Citrus Sinensis ID: 007742

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-
Protein Sequence
MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccEEEccccccccHHHHHHHHHccccEEEEEEEEcccccccccEEEEEEcccccHHHHHHcccccccccEEEEccccHHHHHHcccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEcccccccccccEEEEEEccHHHHHHHHHHHcccEEEcccEEEEEEEcccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccEEEEccccccccccccHHHHHHHHHHHHHHHccccEEEEEEcccccccEEEEEccHHHHHHHHHHHcccccccEEEEEEEccHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEcEEccccccccccEEEEEcccHHHHHHHHHccccccccEEEEcccccccccccccccccccHHcccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEEcccccccEEEEEEEccHHHHHHHHHHccccccccEEEEEcccccHHHHHHHHHHHHHcccccccccEEEEEEcccccccHHHHHHHHHccccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHcccEEEcccEEEEEEEEcccHHHHHHHHHcccccHHHcHHHHccccccccEEEEccccccccccccccccccccHHHHHHHHHccHHccccccccccccccccccHHHccccccHHHEEEHccccccccccccccHHHHHHHHHHHcccccEEEEEEccccccEEEEEcccHHHHHHHHHHHcccEEcccEEEEEEcccHHHHHHccc
Coil and Loop (DISEMBL)
MEFDEYEYLEKTVEEQRQqkqdddssskkKAKREEKSERsyrkredseeeeEEEKsrsgkrsrrdedeengsrrdrdrdrdrdkerhrrdrdrdrdrgrerereTERDRERSRERREKEKERERRERRDREKERererdgerrsssrsrrsssqsrrsssrsrreRERESERERELELERERERERELRERERDLEMRESRrykekkevvepeadperdqrTVFAYQMPLKATERDVYEFFSkagkvrdvrLIMDrnsrrskgvgyiefydvMSVPMAIALSGqlllgqpvmvkpseaEKNLVQsntsaggtatgpygaidrkLYVGNLHFNMTETQLRKlfepfgpvelvqlpldietgqckgfgfVQFAQLEHAKAAQSALNGKLEIVGRTLkvssvtdhvgtqdtaaksadfddddggglaLNAQSRALLMQKLDRTGIATSIAgslgvapavngsavnqqaislpvvgqpavpvpavtapvipnmaaefigspseclllknmfdpametdpdfdleIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFmkpedyeakfks
Flexible Loop (DISEMBL)
MEFDEYEYLEKTveeqrqqkqdddssskkkakreeksersyrkredseeeeeeeksrsgkrsrrdedeengsrrdrdrdrdrdkerhrrdrdrdrdrgrerereterdrersrerrekekererrerrdrekerererdgerrsssrsrrsssqsrrsssrsrrereresererelelererererelrererdlemresrrykekkevvepeadperdqrtVFAYQmplkaterdVYEFFskagkvrdvrlimdrnsrrskgvgyIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVqsntsaggtatgpyGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDtaaksadfddddGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS
Low Complexity Region (SEG)
MEFDEYEYLEKTVeeqrqqkqdddssskkkakreeksersyrkredseeeeeeeksrsgkrsrrdedeengsrrdrdrdrdrdkerhrrdrdrdrdrgrerereterdrersrerrekekererrerrdrekerererdgerrsssrsrrsssqsrrsssrsrrereresererelelererererelrererdlemresrrYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAdfddddgggLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLpvvgqpavpvpavtapvipNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS
Disordered region (IsUnstruct)
******************************************************************************************************************************************************************************************************************************VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMV********************TGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT*****************************RALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMK**********
Disordered Region (DISOPRED)
*EFDEYE*********************************************************************************************************************************************************************************************************************RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK****************************KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS******************************************************************************************************CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFK*
Disordered Region (DISEMBL)
*************************************************************************************************************************************************************************************************************************RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS
Disordered Region (DISPRO)
*EFDEYEYLEKTVE************************************************************************************************************************************RSRR*SSQSRRSSSRSRRERERESERERELELERERERERELRERER***********************ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQS*********GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMA*EFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDGERRSSSRSRRSSSQSRRSSSxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS
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	591	2.2.26 [Sep-21-2011]
Q5RC80	524	RNA-binding protein 39 OS	yes	no	0.622	0.702	0.427	8e-70
Q14498	530	RNA-binding protein 39 OS	no	no	0.617	0.688	0.428	2e-69
Q8VH51	530	RNA-binding protein 39 OS	yes	no	0.617	0.688	0.428	2e-69
O13845	603	RNA-binding protein rsd1	yes	no	0.597	0.585	0.361	2e-52
Q86U06	439	Probable RNA-binding prot	no	no	0.551	0.742	0.379	5e-48
Q2QKB3	591	Splicing factor U2af larg	N/A	no	0.296	0.296	0.288	3e-12
Q2QKB4	543	Splicing factor U2af larg	N/A	no	0.311	0.338	0.286	3e-12
Q8L716	589	Splicing factor U2af larg	no	no	0.296	0.297	0.293	1e-11
Q2R0Q1	574	Splicing factor U2af larg	no	no	0.311	0.320	0.281	4e-11
Q2QZL4	548	Splicing factor U2af larg	no	no	0.311	0.335	0.286	6e-11

