986554     448999999999987632   24799999999999999999 79999985 57778


Q ss_pred             EEcccc
Q 025973           91 QYAKTK   96 (245)
Q Consensus        91 ~~~~~~   96 (245)
                      .+...+
T Consensus        92 ~p~~d~   97 (119)
T 1wwh_A           92 KPCIDK   97 (119)
T ss_dssp             EECCCH
T ss_pred             EECCCH
Confidence            776433

>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=97.57  E-value=0.00075  Score=44.05  Aligned_cols=57  Identities=21%  Similarity=0.395  Sum_probs=46.2

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQ  229 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~  229 (245)
                      ...+++++ ++|....-.||.++|++||.| .|+-+.+  .-|||.|.+++.|..|+..+.
T Consensus        14 ~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidD--TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           14 KRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD--TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEET--TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcC--CeEEEEecCHHHHHHHHHhcc
Confidence            35567888 999999999999999999864 2232334  479999999999999999773

>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=97.45  E-value=0.00098  Score=45.47  Aligned_cols=69  Identities=14%  Similarity=0.211  Sum_probs=55.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC-CeEEEEEE
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITY  242 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~  242 (245)
                      ..-|.|.+.|... -..+...|+.||.|.+...... .++-.|.|.++.+|.+||. .||..|+ +-.|-|..
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-ASYILLQFAQYGNILKHVMSNT-GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   93 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSS-SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCC-CCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEE
Confidence            4568888888764 6677888999999988877333 4799999999999999998 6999998 46666654

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.38  E-value=0.00038  Score=45.66  Aligned_cols=64  Identities=9%  Similarity=0.200  Sum_probs=53.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-------CeEEEEEeCCHHHHHHHHHHhCCCeeC
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-------PGIAFVEYGDEMQATVAMQSLQSLKIG  234 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-------~g~afv~f~~~~~A~~A~~~l~g~~~~  234 (245)
                      +-.|.|+.||+.+|++++.+.++..-.+.+..+++++       ..-|+|.|.+.++.....+.++|..|-
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            3469999999999999999999887777666666643       246899999999999999999998874

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.22  E-value=0.0004  Score=48.07  Aligned_cols=75  Identities=21%  Similarity=0.240  Sum_probs=56.9

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEE-ecCC-----------C-----CeeeEEEEEecCHHHHHHHHHHH
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEIL-AFKT-----------L-----KHKGQAWLVFKDVASATAAVEKM   78 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~-~~~~-----------~-----~~kg~afV~F~~~~~A~~a~~~l   78 (245)
                      .-|.|=|.|.+.+..-     -+.|++||.|.+-. ..++           .     ...++-.|.|.+..+|.+|+. .
T Consensus         8 ~~VtVFGFp~~~~~~V-----I~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~   81 (132)
T 3p3d_A            8 LAILVFGYPETMANQV-----IAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-E   81 (132)
T ss_dssp             CEEEEECCCGGGHHHH-----HHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-T
T ss_pred             eEEEEEecCHHHHHHH-----HHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-h
Confidence            4577788888876654     48999999997721 1110           0     134678999999999999999 7


Q ss_pred             cCCccCCceEEEEEcccc
Q 025973           79 QGFPFYDKPMRIQYAKTK   96 (245)
Q Consensus        79 ~~~~~~g~~i~v~~~~~~   96 (245)
                      ||..|.|..|-|.+..+.
T Consensus        82 NG~ii~G~mIGV~Py~~~   99 (132)
T 3p3d_A           82 NGAVFNGVLLGVIPYTKD   99 (132)
T ss_dssp             TTCEETTEECEEEECCHH
T ss_pred             CCeEeCcEEEEEEECCHH
Confidence            999999999999887543

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.19  E-value=0.001  Score=43.63  Aligned_cols=76  Identities=16%  Similarity=0.283  Sum_probs=51.6

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-----CCCeeeEEEEEecCHHHHHHHHHHHcCCccCC---c
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-----TLKHKGQAWLVFKDVASATAAVEKMQGFPFYD---K   86 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-----~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g---~   86 (245)
                      +-+|-|+.||+.+||++    +.+.++.+-.+.......     ....-..|||.|.+.++.......++|..|.+   .
T Consensus         9 ~~KvVIRrLPP~Ltee~----F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~   84 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQ----LEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGL   84 (97)
T ss_dssp             CCCEEEECCCSCSCHHH----HTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCC
T ss_pred             ceeEEEeCCCCCCCHHH----HHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCC
Confidence            56899999999999998    444444443332222211     11122579999999999999999999987753   2


Q ss_pred             --eEEEEEcc
Q 025973           87 --PMRIQYAK   94 (245)
Q Consensus        87 --~i~v~~~~   94 (245)
                        .-.|++|.
T Consensus        85 ~~~a~VE~AP   94 (97)
T 2l08_A           85 EYPAVVEFAP   94 (97)
T ss_dssp             EEEEEEEECC
T ss_pred             EeeeEEEecC
Confidence              44566653

>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=97.17  E-value=0.00094  Score=43.72  Aligned_cols=55  Identities=22%  Similarity=0.419  Sum_probs=45.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhC
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQ  229 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~  229 (245)
                      .++++| ++|....-.||.++|++||.| .|.-+.+  .-|||.|.+++.|..|+..+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidD--TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD--TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEET--TEEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcC--CeEEEEecCHHHHHHHHHhcc
Confidence            467777 999999999999999999953 3444444  379999999999999999875

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.55  E-value=0.0036  Score=43.28  Aligned_cols=70  Identities=14%  Similarity=0.141  Sum_probs=51.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeE-EEE----------------ecC--CCeEEEEEeCCHHHHHHHHHHhCCCe
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKE-VRM----------------VEA--KPGIAFVEYGDEMQATVAMQSLQSLK  232 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~-v~l----------------~~~--~~g~afv~f~~~~~A~~A~~~l~g~~  232 (245)
                      .-|.|.+.|... ...+.+.|++||.|.. +..                ++.  ..++.-|+|+++.+|.+||+ .||..
T Consensus         8 ~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            347777776554 4556678899999854 211                111  13588999999999999998 79999


Q ss_pred             eCCeEEEEEEe
Q 025973          233 IGQQQLLITYA  243 (245)
Q Consensus       233 ~~g~~i~v~~a  243 (245)
                      |.|..|-|.+-
T Consensus        86 i~G~mIGV~Py   96 (132)
T 3p3d_A           86 FNGVLLGVIPY   96 (132)
T ss_dssp             ETTEECEEEEC
T ss_pred             eCcEEEEEEEC
Confidence            99998877653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.33  E-value=0.0021  Score=54.52  Aligned_cols=54  Identities=15%  Similarity=0.188  Sum_probs=42.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHH
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQ  226 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~  226 (245)
                      +.|+|. .|..+++.+|.+.|++||.|.++.+..++.-||+|+|.+.+++..++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            459997 799999999999999999999999998876699999999998887764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.07  E-value=0.0031  Score=53.57  Aligned_cols=56  Identities=20%  Similarity=0.255  Sum_probs=41.9

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHH
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE   76 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~   76 (245)
                      +.+.|+|. .|...++++    |.++|++||+|..+...++.  .-||.|+|.+.+++..++.
T Consensus        52 a~rsv~v~-~~~~~~~~~----l~~y~~~~g~i~~~~~~~~~--g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENK----FLKYLSQFGPINNHFFYESF--GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CH----HHHHHGGGSCCCCEEEECSS--SEEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHH----HHHHHHhcCCcceEEEEccC--CeEEEEEeCCHHHHHHHHh
Confidence            45789997 799999999    77999999999998777543  2699999999999987765

>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=95.00  E-value=0.099  Score=45.14  Aligned_cols=59  Identities=15%  Similarity=0.202  Sum_probs=46.9

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcC
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQG   80 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~   80 (245)
                      +.....++|+ +|..+...+    |.++|+.||.+.-.++..     ..|||.|.+.+.|..++..+..
T Consensus       437 ~~R~~vl~v~-f~~~~~~~~----i~~~fs~fg~v~V~widd-----t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          437 PKRDHVLHVT-FPKEWKTSD----LYQLFSAFGNIQISWIDD-----TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             CCGGGEEEEE-CCTTCCHHH----HHHHGGGGCCCEEEECSS-----SEEEEECSCHHHHHHHHHHHTT
T ss_pred             CCcCcEEEEe-CCCCCCHHH----HHHHHHhcCCEEEEEEcC-----CeEEEEECCHHHHHHHHHHHHh
Confidence            3446677776 999999888    679999999875445543     3699999999999999998854

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=91.59  E-value=0.78  Score=39.58  Aligned_cols=56  Identities=21%  Similarity=0.397  Sum_probs=45.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCC
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQS  230 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g  230 (245)
                      ..+++|+ +|..+...+|.+.|+.||.+ +|+.+.+  ..|||.|.+.+.|..++..++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd--t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD--TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS--SEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC--CeEEEEECCHHHHHHHHHHHHh
Confidence            4577887 88899999999999999964 4544433  4799999999999999998853

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=90.95  E-value=0.35  Score=29.84  Aligned_cols=61  Identities=11%  Similarity=0.237  Sum_probs=40.4

Q ss_pred             CCCCHHHHHHHhccCCC-----eeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          181 HDTTPMALQMFFSQFPG-----FKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       181 ~~~t~~~l~~~f~~~g~-----v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      ..+...+|..++..-+.     |-.|.+..   .+.||+-.. +.|..++..|++..+.|+++.|..+++
T Consensus        11 ~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d---~~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~~~~~   76 (76)
T 2g0c_A           11 KKIRAVDFVGTIAKIDGVSADDIGIITIMD---NASYVEILN-GKGPHVLKVMKNTTVKGKQLKVNKANK   76 (76)
T ss_dssp             ----CHHHHHHHHTSTTCCGGGEEEEEECS---SCEEEEECT-TCHHHHHHHHTTCCC---CCCEEECC-
T ss_pred             cCCCHHHHHHHHHHccCCChhhccEEEEeC---CcEEEEECH-HHHHHHHHHhccccCcCceEEEEECCC
Confidence            55666777777765554     34555532   489999886 678889999999999999999999875

---

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	245
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-23
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-08
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-18
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-14
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-14
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-14
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	5e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-13
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-06
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-13
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-12
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-08
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-12
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-05
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	6e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-11
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-06
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-08
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-11
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	4e-11
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	9e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-11
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-07
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	8e-11
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-06
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-10
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-06
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-10
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	5e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	9e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-10
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-10
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-09
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	9e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-08
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.003
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-08
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	7e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-08
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	8e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.002
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	8e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	8e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	4e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	5e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	7e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.004
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	7e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	4e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	7e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	7e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	8e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	9e-06
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 9e-06
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 6e-04
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-06
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-05
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-05
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	0.003
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-05
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	3e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	9e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	7e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	0.003
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-04
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	6e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.001
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.001
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	0.002
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	0.002

>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 = 89.0 bits (220), Expect = 1e-23
 Identities = 63/89 (70%), Positives = 79/89 (88%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
           PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL  ++LK +GQA+++FK+V+SAT 
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 74  AVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
           A+  MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 90

>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 = 48.1 bits (114), Expect = 2e-08
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 170 PNNILFVQNVPHDTTPMALQM----FFSQFPGFKEVRMVEA--KPGIAFVEYGDEMQATV 223
           PN+ +++ N+        L+      FS+F    ++ +  +    G AFV + +   AT 
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 224 AMQSLQSLKIGQQQLLITYAKK 245
           A++S+Q      + + I YAK 
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKT 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 = 75.1 bits (184), Expect = 5e-18
 Identities = 26/118 (22%), Positives = 54/118 (45%), Gaps = 13/118 (11%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
            N  +YI NL  K+  +++      +F ++G I +I    T + +G A++V++D+  A  
Sbjct: 6   VNRILYIRNLPYKITAEEMYD----IFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 61

Query: 74  AVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQ 131
           A + + GF   ++ + + Y                 +   K+ EE+ K  K+++  N 
Sbjct: 62  ACDHLSGFNVCNRYLVVLYYNANRAF---------QKMDTKKKEEQLKLLKEKYGINT 110

>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 = 56.2 bits (135), Expect = 5e-11
 Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP--GIAFVEYGDEMQATVA 224
           P   N IL+++N+P+  T   +   F ++   +++R+       G A+V Y D   A  A
Sbjct: 3   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 62

Query: 225 MQSLQSLKIGQQQLLITYAK 244
              L    +  + L++ Y  
Sbjct: 63  CDHLSGFNVCNRYLVVLYYN 82

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.0 bits (158), Expect = 2e-14
 Identities = 22/95 (23%), Positives = 39/95 (41%), Gaps = 9/95 (9%)

Query: 4  EVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWL 63
          +V NQ +    N T+Y   +   +    ++Q     F  FG I+EI   +    KG +++
Sbjct: 9  DVVNQSS--PKNCTVYCGGIASGLTDQLMRQ----TFSPFGQIMEI---RVFPEKGYSFV 59

Query: 64 VFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           F    SA  A+  + G       ++  + K   D
Sbjct: 60 RFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD 94

>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 = 56.5 bits (136), Expect = 2e-11
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 1/82 (1%)

Query: 163 IPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQAT 222
           +    +P N  ++   +    T   ++  FS F    E+R+   + G +FV +     A 
Sbjct: 10  VVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-EKGYSFVRFSTHESAA 68

Query: 223 VAMQSLQSLKIGQQQLLITYAK 244
            A+ S+    I    +   + K
Sbjct: 69  HAIVSVNGTTIEGHVVKCYWGK 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 = 63.3 bits (154), Expect = 8e-14
 Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 8/93 (8%)

Query: 6  ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
          + + +  S N+ ++I NLN  V        + A+F ++G I+         HKG A++ +
Sbjct: 6  SGKTDPRSMNSRVFIGNLNTLVVKKSD---VEAIFSKYGKIVGCS-----VHKGFAFVQY 57

Query: 66 KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           +  +A AAV    G     + + I  A     
Sbjct: 58 VNERNARAAVAGEDGRMIAGQVLDINLAAEPKV 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 = 50.6 bits (121), Expect = 3e-09
 Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 4/80 (5%)

Query: 167 PAPPNNILFVQNV-PHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAM 225
           P   N+ +F+ N+         ++  FS++       +     G AFV+Y +E  A  A+
Sbjct: 11  PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAV 67

Query: 226 QSLQSLKIGQQQLLITYAKK 245
                  I  Q L I  A +
Sbjct: 68  AGEDGRMIAGQVLDINLAAE 87

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 8e-14
 Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 4/84 (4%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          + +  IY+ NL   ++   ++     VF ++G I +I           A++ F+D   A 
Sbjct: 12 NNDCRIYVGNLPPDIRTKDIED----VFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAE 67

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTK 96
           AV    G+ +    +R+++ ++ 
Sbjct: 68 DAVYGRDGYDYDGYRLRVEFPRSG 91

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 5e-08
 Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 3/82 (3%)

Query: 166 APAPPNNI-LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV--EAKPGIAFVEYGDEMQAT 222
            PA  N+  ++V N+P D     ++  F ++   +++ +      P  AFVE+ D   A 
Sbjct: 8   GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAE 67

Query: 223 VAMQSLQSLKIGQQQLLITYAK 244
            A+           +L + + +
Sbjct: 68  DAVYGRDGYDYDGYRLRVEFPR 89

>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 = 62.5 bits (151), Expect = 2e-13
 Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 4/87 (4%)

Query: 13 SPNNTIYINNLNEKV-KIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASA 71
          S ++ +     N+ V    + +    ++F+ +        F+  K   +  + F +  SA
Sbjct: 3  SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTT---FQYFKSFKRVRINFSNPLSA 59

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            A  ++    F  K M++ +A+T   
Sbjct: 60 ADARLRLHKTEFLGKEMKLYFAQTLHI 86

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.9 bits (100), Expect = 3e-06
 Identities = 7/82 (8%), Positives = 25/82 (30%), Gaps = 6/82 (7%)

Query: 169 PPNNILFVQNVP-----HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATV 223
             ++ L              T    +  F  +      +  ++      + + + + A  
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-KRVRINFSNPLSAAD 61

Query: 224 AMQSLQSLKIGQQQLLITYAKK 245
           A   L   +   +++ + +A+ 
Sbjct: 62  ARLRLHKTEFLGKEMKLYFAQT 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 = 61.1 bits (148), Expect = 4e-13
 Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 7/81 (8%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEIL---AFKTLKHKGQAWLVFKDVASATA 73
          ++Y+ +L+  V    L +     F   G IL I       T +  G A++ F+  A A  
Sbjct: 2  SLYVGDLHPDVTEAMLYE----KFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 57

Query: 74 AVEKMQGFPFYDKPMRIQYAK 94
          A++ M       KP+RI +++
Sbjct: 58 ALDTMNFDVIKGKPVRIMWSQ 78

>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 = 51.8 bits (124), Expect = 8e-10
 Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 5/77 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV-----EAKPGIAFVEYGDEMQATVAMQSL 228
           L+V ++  D T   L   FS       +R+          G A+V +     A  A+ ++
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 229 QSLKIGQQQLLITYAKK 245
               I  + + I ++++
Sbjct: 63  NFDVIKGKPVRIMWSQR 79

>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 = 60.1 bits (145), Expect = 1e-12
 Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 7/88 (7%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVAS 70
           N TI + NL+E  +   L++    +F+ FG+I  I   K   T + KG A++ F     
Sbjct: 7  DNATIRVTNLSEDTRETDLQE----LFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 62

Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
          A  A+  + GF +    + +++AK  ++
Sbjct: 63 AARAIAGVSGFGYDHLILNVEWAKPSTN 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 = 47.3 bits (112), Expect = 4e-08
 Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 5/86 (5%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDE 218
           P   A  N  + V N+  DT    LQ  F  F     + + + K      G AF+ +   
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 219 MQATVAMQSLQSLKIGQQQLLITYAK 244
             A  A+  +         L + +AK
Sbjct: 61  EDAARAIAGVSGFGYDHLILNVEWAK 86

>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 = 59.3 bits (143), Expect = 2e-12
 Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 7/90 (7%)

Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKD 67
          E + + T+Y+  L+EKV    L +    +F Q G ++         T +H+G  ++ F  
Sbjct: 5  ERNQDATVYVGGLDEKVSEPLLWE----LFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 60

Query: 68 VASATAAVEKMQGFPFYDKPMRIQYAKTKS 97
             A  A++ M     Y KP+R+  A   +
Sbjct: 61 EEDADYAIKIMDMIKLYGKPIRVNKASAHN 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 = 48.9 bits (116), Expect = 2e-08
 Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 5/87 (5%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-----KPGIAFVEYGDE 218
           P +    +  ++V  +    +   L   F Q        M +        G  FVE+  E
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 219 MQATVAMQSLQSLKIGQQQLLITYAKK 245
             A  A++ +  +K+  + + +  A  
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASA 88

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 58.5 bits (141), Expect = 4e-12
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 7/83 (8%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKG---QAWLVFKDVASA 71
          N  + +N L + +   +L      +F+  G I      +  K       A++ F     +
Sbjct: 2  NTNLIVNYLPQDMTDRELYA----LFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDS 57

Query: 72 TAAVEKMQGFPFYDKPMRIQYAK 94
            A++ + G    +K +++ YA+
Sbjct: 58 QRAIKVLNGITVRNKRLKVSYAR 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 = 45.4 bits (107), Expect = 2e-07
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 5/79 (6%)

Query: 171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-----KPGIAFVEYGDEMQATVAM 225
           N  L V  +P D T   L   F         R++         G AFV++  EM +  A+
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 226 QSLQSLKIGQQQLLITYAK 244
           + L  + +  ++L ++YA+
Sbjct: 62  KVLNGITVRNKRLKVSYAR 80

>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 = 58.1 bits (140), Expect = 5e-12
 Identities = 14/89 (15%), Positives = 41/89 (46%), Gaps = 7/89 (7%)

Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
            +  + +++ NL   +  +++++    +F+++G   E+   K    KG  ++  +    
Sbjct: 4  TFTQRSRLFVGNLPPDITEEEMRK----LFEKYGKAGEVFIHK---DKGFGFIRLETRTL 56

Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDI 99
          A  A  ++   P   K +R+++A   + +
Sbjct: 57 AEIAKVELDNMPLRGKQLRVRFACHSASL 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 = 44.6 bits (105), Expect = 4e-07
 Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
           LFV N+P D T   ++  F ++    EV + +   G  F+       A +A   L ++ +
Sbjct: 11  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-DKGFGFIRLETRTLAEIAKVELDNMPL 69

Query: 234 GQQQLLITYAKK 245
             +QL + +A  
Sbjct: 70  RGKQLRVRFACH 81

>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 = 58.2 bits (140), Expect = 5e-12
 Identities = 15/86 (17%), Positives = 35/86 (40%), Gaps = 1/86 (1%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          S    +++  L+       L+Q      +    ++     +T + +G  ++ F+++  A 
Sbjct: 3  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVK-DRETQRSRGFGFVTFENIDDAK 61

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A+  M G     + +R+  A   SD
Sbjct: 62 DAMMAMNGKSVDGRQIRVDQAGKSSD 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 = 40.5 bits (94), Expect = 1e-05
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           LFV  +  DT   +L+  FS++    EV +V+ +      G  FV + +   A  AM ++
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 229 QSLKIGQQQLLITYAKK 245
               +  +Q+ +  A K
Sbjct: 68  NGKSVDGRQIRVDQAGK 84

>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 = 58.1 bits (140), Expect = 5e-12
 Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 5/87 (5%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASA 71
          S    I+I NL++ +    L       F  FG IL   +       KG  ++ F+   +A
Sbjct: 6  SGVGNIFIKNLDKSIDNKALYD----TFSAFGNILSCKVVCDENGSKGYGFVHFETQEAA 61

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            A+EKM G    D+ + +   K++ +
Sbjct: 62 ERAIEKMNGMLLNDRKVFVGRFKSRKE 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 = 44.3 bits (104), Expect = 5e-07
 Identities = 14/75 (18%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPG---IAFVEYGDEMQATVAMQSLQS 230
           +F++N+       AL   FS F      ++V  + G     FV +  +  A  A++ +  
Sbjct: 11  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 70

Query: 231 LKIGQQQLLITYAKK 245
           + +  +++ +   K 
Sbjct: 71  MLLNDRKVFVGRFKS 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 = 58.1 bits (140), Expect = 7e-12
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 6/87 (6%)

Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
          ++    T+   NL+  +  D+LK+    VF+    I  +   +  K KG A++ FK  A 
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKE----VFEDALEIRLV--SQDGKSKGIAYIEFKSEAD 65

Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKS 97
          A   +E+ QG     + + + Y   K 
Sbjct: 66 AEKNLEEKQGAEIDGRSVSLYYTGEKG 92

>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 = 50.0 bits (119), Expect = 5e-09
 Identities = 15/82 (18%), Positives = 30/82 (36%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATV 223
                     L  +N+  + T   L+  F      + V       GIA++E+  E  A  
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 224 AMQSLQSLKIGQQQLLITYAKK 245
            ++  Q  +I  + + + Y  +
Sbjct: 69  NLEEKQGAEIDGRSVSLYYTGE 90

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 2e-11
 Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 7/87 (8%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVA 69
          +    +Y+  L E+V    L       F  FG I +I       T KH+G A++ F+   
Sbjct: 3  TTKRVLYVGGLAEEVDDKVLHA----AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 58

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTK 96
           A AA++ M     + + +R+  AK  
Sbjct: 59 DAAAAIDNMNESELFGRTIRVNLAKPM 85

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 6e-06
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 5/82 (6%)

Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE-----AKPGIAFVEYGDEMQAT 222
           A    +L+V  +  +     L   F  F    ++++          G AFVE+     A 
Sbjct: 2   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61

Query: 223 VAMQSLQSLKIGQQQLLITYAK 244
            A+ ++   ++  + + +  AK
Sbjct: 62  AAIDNMNESELFGRTIRVNLAK 83

>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 = 57.1 bits (137), Expect = 2e-11
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 1/85 (1%)

Query: 14  PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
           PN  +Y+ NL+ +V    L       F++           T + +GQA++ F +   A  
Sbjct: 17  PNKVLYLKNLSPRVTERDLVSLFA-RFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 75

Query: 74  AVEKMQGFPFYDKPMRIQYAKTKSD 98
           A+  + G+  Y K + I++ K K  
Sbjct: 76  ALHLVNGYKLYGKILVIEFGKNKKQ 100

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 1e-06
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQA 221
           P  PN +L+++N+    T   L   F++F   K   +          G AF+ + ++  A
Sbjct: 14  PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIA 73

Query: 222 TVAMQSLQSLKIGQQQLLITYAK 244
             A+  +   K+  + L+I + K
Sbjct: 74  WQALHLVNGYKLYGKILVIEFGK 96

>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 = 56.5 bits (136), Expect = 2e-11
 Identities = 14/91 (15%), Positives = 37/91 (40%), Gaps = 9/91 (9%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK----TLKHKGQAWLVFKDVA 69
            + I + N+  +    ++++    +F  FG +  +   K    T  H+G  ++ F    
Sbjct: 7  TTSKILVRNIPFQANQREIRE----LFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 70 SATAAVEKM-QGFPFYDKPMRIQYAKTKSDI 99
           A  A   +      Y + + +++A ++  +
Sbjct: 63 DAKKAFNALCHSTHLYGRRLVLEWADSEVTV 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 = 48.8 bits (116), Expect = 1e-08
 Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK------PGIAFVEYGDEMQAT 222
              + + V+N+P       ++  FS F   K VR+ +         G  FV++  +  A 
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 223 VAMQSL-QSLKIGQQQLLITYAKK 245
            A  +L  S  +  ++L++ +A  
Sbjct: 66  KAFNALCHSTHLYGRRLVLEWADS 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 = 56.1 bits (135), Expect = 2e-11
 Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFKDVASATAAV 75
          + ++NL+  V    +++    +F +FGT+ +  +   ++ +  G A + F+  A A  A+
Sbjct: 3  LLVSNLDFGVSDADIQE----LFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAM 58

Query: 76 EKMQGFPFYDKPMRIQYAKT 95
          ++  G P   +PM IQ   +
Sbjct: 59 KQYNGVPLDGRPMNIQLVTS 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 = 48.4 bits (115), Expect = 1e-08
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 4/74 (5%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV----EAKPGIAFVEYGDEMQATVAMQSLQ 229
           L V N+    +   +Q  F++F   K+  +         G A V +  +  A  AM+   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 230 SLKIGQQQLLITYA 243
            + +  + + I   
Sbjct: 63  GVPLDGRPMNIQLV 76

>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 = 56.2 bits (135), Expect = 3e-11
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 5/89 (5%)

Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF-KTLKHKGQAWLVFKDVA 69
          +     T+Y+ NL+  V    + Q    +F Q G         +   +    ++ F +  
Sbjct: 4  DDGQPRTLYVGNLSRDVTEVLILQ----LFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 59