>sp|Q5RC80|RBM39_PONAB RNA-binding protein 39 OS=Pongo abelii GN=RBM39 PE=2 SV=1

 Score =  265 bits (677), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 169/395 (42%), Positives = 229/395 (57%), Gaps = 27/395 (6%)

Query: 204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
           K+K  V EP     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct: 133 KDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRR 192

Query: 261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKN--LVQSNTSAGGTATGPYG 318
           SKG+ Y+EF DV SVP+AI L+GQ +LG P++V+ S+AEKN     +N    G+A GP  
Sbjct: 193 SKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQKGSA-GPM- 250

Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
               +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK 
Sbjct: 251 ----RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 306

Query: 379 AQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDG--GGLALNAQSRALLMQK 436
           A   LNG  E+ GR +KV  VT+     D ++ S+  D D+    G+ L    R  LM +
Sbjct: 307 ALEQLNG-FELAGRPMKVGHVTERT---DASSASSFLDSDELERTGIDLGTTGRLQLMAR 362

Query: 437 L-DRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIG 495
           L + TG        L + PA   +     +++   V      +   T       AA    
Sbjct: 363 LAEGTG--------LQIPPAAQQALQMSGSLAFGAVADLQTRLSQQTEASALAAAASVQP 414

Query: 496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFES 554
             ++C  L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S
Sbjct: 415 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPS 474

Query: 555 TEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
             AA +A  A+H RWFA ++I+A ++    Y   F
Sbjct: 475 IAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLF 509

Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1 (By similarity). May be involved in pre-mRNA splicing process.
Pongo abelii (taxid: 9601)

>sp|Q14498|RBM39_HUMAN RNA-binding protein 39 OS=Homo sapiens GN=RBM39 PE=1 SV=2

 Score =  264 bits (674), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 173/404 (42%), Positives = 233/404 (57%), Gaps = 39/404 (9%)

Query: 204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
           K+K  V EP     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct: 133 KDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRR 192

Query: 261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKN--LVQSNTSAGGTATGPYG 318
           SKG+ Y+EF DV SVP+AI L+GQ +LG P++V+ S+AEKN     +N    G+A GP  
Sbjct: 193 SKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQKGSA-GPM- 250

Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
               +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK 
Sbjct: 251 ----RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 306

Query: 379 AQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDG--GGLALNAQSRALLMQK 436
           A   LNG  E+ GR +KV  VT+     D ++ S+  D D+    G+ L    R  LM +
Sbjct: 307 ALEQLNG-FELAGRPMKVGHVTERT---DASSASSFLDSDELERTGIDLGTTGRLQLMAR 362

Query: 437 L-DRTGI--------ATSIAGSLGVAPAVNGSAVNQQAISLPV-VGQPAVPVPAVTAPVI 486
           L + TG+        A  ++GSL        S V    I L   + Q         A  +
Sbjct: 363 LAEGTGLQIPPAAQQALQMSGSLAFGAVAEFSFV----IDLQTRLSQQTEASALAAAASV 418

Query: 487 PNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA- 545
             +A       ++C  L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA 
Sbjct: 419 QPLA-------TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQ 471

Query: 546 GFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
           G VY++  S  AA +A  A+H RWFA ++I+A ++    Y   F
Sbjct: 472 GNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLF 515

Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1 (By similarity). May be involved in pre-mRNA splicing process.

Homo sapiens (taxid: 9606)

>sp|Q8VH51|RBM39_MOUSE RNA-binding protein 39 OS=Mus musculus GN=Rbm39 PE=1 SV=2

 Score =  264 bits (674), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 173/404 (42%), Positives = 233/404 (57%), Gaps = 39/404 (9%)

Query: 204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
           K+K  V EP     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct: 133 KDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRR 192

Query: 261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKN--LVQSNTSAGGTATGPYG 318
           SKG+ Y+EF DV SVP+AI L+GQ +LG P++V+ S+AEKN     +N    G+A GP  
Sbjct: 193 SKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQKGSA-GPM- 250

Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
               +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK 
Sbjct: 251 ----RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 306

Query: 379 AQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDG--GGLALNAQSRALLMQK 436
           A   LNG  E+ GR +KV  VT+     D ++ S+  D D+    G+ L    R  LM +
Sbjct: 307 ALEQLNG-FELAGRPMKVGHVTERT---DASSASSFLDSDELERTGIDLGTTGRLQLMAR 362

Query: 437 L-DRTGI--------ATSIAGSLGVAPAVNGSAVNQQAISLPV-VGQPAVPVPAVTAPVI 486
           L + TG+        A  ++GSL        S V    I L   + Q         A  +
Sbjct: 363 LAEGTGLQIPPAAQQALQMSGSLAFGAVAEFSFV----IDLQTRLSQQTEASALAAAASV 418

Query: 487 PNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA- 545
             +A       ++C  L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA 
Sbjct: 419 QPLA-------TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQ 471

Query: 546 GFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
           G VY++  S  AA +A  A+H RWFA ++I+A ++    Y   F
Sbjct: 472 GNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLF 515

Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1. May be involved in pre-mRNA splicing process.

Mus musculus (taxid: 10090)

>sp|O13845|RSD1_SCHPO RNA-binding protein rsd1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rsd1 PE=1 SV=2

 Score =  207 bits (526), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 138/382 (36%), Positives = 208/382 (54%), Gaps = 29/382 (7%)

Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
           ERD+RTVF  Q+  + T R++Y+FF +AG VRD +++ D+ S RSKGV Y+EF    SV 
Sbjct: 236 ERDRRTVFVSQLANRLTSRELYDFFEQAGPVRDAQIVRDKISGRSKGVAYVEFCHEDSVQ 295

Query: 277 MAIALSGQLLLGQPVMVKPSEAEKN---LVQSNTSAGGTATGPYGAIDRKLYVGNLHFNM 333
            AIALSG+ LLG PV+V+ +EAEKN      +  +   +A  P+     +L V N+HFN+
Sbjct: 296 AAIALSGKRLLGLPVIVQLTEAEKNRKAREAAELARAASAEIPF----HRLCVSNIHFNL 351

Query: 334 TETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRT 393
           T+  ++ +FEPFG +E V L  D +  + KGFG++Q+     A+ A   +NG  ++ GR 
Sbjct: 352 TDEDVKAIFEPFGDIEFVHLQRD-DQNRSKGFGYIQYRNPISARNALEKMNG-FDLAGRN 409

Query: 394 LKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVA 453
           ++V    D   T+ T++    FD+       L  Q R+   Q   R G  +S   S    
Sbjct: 410 MRVCLGNDKFTTETTSSMLKRFDE------TLARQERS---QPSQRNG-GSSTYESQDYR 459

Query: 454 PAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSP-----SECLLLKNMFD 508
            A   S   ++  S P+     +   A +  +  N  ++ +  P     S C LL+NMF+
Sbjct: 460 EAAPLSPTEEE--SRPITRDELMKKLARSEDISDN--SKLVSEPEPPIRSRCALLENMFN 515

Query: 509 PAMETDPDFDLEIQGDVEEECS-KYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHM 567
           PA ET P++  E++ DV+EEC  KYG+V HI V     G ++++FE+ + A  A   +H 
Sbjct: 516 PAEETSPNWVQELEQDVKEECDEKYGKVVHIAVVPNELGQIFVKFENADFAEKAITGLHQ 575

Query: 568 RWFARRLISAIFMKPEDYEAKF 589
           RWF  R I A  +   DY  KF
Sbjct: 576 RWFGGRTIKASILPETDYYFKF 597

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

>sp|Q86U06|RBM23_HUMAN Probable RNA-binding protein 23 OS=Homo sapiens GN=RBM23 PE=1 SV=1