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A AA+  M G     K +++ +A T S 
Sbjct: 60 DAAAALAAMNGRKILGKEVKVNWATTPSS 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 = 45.8 bits (108), Expect = 2e-07
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAM 225
                L+V N+  D T + +   FSQ    K  +M+          FVE+ +   A  A+
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAAL 65

Query: 226 QSLQSLKIGQQQLLITYAKK 245
            ++   KI  +++ + +A  
Sbjct: 66  AAMNGRKILGKEVKVNWATT 85

>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 = 55.8 bits (134), Expect = 3e-11
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 10/86 (11%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILA------FKTLKHKGQAWLVFKDVASA 71
          ++I NLN     + LK     VF + G I              L   G  ++ +K    A
Sbjct: 1  LFIKNLNFSTTEETLKG----VFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 56

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKS 97
            A++++QG       + ++ ++  +
Sbjct: 57 QKALKQLQGHTVDGHKLEVRISERAT 82

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.9 bits (103), Expect = 8e-07
 Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 8/80 (10%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGI--------AFVEYGDEMQATVAM 225
           LF++N+   TT   L+  FS+    K   + + K            FVEY    QA  A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 226 QSLQSLKIGQQQLLITYAKK 245
           + LQ   +   +L +  +++
Sbjct: 61  KQLQGHTVDGHKLEVRISER 80

>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 = 56.2 bits (135), Expect = 3e-11
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 5/87 (5%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF-KTLKHKGQAWLVFKDVASA 71
          S    ++++N+  + +   L+Q    +F QFG IL++         KG  ++ F++ A A
Sbjct: 9  STPKRLHVSNIPFRFRDPDLRQ----MFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 64

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            A EK+ G     + + +  A  +  
Sbjct: 65 DRAREKLHGTVVEGRKIEVNNATARVM 91

>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 = 45.1 bits (106), Expect = 4e-07
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 4/85 (4%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP---GIAFVEYGDEMQ 220
            E+ + P   L V N+P       L+  F QF    +V ++  +    G  FV + +   
Sbjct: 5   SESKSTPKR-LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD 63

Query: 221 ATVAMQSLQSLKIGQQQLLITYAKK 245
           A  A + L    +  +++ +  A  
Sbjct: 64  ADRAREKLHGTVVEGRKIEVNNATA 88

>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 = 56.2 bits (135), Expect = 4e-11
 Identities = 29/94 (30%), Positives = 46/94 (48%), Gaps = 7/94 (7%)

Query: 13  SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
           SP   I + NL   V +D L Q    +F +FGT+L+I+ F    ++ QA L + D  SA 
Sbjct: 5   SPVLRIIVENLFYPVTLDVLHQ----IFSKFGTVLKIITFTK-NNQFQALLQYADPVSAQ 59

Query: 73  AAVEKMQGFPFYD--KPMRIQYAKTKSDIIAKAD 104
            A   + G   Y+    +RI ++K  S  +   +
Sbjct: 60  HAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNN 93

>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 = 44.2 bits (104), Expect = 9e-07
 Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 3/83 (3%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-GIAFVEYGDEMQATVA 224
           A   P   + V+N+ +  T   L   FS+F    ++          A ++Y D + A  A
Sbjct: 2   AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHA 61

Query: 225 MQSL--QSLKIGQQQLLITYAKK 245
             SL  Q++      L I ++K 
Sbjct: 62  KLSLDGQNIYNACCTLRIDFSKL 84

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.9 bits (134), Expect = 4e-11
 Identities = 30/98 (30%), Positives = 45/98 (45%), Gaps = 15/98 (15%)

Query: 10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-----------LAFKTLKHK 58
          +E S N+ IY+  LN+ V +D L       FKQ G +              L  +T K K
Sbjct: 3  DEDSDNSAIYVQGLNDSVTLDDLAD----FFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 58

Query: 59 GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTK 96
          G A + ++D  +A AAVE   G  F    +++  A+ K
Sbjct: 59 GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>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 = 37.8 bits (87), Expect = 1e-04
 Identities = 19/90 (21%), Positives = 30/90 (33%), Gaps = 13/90 (14%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-------------PGIAFVEY 215
             N+ ++VQ +    T   L  FF Q    K  +                   G A V Y
Sbjct: 6   SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 65

Query: 216 GDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
            D   A  A++          +L ++ A+K
Sbjct: 66  EDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 55.1 bits (132), Expect = 6e-11
 Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 8/85 (9%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEI----LAFKTLKHKGQAWLVFKDVASATA 73
          I+I NL+ ++    L       F  FG IL+         T   KG A++ F    ++ A
Sbjct: 1  IFIGNLDPEIDEKLLYD----TFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 56

Query: 74 AVEKMQGFPFYDKPMRIQYAKTKSD 98
          A+E M G    ++P+ + YA  K  
Sbjct: 57 AIEAMNGQYLCNRPITVSYAFKKDS 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 = 44.0 bits (103), Expect = 7e-07
 Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV------EAKPGIAFVEYGDEMQATVAMQS 227
           +F+ N+  +     L   FS F    +   +          G AF+ +     +  A+++
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 228 LQSLKIGQQQLLITYAKK 245
           +    +  + + ++YA K
Sbjct: 61  MNGQYLCNRPITVSYAFK 78

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.0 bits (132), Expect = 8e-11
 Identities = 16/90 (17%), Positives = 37/90 (41%), Gaps = 7/90 (7%)

Query: 12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDV 68
          +  + T+Y+ NL+     +Q+ +    +F + G I +I+           G  ++ +   
Sbjct: 4  LKKSCTLYVGNLSFYTTEEQIYE----LFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSR 59

Query: 69 ASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
          A A  A+  + G    D+ +R  +     +
Sbjct: 60 ADAENAMRYINGTRLDDRIIRTDWDAGFKE 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 = 45.7 bits (108), Expect = 2e-07
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGI-----AFVEYGDEMQATVAMQSL 228
           L+V N+   TT   +   FS+    K++ M   K         FVEY     A  AM+ +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 229 QSLKIGQQQLLITYAK 244
              ++  + +   +  
Sbjct: 70  NGTRLDDRIIRTDWDA 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 = 54.3 bits (130), Expect = 1e-10
 Identities = 17/80 (21%), Positives = 38/80 (47%), Gaps = 7/80 (8%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVAS 70
          PN  + +  L+       L++    VF ++G I ++      ++ + +G A++ F++V  
Sbjct: 8  PNCCLGVFGLSLYTTERDLRE----VFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 63

Query: 71 ATAAVEKMQGFPFYDKPMRI 90
          A  A E+  G     + +R+
Sbjct: 64 AKEAKERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 5e-07
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE-----AKPGIAFVEYGDEMQATV 223
            PN  L V  +   TT   L+  FS++    +V +V         G AFV + +   A  
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 224 AMQSLQSLKIGQQQLLI 240
           A +    +++  +++ +
Sbjct: 67  AKERANGMELDGRRIRV 83

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 1e-10
 Identities = 11/78 (14%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
           + +N L + +  ++ +        +  +   +    T +  G  ++ + D   A  A+ 
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFG-SIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 77 KMQGFPFYDKPMRIQYAK 94
           + G     K +++ YA+
Sbjct: 63 TLNGLRLQTKTIKVSYAR 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 = 41.6 bits (97), Expect = 5e-06
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-----KPGIAFVEYGDEMQATVAMQSL 228
           L V  +P + T    +  F      +  ++V         G  FV Y D   A  A+ +L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 229 QSLKIGQQQLLITYAK 244
             L++  + + ++YA+
Sbjct: 65  NGLRLQTKTIKVSYAR 80

>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 = 54.3 bits (130), Expect = 1e-10
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 1/82 (1%)

Query: 16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAV 75
          + ++I  L   +  DQ+K+ L + F        +    T   KG A+  + D+     A+
Sbjct: 2  HKLFIGGLPNYLNDDQVKELLTS-FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 76 EKMQGFPFYDKPMRIQYAKTKS 97
            + G    DK + +Q A   +
Sbjct: 61 AGLNGMQLGDKKLLVQRASVGA 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 = 46.9 bits (111), Expect = 6e-08
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           LF+  +P+      ++   + F   K   +V+        G AF EY D      A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 229 QSLKIGQQQLLITYAK 244
             +++G ++LL+  A 
Sbjct: 64  NGMQLGDKKLLVQRAS 79

>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 = 54.3 bits (130), Expect = 2e-10
 Identities = 12/91 (13%), Positives = 38/91 (41%), Gaps = 11/91 (12%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEIL-----AFKTLKHKGQAWLVFKDVA 69
          N  ++I  + +  K +++ +       +    +  +     A   +K++G A++ ++   
Sbjct: 1  NCRLFIGGIPKMKKREEILE----EIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 56

Query: 70 SATAAVEKMQG--FPFYDKPMRIQYAKTKSD 98
          +A  A  K+       +   + + +A+ + D
Sbjct: 57 AAAMARRKLMPGRIQLWGHQIAVDWAEPEID 87

>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 = 39.7 bits (92), Expect = 3e-05
 Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 9/83 (10%)

Query: 171 NNILFVQNVPHDTTPMALQMFFSQF-PGFKEVRMVEAKP------GIAFVEYGDEMQATV 223
           N  LF+  +P       +    ++   G  +V +  +        G AFVEY     A +
Sbjct: 1   NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 60

Query: 224 AMQSLQS--LKIGQQQLLITYAK 244
           A + L    +++   Q+ + +A+
Sbjct: 61  ARRKLMPGRIQLWGHQIAVDWAE 83

>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 = 54.3 bits (130), Expect = 2e-10
 Identities = 15/86 (17%), Positives = 35/86 (40%), Gaps = 1/86 (1%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          S +  +++ NL+     + L++     +     +   +   T K KG A++ F     A 
Sbjct: 6  SGSGRLFVRNLSYTSSEEDLEKLFS-AYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A  ++ G  F  + + +  +  K +
Sbjct: 65 KAYAEVDGQVFQGRMLHVLPSTIKKE 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 = 42.0 bits (98), Expect = 4e-06
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQAT 222
           +  +  LFV+N+ + ++   L+  FS +    E+            G AFV +     A 
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 223 VAMQSLQSLKIGQQQLLITYAKK 245
            A   +       + L +  +  
Sbjct: 65  KAYAEVDGQVFQGRMLHVLPSTI 87

>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 = 53.8 bits (129), Expect = 2e-10
 Identities = 18/90 (20%), Positives = 39/90 (43%), Gaps = 10/90 (11%)

Query: 9  GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVF 65
          G  I  +  +Y+ NL   +  DQL      +F ++G+I++        T + +G A++ +
Sbjct: 1  GESIK-DTNLYVTNLPRTITDDQLDT----IFGKYGSIVQKNILRDKLTGRPRGVAFVRY 55

Query: 66 KDVASATAAVEKMQGFPF--YDKPMRIQYA 93
               A  A+  +         +P+ ++ A
Sbjct: 56 NKREEAQEAISALNNVIPEGGSQPLSVRLA 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 = 43.0 bits (101), Expect = 1e-06
 Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 7/77 (9%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-----KPGIAFVEYGDEMQATVAMQSL 228
           L+V N+P   T   L   F ++    +  ++         G+AFV Y    +A  A+ +L
Sbjct: 9   LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 68

Query: 229 --QSLKIGQQQLLITYA 243
                + G Q L +  A
Sbjct: 69  NNVIPEGGSQPLSVRLA 85

>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 = 53.7 bits (128), Expect = 2e-10
 Identities = 40/82 (48%), Positives = 54/82 (65%), Gaps = 1/82 (1%)

Query: 165 EAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVA 224
           +   PPN ILF+ N+P +T  M L M F+QFPGFKEVR+V  +  IAFVE+  E+Q+  A
Sbjct: 2   QTEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAA 61

Query: 225 MQSLQSLKI-GQQQLLITYAKK 245
            ++LQ  KI     + IT+AKK
Sbjct: 62  KEALQGFKITPTHAMKITFAKK 83

>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 = 44.5 bits (104), Expect = 5e-07
 Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 7/82 (8%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
          PN  +++ NL E+         L  +F QF    E+           A++ F     + A
Sbjct: 7  PNQILFLTNLPEETNEMM----LSMLFNQFPGFKEV--RLVPNRHDIAFVEFTTELQSNA 60

Query: 74 AVEKMQGFPFYD-KPMRIQYAK 94
          A E +QGF       M+I +AK
Sbjct: 61 AKEALQGFKITPTHAMKITFAK 82

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 2e-10
 Identities = 19/93 (20%), Positives = 37/93 (39%), Gaps = 1/93 (1%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
           A    E      ++I +L ++     L Q            + I        K   ++ +
Sbjct: 9   AGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN-LSKCFGFVSY 67

Query: 66  KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            +  SA AA++ M GF    K +++Q  ++K+D
Sbjct: 68  DNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 100

>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 = 43.9 bits (103), Expect = 9e-07
 Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDE 218
            +   P    LF+ ++P +     L   F  F      ++   K         FV Y + 
Sbjct: 11  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 70

Query: 219 MQATVAMQSLQSLKIGQQQLLITYAKK 245
           + A  A+QS+   +IG ++L +   + 
Sbjct: 71  VSAQAAIQSMNGFQIGMKRLKVQLKRS 97

>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 = 53.5 bits (128), Expect = 2e-10
 Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAV 75
          N +YI NL+  V  D L+Q    +F      L     + L   G A++ + D   A  A+
Sbjct: 2  NKLYIGNLSPAVTADDLRQ----LFGDRKLPLA---GQVLLKSGYAFVDYPDQNWAIRAI 54

Query: 76 EKMQG-FPFYDKPMRIQYAKTK 96
          E + G    + K M + Y+ +K
Sbjct: 55 ETLSGKVELHGKIMEVDYSVSK 76

>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 = 41.6 bits (97), Expect = 4e-06
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQ-S 230
           N L++ N+    T   L+  F           V  K G AFV+Y D+  A  A+++L   
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDR-KLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGK 60

Query: 231 LKIGQQQLLITYAK 244
           +++  + + + Y+ 
Sbjct: 61  VELHGKIMEVDYSV 74

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.3 bits (125), Expect = 6e-10
 Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 7/87 (8%)

Query: 10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVA 69
          + +S    +Y+ NL      + +        K+F  I      +  K +  A++ F +  
Sbjct: 3  DTMSSVKILYVRNLMLSTSEEMI-------EKEFNNIKPGAVERVKKIRDYAFVHFSNRE 55

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTK 96
           A  A++ + G      P+ +  AK  
Sbjct: 56 DAVEAMKALNGKVLDGSPIEVTLAKPV 82

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 3e-08
 Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLK 232
           IL+V+N+   T+   ++  F+        R+ + +   AFV + +   A  AM++L    
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-YAFVHFSNREDAVEAMKALNGKV 68

Query: 233 IGQQQLLITYAK 244
           +    + +T AK
Sbjct: 69  LDGSPIEVTLAK 80

>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 = 52.9 bits (126), Expect = 7e-10
 Identities = 17/89 (19%), Positives = 35/89 (39%), Gaps = 9/89 (10%)

Query: 10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVA 69
          +++S +  +++  L E V    L ++L         ++          K QA + F+++ 
Sbjct: 10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-------FKRQALVEFENID 62

Query: 70 SATAAVEKMQGFPFY--DKPMRIQYAKTK 96
          SA   V      P Y   +     Y+ +K
Sbjct: 63 SAKECVTFAADVPVYIAGQQAFFNYSTSK 91

>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 = 48.3 bits (114), Expect = 3e-08
 Identities = 15/90 (16%), Positives = 28/90 (31%), Gaps = 3/90 (3%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYG 216
           G + S         + ++ V+ +        L     +F     V M+      A VE+ 
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFE 59

Query: 217 DEMQATVAMQSLQS--LKIGQQQLLITYAK 244
           +   A   +       + I  QQ    Y+ 
Sbjct: 60  NIDSAKECVTFAADVPVYIAGQQAFFNYST 89

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 52.0 bits (124), Expect = 1e-09
 Identities = 15/86 (17%), Positives = 37/86 (43%), Gaps = 7/86 (8%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKT---LKHKGQAWLVFKDVAS 70
              +++ +++E+ + D++++     F  +G I  I           KG A + ++    
Sbjct: 6  EGWILFVTSIHEEAQEDEIQE----KFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 61

Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTK 96
          A AA E + G     + +++ +   K
Sbjct: 62 ALAAKEALNGAEIMGQTIQVDWCFVK 87

>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 = 5e-06
 Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGF-----KEVRMVEAKPGIAFVEYGDEMQAT 222
           +    ILFV ++  +     +Q  F  +           R      G A VEY    QA 
Sbjct: 4   SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 63

Query: 223 VAMQSLQSLKIGQQQLLITYAKK 245
            A ++L   +I  Q + + +   
Sbjct: 64  AAKEALNGAEIMGQTIQVDWCFV 86

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.1 bits (124), Expect = 1e-09
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
          ++++ N+  +   +QLK     V       L        K KG  +  ++D  +A +A+ 
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETG-KPKGYGFCEYQDQETALSAMR 68

Query: 77 KMQGFPFYDKPMRIQYAKTKSD 98
           + G  F  + +R+  A ++ +
Sbjct: 69 NLNGREFSGRALRVDNAASEKN 90

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 2e-04
 Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-----KPGIAFVEYGDEMQATVAMQSL 228
           +FV N+P++ T   L+  FS+       R+V         G  F EY D+  A  AM++L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70

Query: 229 QSLKIGQQQLLITYAKK 245
              +   + L +  A  
Sbjct: 71  NGREFSGRALRVDNAAS 87

>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 = 51.7 bits (123), Expect = 1e-09
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 8/85 (9%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          S ++ I + NL +        Q +H + K +            ++K  A++   +   A 
Sbjct: 3  SGSSGILVKNLPQDSN----CQEVHDLLKDYDLK----YCYVDRNKRTAFVTLLNGEQAQ 54

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKS 97
           A++    + F  K + +Q   T +
Sbjct: 55 NAIQMFHQYSFRGKDLIVQLQPTDA 79

>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 = 44.3 bits (104), Expect = 5e-07
 Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 2/72 (2%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
           + V+N+P D+    +      +   K   +       AFV   +  QA  A+Q       
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDR-NKRTAFVTLLNGEQAQNAIQMFHQYSF 65

Query: 234 GQQQLLITYAKK 245
             + L++     
Sbjct: 66  RGKDLIVQLQPT 77

>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 = 49.7 bits (118), Expect = 9e-09
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 9/85 (10%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
          P   +++  L     +  L +       +F     I     +K    A++ ++ + +A A
Sbjct: 16 PTTRLWVGGLGPNTSLAALAR-------EFDRFGSIRTIDHVKGDSFAYIQYESLDAAQA 68

Query: 74 AVEKMQGFPFY--DKPMRIQYAKTK 96
          A  KM+GFP    D+ +R+ +AK+ 
Sbjct: 69 ACAKMRGFPLGGPDRRLRVDFAKSG 93

>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 = 43.1 bits (101), Expect = 2e-06
 Identities = 20/89 (22%), Positives = 39/89 (43%), Gaps = 3/89 (3%)

Query: 158 GAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGD 217
           G+   I    A P   L+V  +  +T+  AL   F +F   + +  V+     A+++Y  
Sbjct: 4   GSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYES 62

Query: 218 EMQATVAMQSLQSLKIG--QQQLLITYAK 244
              A  A   ++   +G   ++L + +AK
Sbjct: 63  LDAAQAACAKMRGFPLGGPDRRLRVDFAK 91

>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 = 48.5 bits (115), Expect = 2e-08
 Identities = 16/84 (19%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASA 71
          +  +Y++ L + +   +L+Q    +F Q+G I+         T   +G  ++ F     A
Sbjct: 6  DANLYVSGLPKTMTQKELEQ----LFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 61

Query: 72 TAAVEKMQGFPFY--DKPMRIQYA 93
            A++ + G       +P+ +++A
Sbjct: 62 EEAIKGLNGQKPSGATEPITVKFA 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 = 43.9 bits (103), Expect = 7e-07
 Identities = 16/80 (20%), Positives = 35/80 (43%), Gaps = 7/80 (8%)

Query: 171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAM 225
           +  L+V  +P   T   L+  FSQ+      R++  +      G+ F+ +   ++A  A+
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 226 QSLQSLKIG--QQQLLITYA 243
           + L   K     + + + +A
Sbjct: 66  KGLNGQKPSGATEPITVKFA 85

>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 = 49.0 bits (116), Expect = 2e-08
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 7/84 (8%)

Query: 15 NNTIYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
          N+ + ++NLN E+V    L              +          K  A +   D   A  
Sbjct: 2  NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF------NKKENALVQMADGNQAQL 55

Query: 74 AVEKMQGFPFYDKPMRIQYAKTKS 97
          A+  + G   + KP+RI  +K ++
Sbjct: 56 AMSHLNGHKLHGKPIRITLSKHQN 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 = 47.4 bits (112), Expect = 7e-08
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 171 NNILFVQNV-PHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQ 229
           N++L V N+ P   TP +L + F  +   + V+++  K   A V+  D  QA +AM  L 
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 230 SLKIGQQQLLITYAKK 245
             K+  + + IT +K 
Sbjct: 62  GHKLHGKPIRITLSKH 77

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.7 bits (115), Expect = 2e-08
 Identities = 16/95 (16%), Positives = 37/95 (38%), Gaps = 7/95 (7%)

Query: 10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVA 69
          ++++   T++I NL+   + + L + L         +  +L   T   KG A+  F    
Sbjct: 3  SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLK-YVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 70 SATAAVEKMQ------GFPFYDKPMRIQYAKTKSD 98
          +A   +          G     + +++  A T+ +
Sbjct: 62 AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.0 bits (77), Expect = 0.003
 Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 12/94 (12%)

Query: 163 IPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEV-----RMVEAKPGIAFVEYGD 217
           +P +       +F++N+  D+   AL     QF   K V        E   G AF ++  
Sbjct: 1   LP-SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMT 59

Query: 218 EMQATVAMQSLQS------LKIGQQQLLITYAKK 245
           +  A   + +         LK+  +QL +  A  
Sbjct: 60  QEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 93

>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 = 47.9 bits (113), Expect = 2e-08
 Identities = 9/83 (10%), Positives = 26/83 (31%), Gaps = 7/83 (8%)

Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTL---KHKGQAWLVFKDVASA 71
            T+++ N         ++     + +    +   +   +L     +  A++       A
Sbjct: 1  ECTLWMTNFPPSYTQRNIRD----LLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 56

Query: 72 TAAVEKMQGFPFYDKPMRIQYAK 94
             VEK+ G       +  + + 
Sbjct: 57 RYCVEKLNGLKIEGYTLVTKVSN 79

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 35.5 bits (81), Expect = 5e-04
 Identities = 11/76 (14%), Positives = 25/76 (32%), Gaps = 5/76 (6%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-----KPGIAFVEYGDEMQATVAMQSL 228
           L++ N P   T   ++              + +         A+++   +  A   ++ L
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 229 QSLKIGQQQLLITYAK 244
             LKI    L+   + 
Sbjct: 64  NGLKIEGYTLVTKVSN 79

>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 = 48.2 bits (114), Expect = 2e-08
 Identities = 17/91 (18%), Positives = 36/91 (39%), Gaps = 6/91 (6%)

Query: 7  NQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFK 66
          N  N   P+ T++++N+   V  + LK     +F   G +++   F     K        
Sbjct: 2  NFQNIFPPSATLHLSNIPPSVSEEDLKV----LFSSNGGVVKGFKFFQKDRKMALI-QMG 56

Query: 67 DVASATAAVEKMQGFPFYD-KPMRIQYAKTK 96
           V  A  A+  +      +   +R+ ++K+ 
Sbjct: 57 SVEEAVQALIDLHNHDLGENHHLRVSFSKST 87

>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 = 44.0 bits (103), Expect = 7e-07
 Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV-EAKPGIAFVEYGDEMQATVAMQS 227
           PP+  L + N+P   +   L++ FS   G  +     +    +A ++ G   +A  A+  
Sbjct: 8   PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID 67

Query: 228 LQSLKIGQ-QQLLITYAK 244
           L +  +G+   L ++++K
Sbjct: 68  LHNHDLGENHHLRVSFSK 85

>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 = 47.3 bits (112), Expect = 6e-08
 Identities = 15/89 (16%), Positives = 37/89 (41%), Gaps = 8/89 (8%)

Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKD 67
          E     T++   L  +++   L+      F   G + ++       + + KG A++ F +
Sbjct: 14 EERDARTVFCMQLAARIRPRDLED----FFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 69

Query: 68 VASATAAVEKMQGFPFYDKPMRIQYAKTK 96
          + S   A+  + G      P+ +Q ++ +
Sbjct: 70 IQSVPLAI-GLTGQRLLGVPIIVQASQAE 97

>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 = 36.9 bits (85), Expect = 3e-04
 Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSL 228
           +F   +     P  L+ FFS     ++VR++  +      GIA+VE+ +          L
Sbjct: 21  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP-LAIGL 79

Query: 229 QSLKIGQQQLLITYAK 244
              ++    +++  ++
Sbjct: 80  TGQRLLGVPIIVQASQ 95

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 48.0 bits (113), Expect = 8e-08
 Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 1/88 (1%)

Query: 11  EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           E      + +N +   V   QL+Q     +    ++  +   +T + +G  ++ F+  +S
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFE-RYGPIESVKIVCDRETRQSRGYGFVKFQSGSS 96

Query: 71  ATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A  A+  + GF   +K +++  A +   
Sbjct: 97  AQQAIAGLNGFNILNKRLKVALAASGHQ 124

>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 = 34.9 bits (79), Expect = 0.002
 Identities = 20/109 (18%), Positives = 37/109 (33%), Gaps = 6/109 (5%)

Query: 142 GAYGATPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEV 201
           G       L Q        + +   P    N L V  +P     + L+  F ++   + V
Sbjct: 14  GQTAQLQQLQQQQQQHIPPTQMNPEPDVLRN-LMVNYIPTTVDEVQLRQLFERYGPIESV 72

Query: 202 RMVEAKPGI-----AFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
           ++V  +         FV++     A  A+  L    I  ++L +  A  
Sbjct: 73  KIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS 121

>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 = 46.6 bits (110), Expect = 8e-08
 Identities = 14/86 (16%), Positives = 36/86 (41%), Gaps = 8/86 (9%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          S ++ +++      +  D+L++     F Q+G ++++  F     +  A++ F D   A 
Sbjct: 3  SGSSGVFVGRCTGDMTEDELRE----FFSQYGDVMDV--FIPKPFRAFAFVTFADDQIAQ 56

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSD 98
          +     +        + I  A+ K +
Sbjct: 57 SLC--GEDLIIKGISVHISNAEPKHN 80