 Score =  192 bits (489), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 138/364 (37%), Positives = 192/364 (52%), Gaps = 38/364 (10%)

Query: 161 RSRRERERESERERELELERERERERELRERERDLEMRESRRY--------KEKKEVVEP 212
           R  R R R  +R    E  R R+  RE R   R   +    RY        +EK  V EP
Sbjct: 96  RQCRHRSRSWDRRHGSE-SRSRDHRREDRVHYRSPPLATGYRYGHSKSPHFREKSPVREP 154

Query: 213 --EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
                PE RD RTVF  Q+  +   RD+ +FFS  GKVRDVR+I DRNSRRSKG+ Y+EF
Sbjct: 155 VDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 214

Query: 270 YDVMSVPMAIALSGQLLLGQPVMVKPSEAEKN--LVQSNTSAGGTATGPYGAIDRKLYVG 327
            ++ SVP+AI L+GQ LLG P++V+ S+AEKN     +N    G   GP      +LYVG
Sbjct: 215 CEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLAAMANNLQKGNG-GPM-----RLYVG 268

Query: 328 NLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKL 387
           +LHFN+TE  LR +FEPFG ++ + L  D +TG+ KG+GF+ F+  E A+ A   LNG  
Sbjct: 269 SLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNG-F 327

Query: 388 EIVGRTLKVSSVTDHV-GTQDTAAKSADFDDDDGGGLALNAQSRALLMQKL-DRTGIATS 445
           E+ GR ++V  VT+ + G  D      D + D G     +A  R  LM KL +  GI   
Sbjct: 328 ELAGRPMRVGHVTERLDGGTDITFPDGDQELDLG-----SAGGRFQLMAKLAEGAGIQL- 381

Query: 446 IAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKN 505
                   P+   +A    A +  +    AVP+ A+    +  ++   +   S+C  L +
Sbjct: 382 --------PSTAAAAAAAAAQAAALQLNGAVPLGALNPAALTALSPA-LNLASQCFQLSS 432

Query: 506 MFDP 509
           +F P
Sbjct: 433 LFTP 436

Probable RNA-binding protein. May be involved in pre-mRNA splicing process.

Homo sapiens (taxid: 9606)

>sp|Q2QKB3|U2A2A_WHEAT Splicing factor U2af large subunit A OS=Triticum aestivum GN=U2AF65A PE=2 SV=1

 Score = 74.3 bits (181), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 58/201 (28%), Positives = 90/201 (44%), Gaps = 26/201 (12%)

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSK-----AGKVRDV-RLIMDRNSRRSKGVGYIEFYD 271
           R  R V+   +P  A E+ V  FF++      G    +   +++      K   ++E   
Sbjct: 269 RHARRVYVGGLPPIANEQTVAVFFNQVMAAIGGNTFALGHAVVNVYINHDKKFAFVEMRS 328

Query: 272 VMSVPMAIALSGQLLLGQPVMVK--------------PSEAEKNLVQSNTSAGGTATGPY 317
           V     A+AL G +  G PV V+              PS+   NL   N +A G   G  
Sbjct: 329 VEEASNAMALDGIMFEGAPVKVRRPTDYNPSQAAALGPSQPNPNL---NLAAVGLTPGAG 385

Query: 318 GAIDR--KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH 375
           G ++   +++VG L +  TE Q+R+L E FGP+    +  D ETG  KG+ F  +     
Sbjct: 386 GGLEGPDRIFVGGLPYYFTEAQVRELLETFGPLRGFDIVKDKETGNSKGYAFCLYKDGTV 445

Query: 376 AKAAQSALNGKLEIVGRTLKV 396
              A +ALNG +++  RTL V
Sbjct: 446 TDIACAALNG-IQLGDRTLTV 465

Necessary for the splicing of pre-mRNA.

Triticum aestivum (taxid: 4565)

>sp|Q2QKB4|U2A2B_WHEAT Splicing factor U2af large subunit B OS=Triticum aestivum GN=U2AF65B PE=2 SV=1

 Score = 73.9 bits (180), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/213 (28%), Positives = 95/213 (44%), Gaps = 29/213 (13%)

Query: 209 VVEPEA---DPERDQRTVFAYQMPLKATERDVYEFFSK------AGKVRDVRLIMDRNSR 259
           V++P+A      R  R V+   +P  A E+ V  +F++               +++    
Sbjct: 192 VMQPQAMTQQATRHARRVYVGGLPPSANEQSVAIYFNQVMAAIGGNTAGPGDAVLNVYIN 251

Query: 260 RSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK--------------PSEAEKNLVQS 305
             K   ++E   V     A+AL G L  G PV V+              PS+   NL   
Sbjct: 252 HDKKFAFVEMRSVEEASNAMALDGILFEGAPVKVRRPTDYNPSLAAALGPSQPSSNL--- 308

Query: 306 NTSAGGTATGPYGAIDR--KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 363
           N +A G   G  G ++   +++VG L +  TE Q+R+L E FGP+    L  D ETG  K
Sbjct: 309 NLAAVGLTPGSAGGLEGPDRIFVGGLPYYFTEAQVRELLESFGPLRGFDLVKDRETGNSK 368

Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           G+ F  +  L     A +ALNG +++  +TL V
Sbjct: 369 GYAFCVYQDLNVTDIACAALNG-IKMGDKTLTV 400

Necessary for the splicing of pre-mRNA.

Triticum aestivum (taxid: 4565)

>sp|Q8L716|U2A2B_ARATH Splicing factor U2af large subunit B OS=Arabidopsis thaliana GN=U2AF65B PE=2 SV=2

 Score = 71.6 bits (174), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 90/201 (44%), Gaps = 26/201 (12%)

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSK------AGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           R  R V+   +P  A E+ V  FFS+               +++      K   ++E   
Sbjct: 252 RHARRVYVGGLPPTANEQSVSTFFSQVMSAIGGNTAGPGDAVVNVYINHEKKFAFVEMRS 311

Query: 272 VMSVPMAIALSGQLLLGQPVMVK--------------PSEAEKNLVQSNTSAGGTATGPY 317
           V     A+AL G +L G PV V+              PS+   NL   N  A G ++G  
Sbjct: 312 VEEASNAMALDGIILEGVPVKVRRPTDYNPSLAATLGPSQPNPNL---NLGAVGLSSGST 368

Query: 318 GAIDR--KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH 375
           G ++   +++VG L +  TE Q+R+L E FGP+    L  D ETG  KG+ F  +     
Sbjct: 369 GGLEGPDRIFVGGLPYYFTEVQIRELLESFGPLRGFNLVKDRETGNSKGYAFCVYQDPSV 428

Query: 376 AKAAQSALNGKLEIVGRTLKV 396
              A +ALNG +++  +TL V
Sbjct: 429 TDIACAALNG-IKMGDKTLTV 448

Necessary for the splicing of pre-mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|Q2R0Q1|U2A2A_ORYSJ Splicing factor U2af large subunit A OS=Oryza sativa subsp. japonica GN=U2AF65A PE=2 SV=2

 Score = 70.5 bits (171), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 60/213 (28%), Positives = 94/213 (44%), Gaps = 29/213 (13%)

Query: 209 VVEPEA---DPERDQRTVFAYQMPLKATERDVYEFFSK------AGKVRDVRLIMDRNSR 259
           V++P+A      R  R V+   +P  A E  V  +F++               +++    
Sbjct: 223 VIQPQAMTQQATRHARRVYVGGLPPTANEHTVAVYFNQVMAAVGGNTAGPGDAVLNVYIN 282

Query: 260 RSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK--------------PSEAEKNLVQS 305
             K   ++E   V     A+AL G +  G PV V+              PS+   NL   
Sbjct: 283 HDKKFAFVEMRSVEEASNAMALDGIMFEGAPVKVRRPTDYNPSLAAALGPSQPNPNL--- 339

Query: 306 NTSAGGTATGPYGAIDR--KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 363
           N +A G   G  G ++   +++VG L +  TE Q+R+L E FGP+    L  D ETG  K
Sbjct: 340 NLAAVGLTPGSAGGLEGPDRIFVGGLPYYFTEAQVRELLESFGPLRGFDLVKDRETGNSK 399

Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           G+ F  +  L     A +ALNG +++  +TL V
Sbjct: 400 GYAFCVYQDLNVTDIACAALNG-IKMGDKTLTV 431

Necessary for the splicing of pre-mRNA.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q2QZL4|U2A2B_ORYSJ Splicing factor U2af large subunit B OS=Oryza sativa subsp. japonica GN=U2AF65B PE=2 SV=2