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 2/77 (2%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL 228
             ++ +FV     D T   L+ FFSQ+    +V + +     AFV + D+  A       
Sbjct: 3   SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG-- 60

Query: 229 QSLKIGQQQLLITYAKK 245
           + L I    + I+ A+ 
Sbjct: 61  EDLIIKGISVHISNAEP 77

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 46.7 bits (110), Expect = 8e-08
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 15 NNTIYINNLNEKV-KIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
             I I NL+ ++   + L++S           +     +   +   A++VF++  SA  
Sbjct: 4  GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 74 AVEKMQGFPFYDKPMRIQYAKTK 96
          A++ M      ++ + +  A  K
Sbjct: 64 ALQ-MNRSLLGNREISVSLADKK 85

>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 = 45.8 bits (108), Expect = 1e-07
 Identities = 15/83 (18%), Positives = 36/83 (43%), Gaps = 9/83 (10%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
            NT+Y+   +  +    L+      F  FG I+++        +  A++ ++ + SA  
Sbjct: 4  KGNTLYVYGED--MTPTLLRG----AFSPFGNIIDL---SMDPPRNCAFVTYEKMESADQ 54

Query: 74 AVEKMQGFPFYDKPMRIQYAKTK 96
          AV ++ G       +++  A+ +
Sbjct: 55 AVAELNGTQVESVQLKVNIARKQ 77

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.5 bits (97), Expect = 4e-06
 Identities = 24/79 (30%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 168 AP-PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQ 226
           AP   N L+V     D TP  L+  FS F    ++ M       AFV Y     A  A+ 
Sbjct: 1   APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP-PRNCAFVTYEKMESADQAVA 57

Query: 227 SLQSLKIGQQQLLITYAKK 245
            L   ++   QL +  A+K
Sbjct: 58  ELNGTQVESVQLKVNIARK 76

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 1e-07
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 2/86 (2%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          SP  T ++ NL   V  + +K+            L        + KG  +  F+D+ S  
Sbjct: 13 SPPYTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSD 98
          +A+  +      +K +R+  A    D
Sbjct: 72 SAL-SLNEESLGNKRIRVDVADQAQD 96

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 6e-05
 Identities = 16/93 (17%), Positives = 36/93 (38%), Gaps = 4/93 (4%)

Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEY- 215
           G + S     P  P    F+ N+P+D T  +++ FF            E         + 
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 216 ---GDEMQATVAMQSLQSLKIGQQQLLITYAKK 245
               +++ + ++  SL    +G +++ +  A +
Sbjct: 61  YAEFEDLDSLLSALSLNEESLGNKRIRVDVADQ 93

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.5 bits (107), Expect = 2e-07
 Identities = 8/85 (9%), Positives = 22/85 (25%), Gaps = 8/85 (9%)

Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
           +  + ++ L        LK  +               +  ++  G   + +        
Sbjct: 14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVC--------YADVQKDGMGMVEYLRKEDMEY 65

Query: 74 AVEKMQGFPFYDKPMRIQYAKTKSD 98
          A+ K+    F        Y +   +
Sbjct: 66 ALRKLDDTKFRSHEGETSYIRVYPE 90

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 5e-04
 Identities = 12/78 (15%), Positives = 26/78 (33%), Gaps = 2/78 (2%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQ 226
               +  + V  +P   +   L+    +        +   K G+  VEY  +     A++
Sbjct: 11  TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ--KDGMGMVEYLRKEDMEYALR 68

Query: 227 SLQSLKIGQQQLLITYAK 244
            L   K    +   +Y +
Sbjct: 69  KLDDTKFRSHEGETSYIR 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 = 45.0 bits (106), Expect = 3e-07
 Identities = 15/81 (18%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
               I + N+   V ID++    +      G++  +   +     G+A + F+    AT
Sbjct: 7  PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVC-LKYNEKGMPTGEAMVAFESRDEAT 65

Query: 73 AAVEKMQGFPFYDKPMRIQYA 93
          AAV  +   P   + +++   
Sbjct: 66 AAVIDLNDRPIGSRKVKLVLG 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 = 43.5 bits (102), Expect = 1e-06
 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 5/80 (6%)

Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATV 223
           P   I+ VQN+P   +   +  FF  +        ++        G A V +    +AT 
Sbjct: 7   PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 66

Query: 224 AMQSLQSLKIGQQQLLITYA 243
           A+  L    IG +++ +   
Sbjct: 67  AVIDLNDRPIGSRKVKLVLG 86

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.8 bits (105), Expect = 3e-07
 Identities = 18/88 (20%), Positives = 32/88 (36%), Gaps = 9/88 (10%)

Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
          + +P+  ++I  L  +V   ++        K             LK K QA+L      +
Sbjct: 4  DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTN-------ILMLKGKNQAFLELATEEA 56

Query: 71 ATAAVEKMQ--GFPFYDKPMRIQYAKTK 96
          A   V           ++P+ IQY+  K
Sbjct: 57 AITMVNYYSAVTPHLRNQPIYIQYSNHK 84

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.3 bits (88), Expect = 7e-05
 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 3/81 (3%)

Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQ 226
              P+ +L ++ +P + T   +      F       ++      AF+E   E  A   + 
Sbjct: 4   DGAPSRVLHIRKLPGEVTETEVIALGLPFG-KVTNILMLKGKNQAFLELATEEAAITMVN 62

Query: 227 SLQ--SLKIGQQQLLITYAKK 245
                +  +  Q + I Y+  
Sbjct: 63  YYSAVTPHLRNQPIYIQYSNH 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 = 44.5 bits (105), Expect = 6e-07
 Identities = 17/89 (19%), Positives = 39/89 (43%), Gaps = 8/89 (8%)

Query: 17 TIYINNL-------NEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVA 69
           + I N+       ++ + ++++++ L     +FG I ++L F      G A + F+D  
Sbjct: 10 VVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR-HPDGVASVSFRDPE 68

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
           A   ++ + G  F  + +  Q     +D
Sbjct: 69 EADYCIQTLDGRWFGGRQITAQAWDGTTD 97

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.7 bits (77), Expect = 0.004
 Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 188 LQMFFSQFPGFKEVRMVEAKP-GIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
           L++  S+F   +++ + +  P G+A V + D  +A   +Q+L     G +Q+      
Sbjct: 36  LRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWD 93

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.9 bits (103), Expect = 7e-07
 Identities = 16/91 (17%), Positives = 32/91 (35%), Gaps = 8/91 (8%)

Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
           +     ++I +         L+  L  + + FG I        L    +A++       
Sbjct: 4  RVETRRVVHIMDFQRGKN---LRYQLLQLVEPFGVISNH---LILNKINEAFIEMATTED 57

Query: 71 ATAAVE--KMQGFPFYDKPMRIQYAKTKSDI 99
          A AAV+         + KP+R+  ++    I
Sbjct: 58 AQAAVDYYTTTPALVFGKPVRVHLSQKYKRI 88

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 43.4 bits (101), Expect = 1e-06
 Identities = 12/91 (13%), Positives = 37/91 (40%), Gaps = 7/91 (7%)

Query: 8  QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVF 65
          +G+E +    ++I NLN    + +L         +     ++     +T  ++   ++ F
Sbjct: 6  EGSESTTPFNLFIGNLNPNKSVAEL----KVAISELFAKNDLAVVDVRTGTNRKFGYVDF 61

Query: 66 KDVASATAAVEKMQGFPFYDKPMRIQYAKTK 96
          +       A+ ++ G   +   ++++  K +
Sbjct: 62 ESAEDLEKAL-ELTGLKVFGNEIKLEKPKGR 91

>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 = 43.4 bits (101), Expect = 2e-06
 Identities = 14/123 (11%), Positives = 35/123 (28%), Gaps = 16/123 (13%)

Query: 6   ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVF 65
            + G+       I   NL       +++++                    +    A + F
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLG-------RVLLPEGGITAIVEF 53

Query: 66  KDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKD 125
            +   A  A   +    F+  P+ +++A             F    ++K  + +    K 
Sbjct: 54  LEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV---------FGAAPQKKDSQHEQPAEKA 104

Query: 126 QHD 128
           +  
Sbjct: 105 ESG 107

>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 = 42.2 bits (98), Expect = 5e-06
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 166 APAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAM 225
           +      ++  +N+P  T    +Q  FS+F     V + E     A VE+ + ++A  A 
Sbjct: 5   SSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-GGITAIVEFLEPLEARKAF 63

Query: 226 QSLQSLKIGQQQLLITYAKK 245
           + L   K     L + +A  
Sbjct: 64  RHLAYSKFHHVPLYLEWAPI 83

>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 = 4e-06
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 5/58 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQ 226
           +F+  +   TT   L+ +F QF   KE  ++         G  FV + D+      + 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>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 = 41.7 bits (97), Expect = 4e-06
 Identities = 9/81 (11%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK------TLKHKGQAWLVFKDVA 69
          N +++  L++++   ++ +     F +FG I +++         +      A++ +    
Sbjct: 9  NLVFVVGLSQRLADPEVLK-RPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 67

Query: 70 SATAAVEKMQGFPFYDKPMRI 90
           A  A++ +       + ++ 
Sbjct: 68 DALRAIQCVNNVVVDGRTLKA 88

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 7e-06
 Identities = 11/79 (13%), Positives = 24/79 (30%), Gaps = 2/79 (2%)

Query: 16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAV 75
            +YI+NL   +   +L+  L    +   T +      +   +G  +   +      A +
Sbjct: 19 TNLYISNLPLSMDEQELENMLKPFGQVISTRILR--DSSGTSRGVGFARMESTEKCEAVI 76

Query: 76 EKMQGFPFYDKPMRIQYAK 94
              G      P      +
Sbjct: 77 GHFNGKFIKTPPGVSAPTE 95

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 7e-06
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 4/85 (4%)

Query: 10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVA 69
          N++  N ++YI        +D +K+ L    +     +     K    KG  ++VF  + 
Sbjct: 2  NDVK-NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHK--AFKGSIFVVFDSIE 58

Query: 70 SATAAVEKMQGFPFYDKPMRIQYAK 94
          SA   VE   G  + +  + I +  
Sbjct: 59 SAKKFVE-TPGQKYKETDLLILFKD 82

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 7e-04
 Identities = 12/78 (15%), Positives = 26/78 (33%), Gaps = 5/78 (6%)

Query: 171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPG----IAFVEYGDEMQATVAMQ 226
           N  ++++  P D T   ++ +         ++M            FV +     A   ++
Sbjct: 6   NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 65

Query: 227 SLQSLKIGQQQLLITYAK 244
                K  +  LLI +  
Sbjct: 66  -TPGQKYKETDLLILFKD 82

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (95), Expect = 8e-06
 Identities = 14/83 (16%), Positives = 23/83 (27%), Gaps = 8/83 (9%)

Query: 16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAV 75
          N + ++ L        LK  +               +  +   G   + F      T AV
Sbjct: 1  NRVVVSGLPPSGSWQDLKDHMREAGDVC--------YADVYRDGTGVVEFVRKEDMTYAV 52

Query: 76 EKMQGFPFYDKPMRIQYAKTKSD 98
           K+    F        Y + K D
Sbjct: 53 RKLDNTKFRSHEGETAYIRVKVD 75

>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 = 41.2 bits (96), Expect = 9e-06
 Identities = 11/88 (12%), Positives = 26/88 (29%), Gaps = 8/88 (9%)

Query: 165 EAPAPPNNILFVQ--NVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQAT 222
           E  +     L V    + +  +   L     +      + M       +F  Y    ++ 
Sbjct: 12  ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESK 70

Query: 223 VAMQSLQSLKIGQQQ-----LLITYAKK 245
            A  +L   ++         L + + +K
Sbjct: 71  RAYVTLNGKEVVDDLGQKITLYLNFVEK 98

>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 = 41.2 bits (96), Expect = 9e-06
 Identities = 11/94 (11%), Positives = 35/94 (37%), Gaps = 8/94 (8%)

Query: 3   PEVANQGNEISPNNT--IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHK 58
           P+ ++Q  +   +    + +    ++   +   +    + +++G + E+           
Sbjct: 13  PQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTE----MEEKYGEVEEMNVCDNLGDHLV 68

Query: 59  GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY 92
           G  ++ F+    A  AV  +    F  +P+  + 
Sbjct: 69  GNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.2 bits (83), Expect = 6e-04
 Identities = 8/73 (10%), Positives = 23/73 (31%), Gaps = 4/73 (5%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPG----IAFVEYGDEMQATVAMQSLQ 229
           + +Q    +           ++   +E+ + +          +V++  E  A  A+  L 
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 230 SLKIGQQQLLITY 242
           +     Q +    
Sbjct: 90  NRWFNGQPIHAEL 102

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.2 bits (96), Expect = 9e-06
 Identities = 12/92 (13%), Positives = 38/92 (41%), Gaps = 8/92 (8%)

Query: 10  NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFK 66
            E      ++I  L+ +   + L+      ++Q+G + + +  +   + + +G  ++ F 
Sbjct: 15  REKEQFRKLFIGGLSFETTEESLRN----YYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 70

Query: 67  DVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
            +A   AA+   +      + +  + A  + +
Sbjct: 71  SMAEVDAAMA-ARPHSIDGRVVEPKRAVAREE 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 = 38.5 bits (89), Expect = 9e-05
 Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 6/77 (7%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
           LF+  +  +TT  +L+ ++ Q+    +  ++         G  FV +    +   AM   
Sbjct: 23  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-A 81

Query: 229 QSLKIGQQQLLITYAKK 245
           +   I  + +    A  
Sbjct: 82  RPHSIDGRVVEPKRAVA 98

>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 = 40.7 bits (95), Expect = 1e-05
 Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 5/63 (7%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSL 228
           L V  +P  TT   L+ +FS F     V++ +        G  FV + +       M   
Sbjct: 11  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 70

Query: 229 QSL 231
             +
Sbjct: 71  HMI 73

>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 = 40.7 bits (95), Expect = 1e-05
 Identities = 11/87 (12%), Positives = 27/87 (31%), Gaps = 3/87 (3%)

Query: 12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASA 71
          +   + + +  L  K     LK+     F +   +      KT   KG  ++ F +  + 
Sbjct: 5  VQKTSDLIVLGLPWKTTEQDLKEYFST-FGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 72 TAAVEKMQGFPFYDKPMRIQYAKTKSD 98
             + +        +    +   +K  
Sbjct: 64 VKVMSQRHM--IDGRWCDCKLPNSKQS 88

>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 = 39.7 bits (92), Expect = 2e-05
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 8/79 (10%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTIL---EILAFKTLKHKGQAWLVFKDVASATAA 74
          I++  L+    ++ +K      F+QFG +     +    T +H+G  ++ F+        
Sbjct: 2  IFVGGLSVNTTVEDVKH----YFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57

Query: 75 VEKMQGFPFYDKPMRIQYA 93
           E +      +K +  + A
Sbjct: 58 CE-IHFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.5 bits (76), Expect = 0.003
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV-----EAKPGIAFVEYGDEMQATVAMQSL 228
           +FV  +  +TT   ++ +F QF    +  ++         G  FV +  E       + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 229 QSLKIGQQQLLITYA 243
              +I  + +    A
Sbjct: 61  HFHEINNKMVECKKA 75

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.5 bits (96), Expect = 3e-05
 Identities = 17/93 (18%), Positives = 34/93 (36%), Gaps = 8/93 (8%)

Query: 10  NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFK 66
                   I++  + E  +   L+      F+Q+G I  I       + K +G A++ F 
Sbjct: 92  GAHLTVKKIFVGGIKEDTEEHHLRD----YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 147

Query: 67  DVASATAAVEKMQGFPFYDKPMRIQYAKTKSDI 99
           D  S    V   +          ++ A +K ++
Sbjct: 148 DHDSVDKIVI-QKYHTVNGHNCEVRKALSKQEM 179

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.7 bits (86), Expect = 5e-04
 Identities = 12/75 (16%), Positives = 29/75 (38%), Gaps = 7/75 (9%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATA 73
           ++I  L+ +   + L+      F+Q+GT+ + +      T + +G  ++ +  V    A
Sbjct: 8  KLFIGGLSFETTDESLRS----HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 74 AVEKMQGFPFYDKPM 88
          A+             
Sbjct: 64 AMNARPHKVDGRVVE 78

>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 = 39.0 bits (90), Expect = 3e-05
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 1/72 (1%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEK 77
          +YI  L        L +      K   T   IL   T K KG  ++ F   ++A  AV  
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTK-AILDKTTNKCKGYGFVDFDSPSAAQKAVTA 59

Query: 78 MQGFPFYDKPMR 89
          ++      +  +
Sbjct: 60 LKASGVQAQMAK 71

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 3e-05
 Identities = 11/85 (12%), Positives = 27/85 (31%), Gaps = 2/85 (2%)

Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
          +    I++  L        L++           ++     +T K +G  ++   D A+A 
Sbjct: 8  TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVIT-DRQTGKSRGYGFVTMADRAAAE 66

Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKS 97
           A +         +   +  A   +
Sbjct: 67 RACKDPNPI-IDGRKANVNLAYLGA 90

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 3e-05
 Identities = 18/115 (15%), Positives = 35/115 (30%), Gaps = 13/115 (11%)

Query: 8   QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKD 67
           +G+  S     +I N+   +    + Q L          + +L     +  GQA + FK+
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLE-GIPVDENAVHVLVDNNGQGLGQALVQFKN 59

Query: 68  VASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKK 122
              A  +   +       +   +     +             RE  K    +GK 
Sbjct: 60  EDDARKSER-LHRKKLNGREAFVHVVTLED-----------MREIEKNPPAQGKS 102

>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 = 37.6 bits (87), Expect = 9e-05
 Identities = 9/58 (15%), Positives = 21/58 (36%), Gaps = 5/58 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGI-----AFVEYGDEMQATVAMQ 226
           +FV  +  DT    ++ +F  F   + + +             F+ + +E      M+
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

>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 = 35.3 bits (81), Expect = 7e-04
 Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 8/79 (10%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAA 74
          I++  L+     +++++     F  FG +  I       T K +G  ++ FK+       
Sbjct: 2  IFVGGLSPDTPEEKIRE----YFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57

Query: 75 VEKMQGFPFYDKPMRIQYA 93
          +EK            I+ A
Sbjct: 58 MEKK-YHNVGLSKCEIKVA 75

>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 = 37.7 bits (87), Expect = 1e-04
 Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 5/58 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPG-----IAFVEYGDEMQATVAMQ 226
           LF+  +  +TT  +L+  F Q+    +  ++            FV Y    +   AM 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

>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 = 33.5 bits (76), Expect = 0.003
 Identities = 13/80 (16%), Positives = 34/80 (42%), Gaps = 8/80 (10%)

Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATA 73
           ++I  L+ +   + L+      F+Q+GT+ + +      T + +G  ++ +  V    A
Sbjct: 8  KLFIGGLSFETTDESLRS----HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 74 AVEKMQGFPFYDKPMRIQYA 93
          A+   +      + +  + A
Sbjct: 64 AMN-ARPHKVDGRVVEPKRA 82

>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 = 36.5 bits (84), Expect = 2e-04
 Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 5/58 (8%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQ 226
           +F+  +  DTT   L+ +FS+F    +  +          G  FV + +       M 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 59

>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 = 34.2 bits (78), Expect = 0.002
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 8/79 (10%)

Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAA 74
          ++I  L+       LK      F +FG +++        T + +G  +++FK+  S    
Sbjct: 2  MFIGGLSWDTTKKDLKD----YFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV 57

Query: 75 VEKMQGFPFYDKPMRIQYA 93
          ++  +      K +  + A
Sbjct: 58 MD-QKEHKLNGKVIDPKRA 75

>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 = 35.7 bits (81), Expect = 6e-04
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 2/72 (2%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
           + ++ +P D T   +    S +        V+   G AFV   +  QA  A+ +    ++
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKY--CFVDKYKGTAFVTLLNGEQAEAAINTFHQSRL 58

Query: 234 GQQQLLITYAKK 245
            +++L +     
Sbjct: 59  RERELSVQLQPT 70

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 34.4 bits (78), Expect = 0.001
 Identities = 11/73 (15%), Positives = 29/73 (39%), Gaps = 4/73 (5%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP---GIAFVEYGDEMQATVAMQSLQS 230
           + V+N+P       +  +F        V + ++       A +E+     A  A+     
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 62

Query: 231 LKIGQQQLLITYA 243
             +GQ ++++++ 
Sbjct: 63  -VVGQNEIIVSHL 74

>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 = 34.7 bits (79), Expect = 0.001
 Identities = 18/81 (22%), Positives = 27/81 (33%), Gaps = 11/81 (13%)

Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP----------GIAFVEYGDEMQATV 223
           L+V N+P   T  A+  FF+       +      P            AF+E+    + T 
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 224 AMQSLQSLKIGQQQLLITYAK 244
           AM     +    Q L I    
Sbjct: 64  AMA-FDGIIFQGQSLKIRRPH 83

>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 = 34.8 bits (79), Expect = 0.002
 Identities = 11/108 (10%), Positives = 36/108 (33%), Gaps = 8/108 (7%)

Query: 17  TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWL-VFKDVASATAAV 75
             +  +L+++   + L      +F   G I  I     ++   +  +   +    A    
Sbjct: 13  LKFSGDLDDQTCREDLHI----LFSNHGEIKWI---DFVRGAKEGIILFKEKAKEALGKA 65

Query: 76  EKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPRERRKRHEEKGKKR 123
           +         +   + +   + ++  +A    +  ++   ++ K K R
Sbjct: 66  KDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKSKGR 113

>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 = 34.8 bits (79), Expect = 0.002
 Identities = 9/73 (12%), Positives = 22/73 (30%)

Query: 173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLK 232
           + F  ++   T    L + FS     K +  V        +      +A    +   +  
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGN 72

Query: 233 IGQQQLLITYAKK 245
           +  +   +T+   
Sbjct: 73  LQLRNKEVTWEVL 85

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	245
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.89
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.89
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.86
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.85
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.85
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.84
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.84
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.84
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.84
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.84
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.84
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.84
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.84
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.84
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.84
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.83
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.83
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.83
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.83
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.83
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.83
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.83
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.83
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.83
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.82
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.82
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.82
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.82
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.82
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.82
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.82
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.81
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.81
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.81
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.81
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.81
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.81
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.81
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.81
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.81
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.8
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.8
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.8
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.8
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.8
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.8
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.8
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.8
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.79
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.79
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.79
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.79
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.79
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.79
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.79
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.79
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.79
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.79
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.79
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.78
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.78
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.78
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.78
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.78
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.78
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.78
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.77
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.77
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.77
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.77
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.77
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.77
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.77
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.77
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.77
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.77
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.77
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.77
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.77
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.77
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.77
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.77
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.77
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.76
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.76
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.76
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.76
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.76
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.76
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.76
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.76
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.76
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.76
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.76
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.76
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.76
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.75
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.75
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.75
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.75
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.74
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.73
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.73
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.73
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.72
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.72
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.72
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.72
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.7
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.65
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.64
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.63
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.6
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.59
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.58
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	99.58
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	99.56
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.56
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.55
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.52
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.52
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.5
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.48
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.48
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.58
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.4
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.19
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.97
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.8
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.78
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.22
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.12

>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=9.8e-32  Score=202.60  Aligned_cols=162  Identities=17%  Similarity=0.298  Sum_probs=135.8

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ..++|||+|||+.+|+++    |+++|++||.|.++.+.   .++.++|||||+|.+.++|.+|+. +++..+.++.+.+
T Consensus         5 ~~r~lfV~nLp~~~te~~----L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~   79 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDES----LRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEP   79 (183)
T ss_dssp             HHHEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEE
T ss_pred             CCCEEEEECCCCCCCHHH----HHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhh
Confidence            457999999999999999    77999999999988654   478899999999999999999999 6677777777777


Q ss_pred             EEccccchHhhhcCCCcccchhhhhhhhhhhhccchhhHhhhcCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025973           91 QYAKTKSDIIAKADGTFVPRERRKRHEEKGKKRKDQHDANQAGMGLNPAYAGAYGATPPLSQIPYPGGAKSVIPEAPAPP  170 (245)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (245)
                      ...........                                                               ......
T Consensus        80 ~~~~~~~~~~~---------------------------------------------------------------~~~~~~   96 (183)
T d1u1qa_          80 KRAVSREDSQR---------------------------------------------------------------PGAHLT   96 (183)
T ss_dssp             EECCCTTGGGS---------------------------------------------------------------TTTTCC
T ss_pred             hhhhhcccccc---------------------------------------------------------------cccccc
Confidence            66543322110                                                               001134


Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++|||+|||..+|+++|+++|+.||.|..+.++.++     +|||||+|.++++|.+|++ +++..+.|++|+|.+|.
T Consensus        97 ~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~  174 (183)
T d1u1qa_          97 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKAL  174 (183)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECC
T ss_pred             cceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecC
Confidence            5679999999999999999999999999999998753     6899999999999999997 78999999999999984

>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=99.89  E-value=4.5e-23  Score=134.26  Aligned_cols=79  Identities=51%  Similarity=0.868  Sum_probs=74.6

Q ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC-CeEEEEEEecC
Q 025973          167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITYAKK  245 (245)
Q Consensus       167 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~ak~  245 (245)
                      ..||+++|||+|||..+++++|.++|+.||.|..++++++++|+|||+|.+.++|..|+..|||..|. |++|+|.||||
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~akk   83 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAKK   83 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEecC
Confidence            34678999999999999999999999999999999999988899999999999999999999999985 79999999997

>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=99.89  E-value=1.3e-23  Score=139.35  Aligned_cols=88  Identities=69%  Similarity=1.118  Sum_probs=82.7

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      .|+++|||+|||..++++||++.|+++|++||.|.+|.+.+++.++|||||+|.+.++|..|++.+||..+.|+.|+|.|
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            47899999999999999999999999999999999999988888999999999999999999999999999999999999


Q ss_pred             ccccchHh
Q 025973           93 AKTKSDII  100 (245)
Q Consensus        93 ~~~~~~~~  100 (245)
                      ++.+++..
T Consensus        81 ak~~~~~~   88 (91)
T d1nu4a_          81 AKTDSDII   88 (91)
T ss_dssp             CSSCCTHH
T ss_pred             eCCCchhh
Confidence            98876643

>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=1.4e-21  Score=126.86  Aligned_cols=74  Identities=27%  Similarity=0.495  Sum_probs=69.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +++|||+|||..+++++|+++|+.||.|.+++++.++     +|||||+|.++++|.+|++.|||..+.|++|+|+||+
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 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   80 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4679999999999999999999999999999998753     6899999999999999999999999999999999996

>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=99.86  E-value=8.1e-22  Score=136.23  Aligned_cols=81  Identities=25%  Similarity=0.501  Sum_probs=76.2