 Score = 69.7 bits (169), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 61/213 (28%), Positives = 96/213 (45%), Gaps = 29/213 (13%)

Query: 209 VVEPEADPE---RDQRTVFAYQMPLKATERDVYEFFSK------AGKVRDVRLIMDRNSR 259
           V++P+A  +   R  R V+   +P  A E+ V  +F++               +++    
Sbjct: 199 VIQPQAMTQQATRHARRVYVGGLPPTANEQSVAIYFNQVMAAIGGNTAGPGDAVLNVYIN 258

Query: 260 RSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK--------------PSEAEKNLVQS 305
             K   ++E   V     A+AL G L  G PV V+              PS+   NL   
Sbjct: 259 HDKKFAFVEMRSVEEASNAMALDGILFEGAPVKVRRPTDYNPSLAAALGPSQPSPNL--- 315

Query: 306 NTSAGGTATGPYGAIDR--KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 363
           N +A G   G  G ++   +++VG L +  TE Q+R+L E FGP+    L  D ETG  K
Sbjct: 316 NLAAVGLTPGSAGGLEGPDRIFVGGLPYYFTEAQVRELLESFGPLRGFDLVKDRETGNSK 375

Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           G+ F  +  L     A +ALNG +++  +TL V
Sbjct: 376 GYAFCVYQDLNVTDIACAALNG-IKMGDKTLTV 407

Necessary for the splicing of pre-mRNA.

Oryza sativa subsp. japonica (taxid: 39947)

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	591
449448446	598	PREDICTED: RNA-binding protein 39-like [	0.969	0.958	0.649	0.0
449497695	598	PREDICTED: RNA-binding protein 39-like [	0.969	0.958	0.649	0.0
357519763	567	RNA-binding protein [Medicago truncatula	0.937	0.977	0.648	0.0
297811089	520	predicted protein [Arabidopsis lyrata su	0.871	0.990	0.627	0.0
296082546	504	unnamed protein product [Vitis vinifera]	0.683	0.801	0.765	1e-179
28059803	527	splicing factor-like protein [Arabidopsi	0.883	0.990	0.624	1e-178
356512787	554	PREDICTED: RNA-binding protein 39-like [	0.920	0.981	0.636	1e-178
18416114	527	RNA-binding protein 39 [Arabidopsis thal	0.881	0.988	0.623	1e-177
147856399	461	hypothetical protein VITISV_002664 [Viti	0.764	0.980	0.706	1e-175
9758966	604	splicing factor-like protein [Arabidopsi	0.862	0.844	0.624	1e-173

>gi|449448446|ref|XP_004141977.1| PREDICTED: RNA-binding protein 39-like [Cucumis sativus]

 Score =  690 bits (1780), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/611 (64%), Positives = 465/611 (76%), Gaps = 38/611 (6%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEE------EEEEE 54
           M+FDEY+YLEK VEEQ     DD  + K K    E++E+S RKRE  EE      E+EE 
Sbjct: 1   MDFDEYDYLEKAVEEQ-----DDRETKKPKRSDSERNEKSTRKREVDEEAGSGGREDEEV 55

Query: 55  KSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRE 114
           K    KRSR   + ENG + DRD    R ++RHRRDR+ + D G+ER++E  R RER   
Sbjct: 56  KV---KRSR--SEHENG-KEDRDHS-GRARDRHRRDREEETDGGKERDKERNRTRERGSS 108

Query: 115 RR---------------EKEKERER-RERRDREKERERERDGERRSSSRSRRSSSQSRRS 158
            +                KEKERER ++R+D+E++RER ++ +R      R    +  + 
Sbjct: 109 EKERERDRDREERDRDRHKEKERERDKDRKDKERDRERHKEKDRERDKDRRDKEREREKE 168

Query: 159 SSRSRRERERESERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPER 218
             + R  R+RE       E    R R R +RERER++++RESRR KEKK+  EPEADPER
Sbjct: 169 KEKERERRDRERREREREEERSRRSRSRSVREREREVDVRESRRMKEKKDTTEPEADPER 228

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
           DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGY+EFYD MSVPMA
Sbjct: 229 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYVEFYDAMSVPMA 288

Query: 279 IALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQL 338
           IALSGQLLLGQPVMVKPSEAEKNLVQSNT+ G +  GPYGA+DRKLYVGNLHFNMTET L
Sbjct: 289 IALSGQLLLGQPVMVKPSEAEKNLVQSNTT-GASGAGPYGAVDRKLYVGNLHFNMTETHL 347

Query: 339 RKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS 398
           R++FE FGPVELVQLPLD+E+G CKGFGFVQFA LEHAKAAQS LNGKLEI GRT+KVSS
Sbjct: 348 REIFEAFGPVELVQLPLDLESGHCKGFGFVQFAHLEHAKAAQS-LNGKLEIAGRTIKVSS 406

Query: 399 VTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNG 458
           VTDH+G Q++ AKS D DDD+GGGLALNAQSRALLMQKLDRTGIATSIAGSLG AP +NG
Sbjct: 407 VTDHIGAQESVAKSNDLDDDEGGGLALNAQSRALLMQKLDRTGIATSIAGSLG-APVLNG 465

Query: 459 SAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFD 518
           SA NQ++ SLPV GQ AV  P + A   P +  + +GSPSECLLLKNMFDP+ ET PDFD
Sbjct: 466 SAPNQRSTSLPVNGQAAVAAPVLPANFTPPV-LQSVGSPSECLLLKNMFDPSTETAPDFD 524

Query: 519 LEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAI 578
           +EI+ DVEEECSKYGRVKHIYVDK SAG VYL++++ EAA +AQRAMH+RWFA R IS +
Sbjct: 525 MEIKEDVEEECSKYGRVKHIYVDKNSAGCVYLQYDTVEAAINAQRAMHLRWFAGRQISVL 584

Query: 579 FMKPEDYEAKF 589
           FM+P+ YEAKF
Sbjct: 585 FMQPQVYEAKF 595

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449497695|ref|XP_004160482.1| PREDICTED: RNA-binding protein 39-like [Cucumis sativus]

 Score =  688 bits (1776), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/611 (64%), Positives = 464/611 (75%), Gaps = 38/611 (6%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEE------EEEEE 54
           M+FDEY+YLEK VEEQ     DD  + K K    E++E+S RKRE  EE      E+EE 
Sbjct: 1   MDFDEYDYLEKAVEEQ-----DDRETKKPKRSDSERNEKSTRKREVDEEAGSGGREDEEV 55

Query: 55  KSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRE 114
           K    KRSR   + ENG + DRD    R ++RHRRDR+ + D G+ER++E  R RER   
Sbjct: 56  KV---KRSR--SEHENG-KEDRDHS-GRARDRHRRDREEETDGGKERDKERNRTRERGSS 108

Query: 115 RR---------------EKEKERER-RERRDREKERERERDGERRSSSRSRRSSSQSRRS 158
            +                KEKERER ++R+D+E++RER ++ +R      R    +  + 
Sbjct: 109 EKERERDRDREERDRDRHKEKERERDKDRKDKERDRERHKEKDRERDKDRRDKEREREKE 168

Query: 159 SSRSRRERERESERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPER 218
             + R  R+RE       E    R R R +RERER++++RESRR KEKK   EPEADPER
Sbjct: 169 KEKERERRDRERREREREEERSRRSRSRSVREREREVDVRESRRMKEKKGTTEPEADPER 228

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
           DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGY+EFYD MSVPMA
Sbjct: 229 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYVEFYDAMSVPMA 288

Query: 279 IALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQL 338
           IALSGQLLLGQPVMVKPSEAEKNLVQSNT+ G +  GPYGA+DRKLYVGNLHFNMTET L
Sbjct: 289 IALSGQLLLGQPVMVKPSEAEKNLVQSNTT-GASGAGPYGAVDRKLYVGNLHFNMTETHL 347

Query: 339 RKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS 398
           R++FE FGPVELVQLPLD+E+G CKGFGFVQFA LEHAKAAQS LNGKLEI GRT+KVSS
Sbjct: 348 REIFEAFGPVELVQLPLDLESGHCKGFGFVQFAHLEHAKAAQS-LNGKLEIAGRTIKVSS 406

Query: 399 VTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNG 458
           VTDH+G Q++ AKS D DDD+GGGLALNAQSRALLMQKLDRTGIATSIAGSLG AP +NG
Sbjct: 407 VTDHIGAQESVAKSNDLDDDEGGGLALNAQSRALLMQKLDRTGIATSIAGSLG-APVLNG 465