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      ++.+++|||+|||.++++++    |+++|+.||.|.+|++..++.++|||||+|.+.++|..|++.|||..|.|+.|.|.
T Consensus         4 p~~~r~l~V~nLp~~~te~~----l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   79 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEE----MYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVL   79 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCEEEEECCCCCCCHHH----HHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45689999999999999999    77999999999999999999999999999999999999999999999999999999


Q ss_pred             Ecccc
Q 025973           92 YAKTK   96 (245)
Q Consensus        92 ~~~~~   96 (245)
                      ++...
T Consensus        80 ~a~~~   84 (114)
T d2f9da1          80 YYNAN   84 (114)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            98654

>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=99.85  E-value=1.7e-21  Score=125.69  Aligned_cols=73  Identities=21%  Similarity=0.290  Sum_probs=69.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .|||+|||..+|+++|+++|+.||.|.+++++.++     +|||||+|.++++|..|++.|||..++|++|+|.||+|
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            49999999999999999999999999999999864     58999999999999999999999999999999999986

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.5e-21  Score=128.54  Aligned_cols=84  Identities=27%  Similarity=0.432  Sum_probs=75.8

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      .+..++++|||+|||.++++++    |+++|++||.|.+|.+.   .+|.++|||||+|.+.++|.+|++.|||..+.|+
T Consensus         4 ~~~~~~~tlfV~nLp~~~t~~~----l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~   79 (93)
T d1x5ua1           4 SERNQDATVYVGGLDEKVSEPL----LWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGK   79 (93)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSC
T ss_pred             CcCCCCCEEEEeCCCCcCCHHH----HHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            3455678999999999999999    66999999999998765   3688999999999999999999999999999999


Q ss_pred             eEEEEEccccc
Q 025973           87 PMRIQYAKTKS   97 (245)
Q Consensus        87 ~i~v~~~~~~~   97 (245)
                      .|+|.+|.++.
T Consensus        80 ~l~V~~A~~~~   90 (93)
T d1x5ua1          80 PIRVNKASAHN   90 (93)
T ss_dssp             BCEEEETTTTS
T ss_pred             EEEEEEcCCCC
Confidence            99999997654

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.85  E-value=2.3e-21  Score=125.86  Aligned_cols=77  Identities=23%  Similarity=0.400  Sum_probs=71.4

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      +++|||+|||.++++++    |+++|++||.|.++.+.   .+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus         2 ~t~l~V~nLp~~~t~~~----l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~   77 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRE----LYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVS   77 (82)
T ss_dssp             CSEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            67899999999999999    66999999999998654   478899999999999999999999999999999999999


Q ss_pred             Eccc
Q 025973           92 YAKT   95 (245)
Q Consensus        92 ~~~~   95 (245)
                      |+++
T Consensus        78 ~a~p   81 (82)
T d1b7fa1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9865

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=4.6e-21  Score=124.43  Aligned_cols=73  Identities=25%  Similarity=0.486  Sum_probs=69.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ++|||+|||..+++++|+++|+.||.|.+++++.+.     +|||||+|.++++|..|++.|||..|+|++|+|.|||
T Consensus         3 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           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            469999999999999999999999999999998753     6899999999999999999999999999999999996

>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=3.3e-21  Score=128.54  Aligned_cols=75  Identities=21%  Similarity=0.341  Sum_probs=71.6

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .+++|||+|||..+++++|+++|++||.|.+|++++++ |||||+|.++++|..|+..|||..|+|++|+|.|||.
T Consensus        17 ~~~~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          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecc-eEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45689999999999999999999999999999999986 8999999999999999999999999999999999974

>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=4.3e-21  Score=126.06  Aligned_cols=81  Identities=20%  Similarity=0.330  Sum_probs=72.9

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..++++|||+|||.++++++    |+++|+.||.|.+|++.   .+|.++|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~----l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l   79 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDE----IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI   79 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34678999999999999999    67999999999988654   478899999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      +|+|+.++
T Consensus        80 ~V~~a~~k   87 (88)
T d1rk8a_          80 QVDWCFVK   87 (88)
T ss_dssp             EEEESEEC
T ss_pred             EEEEecCC
Confidence            99998754

>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=5.6e-21  Score=126.12  Aligned_cols=75  Identities=24%  Similarity=0.395  Sum_probs=71.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++|||+|||..+++++|+++|+.||.|.++.++.++     +|||||+|.+.++|..|++.|||..|+|++|+|+|||
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~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            45789999999999999999999999999999999864     6899999999999999999999999999999999997

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=7.6e-21  Score=128.34  Aligned_cols=77  Identities=23%  Similarity=0.452  Sum_probs=71.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +++++|||+|||..+++++|+++|+.||.|..+.++.++     +|||||+|.++++|..|++.|||..|+|++|+|+||
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456679999999999999999999999999999988754     689999999999999999999999999999999998


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus        96 ~~   97 (102)
T d2cpza1          96 RS   97 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            73

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=3.7e-21  Score=126.99  Aligned_cols=82  Identities=28%  Similarity=0.477  Sum_probs=74.4

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..+.++|||+|||.++++++    |+++|+.||.|..|.+.   .+|.++|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~----l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i   80 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETD----LQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL   80 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHH----HHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCEEEEECCCCCCCHHH----HHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34568999999999999999    77999999999998655   367899999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 025973           89 RIQYAKTKS   97 (245)
Q Consensus        89 ~v~~~~~~~   97 (245)
                      +|.|+++++
T Consensus        81 ~v~~akp~~   89 (90)
T d2cq0a1          81 NVEWAKPST   89 (90)
T ss_dssp             EEEESSCCC
T ss_pred             EEEeeeCCC
Confidence            999998764

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=2.9e-21  Score=130.41  Aligned_cols=87  Identities=23%  Similarity=0.375  Sum_probs=77.0

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEe---cCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILA---FKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~---~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      +....+++++|||+|||.++++++    |+++|+.||.|.++.+   ..+|.++|||||+|.+.++|..|++.|||..+.
T Consensus        11 ~~~~~p~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~   86 (102)
T d2cpza1          11 SQKEGPEGANLFIYHLPQEFGDQD----LLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIG   86 (102)
T ss_dssp             CCCCCSTTCCEEEESCCSSCCHHH----HHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHH----HHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEEC
Confidence            444567789999999999999999    7799999999888644   357889999999999999999999999999999


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |+.|+|.|+.++.+
T Consensus        87 g~~i~V~~a~~k~~  100 (102)
T d2cpza1          87 MKRLKVQLKRSKND  100 (102)
T ss_dssp             TEECEEECCCCSCC
T ss_pred             CEEEEEEEeCCCCC
Confidence            99999999987654

>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=99.84  E-value=6.4e-21  Score=126.52  Aligned_cols=81  Identities=20%  Similarity=0.287  Sum_probs=73.8

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ..++++|||+|||.++++++    |+++|++||.|.+|.+.   .++.++|||||+|.+.++|..|++.|||..+.|+.|
T Consensus         4 ~~~s~tlfV~nlp~~~te~~----l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i   79 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQ----IYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRII   79 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHH----HHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            45789999999999999999    67999999999998654   467899999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      +|.|+...
T Consensus        80 ~V~~a~~~   87 (93)
T d1h2vz_          80 RTDWDAGF   87 (93)
T ss_dssp             EEEEESCC
T ss_pred             EEEEcCCC
Confidence            99998654

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=8.2e-21  Score=126.25  Aligned_cols=83  Identities=17%  Similarity=0.348  Sum_probs=74.6

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC----CCCeeeEEEEEecCHHHHHHHHHHH-cCCccCC
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK----TLKHKGQAWLVFKDVASATAAVEKM-QGFPFYD   85 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~----~~~~kg~afV~F~~~~~A~~a~~~l-~~~~~~g   85 (245)
                      ...++++|||+|||.++++++    |+.+|+.||.|..|.+..    +|.++|||||+|.+.++|.+|+..| |+..+.|
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~----l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~G   79 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQRE----IRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG   79 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHH----HHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECC
Confidence            346778999999999999999    779999999999997743    5788999999999999999999998 8999999


Q ss_pred             ceEEEEEccccc
Q 025973           86 KPMRIQYAKTKS   97 (245)
Q Consensus        86 ~~i~v~~~~~~~   97 (245)
                      +.|+|.|+..+.
T Consensus        80 r~l~V~~A~~~~   91 (94)
T d2cpha1          80 RRLVLEWADSEV   91 (94)
T ss_dssp             CBCEEEECCCCC
T ss_pred             EEEEEEEcCCCC
Confidence            999999997653

>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=1e-20  Score=126.10  Aligned_cols=84  Identities=21%  Similarity=0.389  Sum_probs=77.4

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ++...++++|||+|||+++++++    |+++|+.||.|..+.+..++..++||||+|.+.++|..|++.||+..|.|+.|
T Consensus         8 ~p~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l   83 (95)
T d1x4aa1           8 GPAGNNDCRIYVGNLPPDIRTKD----IEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRL   83 (95)
T ss_dssp             CCCCCCSSEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCEEEEECCCCCCCHHH----HHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            35567789999999999999999    66999999999999988888889999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      +|.|++..
T Consensus        84 ~V~~a~~~   91 (95)
T d1x4aa1          84 RVEFPRSG   91 (95)
T ss_dssp             EEECCCCC
T ss_pred             EEEeccCC
Confidence            99998753

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=8e-21  Score=123.30  Aligned_cols=77  Identities=18%  Similarity=0.390  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      .++|||+|||.++++++    |+++|++||.|.+|++.   .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus         2 ~t~l~V~nLp~~~te~~----l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~   77 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEE----FRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVS   77 (82)
T ss_dssp             CSEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEECCCCCCCHHH----HHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            46799999999999999    66999999999998654   467899999999999999999999999999999999999


Q ss_pred             Eccc
Q 025973           92 YAKT   95 (245)
Q Consensus        92 ~~~~   95 (245)
                      |+++
T Consensus        78 ~AkP   81 (82)
T d1fxla1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EeeC
Confidence            9875

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.84  E-value=1.4e-20  Score=123.58  Aligned_cols=75  Identities=24%  Similarity=0.361  Sum_probs=70.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.+|||+|||..+++++|+++|+.||.|.+|+++.++     +|||||+|.+.++|..|+..|||..+.|++|+|+||+
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~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            45789999999999999999999999999999998764     6899999999999999999999999999999999985

>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=99.84  E-value=1.7e-20  Score=124.41  Aligned_cols=76  Identities=24%  Similarity=0.314  Sum_probs=71.3

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ..+++|||+|||..+|+++|+++|+.||.|.+|.++.++     +|||||+|.+.++|..|++.|||..++|++|+|.||
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            356789999999999999999999999999999998864     589999999999999999999999999999999998


Q ss_pred             c
Q 025973          244 K  244 (245)
Q Consensus       244 k  244 (245)
                      .
T Consensus        85 ~   85 (93)
T d1h2vz_          85 A   85 (93)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.84  E-value=1.4e-20  Score=124.11  Aligned_cols=76  Identities=24%  Similarity=0.395  Sum_probs=71.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      +.++|||+|||..+|+++|+++|+.||.|.+|.++.++   +|||||+|.+.++|..|+..+||..++|+.|+|.||+.
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            45689999999999999999999999999999998754   68999999999999999999999999999999999963

>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=3.4e-20  Score=123.01  Aligned_cols=76  Identities=21%  Similarity=0.355  Sum_probs=71.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      ..++|||+|||..+++++|+++|+.||.|.+|.++.++   +|||||+|.++++|.+|+..|||..|+|++|+|.||+.
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~   88 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   88 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCc
Confidence            34579999999999999999999999999999999864   68999999999999999999999999999999999973

>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=99.84  E-value=1.1e-20  Score=125.38  Aligned_cols=75  Identities=19%  Similarity=0.274  Sum_probs=70.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.+|||+|||..+|+++|+++|+.||.|.+++++.++     +|||||+|.+.++|..|++.|||..|+|++|+|.||+
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999998753     6899999999999999999999999999999999986

>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=7.5e-21  Score=123.61  Aligned_cols=78  Identities=22%  Similarity=0.417  Sum_probs=70.4

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD   85 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g   85 (245)
                      ..++.++++|||+|||.++++++    |+++|++||.|.+|.+.   .+++++|||||+|.+.++|.+|+..||+..+.|
T Consensus         3 r~~p~~~~~l~V~nL~~~~te~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   78 (83)
T d2cqca1           3 RANPDPNCCLGVFGLSLYTTERD----LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG   78 (83)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHH----HHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHH----HHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECC
Confidence            34566789999999999999999    67999999999988654   468899999999999999999999999999999


Q ss_pred             ceEEE
Q 025973           86 KPMRI   90 (245)
Q Consensus        86 ~~i~v   90 (245)
                      +.|+|
T Consensus        79 r~i~V   83 (83)
T d2cqca1          79 RRIRV   83 (83)
T ss_dssp             EEEEE
T ss_pred             EEeEC
Confidence            99987

>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=99.83  E-value=4.1e-21  Score=126.50  Aligned_cols=80  Identities=31%  Similarity=0.516  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ..+++|||+|||.++++++    |+++|+.||.|.+|.+..   +|.++|||||+|.+.++|..|+..||+..+.|+.|+
T Consensus         3 ~~~~tlfV~nLp~~~te~~----l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~   78 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKV----LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR   78 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHH----HHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCcEEEEeCCCCcCCHHH----HHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3468999999999999999    679999999999987653   678999999999999999999999999999999999


Q ss_pred             EEEcccc
Q 025973           90 IQYAKTK   96 (245)
Q Consensus        90 v~~~~~~   96 (245)
                      |.++.++
T Consensus        79 v~~a~p~   85 (89)
T d2cqba1          79 VNLAKPM   85 (89)
T ss_dssp             EEECCCC
T ss_pred             EEEeCCC
Confidence            9999764

>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=99.83  E-value=5.5e-21  Score=130.94  Aligned_cols=74  Identities=30%  Similarity=0.450  Sum_probs=70.7

Q ss_pred             ccEEEEcCCC-CCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVP-HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~-~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +++|||+||| ..+|+++|+++|+.||.|..|.++++++|+|||+|.++++|.+|++.|||..|.|++|+|.||+
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 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            5789999995 5699999999999999999999999989999999999999999999999999999999999986

>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=99.83  E-value=7.6e-21  Score=125.20  Aligned_cols=75  Identities=19%  Similarity=0.352  Sum_probs=70.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++|||+|||..+++++|+++|+.||.|.++.++.++     +|||||+|.++++|..|+..|||..|+|++|.|.||+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45789999999999999999999999999999998753     7899999999999999999999999999999999986

>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=99.83  E-value=1.6e-20  Score=123.48  Aligned_cols=76  Identities=24%  Similarity=0.427  Sum_probs=69.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-CeEEEEEeCCHHHHHHHHHHhCCCeeC-CeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-PGIAFVEYGDEMQATVAMQSLQSLKIG-QQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-~g~afv~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~ak  244 (245)
                      ||+++|||+|||..+++++|+++|+.||.|..+.+...+ +|+|||+|.++++|..|+..|||..+. |++|+|+|||
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            578899999999999999999999999999877766543 689999999999999999999999985 9999999997

>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=99.83  E-value=8.6e-21  Score=122.37  Aligned_cols=75  Identities=28%  Similarity=0.406  Sum_probs=69.4

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      .|||+|||+.+++++    |+++|++||.|.+|++.   .+|+++|||||+|.+.++|..|++.|||..+.|+.|+|.|+
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   77 (80)
T d1cvja1           2 SLYVGDLHPDVTEAM----LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   77 (80)
T ss_dssp             EEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEEC
T ss_pred             EEEEeCCCCcCCHHH----HHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            699999999999999    77999999999998665   46889999999999999999999999999999999999998


Q ss_pred             cc
Q 025973           94 KT   95 (245)
Q Consensus        94 ~~   95 (245)
                      +.
T Consensus        78 ~~   79 (80)
T d1cvja1          78 QR   79 (80)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=3.7e-20  Score=123.39  Aligned_cols=76  Identities=18%  Similarity=0.397  Sum_probs=70.8

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++++|||+|||..+++++|+++|+.||.|..+.+..+.  ++||||+|.++++|..|++.|||+.|.|++|+|+|||
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            456789999999999999999999999999999987643  7899999999999999999999999999999999997

>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=1.5e-20  Score=120.62  Aligned_cols=74  Identities=26%  Similarity=0.445  Sum_probs=69.0

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEcc
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAK   94 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~   94 (245)
                      +|||+|||+++++++    |+++|+.||.|.+|.+.  ++++++|||||+|.+.++|..|++.|||..+.|+.|+|.++.
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 KLLVSNLDFGVSDAD----IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHH----HHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHH----HHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            699999999999999    66999999999998766  478889999999999999999999999999999999999975

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=2.4e-20  Score=123.98  Aligned_cols=76  Identities=24%  Similarity=0.470  Sum_probs=70.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC------CeEEEEEeCCHHHHHHHHHHh-CCCeeCCeEEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK------PGIAFVEYGDEMQATVAMQSL-QSLKIGQQQLLITY  242 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~------~g~afv~f~~~~~A~~A~~~l-~g~~~~g~~i~v~~  242 (245)
                      .+++|||+|||..+++++|+.+|+.||.|.+++++.+.      +|||||+|.++++|..|+..| ||..|.|++|.|.|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            45679999999999999999999999999999997642      689999999999999999998 89999999999999


Q ss_pred             ecC
Q 025973          243 AKK  245 (245)
Q Consensus       243 ak~  245 (245)
                      |+.
T Consensus        87 A~~   89 (94)
T d2cpha1          87 ADS   89 (94)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            973

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.3e-20  Score=123.09  Aligned_cols=84  Identities=21%  Similarity=0.327  Sum_probs=73.6

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ++..+.++|||+|||.++++++    |+++|+.||.|..|.+.. ....+|||||+|.+.++|..|+..|||..+.|+.|
T Consensus         3 ~d~~~~~tl~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i   78 (90)
T d2cqia1           3 EDDGQPRTLYVGNLSRDVTEVL----ILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEV   78 (90)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHH----HHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHH----HHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3456678999999999999999    669999999999987654 33458999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 025973           89 RIQYAKTKS   97 (245)
Q Consensus        89 ~v~~~~~~~   97 (245)
                      +|.|+.+..
T Consensus        79 ~v~~a~~~~   87 (90)
T d2cqia1          79 KVNWATTPS   87 (90)
T ss_dssp             EEEECCCTT
T ss_pred             EEEEcCCCC
Confidence            999987543

>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=99.83  E-value=2.5e-20  Score=121.75  Aligned_cols=73  Identities=26%  Similarity=0.425  Sum_probs=69.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++|||+|||..+++++|+++|+.||.|.+|.+.+++ |||||+|.+.++|..|+..|||..|.|++|+|+||.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k-~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT-TEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeeccc-ceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            4569999999999999999999999999999999886 899999999999999999999999999999999986

>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=2.6e-20  Score=125.09  Aligned_cols=83  Identities=22%  Similarity=0.318  Sum_probs=74.7

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ....++|||+|||..+++++    |+++|++||.|.+|++..   +++++|||||+|.+.++|.+|++.||+..+.|+.|
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~----l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i   80 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEED----LEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRML   80 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEE
T ss_pred             CCCCCEEEEECCCCcCCHHH----HHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34577899999999999999    669999999999997753   67889999999999999999999999999999999


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      +|.++..+..
T Consensus        81 ~V~~a~~~~~   90 (99)
T d1whwa_          81 HVLPSTIKKE   90 (99)
T ss_dssp             EEEECCCCST
T ss_pred             EEEECCCCCc
Confidence            9999887543

>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=3.3e-20  Score=121.06  Aligned_cols=78  Identities=21%  Similarity=0.415  Sum_probs=70.2

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC--c
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD--K   86 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g--~   86 (245)
                      ...+++|||+|||.++++++    |+++|++||.|..+++.   .+|.++|||||+|.+.++|.+|++.||+..+.|  +
T Consensus         3 ~~~~t~lfV~nlp~~~te~~----l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   78 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQ----LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQ   78 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHH----HHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCe
Confidence            44667899999999999999    77999999999998654   478899999999999999999999999999986  7


Q ss_pred             eEEEEEc
Q 025973           87 PMRIQYA   93 (245)
Q Consensus        87 ~i~v~~~   93 (245)
                      +|+|.||
T Consensus        79 ~l~V~~A   85 (85)
T d1b7fa2          79 PLSVRLA   85 (85)
T ss_dssp             CCEEEEC
T ss_pred             EEEEEEC
Confidence            8999986

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=2.6e-20  Score=119.40  Aligned_cols=72  Identities=19%  Similarity=0.303  Sum_probs=68.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .|||+|||..+++++|+++|+.||.|.++.+..++    +|||||+|.++++|..|++.|||..++|++|+|++|.
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            49999999999999999999999999999998864    6799999999999999999999999999999999985

>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=99.82  E-value=3.9e-20  Score=127.63  Aligned_cols=75  Identities=24%  Similarity=0.468  Sum_probs=70.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++|||+|||..+++++|.++|+.||.|.+|++..+.  +|||||+|.+.++|..|++.|||..|.|++|.|.||+
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 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            56789999999999999999999999999999998754  7999999999999999999999999999999999985

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4.6e-20  Score=122.38  Aligned_cols=85  Identities=22%  Similarity=0.366  Sum_probs=74.9

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      .+.....++|||+|||..+++++    |+++|+.||.|.+|.+.. .+.++|||||+|.+.++|.+|+..||+..+.|+.
T Consensus         5 ~~~~~~~~~l~v~nLp~~~t~~~----L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~   80 (93)
T d2cq3a1           5 SESKSTPKRLHVSNIPFRFRDPD----LRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRK   80 (93)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHH----HHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHH----HHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            34556678899999999999999    779999999999987654 3446899999999999999999999999999999


Q ss_pred             EEEEEccccc
Q 025973           88 MRIQYAKTKS   97 (245)
Q Consensus        88 i~v~~~~~~~   97 (245)
                      |+|.+++++.
T Consensus        81 l~V~~A~~r~   90 (93)
T d2cq3a1          81 IEVNNATARV   90 (93)
T ss_dssp             CEEEECCSSC
T ss_pred             EEEEecCcCC
Confidence            9999998753

>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=1.8e-20  Score=122.39  Aligned_cols=72  Identities=29%  Similarity=0.457  Sum_probs=67.7

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC--------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK--------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       174 l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~--------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      |||+|||..+|+++|+++|+.||.|.++.++.++        +|||||+|.++++|..|++.|||..++|++|.|+||++
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            7999999999999999999999999999998642        58999999999999999999999999999999999864

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=3.3e-20  Score=120.95  Aligned_cols=73  Identities=22%  Similarity=0.477  Sum_probs=67.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCC--eEEEEEEe
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQ--QQLLITYA  243 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~a  243 (245)
                      +++|||+|||..+|+++|+++|++||.|.+++++.++     +|||||+|.++++|..|++.|||..+.|  ++|+|.||
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            4579999999999999999999999999999998753     6899999999999999999999999987  66999997

>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=99.82  E-value=5.7e-20  Score=119.31  Aligned_cols=79  Identities=29%  Similarity=0.468  Sum_probs=71.5

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC-CceE
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY-DKPM   88 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~-g~~i   88 (245)
                      .+.+|+++|||+|||.++++++    |+++|+.||.|..|++.++  .+|||||+|.+.++|..|++.|||..+. |+.|
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~----l~~~f~~~G~i~~v~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i   76 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMM----LSMLFNQFPGFKEVRLVPN--RHDIAFVEFTTELQSNAAKEALQGFKITPTHAM   76 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHH----HHHHHTTSTTEEEEEECTT--TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBC
T ss_pred             CCCCCCCEEEEECCCCCCCHHH----HHhhhccCccEEEeeeecc--cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEE
Confidence            4567899999999999999999    7799999999999988764  3689999999999999999999998885 6899


Q ss_pred             EEEEcc
Q 025973           89 RIQYAK   94 (245)
Q Consensus        89 ~v~~~~   94 (245)
                      +|.|++
T Consensus        77 ~v~~ak   82 (83)
T d2b0ga1          77 KITFAK   82 (83)
T ss_dssp             EEEECC
T ss_pred             EEEEec
Confidence            999986

>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=2.6e-20  Score=119.76  Aligned_cols=73  Identities=29%  Similarity=0.383  Sum_probs=68.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .+++|||+|++  +|+++|+++|++||.|.++.+.+++ |||||+|.+.++|..|+..|||..++|++|+|+|||+
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-NCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTT-TEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCC-CEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            56789999996  8999999999999999999998876 8999999999999999999999999999999999985

>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=99.82  E-value=5.7e-20  Score=123.44  Aligned_cols=76  Identities=20%  Similarity=0.244  Sum_probs=70.8

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++|||+|||..+++++|+++|+.||.|.++.++.++     +|||||+|.+.++|..|++.|||..|+|++|+|.+|+
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45679999999999999999999999999999998753     6899999999999999999999999999999999986


Q ss_pred             C
Q 025973          245 K  245 (245)
Q Consensus       245 ~  245 (245)
                      .
T Consensus        87 ~   87 (99)
T d1whwa_          87 I   87 (99)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=1.3e-20  Score=121.85  Aligned_cols=77  Identities=10%  Similarity=0.215  Sum_probs=66.0

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      .++|||+|||.++++++    |+++|+.||.|..+...   .+|.++|||||+|.+.++|.+|++.|||..+.|+.|.|.
T Consensus         1 d~tl~v~nLp~~~t~~~----l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~   76 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRN----IRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTK   76 (81)
T ss_dssp             SCEEEEECCCTTCCHHH----HHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CcEEEEECCCCcCCHHH----HHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            47999999999999999    66999999999765433   467889999999999999999999999999999999999


Q ss_pred             Eccc
Q 025973           92 YAKT   95 (245)
Q Consensus        92 ~~~~   95 (245)
                      ++++
T Consensus        77 ~a~P   80 (81)
T d2ghpa1          77 VSNP   80 (81)
T ss_dssp             ECCC
T ss_pred             EccC
Confidence            9875

>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=2e-20  Score=123.18  Aligned_cols=74  Identities=19%  Similarity=0.354  Sum_probs=69.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      .+|||+|||..+++++|+++|+.||.|..+.++.++   +|||||+|.+.++|..|++.|||..|+|++|.|.+|+.
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            469999999999999999999999999999998864   68999999999999999999999999999999999973

>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=99.82  E-value=1.5e-20  Score=129.16  Aligned_cols=76  Identities=24%  Similarity=0.348  Sum_probs=71.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      ..+++|||+|||..+++++|+++|+.||.|.+|.|.+.+ |||||+|.+.++|.+|++.|||..|.|++|.|+||+.
T Consensus         8 r~~~~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_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-ITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSS-SCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccC-ceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            456789999999999999999999999999999987665 8999999999999999999999999999999999863

>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=99.82  E-value=2e-20  Score=121.96  Aligned_cols=78  Identities=22%  Similarity=0.363  Sum_probs=71.6

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      .+|||+|||..+++++    |+++|+.||+|.+|++.   .+|.++|||||+|.+.++|..|++.||+..+.|+.|.|.+
T Consensus         2 ~rlfV~nlp~~~te~~----l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~   77 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQ----VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR   77 (85)
T ss_dssp             CCEEEETCCSSCCSHH----HHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEE
T ss_pred             CEEEEECCCCCCCHHH----HHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            5799999999999999    66999999999998765   4688999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025973           93 AKTKS   97 (245)
Q Consensus        93 ~~~~~   97 (245)
                      +....
T Consensus        78 A~~~~   82 (85)
T d2u2fa_          78 ASVGA   82 (85)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            97643

>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=99.82  E-value=5.9e-20  Score=119.82  Aligned_cols=74  Identities=26%  Similarity=0.438  Sum_probs=68.7

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCC--eEEEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQ--QQLLITY  242 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~  242 (245)
                      .+++|||+|||..+++++|+++|+.||.|.+++++.++     +|||||+|.++++|..|++.|||..+.|  ++|+|+|
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            45679999999999999999999999999999999764     6899999999999999999999999875  8999999


Q ss_pred             e
Q 025973          243 A  243 (245)
Q Consensus       243 a  243 (245)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            8

>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=99.82  E-value=9.4e-20  Score=121.80  Aligned_cols=77  Identities=23%  Similarity=0.429  Sum_probs=71.3

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCC--eEEEEEEecC
Q 025973          168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQ--QQLLITYAKK  245 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~ak~  245 (245)
                      .+|+++|||+|||..+++++|+++|++||.|..+++.+++ ++|||+|.+.++|..|++.|||..|.|  ++|+|.|||.
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~-~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~   92 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD-SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSS-CCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccc-cEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCC
Confidence            3567889999999999999999999999999999999886 899999999999999999999999985  6899999973

>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=99.81  E-value=8.7e-20  Score=118.93  Aligned_cols=77  Identities=19%  Similarity=0.415  Sum_probs=69.1

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc--e
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK--P   87 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~--~   87 (245)
                      ..+++|||+|||..+++++    |+++|++||.|.++.+.   .+|.++|||||+|.+.++|.+|++.|||..+.|+  +
T Consensus         4 ~k~~~lfV~nLp~~~te~~----L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~   79 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKE----LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEP   79 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSC
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEE
Confidence            3468899999999999999    77999999999998654   4688999999999999999999999999999975  6


Q ss_pred             EEEEEc
Q 025973           88 MRIQYA   93 (245)
Q Consensus        88 i~v~~~   93 (245)
                      |.|.||
T Consensus        80 i~V~~A   85 (85)
T d1fxla2          80 ITVKFA   85 (85)
T ss_dssp             CEEEEC
T ss_pred             EEEEeC
Confidence            999886

>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=99.81  E-value=4.3e-20  Score=119.42  Aligned_cols=73  Identities=15%  Similarity=0.212  Sum_probs=67.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ++|||+|||..+|+++|+++|+.||.|..+.++.+.     +|||||+|.++++|..|++.|||..+.|++|.|+||+
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~   79 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN   79 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            579999999999999999999999999877776532     6899999999999999999999999999999999986

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=2.8e-20  Score=121.23  Aligned_cols=72  Identities=25%  Similarity=0.454  Sum_probs=69.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .|||+|||..+|+++|+++|+.||.|.+++++.++     +|||||+|.++++|..|++.|||..++|++|.|.||+
T Consensus         3 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_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS   79 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            59999999999999999999999999999999864     6999999999999999999999999999999999996

>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=99.81  E-value=3.1e-20  Score=122.57  Aligned_cols=80  Identities=21%  Similarity=0.452  Sum_probs=72.0

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ..++|||+|||.++++++    |.++|++||.|..+.+.   .++.++|||||+|.+.++|..|+..|||..+.|+.|+|
T Consensus         4 ~~~kifV~nLp~~~t~~~----l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V   79 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQS----LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   79 (90)
T ss_dssp             CCSEEEEESCCTTCCHHH----HHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCEEEEECCCCcCCHHH----HHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            467899999999999999    66999999999988544   36778999999999999999999999999999999999


Q ss_pred             EEccccc
Q 025973           91 QYAKTKS   97 (245)
Q Consensus        91 ~~~~~~~   97 (245)
                      .++.++.
T Consensus        80 ~~a~~~~   86 (90)
T d1x5sa1          80 DQAGKSS   86 (90)
T ss_dssp             EEEECCC
T ss_pred             EEcCCCC
Confidence            9987654

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=8.6e-20  Score=118.51  Aligned_cols=71  Identities=24%  Similarity=0.332  Sum_probs=66.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLI  240 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v  240 (245)
                      ++++|||+|||..+|+++|+++|+.||.|.++.++.++     +|||||+|.++++|..|+..|||..|+|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            56789999999999999999999999999999998754     689999999999999999999999999999987

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=2e-20  Score=123.09  Aligned_cols=79  Identities=27%  Similarity=0.429  Sum_probs=71.4

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      ..+|||+|||.++++++    |+++|+.||.|.++.+.. .+.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++
T Consensus         8 ~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a   83 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKA----LYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF   83 (89)
T ss_dssp             TTEEEEESCCSSCCHHH----HHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45799999999999999    669999999999987765 4457899999999999999999999999999999999999


Q ss_pred             cccc
Q 025973           94 KTKS   97 (245)
Q Consensus        94 ~~~~   97 (245)
                      .++.
T Consensus        84 ~~~~   87 (89)
T d1cvja2          84 KSRK   87 (89)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            8654

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=5.3e-20  Score=119.57  Aligned_cols=78  Identities=17%  Similarity=0.307  Sum_probs=69.9

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ++..++|||+|||.++++++    |+++|+.||.|..|.+.   .+|.++|||||+|.+.++|.+|++ +++..+.|+.|
T Consensus         3 pe~~~~lfV~nlp~~~te~~----l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i   77 (84)
T d1l3ka1           3 PEQLRKLFIGGLSFETTDES----LRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVV   77 (84)
T ss_dssp             CGGGGEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEEC
T ss_pred             CCCCcEEEEECCCCCCCHHH----HHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEE
Confidence            44567999999999999999    77999999999987554   468899999999999999999998 69999999999


Q ss_pred             EEEEcc
Q 025973           89 RIQYAK   94 (245)
Q Consensus        89 ~v~~~~   94 (245)
                      +|..|.
T Consensus        78 ~V~~A~   83 (84)
T d1l3ka1          78 EPKRAV   83 (84)
T ss_dssp             EEEECC
T ss_pred             EEEeee
Confidence            998874

>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=99.81  E-value=5.9e-20  Score=120.77  Aligned_cols=81  Identities=16%  Similarity=0.244  Sum_probs=71.2

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ....+++|||+|||.++|+++    |+++|+.||.|.+|.+.   .+|.++|||||.|.+.++|.+|++.  +..+.|+.
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~----l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~   77 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQD----LKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRW   77 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHH----HHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEE
T ss_pred             CCcCCCeEEEECCCCCCCHHH----HHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEE
Confidence            456788999999999999999    77999999999998654   4789999999999999999999985  44789999


Q ss_pred             EEEEEccccc
Q 025973           88 MRIQYAKTKS   97 (245)
Q Consensus        88 i~v~~~~~~~   97 (245)
                      |.|.++.++.
T Consensus        78 i~v~~a~~k~   87 (90)
T d2cqga1          78 CDCKLPNSKQ   87 (90)
T ss_dssp             EEEECCCTTC
T ss_pred             eEEEeCCCCC
Confidence            9999987653

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.81  E-value=2.1e-19  Score=128.30  Aligned_cols=75  Identities=21%  Similarity=0.391  Sum_probs=70.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..++|||+|||..+++++|+++|+.||.|.+|.++.++     +|||||+|.+.++|..|++.|||..|+|++|+|.||+
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34679999999999999999999999999999998753     6899999999999999999999999999999999986

>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=99.81  E-value=4.9e-20  Score=120.41  Aligned_cols=79  Identities=24%  Similarity=0.317  Sum_probs=68.5

Q ss_pred             CCCCeEEEcCCCcccC-hHHHHHHHHHhhcccCCeEEEEec----CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           13 SPNNTIYINNLNEKVK-IDQLKQSLHAVFKQFGTILEILAF----KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~-~~~l~~~l~~~F~~~G~v~~i~~~----~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      .++++|||+|||.+++ +++    |+++|+.||.|.+|.+.    .+++++|||||+|.+.++|.+|++ ||+..+.|+.
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~----l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~   76 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENL----LRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNRE   76 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHH----HHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEE
T ss_pred             CCCCEEEEECCCCCcccHHH----HHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEE
Confidence            4679999999999976 566    66999999999999764    267889999999999999999997 9999999999


Q ss_pred             EEEEEcccc
Q 025973           88 MRIQYAKTK   96 (245)
Q Consensus        88 i~v~~~~~~   96 (245)
                      |+|.+++++
T Consensus        77 l~V~~a~~k   85 (86)
T d2ghpa3          77 ISVSLADKK   85 (86)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEEcCCC
Confidence            999998765

>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=99.81  E-value=5.4e-20  Score=122.60  Aligned_cols=79  Identities=23%  Similarity=0.397  Sum_probs=72.2

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      .+..++|||+|||.++++++    |+++|++||.|.+|++.++   +|||||+|.+.++|..|+..|||..+.|+.|+|.
T Consensus        15 ~~~~~~l~v~nL~~~~te~~----L~~~F~~fG~i~~v~i~~~---kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~   87 (96)
T d1x4ga1          15 SPKNCTVYCGGIASGLTDQL----MRQTFSPFGQIMEIRVFPE---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   87 (96)
T ss_dssp             CSSCCEEEEECCSSCCCHHH----HHHHHHHHSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHH----HHHHHHHhCCceEEEEEec---ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            35578999999999999999    7799999999999988765   7999999999999999999999999999999999


Q ss_pred             Eccccc
Q 025973           92 YAKTKS   97 (245)
Q Consensus        92 ~~~~~~   97 (245)
                      |++++.
T Consensus        88 ~ak~~p   93 (96)
T d1x4ga1          88 WGKESP   93 (96)
T ss_dssp             CCCCCC
T ss_pred             EcCCCC
Confidence            987653

>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=99.81  E-value=1.8e-19  Score=118.29  Aligned_cols=77  Identities=19%  Similarity=0.357  Sum_probs=70.9

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHh--CCCeeCCeEEEEEEecC
Q 025973          168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL--QSLKIGQQQLLITYAKK  245 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l--~g~~~~g~~i~v~~ak~  245 (245)
                      .+|+++|||+|||..+++++|+++|+.||.|.++++.+++ ++|||+|.++++|.+|+..+  ++..++|++|+|.||+.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~-~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~   83 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-NQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc-eEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            3578899999999999999999999999999999999886 89999999999999999865  56789999999999974

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.81  E-value=7.6e-20  Score=130.58  Aligned_cols=82  Identities=21%  Similarity=0.395  Sum_probs=73.5

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ....++|||+|||.++++++    |+++|+.||.|.+|.+.   .+|.++|||||+|.+.++|..|++.|||..|.|+.|
T Consensus        39 ~~~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l  114 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQ----LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRL  114 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHH----HHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            44567899999999999999    66999999999987654   478899999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 025973           89 RIQYAKTKS   97 (245)
Q Consensus        89 ~v~~~~~~~   97 (245)
                      +|.++....
T Consensus       115 ~V~~a~~~~  123 (139)
T d1u6fa1         115 KVALAASGH  123 (139)
T ss_dssp             EEEESSCCC
T ss_pred             EEEEcCCCC
Confidence            999987543

>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=99.80  E-value=7.1e-20  Score=120.82  Aligned_cols=76  Identities=26%  Similarity=0.417  Sum_probs=70.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+|||+|||..+++++|+++|+.||.|..+.++.+.     +|||||+|.++++|..|++.|||+.|+|++|+|.+|+
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            34579999999999999999999999999999888743     7899999999999999999999999999999999986


Q ss_pred             C
Q 025973          245 K  245 (245)
Q Consensus       245 ~  245 (245)
                      +
T Consensus        84 ~   84 (90)
T d1x5sa1          84 K   84 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.80  E-value=9.4e-20  Score=119.69  Aligned_cols=80  Identities=19%  Similarity=0.376  Sum_probs=70.5

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCcc-CCceEEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPF-YDKPMRI   90 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~-~g~~i~v   90 (245)
                      .+|+++|||+|||.++++++    |+++|+.||.|..+.... ++++|||||+|.+.++|.+|+..|||..+ .|+.|+|
T Consensus         7 ~pPs~tL~V~NLp~~~te~~----l~~~F~~~G~v~~~~~~~-~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v   81 (88)
T d2adca2           7 FPPSATLHLSNIPPSVSEED----LKVLFSSNGGVVKGFKFF-QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV   81 (88)
T ss_dssp             CCSCSEEEEECCCTTCCHHH----HHHHHHTTSCCEEEEEEC-SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEE
T ss_pred             CCCCCEEEEECCCCCCCHHH----HHHHhhccCCEEEEEEee-ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEE
Confidence            46789999999999999999    679999999998875543 45678999999999999999999999988 4899999


Q ss_pred             EEcccc
Q 025973           91 QYAKTK   96 (245)
Q Consensus        91 ~~~~~~   96 (245)
                      .|++..
T Consensus        82 ~~sk~~   87 (88)
T d2adca2          82 SFSKST   87 (88)
T ss_dssp             EECSSC
T ss_pred             EeCCCC
Confidence            998753

>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=1.6e-19  Score=118.00  Aligned_cols=74  Identities=23%  Similarity=0.309  Sum_probs=69.0

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..++|||+|||..+++++|.++|+.||.|..+.+...+ |||||+|.++++|..|+..|||..|+|++|.|+|||
T Consensus         7 ~~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           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR-DYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECS-SEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcccc-EEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            45789999999999999999999999998887776664 899999999999999999999999999999999986

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=1.3e-19  Score=121.65  Aligned_cols=83  Identities=22%  Similarity=0.388  Sum_probs=72.9

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHc------CC
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQ------GF   81 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~------~~   81 (245)
                      +..++++|||+|||.++++++    |+++|++||.|.++.+..   ++.++|||||+|.+.++|.+|++.||      |.
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~----l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~   79 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEA----LGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL   79 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE
T ss_pred             CCCCCCEEEEcCCCCcCCHHH----HHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCc
Confidence            456789999999999999999    669999999999886654   56789999999999999999999887      56


Q ss_pred             ccCCceEEEEEccccc
Q 025973           82 PFYDKPMRIQYAKTKS   97 (245)
Q Consensus        82 ~~~g~~i~v~~~~~~~   97 (245)
                      .+.|+.|+|.++.++.
T Consensus        80 ~~~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          80 KLDGRQLKVDLAVTRD   95 (98)
T ss_dssp             ESSSCEEEEECCCCCC
T ss_pred             EECCEEEEEEECCCCC
Confidence            7789999999997754

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=5e-20  Score=123.77  Aligned_cols=79  Identities=18%  Similarity=0.399  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ..++|||+|||.++++++    |+++|+.||.|.+|.+..   +|.++|||||+|.+.++|.+|+. |||..|.|+.|.|
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   91 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRD----LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIV   91 (101)
T ss_dssp             HHTEEEEESCCTTCCHHH----HHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHH----HHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEE
Confidence            357899999999999999    669999999999987764   58899999999999999999996 9999999999999


Q ss_pred             EEccccc
Q 025973           91 QYAKTKS   97 (245)
Q Consensus        91 ~~~~~~~   97 (245)
                      .++....
T Consensus        92 ~~a~~~~   98 (101)
T d2cq4a1          92 QASQAEK   98 (101)
T ss_dssp             EEHHHHH
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=5.8e-20  Score=124.56  Aligned_cols=79  Identities=20%  Similarity=0.431  Sum_probs=71.7

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      .++|||+|||.++++++    |.++|++||.|.+|.+.   .+|+++|||||+|.+.++|.+|++.||+..+.|+.|+|.
T Consensus         8 ~rtl~V~nLp~~~te~~----l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~   83 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQ----LKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             HSCEEEESCCTTSCHHH----HHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             CCEEEEECCCCcCCHHH----HHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            47899999999999999    66999999999988654   478899999999999999999999999999999999999


Q ss_pred             Eccccc
Q 025973           92 YAKTKS   97 (245)
Q Consensus        92 ~~~~~~   97 (245)
                      ++....
T Consensus        84 ~a~~~~   89 (104)
T d1p1ta_          84 NAASEK   89 (104)
T ss_dssp             ETTCTT
T ss_pred             ECCCCC
Confidence            986543

>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=99.80  E-value=9.5e-20  Score=118.91  Aligned_cols=78  Identities=18%  Similarity=0.451  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      ...++|||+|||.++++++    |+++|++||.|.+|.+.++   +|||||+|.+.++|..|++.|||..+.|+.|+|.|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~----l~~~F~~~G~i~~i~~~~~---k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~   78 (86)
T d2cpja1           6 TQRSRLFVGNLPPDITEEE----MRKLFEKYGKAGEVFIHKD---KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   78 (86)
T ss_dssp             CCTTEEEEESCCTTCCHHH----HHHHTSTTCCCSEEEEETT---TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             cCCCEEEEECCCCCCCHHH----HHHHHHHhCCceEeeeecc---cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3567899999999999999    6799999999999988754   68999999999999999999999999999999999


Q ss_pred             ccccc
Q 025973           93 AKTKS   97 (245)
Q Consensus        93 ~~~~~   97 (245)
                      +.+..
T Consensus        79 A~~~~   83 (86)
T d2cpja1          79 ACHSA   83 (86)
T ss_dssp             SSCCS
T ss_pred             CCCcC
Confidence            87654

>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=1.8e-19  Score=120.40  Aligned_cols=72  Identities=25%  Similarity=0.310  Sum_probs=66.8

Q ss_pred             CccEEEEcCCC-CCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVP-HDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~-~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.+|||+||| ..+++++|+++|++||.|.++.+.   +|||||+|.+.++|.+|++.|||+.|.|++|+|.||+
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~---rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   86 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH---KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAA   86 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE---TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETT
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe---CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            44569999997 678999999999999999999984   5999999999999999999999999999999999996

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=2.7e-20  Score=118.84  Aligned_cols=73  Identities=22%  Similarity=0.353  Sum_probs=66.5

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      |+|||+|||.++++++    |+++|++||.|.++.+.   .+|.++|||||+|.+.++|.+|++ +++..+.|+.|.|..
T Consensus         1 cklfV~nLp~~~te~~----l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~   75 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEG----LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKV   75 (77)
T ss_dssp             CCEEEESCCSSCCSHH----HHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEE
T ss_pred             CEEEEeCCCCcCCHHH----HHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEE
Confidence            6899999999999999    66999999999887554   468899999999999999999998 799999999999987


Q ss_pred             c
Q 025973           93 A   93 (245)
Q Consensus        93 ~   93 (245)
                      |
T Consensus        76 A   76 (77)
T d1uawa_          76 A   76 (77)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.79  E-value=1.3e-19  Score=119.69  Aligned_cols=76  Identities=26%  Similarity=0.450  Sum_probs=69.2

Q ss_pred             CccEEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          170 PNNILFVQNVPHDTTPMALQ----MFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~----~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      |+++|||+|||..+++++|+    .+|+.||.|.+|.+..+.  +|||||+|.+.++|..|+..+||..|+|++|.|.||
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            57899999999999999885    468999999999987642  699999999999999999999999999999999999


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus        82 k~   83 (91)
T d1nu4a_          82 KT   83 (91)
T ss_dssp             SS
T ss_pred             CC
Confidence            73

>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=99.79  E-value=7.5e-20  Score=125.62  Aligned_cols=81  Identities=19%  Similarity=0.258  Sum_probs=72.7

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ++....+++|||+|||+++++++    |+++|+.||.|..|.+.+   .+|||||+|.+.++|.+|++.|||..|.|+.|
T Consensus         4 ~~~~r~~~~l~V~nLp~~~t~~~----L~~~F~~fG~I~~v~l~~---~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l   76 (111)
T d1whxa_           4 GSSGRSKTVILAKNLPAGTLAAE----IQETFSRFGSLGRVLLPE---GGITAIVEFLEPLEARKAFRHLAYSKFHHVPL   76 (111)
T ss_dssp             GGTSEEEEEEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCS---SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCCCEEEEECCCCCCCHHH----HHhhhhccCCccEEEeec---cCceEEEEEcCHHHHHHHHHHHcCCccCCCeE
Confidence            44556678999999999999999    679999999999998864   46999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      .|.|+...
T Consensus        77 ~v~~a~~~   84 (111)
T d1whxa_          77 YLEWAPIG   84 (111)
T ss_dssp             EEEEEETT
T ss_pred             EEEECCCC
Confidence            99998654

>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=6.4e-19  Score=119.23  Aligned_cols=77  Identities=18%  Similarity=0.191  Sum_probs=70.4

Q ss_pred             CCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHh--CCCeeCCeEEEEEEecC
Q 025973          168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL--QSLKIGQQQLLITYAKK  245 (245)
Q Consensus       168 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l--~g~~~~g~~i~v~~ak~  245 (245)
                      .+++.+|||+|||..+++++|.++|+.||.|.++.+.+.+ ++|||+|.++++|..|+..+  ++..++|++|+|+||+.
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k-~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~   90 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK-RQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTT-TEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecc-eeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCC
Confidence            3578899999999999999999999999999999998876 89999999999999999977  55678899999999863

>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=99.79  E-value=2.3e-19  Score=120.19  Aligned_cols=76  Identities=16%  Similarity=0.250  Sum_probs=69.6

Q ss_pred             CCccEEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHH--HhCCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPH-DTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQ--SLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~-~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~--~l~g~~~~g~~i~v~~ak~  245 (245)
                      .++++|||+|||. .+|+++|.++|+.||.|.++.+.+++ |+|||+|.+.++|..|++  .+++..|+|++|+|.||++
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k-~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK-SQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT-TEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC-CcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            4567899999997 58999999999999999999999886 899999999999999997  5788899999999999974

>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=99.79  E-value=1.4e-19  Score=121.51  Aligned_cols=73  Identities=21%  Similarity=0.433  Sum_probs=68.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++|||+|||..+++++|+++|+.||.|.+|.++.++     +|||||+|.++++|..|+. |||..|.|++|.|++|+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            4689999999999999999999999999999999863     7899999999999999995 99999999999999974

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.7e-19  Score=114.62  Aligned_cols=72  Identities=18%  Similarity=0.339  Sum_probs=65.3

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      +|||+|||+++++++    |+++|++||.|..+.+..   +++++|||||+|.+.++|.+|++ +++..+.|+.|.|..|
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 KMFIGGLSWDTTKKD----LKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHH----HHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            599999999999999    779999999999987654   67899999999999999999998 7999999999998653

>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=2.4e-19  Score=121.08  Aligned_cols=80  Identities=20%  Similarity=0.252  Sum_probs=70.7

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      ....++|||+|||..+++++    |+++|+.||.|.+|.+..   +|+++|||||+|.+.++|.+|++.+|+ .+.|+.|
T Consensus         7 d~~~~~lfV~nLp~~~te~~----l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l   81 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDAS----LRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKA   81 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHH----HHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEEC
T ss_pred             CCCCcEEEEeCCCCcCcHHH----HHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEE
Confidence            34457899999999999999    679999999999987754   578999999999999999999998876 6899999


Q ss_pred             EEEEcccc
Q 025973           89 RIQYAKTK   96 (245)
Q Consensus        89 ~v~~~~~~   96 (245)
                      .|.++...
T Consensus        82 ~V~~a~~~   89 (103)
T d2cqda1          82 NVNLAYLG   89 (103)
T ss_dssp             EEEESTTT
T ss_pred             EEEEcCCC
Confidence            99998654

>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=1.6e-19  Score=121.56  Aligned_cols=81  Identities=15%  Similarity=0.261  Sum_probs=71.3

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .....++|||+|||.++++++    |+++|+.||.|..+.+.  .++.++|||||+|.+.++|.+|++.|||..+.|+++
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~----L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~   89 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQE----LENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   89 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHH----HHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             ccCCCCEEEEeCCCCCCCHHH----HHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCC
Confidence            344568999999999999999    77999999999887544  477889999999999999999999999999999998


Q ss_pred             EEEEccc
Q 025973           89 RIQYAKT   95 (245)
Q Consensus        89 ~v~~~~~   95 (245)
                      .|.++++
T Consensus        90 ~v~~~~P   96 (101)
T d1x5oa1          90 VSAPTEP   96 (101)
T ss_dssp             SCCCSSC
T ss_pred             ccCCCCC
Confidence            8877654

>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=99.79  E-value=1.4e-19  Score=118.01  Aligned_cols=75  Identities=21%  Similarity=0.365  Sum_probs=66.8

Q ss_pred             EEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CC---CeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TL---KHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        18 l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~---~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      |||+|||.++++++    |+++|+.||.|.+|.+..   ++   .++|||||+|.+.++|.+|++.|||..+.|+.|.|.
T Consensus         1 LfV~nLp~~~t~~~----l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~   76 (85)
T d2cpfa1           1 LFIKNLNFSTTEET----LKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   76 (85)
T ss_dssp             EEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CEEcCCCCCCCHHH----HHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            79999999999999    679999999999876543   22   468999999999999999999999999999999999


Q ss_pred             Ecccc
Q 025973           92 YAKTK   96 (245)
Q Consensus        92 ~~~~~   96 (245)
                      ++...
T Consensus        77 ~a~~~   81 (85)
T d2cpfa1          77 ISERA   81 (85)
T ss_dssp             CSSCS
T ss_pred             ECCCC
Confidence            98543

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.79  E-value=1.6e-19  Score=117.89  Aligned_cols=74  Identities=16%  Similarity=0.331  Sum_probs=66.3

Q ss_pred             ccEEEEcCCCCCCC-HHHHHHHhccCCCeeEEEEecCC------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          171 NNILFVQNVPHDTT-PMALQMFFSQFPGFKEVRMVEAK------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       171 ~~~l~v~nl~~~~t-~~~l~~~f~~~g~v~~v~l~~~~------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +++|||+|||..++ +++|+++|+.||.|.++.+..+.      +|||||+|.+.++|..|++ |||..|+|++|+|+||
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEEC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEc
Confidence            56899999998876 56699999999999999987531      6899999999999999996 9999999999999999


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      ++
T Consensus        83 ~~   84 (86)
T d2ghpa3          83 DK   84 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>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=1e-19  Score=121.41  Aligned_cols=84  Identities=25%  Similarity=0.354  Sum_probs=74.5

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .....++++|||+|||.++++++    |+++|+.||.|..+.  .++.++|||||+|.+.++|.+|++.||+..+.|+.|
T Consensus        10 ~~~~~~~~~l~V~nL~~~~te~~----l~~~F~~~g~v~~~~--~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i   83 (96)
T d1fjca_          10 SKKVRAARTLLAKNLSFNITEDE----LKEVFEDALEIRLVS--QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV   83 (96)
T ss_dssp             TSTTTGGGEEEEESCCSSCCHHH----HHHHHCSEEEECCEE--ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEE
T ss_pred             cCcCCCCCEEEEeCCCCCCCHHH----HHHHHHhcccceeee--ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEE
Confidence            34466789999999999999999    679999999887664  467889999999999999999999999999999999


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      +|.|+.++..
T Consensus        84 ~V~~a~~k~~   93 (96)
T d1fjca_          84 SLYYTGEKGG   93 (96)
T ss_dssp             EEEECSSSCC
T ss_pred             EEEEeCCCCC
Confidence            9999987643

>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=2e-19  Score=117.88  Aligned_cols=73  Identities=18%  Similarity=0.275  Sum_probs=64.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++|||+|||..+++++|+++|+.|| +..+.+... +|||||+|.++++|..|+..|||+.|+|++|.|+||+
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-KRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEGG-GTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeecc-CCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            356799999999999999999999999 333444444 5899999999999999999999999999999999986

>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=99.79  E-value=6.8e-20  Score=117.97  Aligned_cols=71  Identities=21%  Similarity=0.299  Sum_probs=65.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCC-eeCCeEEEEEEec
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSL-KIGQQQLLITYAK  244 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~-~~~g~~i~v~~ak  244 (245)
                      +|||+|||..+|+++|+++|+.||.|..+.+...+ |||||+|.++++|..|++.|||. .++|++|+|+||+
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-GYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSV   74 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEET-TEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEeccc-ceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcC
Confidence            59999999999999999999999999777777665 89999999999999999999996 6999999999985

>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=99.79  E-value=3e-20  Score=125.62  Aligned_cols=85  Identities=27%  Similarity=0.458  Sum_probs=74.9

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEe---cCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILA---FKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~---~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ....|+++|||+|||.++++++    |+++|+.||.|..+.+   ..+|.++|||||+|.+.++|..|++.|||..+.|+
T Consensus        13 ~~~~ps~tl~V~nLp~~~t~~~----l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~   88 (102)
T d2cpxa1          13 NPGEPNKVLYLKNLSPRVTERD----LVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGK   88 (102)
T ss_dssp             CCCSCCSEEEEECCCTTCCHHH----HHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCE
Confidence            3456789999999999999999    6699999998877543   34788999999999999999999999999999999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|+|.|++++..
T Consensus        89 ~l~V~~ak~k~~  100 (102)
T d2cpxa1          89 ILVIEFGKNKKQ  100 (102)
T ss_dssp             BCEEEECCCCSC
T ss_pred             EEEEEeCCCccc
Confidence            999999987543

>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=6.9e-20  Score=119.00  Aligned_cols=76  Identities=32%  Similarity=0.545  Sum_probs=67.7

Q ss_pred             EEEcCCCcccChHHHHHHHHHhhcccCCeEEE-Eec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        18 l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i-~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      |||+|||.++++++    |+++|++||.|.++ ++.   .+|+++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus         1 lfV~nLp~~~te~~----l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a   76 (83)
T d1x5ta1           1 IFIGNLDPEIDEKL----LYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   76 (83)
T ss_dssp             EEEECCCTTCCHHH----HHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CEEcCCCCcCcHHH----HHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEe
Confidence            79999999999999    77999999998653 333   46888999999999999999999999999999999999998


Q ss_pred             cccc
Q 025973           94 KTKS   97 (245)
Q Consensus        94 ~~~~   97 (245)
                      .++.
T Consensus        77 ~~k~   80 (83)
T d1x5ta1          77 FKKD   80 (83)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7653

>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=5.8e-19  Score=112.00  Aligned_cols=69  Identities=19%  Similarity=0.349  Sum_probs=63.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       174 l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      |||+|||..+++++|+++|++|| +..+.+.+. +|+|||+|.+.++|.+|++.|||..++|++|+|+||+
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-KGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQP   69 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeeccc-ceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeC
Confidence            79999999999999999999999 666666655 4999999999999999999999999999999999996

>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=1.8e-20  Score=123.73  Aligned_cols=83  Identities=16%  Similarity=0.355  Sum_probs=72.5

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEe--cCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILA--FKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~--~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ..++....+|||+|||.++++++    |+++|+.||.|..+.+  ..+|+++|||||+|.+.++|.+|++ ||+..+.|+
T Consensus         7 ~~~~~~~~~ifV~nL~~~~te~~----l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~   81 (91)
T d1fjeb1           7 GSESTTPFNLFIGNLNPNKSVAE----LKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGN   81 (91)
T ss_dssp             SSSCSSSEEEEEECCCTTSCHHH----HHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTE
T ss_pred             CCCCCCCcEEEEeCccCcchHHH----HHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCE
Confidence            34455677999999999999999    6699999998877644  3478899999999999999999997 999999999


Q ss_pred             eEEEEEcccc
Q 025973           87 PMRIQYAKTK   96 (245)
Q Consensus        87 ~i~v~~~~~~   96 (245)
                      .|+|.+++.+
T Consensus        82 ~i~V~~ak~k   91 (91)
T d1fjeb1          82 EIKLEKPKGR   91 (91)
T ss_dssp             EEEEECCCCS
T ss_pred             EEEEEecCCC
Confidence            9999998753

>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=99.78  E-value=3.2e-19  Score=116.11  Aligned_cols=76  Identities=22%  Similarity=0.417  Sum_probs=69.1

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec--CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF--KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~--~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      ..++|||+|||.++++++    |+++|+.||.|..|.+.  .+|.++|||||+|.+.++|.+|++ +++..+.|+.|.|.
T Consensus         5 ~~rtvfV~nlp~~~te~~----l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~   79 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDD----IKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLIL   79 (85)
T ss_dssp             HTTEEEEECCCTTCCHHH----HHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEE
T ss_pred             CcCEEEEECCCCCCCHHH----HHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            468999999999999999    66999999999998665  478899999999999999999997 79999999999999


Q ss_pred             Ecc
Q 025973           92 YAK   94 (245)
Q Consensus        92 ~~~   94 (245)
                      +..
T Consensus        80 ~~~   82 (85)
T d1zh5a2          80 FKD   82 (85)
T ss_dssp             EGG
T ss_pred             EcC
Confidence            854

>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=99.78  E-value=2.4e-19  Score=116.40  Aligned_cols=71  Identities=17%  Similarity=0.333  Sum_probs=64.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeE-EEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          174 LFVQNVPHDTTPMALQMFFSQFPGFKE-VRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       174 l~v~nl~~~~t~~~l~~~f~~~g~v~~-v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      |||+|||..+|+++|+++|+.||.|.. ++++.++     +|||||+|.++++|..|++.|||..++|++|+|.||+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~   77 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAF   77 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEec
Confidence            799999999999999999999999855 4566543     6899999999999999999999999999999999986

>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=4.3e-19  Score=114.10  Aligned_cols=74  Identities=22%  Similarity=0.326  Sum_probs=67.0

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      .++|||+|||.++|+++    |.++|+.||.|..+.+.   .++.++|||||+|.+.++|.+|++ +|+..|.|+.|+|.
T Consensus         2 ~r~lfV~nLp~~~te~~----l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~   76 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHH----LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVR   76 (79)
T ss_dssp             CSEEEEECCTTTCCHHH----HHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEE
T ss_pred             CCEEEECCCCCcCCHHH----HHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            47999999999999999    66999999999987543   477899999999999999999997 89999999999998


Q ss_pred             Ec
Q 025973           92 YA   93 (245)
Q Consensus        92 ~~   93 (245)
                      .|
T Consensus        77 ~A   78 (79)
T d1l3ka2          77 KA   78 (79)
T ss_dssp             EC
T ss_pred             EC
Confidence            75

>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=99.78  E-value=1.4e-19  Score=122.02  Aligned_cols=80  Identities=14%  Similarity=0.329  Sum_probs=71.5

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEE
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI   90 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v   90 (245)
                      ..++|||+|||+++++++    |+++|++||.|..+.+.   .++.++|||||+|.+.++|.+|++ +++..|.|+.|.|
T Consensus        19 ~~~~lfVgnLp~~~te~~----L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V   93 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEES----LRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEP   93 (103)
T ss_dssp             HHTEEEEECCTTCCCHHH----HHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEE
T ss_pred             CCCEEEEeCCCCcCCHHH----HHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEE
Confidence            358999999999999999    67999999999998764   367889999999999999999997 7999999999999


Q ss_pred             EEccccch
Q 025973           91 QYAKTKSD   98 (245)
Q Consensus        91 ~~~~~~~~   98 (245)
                      .++.++..
T Consensus        94 ~~a~~ke~  101 (103)
T d1x4ba1          94 KRAVAREE  101 (103)
T ss_dssp             ECCSSCCC
T ss_pred             EECcccCC
Confidence            99876543

>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=99.78  E-value=7.5e-19  Score=118.61  Aligned_cols=74  Identities=23%  Similarity=0.356  Sum_probs=68.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ..++|||+|||..+++++|+++|+.||.|.+++++.++     +|||||+|.+.++|.+|++.+|+ .|.|++|.|.+|.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            34679999999999999999999999999999998863     68999999999999999998876 7999999999985

>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=99.78  E-value=3.1e-19  Score=116.60  Aligned_cols=78  Identities=18%  Similarity=0.245  Sum_probs=69.4

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      ...++|||+|||.++++++    |.++|+.||.|..+.+   ++++|||||+|.+.++|..|+..|||..+.|+.|+|.|
T Consensus         6 ~~~k~l~V~nLp~~~te~~----l~~~F~~~g~i~~~~~---~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~   78 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEM----IEKEFNNIKPGAVERV---KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL   78 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHH----HHHHHHTTSTTCEEEE---EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             cCCCEEEEcCCCCCCCHHH----HHHhhcccceeeeEEE---ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4568999999999999999    6699999998877655   34579999999999999999999999999999999999


Q ss_pred             ccccc
Q 025973           93 AKTKS   97 (245)
Q Consensus        93 ~~~~~   97 (245)
                      +++..
T Consensus        79 akP~~   83 (86)
T d2cpda1          79 AKPVD   83 (86)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            97653

>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=3.1e-19  Score=120.38  Aligned_cols=83  Identities=36%  Similarity=0.503  Sum_probs=72.1

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE--------EEe---cCCCCeeeEEEEEecCHHHHHHHHHHHc
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--------ILA---FKTLKHKGQAWLVFKDVASATAAVEKMQ   79 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~--------i~~---~~~~~~kg~afV~F~~~~~A~~a~~~l~   79 (245)
                      +...+++|||+|||..+++++    |+++|+.||.|..        +..   ..+|.++|||||+|.+.++|.+|++.||
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~----l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~   79 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDD----LADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFD   79 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHH----HHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHT
T ss_pred             CCCCCCEEEEECCCCcCCHHH----HHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhC
Confidence            455688999999999999999    6699999998853        222   2357889999999999999999999999


Q ss_pred             CCccCCceEEEEEccccc
Q 025973           80 GFPFYDKPMRIQYAKTKS   97 (245)
Q Consensus        80 ~~~~~g~~i~v~~~~~~~   97 (245)
                      |..|.|+.|+|.+++++.
T Consensus        80 g~~~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          80 GKDFQGSKLKVSLARKKP   97 (101)
T ss_dssp             TCEETTEECEEECSSCCC
T ss_pred             CCEECCEEEEEEEcCCCC
Confidence            999999999999997653

>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=99.78  E-value=2.4e-19  Score=121.44  Aligned_cols=74  Identities=28%  Similarity=0.410  Sum_probs=69.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++|||+|||..+++++|.++|+.||.|.+|.++.++     +|||||+|.+.++|..|++.|||..|.|++|+|.||.
T Consensus         8 ~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_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            3579999999999999999999999999999998753     5899999999999999999999999999999999985

>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=99.78  E-value=9.7e-19  Score=113.51  Aligned_cols=73  Identities=21%  Similarity=0.312  Sum_probs=67.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++|||+|||..+++++|.++|+.||.|..+.++.++     +|||||+|.++++|.+|++ +++..|.|++|.|..|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            3579999999999999999999999999999998764     7899999999999999997 69999999999999884

>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=99.77  E-value=5.1e-19  Score=113.59  Aligned_cols=77  Identities=19%  Similarity=0.396  Sum_probs=69.6

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      +..+++|||+||+  +|+++    |+++|++||.|.+|.+.+.   +|||||+|.+.++|..|+..|||..+.|+.|+|.
T Consensus         2 p~~~~ti~V~~~~--~te~~----L~~~F~~~G~I~~v~~~~~---~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   72 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTL----LRGAFSPFGNIIDLSMDPP---RNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   72 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHH----HHHHHSTTCCCSCEEEETT---TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEECCC--CCHHH----HHHHHhccCccceeeeccC---CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEE
Confidence            5678999999996  89999    7799999999999987643   6899999999999999999999999999999999


Q ss_pred             Eccccc
Q 025973           92 YAKTKS   97 (245)
Q Consensus        92 ~~~~~~   97 (245)
                      |++++.
T Consensus        73 ~a~~~P   78 (79)
T d2bz2a1          73 IARKQP   78 (79)
T ss_dssp             ECCSSC
T ss_pred             EecCCC
Confidence            997653

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.5e-18  Score=111.48  Aligned_cols=71  Identities=18%  Similarity=0.342  Sum_probs=66.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +.|||+|||..+|+++|+++|+.||.|..+.+..++     +|+|||+|.++++|.+|+. +||..|+|++|.|..|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            579999999999999999999999999999998764     6899999999999999996 8999999999999987

>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=99.77  E-value=1.3e-18  Score=114.10  Aligned_cols=81  Identities=26%  Similarity=0.350  Sum_probs=72.0

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHH--cCCccCCce
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKM--QGFPFYDKP   87 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l--~~~~~~g~~   87 (245)
                      .+.+|+++|||+|||.++++++    |+++|++||.|.++.+.+.   +++|||+|.+.++|..|++.+  ++..+.|+.
T Consensus         3 ~~~~Ps~~l~V~nLp~~~t~~~----L~~~f~~~G~i~~v~~~~~---~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~   75 (88)
T d2cq1a1           3 MDGAPSRVLHIRKLPGEVTETE----VIALGLPFGKVTNILMLKG---KNQAFLELATEEAAITMVNYYSAVTPHLRNQP   75 (88)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHH----HHHTTTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHH----HHHHHhccccccccccccc---ceEEEEEeCCHHHHHHHHHHHccCCCccCCCE
Confidence            4578999999999999999999    6799999999999987754   589999999999999999866  567899999


Q ss_pred             EEEEEccccc
Q 025973           88 MRIQYAKTKS   97 (245)
Q Consensus        88 i~v~~~~~~~   97 (245)
                      |+|.|++.+.
T Consensus        76 l~v~~sk~~~   85 (88)
T d2cq1a1          76 IYIQYSNHKE   85 (88)
T ss_dssp             CEEEECSCSS
T ss_pred             EEEEECCCCC
Confidence            9999997654

>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=9.8e-19  Score=110.92  Aligned_cols=71  Identities=15%  Similarity=0.259  Sum_probs=66.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC---CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK---PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~---~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      ++|||+|||..+++++|+++|+.||.|..+.+..++   +++|||+|.++++|.+|+. +|+..|+|++|.|..+
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            369999999999999999999999999999998865   6899999999999999995 8999999999999875

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.2e-19  Score=122.56  Aligned_cols=77  Identities=23%  Similarity=0.372  Sum_probs=70.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC-----CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA-----KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~-----~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++++|||+|||..+++++|.++|+.||.|..+.+..+     .+|||||+|.++++|..|+..|||..|+|++|+|+||
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            46788999999999999999999999999877777652     2689999999999999999999999999999999999


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      +.
T Consensus        96 k~   97 (102)
T d2cpxa1          96 KN   97 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            73

>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=9.2e-19  Score=114.79  Aligned_cols=76  Identities=11%  Similarity=0.159  Sum_probs=69.4

Q ss_pred             CCccEEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHh--CCCeeCCeEEEEEEecC
Q 025973          169 PPNNILFVQNVPHD-TTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL--QSLKIGQQQLLITYAKK  245 (245)
Q Consensus       169 ~~~~~l~v~nl~~~-~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l--~g~~~~g~~i~v~~ak~  245 (245)
                      .++++|||+|||.. +|+++|.++|++||.|.++.+.+++ ++|||+|.+.++|..|+..+  ++..+.|++|+|+||++
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k-~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI-NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS-SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc-eEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence            36788999999975 8899999999999999999999886 79999999999999999966  67789999999999974

>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=99.77  E-value=1.2e-18  Score=116.28  Aligned_cols=80  Identities=26%  Similarity=0.548  Sum_probs=71.8

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCC--ceE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYD--KPM   88 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g--~~i   88 (245)
                      ...|+++|||+|||+++++++    |+++|++||.|..|++.++   ++||||+|.+.++|..|++.||+..+.|  +.|
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~----l~~~f~~~G~i~~~~~~~~---~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l   85 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAA----LAREFDRFGSIRTIDHVKG---DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRL   85 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHH----HHHHHHTTSCEEEEEECSS---SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBC
T ss_pred             CCCCCCEEEEcCCCCCCCHHH----HHHHHHhhcccceEeeecc---ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEE
Confidence            457889999999999999999    7799999999999988754   6899999999999999999999999986  489


Q ss_pred             EEEEccccc
Q 025973           89 RIQYAKTKS   97 (245)
Q Consensus        89 ~v~~~~~~~   97 (245)
                      +|.|+++..
T Consensus        86 ~v~~ak~~~   94 (97)
T d1whya_          86 RVDFAKSGP   94 (97)
T ss_dssp             EEEECCCCC
T ss_pred             EEEeCCCCC
Confidence            999987643

>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=99.77  E-value=2.1e-19  Score=114.65  Aligned_cols=70  Identities=20%  Similarity=0.341  Sum_probs=66.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .|||+|||..+|+++|+++|+.||.|.+++++.++     +|||||+|.++++|.+|+. +|++.++|++|.|.+|
T Consensus         2 klfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            59999999999999999999999999999998764     7999999999999999997 7999999999999987

>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=99.77  E-value=5.9e-19  Score=117.88  Aligned_cols=77  Identities=30%  Similarity=0.420  Sum_probs=68.4

Q ss_pred             CCCCCCeEEEcCCC-cccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           11 EISPNNTIYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        11 ~~~~~~~l~V~nLp-~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      +...+++|||+||| ..+++++    |+++|++||.|..|.+     .+|||||+|.+.++|.+|++.|||..+.|+.|+
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~----L~~~F~~~G~i~~~~i-----~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSD----VEAIFSKYGKIVGCSV-----HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLD   81 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHH----HHHSSTTSSCEEEEEE-----ETEEEEEEESSHHHHHHHHHTTTTCEETTEECE
T ss_pred             CCCCCcEEEEeCCCcccCCHHH----HHHHHhhcCCEEEEEE-----eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34557889999997 5678888    7799999999999987     369999999999999999999999999999999


Q ss_pred             EEEcccc
Q 025973           90 IQYAKTK   96 (245)
Q Consensus        90 v~~~~~~   96 (245)
                      |.++...
T Consensus        82 V~~a~~~   88 (98)
T d1wf2a_          82 INLAAEP   88 (98)
T ss_dssp             EEETTSC
T ss_pred             EEECCCC
Confidence            9998654

>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=5e-19  Score=112.41  Aligned_cols=70  Identities=20%  Similarity=0.308  Sum_probs=65.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .|||+|||..+|+++|.++|+.||.|..+.++.++     +|||||+|.++++|..|++ +++..|.|++|.|..|
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            38999999999999999999999999999998853     6999999999999999997 7999999999999765

>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=99.77  E-value=4.8e-19  Score=118.12  Aligned_cols=80  Identities=15%  Similarity=0.406  Sum_probs=69.5

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCC-eEEEEecC----CCCeeeEEEEEecCHHHHHHHHHHHcC--CccCCce
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGT-ILEILAFK----TLKHKGQAWLVFKDVASATAAVEKMQG--FPFYDKP   87 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~-v~~i~~~~----~~~~kg~afV~F~~~~~A~~a~~~l~~--~~~~g~~   87 (245)
                      +|+|||+|||.++++++    |+++|+.||. |.+|.+.+    +++++|||||+|.+.++|..|++.|++  ..+.|+.
T Consensus         1 n~rLyV~nLp~~~te~~----l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~   76 (96)
T d2disa1           1 NCRLFIGGIPKMKKREE----ILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQ   76 (96)
T ss_dssp             SEEEEEECCCTTSCHHH----HHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBC
T ss_pred             CCEEEEcCCCCcCCHHH----HHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEE
Confidence            57999999999999999    6699999995 88887754    467899999999999999999999865  4557999


Q ss_pred             EEEEEccccch
Q 025973           88 MRIQYAKTKSD   98 (245)
Q Consensus        88 i~v~~~~~~~~   98 (245)
                      |+|.|++++..
T Consensus        77 i~V~~A~p~~~   87 (96)
T d2disa1          77 IAVDWAEPEID   87 (96)
T ss_dssp             CEEEESCSSCS
T ss_pred             EEEEEcCCCCC
Confidence            99999987544

>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=99.77  E-value=6.9e-19  Score=118.41  Aligned_cols=74  Identities=12%  Similarity=0.229  Sum_probs=67.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++|||+|||..+++++|+++|+.||.|..+.+..+.    +|||||+|.++++|..|++.|||..|.|+++.|.+++
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            4579999999999999999999999999999888754    6899999999999999999999999999998887764

>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=99.77  E-value=6.9e-19  Score=120.31  Aligned_cols=76  Identities=25%  Similarity=0.430  Sum_probs=69.2

Q ss_pred             CCeEEEcCCCc-ccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           15 NNTIYINNLNE-KVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        15 ~~~l~V~nLp~-~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      +++|||+|||+ .+++++    |+++|+.||.|..|.+.++.  +|||||+|.+.++|.+|++.|||..+.|+.|+|.|+
T Consensus         2 ~~~l~V~nL~p~~~te~~----L~~~F~~fG~I~~v~i~~~~--kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s   75 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQS----LFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   75 (109)
T ss_dssp             CSEEEEESCCTTTCCHHH----HHHHHHHHTCEEEEEECCTT--SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECC
T ss_pred             CCEEEEeCCCcccCCHHH----HHHHHhhccccceEEEEecc--cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            68999999965 589999    77999999999999988653  689999999999999999999999999999999998


Q ss_pred             ccc
Q 025973           94 KTK   96 (245)
Q Consensus        94 ~~~   96 (245)
                      +..
T Consensus        76 ~~~   78 (109)
T d2adca1          76 KHQ   78 (109)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.1e-18  Score=117.53  Aligned_cols=77  Identities=26%  Similarity=0.314  Sum_probs=67.5

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCee--------EEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCC
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFK--------EVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQ  235 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~--------~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g  235 (245)
                      ..+.+|||+|||..+|+++|+++|+.||.|.        .+.+..++     +|||||+|.++++|..|++.|||..|.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            3567899999999999999999999999874        34444432     5899999999999999999999999999


Q ss_pred             eEEEEEEecC
Q 025973          236 QQLLITYAKK  245 (245)
Q Consensus       236 ~~i~v~~ak~  245 (245)
                      ++|+|+||+.
T Consensus        86 r~i~V~~a~~   95 (101)
T d2cpea1          86 SKLKVSLARK   95 (101)
T ss_dssp             EECEEECSSC
T ss_pred             EEEEEEEcCC
Confidence            9999999974

>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=99.77  E-value=3.7e-19  Score=118.67  Aligned_cols=76  Identities=20%  Similarity=0.306  Sum_probs=68.6

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++++|||+|||..+|+++|+++|+.||.|..+......+|||||+|.+.++|..|++.|||..|.|++|+|.||+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~   89 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            3567899999999999999999999999987776443337999999999999999999999999999999999986

>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=99.77  E-value=1.3e-18  Score=116.17  Aligned_cols=73  Identities=15%  Similarity=0.206  Sum_probs=68.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+|||+|||..+++++|+++|+.||.|.++.+..  +|||||+|.++++|..|++.|||..|.|+.|+|.|++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~--~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK--DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET--TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc--cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            456799999999999999999999999999999875  4899999999999999999999999999999999975

>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=8.2e-19  Score=118.12  Aligned_cols=73  Identities=18%  Similarity=0.305  Sum_probs=67.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++|||+|||..+++++|+++|++||.|..+.|..++     +|||||+|.+.++|..|+. ++|..|.|++|.|.+|+
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-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            3579999999999999999999999999999998753     7999999999999999996 79999999999999986

>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=99.77  E-value=5.4e-19  Score=112.48  Aligned_cols=70  Identities=20%  Similarity=0.310  Sum_probs=65.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .|||+|||..+|+++|+++|+.||.|..+.++.++     +|+|||+|.+.++|..|++ +||..|+|++|.|.+|
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            38999999999999999999999999998887753     6899999999999999997 9999999999999987

>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=1.5e-18  Score=112.80  Aligned_cols=73  Identities=18%  Similarity=0.292  Sum_probs=68.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .++|||+|||..+|+++|+++|+.||.|..|.+..++    +|||||+|.++++|.+|++ ++|..|.|++|.|.|++
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4679999999999999999999999999999998754    6899999999999999996 79999999999999975

>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=99.77  E-value=1.3e-18  Score=114.18  Aligned_cols=73  Identities=21%  Similarity=0.251  Sum_probs=66.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.+|||+|||..+|+++|+++|+.||.|.++.++.++     +|||||+|.++++|.+|++.  +..++|+.|.|.+|+
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            34569999999999999999999999999999999864     68999999999999999984  458999999999985

>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=1.6e-19  Score=118.16  Aligned_cols=70  Identities=16%  Similarity=0.182  Sum_probs=66.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      +|||+|||..+++++|.++|+.||.|.++.+..+  |||||+|.+.++|..|+..|||..|.|+.|.|.+++
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--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   71 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc--ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEe
Confidence            5999999999999999999999999999998764  899999999999999999999999999999988764

>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=99.76  E-value=7.2e-19  Score=119.84  Aligned_cols=75  Identities=25%  Similarity=0.254  Sum_probs=69.3

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-CeEEEEEeCCHHHHHHHHHHhCCCeeC--CeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-PGIAFVEYGDEMQATVAMQSLQSLKIG--QQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-~g~afv~f~~~~~A~~A~~~l~g~~~~--g~~i~v~~ak  244 (245)
                      +...|||+|||..+|+++|+++|++||.|..+.+..++ +|+|||+|.++++|..|+..|||..|.  |++|+|.|++
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            55679999999999999999999999999999988764 689999999999999999999999884  8999999986

>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=99.76  E-value=3.5e-19  Score=116.79  Aligned_cols=73  Identities=26%  Similarity=0.317  Sum_probs=68.2

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+++|||+|||..+|+++|+++|+.||.|.++++....++||||+|.++++|..|+.  +++.|.|++|.|.+|+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            567899999999999999999999999999999888778999999999999999985  7889999999999985

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.76  E-value=1.3e-19  Score=119.41  Aligned_cols=75  Identities=16%  Similarity=0.280  Sum_probs=67.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC----CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA----KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAKK  245 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~----~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak~  245 (245)
                      ...+|||+|||..+++++|+++|+.||.|..+.++.+    .+|||||+|.++++|.+|++ |||..++|++|+|.+||.
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            4568999999999999999999999999877776553    26999999999999999996 999999999999999973

>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=99.76  E-value=1.5e-18  Score=117.44  Aligned_cols=81  Identities=21%  Similarity=0.320  Sum_probs=69.0

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec----CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF----KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~----~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      +..+.++|||+|||.++++++    |+++|+.|| +.++++.    .++.++|||||+|.+.++|.+|++ ||+..|.|+
T Consensus        11 p~~p~~~v~V~nLp~~~te~~----l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr   84 (104)
T d1wi8a_          11 PKSPPYTAFLGNLPYDVTEES----IKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNK   84 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHH----HHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTE
T ss_pred             CCCCCCEEEEeCCCCcCCHHH----HHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCE
Confidence            345678999999999999999    669999999 5565443    257789999999999999987776 999999999


Q ss_pred             eEEEEEccccc
Q 025973           87 PMRIQYAKTKS   97 (245)
Q Consensus        87 ~i~v~~~~~~~   97 (245)
                      .|+|.++..+.
T Consensus        85 ~l~V~~a~~~~   95 (104)
T d1wi8a_          85 RIRVDVADQAQ   95 (104)
T ss_dssp             ECEEEECCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999987653

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=5.7e-19  Score=112.38  Aligned_cols=72  Identities=18%  Similarity=0.395  Sum_probs=65.5

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      +|||+|||+++++++    |+++|+.||.|..+.+.   .++.++|||||+|.+.++|.+|++ +|+..+.|+.|+|.+|
T Consensus         1 rlfV~nLp~~~te~~----l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVED----VKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHH----HHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHH----HHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            599999999999999    66999999999987543   367789999999999999999997 9999999999999875

>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=99.76  E-value=2.2e-18  Score=115.50  Aligned_cols=75  Identities=27%  Similarity=0.396  Sum_probs=68.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhC------CCeeCCeEE
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQ------SLKIGQQQL  238 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~------g~~~~g~~i  238 (245)
                      .+++|||+|||..+|+++|+++|+.||.|..+.++.++     +|||||+|.++++|.+|++.+|      |..+.|++|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            45679999999999999999999999999999988753     6899999999999999999987      567889999


Q ss_pred             EEEEec
Q 025973          239 LITYAK  244 (245)
Q Consensus       239 ~v~~ak  244 (245)
                      +|+||+
T Consensus        87 ~v~~a~   92 (98)
T d1x4ha1          87 KVDLAV   92 (98)
T ss_dssp             EEECCC
T ss_pred             EEEECC
Confidence            999986

>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=99.76  E-value=6.9e-19  Score=115.51  Aligned_cols=71  Identities=18%  Similarity=0.334  Sum_probs=65.6

Q ss_pred             ccEEEEcCCCCCCCHHHH---HHHhccCCCeeEEEEecCC--------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEE
Q 025973          171 NNILFVQNVPHDTTPMAL---QMFFSQFPGFKEVRMVEAK--------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLL  239 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l---~~~f~~~g~v~~v~l~~~~--------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~  239 (245)
                      .++|||+|||..+++++|   .++|++||.|.+|.+++++        .|||||+|.++++|..|++.|||..|+|++|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            456999999999999999   6789999999999998753        38999999999999999999999999999999


Q ss_pred             EE
Q 025973          240 IT  241 (245)
Q Consensus       240 v~  241 (245)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.76  E-value=1.8e-18  Score=112.93  Aligned_cols=75  Identities=24%  Similarity=0.344  Sum_probs=66.4

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKE-VRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~-v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +...+|+|+|||..+++++|+++|+.||.+.. +.+..+.    +|+|||+|.++++|.+|++.|||..++|++|+|++|
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            34567999999999999999999999999854 4555432    689999999999999999999999999999999986

>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=99.76  E-value=3.4e-19  Score=116.73  Aligned_cols=78  Identities=18%  Similarity=0.303  Sum_probs=66.4

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      ..+++|||+|||.+++++|    |+++|+.||. ..+..   +..+|||||+|.+.++|.+|++.||+..+.|+.|+|.+
T Consensus         3 s~s~~i~V~nLp~~~t~~~----l~~lF~~~G~-~~~~~---~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~   74 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQE----VHDLLKDYDL-KYCYV---DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL   74 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHH----HHHHTCSSCC-CCEEE---EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCccChHH----HHHHHHhcCc-eeeee---eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3467899999999999999    6799999992 22222   45679999999999999999999999999999999999


Q ss_pred             ccccch
Q 025973           93 AKTKSD   98 (245)
Q Consensus        93 ~~~~~~   98 (245)
                      ++.+..
T Consensus        75 a~~~~~   80 (88)
T d1wg1a_          75 QPTDAL   80 (88)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            866543

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=4.2e-19  Score=112.49  Aligned_cols=72  Identities=19%  Similarity=0.281  Sum_probs=64.5

Q ss_pred             eEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC---CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        17 ~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~---~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      +|||+|||.++++++    |+++|++||.|..|.+..   ++.++|||||+|.+.++|.+|++ .++..+.|+.|.|..|
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 KIFVGGLSPDTPEEK----IREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHH----HHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHH----HHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            699999999999999    669999999999987654   67899999999999999999998 5778899999988754

>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=99.76  E-value=2.7e-18  Score=112.10  Aligned_cols=78  Identities=21%  Similarity=0.256  Sum_probs=69.1

Q ss_pred             CCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE---EEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceE
Q 025973           12 ISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM   88 (245)
Q Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~---i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i   88 (245)
                      .+..++|||+|||.++++++    |+++|+.||.+..   +....++.++|+|||+|.+.++|.+|++.||+..+.|+.|
T Consensus         6 ~p~~~~l~v~nLp~~~~~~d----i~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i   81 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSIDE----ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV   81 (86)
T ss_dssp             CCSSEEEEEESCCTTCCHHH----HHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCEEEEECCCCCCCHHH----HHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEE
Confidence            34567899999999999999    6699999998754   4555688999999999999999999999999999999999


Q ss_pred             EEEEc
Q 025973           89 RIQYA   93 (245)
Q Consensus        89 ~v~~~   93 (245)
                      +|.++
T Consensus        82 ~v~l~   86 (86)
T d2cqpa1          82 KLVLG   86 (86)
T ss_dssp             EEEES
T ss_pred             EEEEC
Confidence            99874

>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=99.76  E-value=2.6e-19  Score=115.17  Aligned_cols=75  Identities=28%  Similarity=0.400  Sum_probs=65.9

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCC-ccCCceEEEEEcc
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGF-PFYDKPMRIQYAK   94 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~-~~~g~~i~v~~~~   94 (245)
                      ++|||+|||.++++++    |+++|++||.|..+.+.   ..+|||||+|.+.++|.+|++.|||. .+.|+.|+|.|+.
T Consensus         2 n~l~V~nLp~~~te~~----L~~~F~~~G~i~~~~~~---~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~   74 (80)
T d2cqha1           2 NKLYIGNLSPAVTADD----LRQLFGDRKLPLAGQVL---LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSV   74 (80)
T ss_dssp             CCEEEECCCTTCCHHH----HHHHHHHTTCCCSSCEE---EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHH----HHHHHHHhCcEEEeEEe---cccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcC
Confidence            4799999999999999    66999999988664433   45799999999999999999999985 6999999999998


Q ss_pred             ccc
Q 025973           95 TKS   97 (245)
Q Consensus        95 ~~~   97 (245)
                      ++.
T Consensus        75 ~k~   77 (80)
T d2cqha1          75 SKK   77 (80)
T ss_dssp             CCC
T ss_pred             CcC
Confidence            754

>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=99.76  E-value=4.7e-18  Score=115.02  Aligned_cols=74  Identities=24%  Similarity=0.452  Sum_probs=65.4

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC------CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK------PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~------~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      +..+|||+|||..+++++|+++|+.|| +..+.++.+.      +|||||+|.++++|.+|+ .||+..|.|++|+|.||
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            457899999999999999999999998 7777777542      589999999999998777 59999999999999998


Q ss_pred             cC
Q 025973          244 KK  245 (245)
Q Consensus       244 k~  245 (245)
                      ++
T Consensus        92 ~~   93 (104)
T d1wi8a_          92 DQ   93 (104)
T ss_dssp             CC
T ss_pred             CC
Confidence            73

>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=99.76  E-value=1.1e-18  Score=118.93  Aligned_cols=83  Identities=35%  Similarity=0.497  Sum_probs=72.7

Q ss_pred             CCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC--CceE
Q 025973           11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY--DKPM   88 (245)
Q Consensus        11 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~--g~~i   88 (245)
                      ...+..+|||+|||..+|+++    |+++|+.||.|..|.+... +++|||||+|.+.++|..|+..|||..+.  |+.|
T Consensus         3 ~~s~~~~v~V~NL~~~vte~~----L~~~F~~~G~i~~~~i~~~-~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l   77 (108)
T d2adba1           3 GQSPVLRIIVENLFYPVTLDV----LHQIFSKFGTVLKIITFTK-NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL   77 (108)
T ss_dssp             CCCCEEEEESCSCCSTTHHHH----HHHHHTTTSCEEEEEEEEE-TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCC
T ss_pred             CCCCeEEEEEeCcCCCCCHHH----HHHHHccCCcEEEEEEEee-CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEE
Confidence            456788999999999999999    7799999999999877653 35799999999999999999999999885  6799


Q ss_pred             EEEEccccch
Q 025973           89 RIQYAKTKSD   98 (245)
Q Consensus        89 ~v~~~~~~~~   98 (245)
                      +|.|++.+..
T Consensus        78 ~v~~s~~~~~   87 (108)
T d2adba1          78 RIDFSKLTSL   87 (108)
T ss_dssp             EEEECSSCSC
T ss_pred             EEEecCCccc
Confidence            9999876543

>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=99.75  E-value=4.4e-18  Score=115.02  Aligned_cols=85  Identities=21%  Similarity=0.281  Sum_probs=73.9

Q ss_pred             ccCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHc--CCccC
Q 025973            7 NQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQ--GFPFY   84 (245)
Q Consensus         7 ~~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~--~~~~~   84 (245)
                      ......+++++|||+|||..+++++    |.++|+.||.|..|++.+   .|++|||+|.+.++|..|+..++  +..+.
T Consensus         7 g~~~~~~ps~~l~v~nlp~~~te~~----l~~~F~~fG~I~~~~~~~---~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~   79 (104)
T d1wexa_           7 GSHHKVSVSPVVHVRGLCESVVEAD----LVEALEKFGTICYVMMMP---FKRQALVEFENIDSAKECVTFAADVPVYIA   79 (104)
T ss_dssp             CSCCCCCCCSEEEEESCCSSCCHHH----HHHHHTTTSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCCBSS
T ss_pred             CCCCcCCCCCEEEEeCCCCCCCHHH----HHHhhhhcccceEEEEEe---cceeEEEEeCCHHHHHHHHHHHcCCCcEEe
Confidence            3445678899999999999999999    779999999999998865   36899999999999999999884  56678


Q ss_pred             CceEEEEEccccch
Q 025973           85 DKPMRIQYAKTKSD   98 (245)
Q Consensus        85 g~~i~v~~~~~~~~   98 (245)
                      |+.|+|.|++.+..
T Consensus        80 g~~l~v~~s~~~~~   93 (104)
T d1wexa_          80 GQQAFFNYSTSKRI   93 (104)
T ss_dssp             SSBCEEEECSSSSC
T ss_pred             eEEEEEEEcCCCcc
Confidence            99999999976543

>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=99.75  E-value=1.4e-18  Score=110.21  Aligned_cols=72  Identities=19%  Similarity=0.326  Sum_probs=63.9

Q ss_pred             EEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEccccc
Q 025973           18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKS   97 (245)
Q Consensus        18 l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~~~~   97 (245)
                      |||+|||+++++++    |+++|++|| +..+..   ++++|||||.|.+.++|.+|+..|||..+.|+.|+|.++..+.
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 ILIRGLPGDVTNQE----VHDLLSDYE-LKYCFV---DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHH----HHHHTTTSC-EEEEEE---ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHH----HHHHHhccc-ccceee---cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999    679999999 545444   4567999999999999999999999999999999999987654

>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=7.8e-19  Score=111.22  Aligned_cols=70  Identities=19%  Similarity=0.359  Sum_probs=65.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .|||+|||..+|+++|+++|+.||.|.++.++.++     +|||||+|.+.++|.+|++ .++..++|+.|.|..|
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            48999999999999999999999999999999864     7999999999999999997 5788999999999876

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=8.8e-19  Score=114.57  Aligned_cols=73  Identities=18%  Similarity=0.264  Sum_probs=66.9

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEccc
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKT   95 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~~   95 (245)
                      ++|||+|||+.+++++    |+++|++||.|..+.+..+    |||||+|.+.++|.+|+..|||..|.|+.|+|.++..
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 NRVVVSGLPPSGSWQD----LKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CCEEEEECCSSCCTTH----HHHHHGGGSCEEEEEECTT----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CeEEEECCCCcCCHHH----HHHHHhhhccccccccccc----ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            4799999999999999    7799999999999987654    7999999999999999999999999999999988754


Q ss_pred             c
Q 025973           96 K   96 (245)
Q Consensus        96 ~   96 (245)
                      +
T Consensus        73 ~   73 (87)
T d3begb1          73 K   73 (87)
T ss_dssp             E
T ss_pred             C
Confidence            4

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.74  E-value=2.3e-18  Score=109.20  Aligned_cols=73  Identities=18%  Similarity=0.180  Sum_probs=64.7

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC-CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK-TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~-~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      ++|||+|||+++++++    |+++|+.||.|..|++.. .+..++||||+|.+.++|.+|+. +|+..|.|+.|.|..+
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 TTVLVKNLPKSYNQNK----VYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHH----HHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHH----HHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            5899999999999999    779999999999987653 33456799999999999999997 8999999999999864

>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=1.1e-18  Score=110.10  Aligned_cols=68  Identities=22%  Similarity=0.329  Sum_probs=61.8

Q ss_pred             EEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        18 l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      |||+|||.++++++    |+++|+.||.|..+++.   .++.++|+|||+|.+.++|.+|++.|||..+.|+.++
T Consensus         1 lyV~nLp~~~te~~----l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQD----LVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHH----HHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHH----HHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999    77999999999987654   3677899999999999999999999999999998763

>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=1e-17  Score=113.27  Aligned_cols=85  Identities=9%  Similarity=0.082  Sum_probs=72.7

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE-Ee--cCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LA--FKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i-~~--~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ..++...+.+|||+|||+++++++    |+++|+.+|.|..+ .+  ..++.++|||||+|.+.++|.+|++ +|+..|.
T Consensus         8 ~~~~~~~~~~v~v~nLP~~~te~d----I~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~   82 (104)
T d1wg5a_           8 NSPDTANDGFVRLRGLPFGCSKEE----IVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIG   82 (104)
T ss_dssp             CCSSCSCCCEEEEESCCTTCCHHH----HHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSS
T ss_pred             CCCCCCCCcEEEEeCCCCCCCHHH----HHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEc
Confidence            445566677899999999999999    66999999988763 32  2477889999999999999999997 8999999


Q ss_pred             CceEEEEEccccc
Q 025973           85 DKPMRIQYAKTKS   97 (245)
Q Consensus        85 g~~i~v~~~~~~~   97 (245)
                      ||.|.|.++....
T Consensus        83 gR~i~V~~~~~~~   95 (104)
T d1wg5a_          83 HRYIEIFKSSRAE   95 (104)
T ss_dssp             SSCCEEEEECTTT
T ss_pred             ceEEEEEECCHHH
Confidence            9999999987654

>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=99.73  E-value=1.6e-18  Score=116.76  Aligned_cols=83  Identities=18%  Similarity=0.251  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCccc-ChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEE
Q 025973           13 SPNNTIYINNLNEKV-KIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQ   91 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~-~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~   91 (245)
                      ..+++|||+||+.++ +++++++.|+.+|+.||.|.++.+.+   +++||||+|.+.++|.+|+..|||..|.|+.|+|.
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            457899999999997 88888888999999999999998875   46899999999999999999999999999999999


Q ss_pred             Eccccch
Q 025973           92 YAKTKSD   98 (245)
Q Consensus        92 ~~~~~~~   98 (245)
                      |++....
T Consensus        80 ~a~~~~~   86 (104)
T d1weya_          80 FAQTLHI   86 (104)
T ss_dssp             CCCCSSC
T ss_pred             ecccCCC
Confidence            9865533

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=3.1e-18  Score=112.36  Aligned_cols=78  Identities=12%  Similarity=0.270  Sum_probs=65.8

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCC---C---CeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKT---L---KHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~---~---~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ...++|||+|||+++++++|.+ +.++|++||.|..|.+.++   +   ..+|||||+|.+.++|.+|++.|||..+.|+
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~-~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr   84 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLK-RPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   84 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHH-STTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             EecCEEEEECCCCccCHHHHHH-HHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCE
Confidence            3467899999999999999521 2578999999999976542   2   2348999999999999999999999999999


Q ss_pred             eEEEE
Q 025973           87 PMRIQ   91 (245)
Q Consensus        87 ~i~v~   91 (245)
                      .|+|.
T Consensus        85 ~lkvS   89 (89)
T d2cpia1          85 TLKAS   89 (89)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            99884

>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=99.73  E-value=4e-18  Score=113.58  Aligned_cols=74  Identities=22%  Similarity=0.351  Sum_probs=66.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEecCC------CeEEEEEeCCHHHHHHHHHHhCC--CeeCCeEEEEE
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPG-FKEVRMVEAK------PGIAFVEYGDEMQATVAMQSLQS--LKIGQQQLLIT  241 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~-v~~v~l~~~~------~g~afv~f~~~~~A~~A~~~l~g--~~~~g~~i~v~  241 (245)
                      ++.|||+|||..+++++|+++|+.||. |..+.++++.      +|||||+|.++++|..|++.|++  ..++|++|.|.
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            357999999999999999999999995 8999998742      68999999999999999999975  45579999999


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      ||+
T Consensus        81 ~A~   83 (96)
T d2disa1          81 WAE   83 (96)
T ss_dssp             ESC
T ss_pred             EcC
Confidence            996

>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=7.4e-18  Score=113.49  Aligned_cols=75  Identities=17%  Similarity=0.230  Sum_probs=66.0

Q ss_pred             CCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       169 ~~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ....+|||+|||..+|+++|+++|+.||. ..+.++.+.    +|||||+|.++++|.+|++ +|+..|+||.|.|.+++
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            45578999999999999999999999985 466666653    6899999999999999986 89999999999999986


Q ss_pred             C
Q 025973          245 K  245 (245)
Q Consensus       245 ~  245 (245)
                      .
T Consensus        91 ~   91 (102)
T d1weza_          91 T   91 (102)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.72  E-value=8.4e-18  Score=113.21  Aligned_cols=84  Identities=12%  Similarity=0.105  Sum_probs=71.1

Q ss_pred             CCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE-EEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973            9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE-ILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~-i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ......+.+|||+|||+++|+++    |+++|+.+|.+.. +....++..+|||||+|.+.++|.+|++ +|+..|.||.
T Consensus         9 ~~~~~~~~~v~v~nLp~~~te~d----l~~~F~~~~~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~   83 (102)
T d1weza_           9 SFQSTTGHCVHMRGLPYRATEND----IYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRY   83 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHH----HHHSSCSCCCSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSC
T ss_pred             CCcCCCCCEEEEeCCCCcCCHHH----HHHHHhccCcceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEE
Confidence            34456678999999999999999    6699999986532 2344578899999999999999999997 8999999999


Q ss_pred             EEEEEccccc
Q 025973           88 MRIQYAKTKS   97 (245)
Q Consensus        88 i~v~~~~~~~   97 (245)
                      |+|.++....
T Consensus        84 I~V~~s~~~~   93 (102)
T d1weza_          84 VELFLNSTAG   93 (102)
T ss_dssp             CEEEEECCCC
T ss_pred             EEEEEcCCCC
Confidence            9999987653

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.6e-18  Score=113.61  Aligned_cols=78  Identities=18%  Similarity=0.360  Sum_probs=68.8

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      ..+++|||+|||.++++++    |+++|++||.|.+|++..  .+++||||+|.+.++|.+|+.  ++..+.|+.|.|.+
T Consensus         3 ~~s~~lfV~nLp~~~te~~----L~~~F~~~G~v~~v~~~~--~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~   74 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDE----LREFFSQYGDVMDVFIPK--PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISN   74 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHH----HHHHSTTTSCCCEEECCS--SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHHcCCceEEEEee--ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEe
Confidence            4578999999999999999    669999999999987653  467999999999999999986  78889999999999


Q ss_pred             ccccch
Q 025973           93 AKTKSD   98 (245)
Q Consensus        93 ~~~~~~   98 (245)
                      +.++..
T Consensus        75 a~~k~~   80 (88)
T d1wf0a_          75 AEPKHN   80 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.72  E-value=2.4e-18  Score=108.48  Aligned_cols=66  Identities=18%  Similarity=0.300  Sum_probs=62.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEE
Q 025973          174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLL  239 (245)
Q Consensus       174 l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~  239 (245)
                      |||+|||..+|+++|+++|+.||.|..+++..++     +|+|||+|.++++|..|+..|||..|.|+.|+
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            7999999999999999999999999999988753     68999999999999999999999999999874

>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=99.72  E-value=8.2e-18  Score=112.49  Aligned_cols=81  Identities=15%  Similarity=0.247  Sum_probs=70.6

Q ss_pred             CCCCCCCeEEEcCCCcc-cChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHH--HHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEK-VKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE--KMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~-~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~--~l~~~~~~g~   86 (245)
                      +...++++|||+|||.+ +|+++    |..+|+.||.|..|.+.++   +|+|||+|.+.++|..|++  .+++..+.|+
T Consensus        13 ~~~~~~~~l~v~nLp~~~~te~~----l~~~F~~fG~V~~v~~~~~---k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr   85 (99)
T d1x4fa1          13 QKQELGRVIHLSNLPHSGYSDSA----VLKLAEPYGKIKNYILMRM---KSQAFIEMETREDAMAMVDHCLKKALWFQGR   85 (99)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHH----HHTTTTTTSCCSEEEEETT---TTEEEEECSSHHHHHHHHHHHHHSCCCSSSS
T ss_pred             cCCCCCCEEEEeCCcCCccCHHH----HHhhhccccceeEEEEeec---CCcEEEEecchHHHHHHHHHHhcCCceECCE
Confidence            34567899999999985 89999    7799999999999988754   5899999999999999997  4678899999


Q ss_pred             eEEEEEccccc
Q 025973           87 PMRIQYAKTKS   97 (245)
Q Consensus        87 ~i~v~~~~~~~   97 (245)
                      .|+|.|++...
T Consensus        86 ~l~V~~s~~~~   96 (99)
T d1x4fa1          86 CVKVDLSEKYK   96 (99)
T ss_dssp             CCEEEEECSCS
T ss_pred             EEEEEEcCCcc
Confidence            99999987654

>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=99.72  E-value=8.7e-18  Score=112.08  Aligned_cols=77  Identities=12%  Similarity=0.160  Sum_probs=69.4

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQY   92 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~   92 (245)
                      ...++|||+|||.++++++    |.++|+.||.|..+.+..    +|||||+|.+.++|.+|++.||+..|.|+.|+|.+
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~----L~~~F~~~G~v~~~~i~~----~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~   84 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQD----LKDHMREAGDVCYADVQK----DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSY   84 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHH----HHHHHTTSSCEEEEEEET----TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEE
T ss_pred             CCCCEEEEECCCCCCCHHH----HHHHHHhhcccccccccc----cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            4467899999999999999    669999999999998764    47999999999999999999999999999999999


Q ss_pred             ccccc
Q 025973           93 AKTKS   97 (245)
Q Consensus        93 ~~~~~   97 (245)
                      +..+.
T Consensus        85 ~~~~~   89 (98)
T d1wg4a_          85 IRVYP   89 (98)
T ss_dssp             EEEEC
T ss_pred             EecCC
Confidence            86544

>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=3.4e-17  Score=110.63  Aligned_cols=75  Identities=17%  Similarity=0.276  Sum_probs=65.5

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEV-RMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v-~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.+|||+|||..+|+++|+++|+.+|.+... .+..+.    +|+|||+|.++++|.+|++ +|+..|+||.|.|.+++
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            45579999999999999999999999988664 444432    6999999999999999996 89999999999999986


Q ss_pred             C
Q 025973          245 K  245 (245)
Q Consensus       245 ~  245 (245)
                      +
T Consensus        93 ~   93 (104)
T d1wg5a_          93 R   93 (104)
T ss_dssp             T
T ss_pred             H
Confidence            4

>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=99.72  E-value=1.8e-17  Score=108.51  Aligned_cols=80  Identities=19%  Similarity=0.296  Sum_probs=70.3

Q ss_pred             CCCCCCCeEEEcCCCcc-cChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHH--cCCccCCc
Q 025973           10 NEISPNNTIYINNLNEK-VKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKM--QGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~-~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l--~~~~~~g~   86 (245)
                      ....++++|||+|||.. +|++|    |+++|+.||.|.+|.+.++   +++|||+|.+.++|..|+..+  ++..+.|+
T Consensus         3 ~~~~~sr~v~v~nl~~~~~t~~e----L~~lF~~fG~I~~i~i~~~---k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr   75 (89)
T d1x4da1           3 GRVETRRVVHIMDFQRGKNLRYQ----LLQLVEPFGVISNHLILNK---INEAFIEMATTEDAQAAVDYYTTTPALVFGK   75 (89)
T ss_dssp             CCCCCCCEEEEESCCCSSSHHHH----HHTTTGGGSCEEEEEECSS---SSCEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCCCcEEEEECCCCCcCCHHH----HHHHHHhhCCeEEEEeecc---ceEEEEEEcchhhHHHHHHHHhhCCCccCCc
Confidence            34678999999999986 78999    7799999999999988754   579999999999999999976  56789999


Q ss_pred             eEEEEEcccc
Q 025973           87 PMRIQYAKTK   96 (245)
Q Consensus        87 ~i~v~~~~~~   96 (245)
                      +|+|.|++..
T Consensus        76 ~l~V~~s~~~   85 (89)
T d1x4da1          76 PVRVHLSQKY   85 (89)
T ss_dssp             ECEEEEECCC
T ss_pred             eEEEEECCCc
Confidence            9999998653

>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=99.72  E-value=3.6e-18  Score=115.07  Aligned_cols=74  Identities=9%  Similarity=0.144  Sum_probs=67.5

Q ss_pred             CccEEEEcCCCCCC-C----HHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDT-T----PMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~-t----~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.+|||+||+..+ +    +++|.++|+.||.|.++.+.+++ ++|||+|.++++|.+|+..|||..|+|++|+|.||+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~-~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   82 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-KRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT-TEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCC-CEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecc
Confidence            45679999999765 3    36799999999999999999886 799999999999999999999999999999999996

>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=2.2e-17  Score=111.41  Aligned_cols=81  Identities=12%  Similarity=0.079  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE-E--EecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEE
Q 025973           13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE-I--LAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~-i--~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      ....+|||+|||+++++++    |+++|+.||.|.. +  ....+|.++|+|||+|.+.++|.+|+. +|+..|.|+.|.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~----l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~   80 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMD----VLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAF   80 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHH----HHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEE
T ss_pred             CCceEEEEeCCCCCCCHHH----HhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEE
Confidence            3456799999999999999    6699999998754 3  334588899999999999999999997 999999999999


Q ss_pred             EEEccccch
Q 025973           90 IQYAKTKSD   98 (245)
Q Consensus        90 v~~~~~~~~   98 (245)
                      |.++.....
T Consensus        81 V~~~~~~~~   89 (103)
T d2cpya1          81 VHVVTLEDM   89 (103)
T ss_dssp             EEEECHHHH
T ss_pred             EEECCHHHh
Confidence            999765443

>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=99.68  E-value=6.1e-17  Score=110.74  Aligned_cols=85  Identities=14%  Similarity=0.180  Sum_probs=73.5

Q ss_pred             cCCCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEE---EEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973            8 QGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~---i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      +..+..+.++|||+|||+++++++    |.++|+.||.+..   +....+|.++|+|||+|.+.++|.+|++ ||+..|.
T Consensus        11 ~~~~~~~~~~i~v~nLp~~~t~~d----i~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~   85 (112)
T d1wela1          11 SRSPHEAGFCVYLKGLPFEAENKH----VIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMG   85 (112)
T ss_dssp             CSSCCCCCCEEEEECCCTTCCHHH----HHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCST
T ss_pred             CCCCCCCCeEEEEecCCCcCcHHH----HhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCC
Confidence            445566788999999999999999    6699999998754   3555789999999999999999999997 9999999


Q ss_pred             CceEEEEEccccc
Q 025973           85 DKPMRIQYAKTKS   97 (245)
Q Consensus        85 g~~i~v~~~~~~~   97 (245)
                      |+.|.|..+....
T Consensus        86 gR~i~V~~~~~~~   98 (112)
T d1wela1          86 NRFIQVHPITKKG   98 (112)
T ss_dssp             TSCBEEEEECHHH
T ss_pred             CEEEEEEEcChHH
Confidence            9999999876544

>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=99.68  E-value=3.7e-17  Score=110.26  Aligned_cols=74  Identities=19%  Similarity=0.321  Sum_probs=65.1

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKE-VRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~-v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+|||+|||..+|+++|+++|+.||.+.. +.+..+.    +|+|||+|.++++|.+|++ +||..|+|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            4567999999999999999999999999865 4444432    7999999999999999996 99999999999999874

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=7.1e-17  Score=110.41  Aligned_cols=74  Identities=14%  Similarity=0.274  Sum_probs=63.9

Q ss_pred             CccEEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          170 PNNILFVQNVPHDTTPMALQMFFSQFPGFKEV-RMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       170 ~~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v-~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      ...+|||+|||..+|+++|.++|+.||.+..+ .+..+.    +|+|||+|.+.++|.+|+. +||..|+|+.|.|..|.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            45689999999999999999999999988543 333322    7899999999999999996 99999999999998874

>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=99.64  E-value=2.8e-16  Score=105.13  Aligned_cols=75  Identities=16%  Similarity=0.193  Sum_probs=64.2

Q ss_pred             CCccEEEEcC--CCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeC---Ce--EEEEE
Q 025973          169 PPNNILFVQN--VPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIG---QQ--QLLIT  241 (245)
Q Consensus       169 ~~~~~l~v~n--l~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~---g~--~i~v~  241 (245)
                      .|+++|+|.|  ||..+|+++|+++|++||.|..|.+.+++ +||||+|.+.++|..|+..|||+.+.   +.  ++.+.
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k-~~aFV~f~~~e~A~~A~~~lng~~i~~~~~~~i~~~~~   94 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-PYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN   94 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC-SCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCc-cEEEEEECCHHHHHHHHHHhCCCCCCCCCCcEEEEEEE
Confidence            3567788865  99999999999999999999999999886 89999999999999999999998873   33  34446


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      |.+
T Consensus        95 ~~~   97 (101)
T d2cq2a1          95 FVE   97 (101)
T ss_dssp             EES
T ss_pred             eee
Confidence            654

>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=3.7e-18  Score=112.41  Aligned_cols=74  Identities=20%  Similarity=0.369  Sum_probs=63.7

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEE--------EecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCce
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI--------LAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKP   87 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i--------~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~   87 (245)
                      ++|||+|||.++++++    |.++|+.||.|..+        ....+++++|||||+|.+.++|.+|++ |||..+.|+.
T Consensus         2 RrlyVgNLp~~~te~~----l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~   76 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEA----MMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQS   76 (90)
T ss_dssp             CEEEECSCCTTCCTTH----HHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSC
T ss_pred             CEEEEcCCCCccchHH----HHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEE
Confidence            7899999999999999    66999999877653        334566788999999999999999996 9999999999


Q ss_pred             EEEEEcc
Q 025973           88 MRIQYAK   94 (245)
Q Consensus        88 i~v~~~~   94 (245)
                      |+|..++
T Consensus        77 l~V~r~k   83 (90)
T d1u2fa_          77 LKIRRPH   83 (90)
T ss_dssp             CCCBCTT
T ss_pred             EEECCCC
Confidence            9996543

>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=3.2e-15  Score=111.15  Aligned_cols=84  Identities=20%  Similarity=0.294  Sum_probs=74.1

Q ss_pred             CCCCCCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEec---CCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc
Q 025973           10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK   86 (245)
Q Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~---~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~   86 (245)
                      ......++|||+|||..+++++    |+++|+.||.|..+.+.   .+|.++|||||+|.+.++|.+|++ +++..+.|+
T Consensus        92 ~~~~~~~~i~V~~lp~~~te~~----L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~  166 (183)
T d1u1qa_          92 GAHLTVKKIFVGGIKEDTEEHH----LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGH  166 (183)
T ss_dssp             TTTCCCSEEEEECCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTE
T ss_pred             ccccccceeEEccCCCcCCHHH----HhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCE
Confidence            4456678999999999999999    77999999999987544   468899999999999999999998 788899999


Q ss_pred             eEEEEEccccch
Q 025973           87 PMRIQYAKTKSD   98 (245)
Q Consensus        87 ~i~v~~~~~~~~   98 (245)
                      .|+|.++.++..
T Consensus       167 ~i~V~~A~~k~e  178 (183)
T d1u1qa_         167 NCEVRKALSKQE  178 (183)
T ss_dssp             EEEEEECCCHHH
T ss_pred             EEEEEecCCccc
Confidence            999999877654

>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=99.60  E-value=1.2e-15  Score=104.24  Aligned_cols=70  Identities=13%  Similarity=0.208  Sum_probs=63.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCH-HHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDE-MQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~-~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .+||+|||..+|+++|+++|+.||.|.+|.++.++ |+|||.|.++ ++|..|+..+|+..+.++.+.|.|+
T Consensus        13 ~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~k-g~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          13 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             EEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             EEEECCCCCCCCHHHHHHHHHhcCChheEEEecCC-ceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            46999999999999999999999999999999886 8999999996 6888999999999988777777664

>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=99.59  E-value=1.3e-17  Score=109.67  Aligned_cols=72  Identities=24%  Similarity=0.327  Sum_probs=62.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecC----------CCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEE
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA----------KPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLIT  241 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~----------~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~  241 (245)
                      ++|||+|||..+|+++|+++|+.||.+..+.+...          .+|||||+|.++++|..|+. |||+.|.|++|+|.
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            46999999999999999999999998765554431          26899999999999999995 99999999999998


Q ss_pred             Eec
Q 025973          242 YAK  244 (245)
Q Consensus       242 ~ak  244 (245)
                      .+|
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            765

>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=99.58  E-value=3e-15  Score=99.71  Aligned_cols=87  Identities=18%  Similarity=0.363  Sum_probs=73.5

Q ss_pred             CCCCCCCeEEEcCC--CcccC-----hHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCc
Q 025973           10 NEISPNNTIYINNL--NEKVK-----IDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFP   82 (245)
Q Consensus        10 ~~~~~~~~l~V~nL--p~~~~-----~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~   82 (245)
                      +....+++|+|+||  |.++.     ..+|++.|+..|+.||.|..|.+... ..+|+|||.|.+.++|.+|+..|||..
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~-~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR-HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT-CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC-CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            45678999999999  65542     23677778999999999999876543 567999999999999999999999999


Q ss_pred             cCCceEEEEEccccc
Q 025973           83 FYDKPMRIQYAKTKS   97 (245)
Q Consensus        83 ~~g~~i~v~~~~~~~   97 (245)
                      |.|+.|+|.++.++.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999986653

>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=99.58  E-value=2.2e-16  Score=106.18  Aligned_cols=74  Identities=12%  Similarity=0.231  Sum_probs=67.0

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecC--CCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEc
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYA   93 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~--~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~   93 (245)
                      +.++|++++.+++|++    |.++|++||.|.+|.+.+  +++++|+|||+|.+.++|.+|+..|||..+.|++|.|+|+
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 SDVEMQEHYDEFFEEV----FTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHH----HHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHH----HHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4577888888888888    679999999999998764  6788999999999999999999999999999999999986

>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=99.56  E-value=2.4e-16  Score=105.95  Aligned_cols=71  Identities=13%  Similarity=0.127  Sum_probs=66.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC----CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK----PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYA  243 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~----~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  243 (245)
                      .++|++++..+++++|.++|++||.|.+|.++++.    +|+|||+|.+.++|.+|++.|||+.|+|++|.|+|+
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            48888899899999999999999999999998753    699999999999999999999999999999999985

>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=99.56  E-value=8.3e-15  Score=97.49  Aligned_cols=75  Identities=20%  Similarity=0.333  Sum_probs=66.0

Q ss_pred             CCccEEEEcCC--CCCC---------CHHHHHHHhccCCCeeEEEEecCC-CeEEEEEeCCHHHHHHHHHHhCCCeeCCe
Q 025973          169 PPNNILFVQNV--PHDT---------TPMALQMFFSQFPGFKEVRMVEAK-PGIAFVEYGDEMQATVAMQSLQSLKIGQQ  236 (245)
Q Consensus       169 ~~~~~l~v~nl--~~~~---------t~~~l~~~f~~~g~v~~v~l~~~~-~g~afv~f~~~~~A~~A~~~l~g~~~~g~  236 (245)
                      ..+++|+|+||  |..+         .+++|+..|+.||.|..|.+..+. +|+|||+|.++++|.+|+..|||..|+|+
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr   85 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR   85 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCE
Confidence            46789999999  4321         246899999999999999988765 79999999999999999999999999999


Q ss_pred             EEEEEEe
Q 025973          237 QLLITYA  243 (245)
Q Consensus       237 ~i~v~~a  243 (245)
                      +|.|+|+
T Consensus        86 ~i~v~~~   92 (99)
T d2dita1          86 QITAQAW   92 (99)
T ss_dssp             ECEEEEC
T ss_pred             EEEEEEe
Confidence            9999996

>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=99.55  E-value=7.3e-15  Score=98.10  Aligned_cols=67  Identities=15%  Similarity=0.219  Sum_probs=59.4

Q ss_pred             CCCCCCeEEEc--CCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccC
Q 025973           11 EISPNNTIYIN--NLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFY   84 (245)
Q Consensus        11 ~~~~~~~l~V~--nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~   84 (245)
                      ...|+++|+|.  |||.++|+++    |+++|++||.|..|.+.++   ++||||+|.+.++|..|+..|||..+.
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~----L~~~F~~~G~i~~i~~~~~---k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQ----LLPVLEKCGLVDALLMPPN---KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHH----HHHHHHHHSCEEEEECCTT---CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHH----HHHHHHhhCcccEEeeccC---ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            35678899995  5999999999    7799999999999988754   689999999999999999999998774

>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=99.52  E-value=9.1e-15  Score=98.29  Aligned_cols=76  Identities=21%  Similarity=0.343  Sum_probs=65.9

Q ss_pred             CCccEEEEcCC--CCCC--------CHHHHHHHhccCCCeeEEEEecCC-------CeEEEEEeCCHHHHHHHHHHhCCC
Q 025973          169 PPNNILFVQNV--PHDT--------TPMALQMFFSQFPGFKEVRMVEAK-------PGIAFVEYGDEMQATVAMQSLQSL  231 (245)
Q Consensus       169 ~~~~~l~v~nl--~~~~--------t~~~l~~~f~~~g~v~~v~l~~~~-------~g~afv~f~~~~~A~~A~~~l~g~  231 (245)
                      +|+++|.|+||  |..+        ..+||+..|++||.|.+|.+.++.       .|++||+|.++++|.+|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            47889999999  4333        246799999999999999987632       489999999999999999999999


Q ss_pred             eeCCeEEEEEEec
Q 025973          232 KIGQQQLLITYAK  244 (245)
Q Consensus       232 ~~~g~~i~v~~ak  244 (245)
                      .|+||+|.|.|+.
T Consensus        82 ~f~gR~v~v~f~~   94 (104)
T d1o0pa_          82 KFANRVVVTKYCD   94 (104)
T ss_dssp             CSSSSCCEEEEEC
T ss_pred             EECCeEEEEEEcC
Confidence            9999999999974

>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=99.52  E-value=2.1e-14  Score=97.91  Aligned_cols=77  Identities=13%  Similarity=0.196  Sum_probs=64.4

Q ss_pred             CCCCCeE-EEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCH-HHHHHHHHHHcCCccCCceEE
Q 025973           12 ISPNNTI-YINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDV-ASATAAVEKMQGFPFYDKPMR   89 (245)
Q Consensus        12 ~~~~~~l-~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~-~~A~~a~~~l~~~~~~g~~i~   89 (245)
                      .+.++.+ ||+|||..+|+++    |.++|+.||.|..|.+.+.   +|||||.|.+. ++|..|+..+++..+.++.+.
T Consensus         7 ~~~g~~~~fvgnL~~~~tee~----Lk~~F~~fG~V~~v~i~~~---kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~   79 (113)
T d1owxa_           7 EKIGCLLKFSGDLDDQTCRED----LHILFSNHGEIKWIDFVRG---AKEGIILFKEKAKEALGKAKDANNGNLQLRNKE   79 (113)
T ss_dssp             CCCCCEEEEEESCCSSCCHHH----HHHHTCSSCCEEEEECCTT---CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             CCCCCeEEEECCCCCCCCHHH----HHHHHHhcCChheEEEecC---CceEEEEecCcHHHHHHHHHHhcCCceecCceE
Confidence            3444555 9999999999999    6699999999999998854   69999999985 789999999999888877666


Q ss_pred             EEEccc
Q 025973           90 IQYAKT   95 (245)
Q Consensus        90 v~~~~~   95 (245)
                      |.+...
T Consensus        80 v~~~~~   85 (113)
T d1owxa_          80 VTWEVL   85 (113)
T ss_dssp             EEEEEC
T ss_pred             EEEeec
Confidence            666543

>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=99.50  E-value=6.8e-14  Score=93.91  Aligned_cols=84  Identities=14%  Similarity=0.356  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCC--Cccc----ChHHHHHHHHHhhcccCCeEEEEecCC-----CCeeeEEEEEecCHHHHHHHHHHHcCC
Q 025973           13 SPNNTIYINNL--NEKV----KIDQLKQSLHAVFKQFGTILEILAFKT-----LKHKGQAWLVFKDVASATAAVEKMQGF   81 (245)
Q Consensus        13 ~~~~~l~V~nL--p~~~----~~~~l~~~l~~~F~~~G~v~~i~~~~~-----~~~kg~afV~F~~~~~A~~a~~~l~~~   81 (245)
                      +|+++|.|.||  |.+.    ..++|++-|+..|++||.|.+|.+.++     ....|++||+|.+.++|.+|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            68999999999  4433    234566668899999999999987652     234589999999999999999999999


Q ss_pred             ccCCceEEEEEcccc
Q 025973           82 PFYDKPMRIQYAKTK   96 (245)
Q Consensus        82 ~~~g~~i~v~~~~~~   96 (245)
                      .+.||.|.|.|+...
T Consensus        82 ~f~gR~v~v~f~~~~   96 (104)
T d1o0pa_          82 KFANRVVVTKYCDPD   96 (104)
T ss_dssp             CSSSSCCEEEEECHH
T ss_pred             EECCeEEEEEEcCHH
Confidence            999999999998643

>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=99.48  E-value=5.7e-14  Score=89.49  Aligned_cols=74  Identities=15%  Similarity=0.180  Sum_probs=62.8

Q ss_pred             CCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCc-eEEEEEc
Q 025973           15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK-PMRIQYA   93 (245)
Q Consensus        15 ~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~-~i~v~~~   93 (245)
                      ++.|+|.|+|++.+++.    | ++|++||.|.++...+   .+|||||+|.+.++|.+|++ +||..+.|+ .|.|.++
T Consensus         4 ~~wV~V~G~p~~~~~~i----l-~~F~~~G~I~~~~~~~---~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           4 DTWVTVFGFPQASASYI----L-LQFAQYGNILKHVMSN---TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGEEEEECCCGGGHHHH----H-HHHHTTSCEEEEEECS---SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             ccEEEEECCChHHHHHH----H-HHHHhhhhhheEEecC---CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            46799999999998654    4 5799999999998754   46999999999999999997 999999998 4678887


Q ss_pred             cccc
Q 025973           94 KTKS   97 (245)
Q Consensus        94 ~~~~   97 (245)
                      ..+.
T Consensus        75 ~~k~   78 (81)
T d1wwha1          75 IDKN   78 (81)
T ss_dssp             CCHH
T ss_pred             CChh
Confidence            6553

>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=99.48  E-value=7e-14  Score=89.08  Aligned_cols=71  Identities=15%  Similarity=0.242  Sum_probs=61.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeE-EEEEEec
Q 025973          171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQ-LLITYAK  244 (245)
Q Consensus       171 ~~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~-i~v~~ak  244 (245)
                      .+-|+|.++|+..+++.| .+|+.||.|.++++.+++ |||||+|.++++|.+|++ +||..|+|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~-~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTG-NWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSS-SEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCC-CEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            356999999999887655 579999999999987665 899999999999999996 9999999974 6787653

>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=98.58  E-value=2.6e-07  Score=54.67  Aligned_cols=70  Identities=16%  Similarity=0.240  Sum_probs=60.8

Q ss_pred             cccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCccCCceEEEEEcc
Q 025973           25 EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAK   94 (245)
Q Consensus        25 ~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~~i~v~~~~   94 (245)
                      +..++++|++.|.+.|.++|.|.++.+..-....-.|-|...+.++|..|+..||...+++++|.|.++.
T Consensus         2 ~~L~~kelqq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           2 YRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CcCCHHHHHHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4568899999999999999999998776422223469999999999999999999999999999999975

>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=98.40  E-value=8.6e-07  Score=52.37  Aligned_cols=60  Identities=27%  Similarity=0.308  Sum_probs=53.0

Q ss_pred             HHHHHHHhccCCCeeEEEEecCC--CeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q 025973          185 PMALQMFFSQFPGFKEVRMVEAK--PGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK  244 (245)
Q Consensus       185 ~~~l~~~f~~~g~v~~v~l~~~~--~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~ak  244 (245)
                      .+.|.+.|+++|.|.++.+.+-.  .-.|-|...+..+|..|+..||-..|++|+|.|+|+.
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            34567889999999999998744  3479999999999999999999999999999999973

>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=98.19  E-value=2.1e-06  Score=53.35  Aligned_cols=80  Identities=19%  Similarity=0.286  Sum_probs=66.5

Q ss_pred             cCCCCCCCCeEEEcCCCcc-----cChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHcCCc
Q 025973            8 QGNEISPNNTIYINNLNEK-----VKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFP   82 (245)
Q Consensus         8 ~~~~~~~~~~l~V~nLp~~-----~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~~~~   82 (245)
                      +.-..+|.-+|.|.=...+     .-++.|+..|.+.|..||.|.-|++..     +..+|.|.+-++|-+|+. ++|..
T Consensus         8 ~~~qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~-----d~mwVTF~dG~SAL~al~-l~g~~   81 (95)
T d1ufwa_           8 SSFQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ-----GQMLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             SCCCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET-----TEEEEECSCSHHHHHHHH-GGGSE
T ss_pred             ccccCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeC-----CeEEEEECCcHHHHHHhc-cCCeE
Confidence            4456788888888655532     345678888999999999999998875     469999999999999999 99999


Q ss_pred             cCCceEEEEEc
Q 025973           83 FYDKPMRIQYA   93 (245)
Q Consensus        83 ~~g~~i~v~~~   93 (245)
                      +.|+.|+|...
T Consensus        82 v~G~~l~It~~   92 (95)
T d1ufwa_          82 VKGRAVKISGP   92 (95)
T ss_dssp             ETTEEEEEECC
T ss_pred             EcceEEEEecC
Confidence            99999998653

>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=97.97  E-value=2.9e-05  Score=48.94  Aligned_cols=63  Identities=10%  Similarity=0.193  Sum_probs=57.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCC-------CeEEEEEeCCHHHHHHHHHHhCCCeeC
Q 025973          172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-------PGIAFVEYGDEMQATVAMQSLQSLKIG  234 (245)
Q Consensus       172 ~~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~-------~g~afv~f~~~~~A~~A~~~l~g~~~~  234 (245)
                      +.|.|+.||+.+|++++.+.++..|.+.+....+++       ..-|+|.|.+.++.....+.++|+.|-
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            359999999999999999999999999999888864       357999999999999999999998885

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.80  E-value=3.9e-05  Score=47.57  Aligned_cols=53  Identities=15%  Similarity=0.253  Sum_probs=47.7

Q ss_pred             HHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhCCCeeCCeEEEEEE
Q 025973          186 MALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITY  242 (245)
Q Consensus       186 ~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  242 (245)
                      .+|.+.|..||+|.-|+++.+   ...|+|.+-+.|..|+. ++|..+.|+.|.|+.
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d---~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~   91 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG---QMLVTFADSHSALSVLD-VDGMKVKGRAVKISG   91 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT---EEEEECSCSHHHHHHHH-GGGSEETTEEEEEEC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC---eEEEEECCcHHHHHHhc-cCCeEEcceEEEEec
Confidence            468889999999999999865   58899999999999997 899999999999974

>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=97.78  E-value=4.9e-05  Score=47.86  Aligned_cols=75  Identities=17%  Similarity=0.329  Sum_probs=56.9

Q ss_pred             CeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCC----C-CeeeEEEEEecCHHHHHHHHHHHcCCccCCc----
Q 025973           16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKT----L-KHKGQAWLVFKDVASATAAVEKMQGFPFYDK----   86 (245)
Q Consensus        16 ~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~----~-~~kg~afV~F~~~~~A~~a~~~l~~~~~~g~----   86 (245)
                      ++|.|+.||+..|+++    +.+.++..|.+........    + ..-..|||.|.+.++........+|..|.+.    
T Consensus         2 tKvVvRrLPP~Lte~~----F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~   77 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQ----LQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQE   77 (91)
T ss_dssp             CEEEEEEECTTCCHHH----HHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCE
T ss_pred             ceEEEecCCCCCCHHH----HHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCE
Confidence            5799999999999999    6677788888877644331    1 1235799999999999999999999888632    


Q ss_pred             -eEEEEEcc
Q 025973           87 -PMRIQYAK   94 (245)
Q Consensus        87 -~i~v~~~~   94 (245)
                       .-.|++|.
T Consensus        78 ~~a~VE~AP   86 (91)
T d1uw4a_          78 YPAIVEFAP   86 (91)
T ss_dssp             EECEEEECS
T ss_pred             eeeEEEEcC
Confidence             33555553

>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=96.22  E-value=0.0098  Score=37.16  Aligned_cols=57  Identities=18%  Similarity=0.233  Sum_probs=47.1

Q ss_pred             CCCeEEEcCCCcccChHHHHHHHHHhhcccCCeEEEEecCCCCeeeEEEEEecCHHHHHHHHHHHc
Q 025973           14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQ   79 (245)
Q Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~l~~~F~~~G~v~~i~~~~~~~~kg~afV~F~~~~~A~~a~~~l~   79 (245)
                      ...-||.-..|..+...|    |.++|+.||.|.-..+..+     .|||.-.+.++|..++..+.
T Consensus        14 ~RdHVf~~tFP~~Wk~~d----I~~lFSpfG~V~VswIddT-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSD----LYQLFSAFGNIQISWIDDT-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHH----HHHHHTTTCSCCCEEEETT-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhH----HHHHhcCCCceEEEEecCc-----eEEEEecCHHHHHHHHHHhc
Confidence            345577778999999999    7799999999966666544     79999999999999988554

>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=96.12  E-value=0.025  Score=35.27  Aligned_cols=54  Identities=19%  Similarity=0.329  Sum_probs=42.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecCCCeEEEEEeCCHHHHHHHHHHhC
Q 025973          173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQ  229 (245)
Q Consensus       173 ~l~v~nl~~~~t~~~l~~~f~~~g~v~~v~l~~~~~g~afv~f~~~~~A~~A~~~l~  229 (245)
                      -+|.-..|......||.++|++||.|. |.-+.+  .-|||...+.++|..++..+.
T Consensus        17 HVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd--TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          17 HVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD--TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET--TEEEEECSCHHHHHHHHHHHH
T ss_pred             eeEEEeCCcccchhHHHHHhcCCCceE-EEEecC--ceEEEEecCHHHHHHHHHHhc
Confidence            377778999999999999999999862 222233  379999999999998887553