Query: 459 SAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFD 518
           SA NQ++ SLPV GQ AV  P + A   P +  + +GSPSECLLLKNMFDP+ ET PDFD
Sbjct: 466 SAPNQRSTSLPVNGQAAVAAPVLPANFTPPV-LQSVGSPSECLLLKNMFDPSTETAPDFD 524

Query: 519 LEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAI 578
           +EI+ DVEEECSKYGRVKHIYVDK SAG VYL++++ EAA +AQRAMH+RWFA R IS +
Sbjct: 525 MEIKEDVEEECSKYGRVKHIYVDKNSAGCVYLQYDTVEAAINAQRAMHLRWFAGRQISVL 584

Query: 579 FMKPEDYEAKF 589
           FM+P+ YEAKF
Sbjct: 585 FMQPQVYEAKF 595

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357519763|ref|XP_003630170.1| RNA-binding protein [Medicago truncatula] gi|355524192|gb|AET04646.1| RNA-binding protein [Medicago truncatula]

 Score =  679 bits (1753), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 389/600 (64%), Positives = 447/600 (74%), Gaps = 46/600 (7%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREE-KSERSYRKREDSEEEEEEEKSRSG 59
           M+FDEYEYLEKTVEEQ    +D DSS KK     + KSER+YRK    ++ +  E  RS 
Sbjct: 1   MDFDEYEYLEKTVEEQ---PEDKDSSKKKNTDITDIKSERTYRKHGIDDDLDGGEDRRS- 56

Query: 60  KRSRRDEDEENGSRRDRDRDRDRDKERHR------RDRDRDRDRG-RERERETERDRERS 112
           KRSR  +DE NGS++DRDRDRDR+++R        R R+RD +RG RE+ERE + +R   
Sbjct: 57  KRSRGGDDE-NGSKKDRDRDRDRERDREHRERSSGRHRERDGERGSREKEREKDVERGGR 115

Query: 113 RERREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESER 172
            + R++E+E+ER  R    ++    RD ER      R    + R   S SR ER+R    
Sbjct: 116 DKERDREREKERERRDKEREKERERRDKEREKERAEREKEEKERPRRSMSRPERDR---- 171

Query: 173 ERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKA 232
                              ERD E R+ RR+++KKE VEPEADPERDQRTVFAYQMPLKA
Sbjct: 172 ------------------GERDFENRDGRRFRDKKENVEPEADPERDQRTVFAYQMPLKA 213

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD MSVPMAIALSGQLLLGQPVM
Sbjct: 214 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDAMSVPMAIALSGQLLLGQPVM 273

Query: 293 VKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQ 352
           VKPSEAEKNLVQSN S+G    GPYGA+DRKLYVGNLHFNMTE  LR++FEPFG +E+VQ
Sbjct: 274 VKPSEAEKNLVQSNASSGAAVVGPYGAVDRKLYVGNLHFNMTEANLREIFEPFGQIEVVQ 333

Query: 353 LPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKS 412
           LPLD+ETG CKGFGFVQFA LEHAKAAQS LNGKLEI GRT+KVSSVTDHVG+QDT  KS
Sbjct: 334 LPLDMETGHCKGFGFVQFAHLEHAKAAQS-LNGKLEIAGRTIKVSSVTDHVGSQDTTTKS 392

Query: 413 ADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVG 472
           ADFDDD+ GGL LNA SRALLMQ+L  T I TSI       P VNGS   QQA S+P  G
Sbjct: 393 ADFDDDE-GGLTLNAHSRALLMQRLAGTDITTSIG-----VPTVNGSVPVQQAFSMP-FG 445

Query: 473 QPAVPVPAVTAP--VIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECS 530
            P V +PA   P  V+P   AE +G PSECLLLKNMFDP+ E +PDFD++I+ DVEEECS
Sbjct: 446 NPGV-IPASVLPTQVMPTPVAEPVGIPSECLLLKNMFDPSTEIEPDFDIDIKEDVEEECS 504

Query: 531 KYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFK 590
           KYGRV HIYVDKRSAGFVYL+FE+ EA+++AQRAMHMRWFARRLI+AIFM+P  YEAKFK
Sbjct: 505 KYGRVMHIYVDKRSAGFVYLQFETVEASSAAQRAMHMRWFARRLITAIFMQPHLYEAKFK 564

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297811089|ref|XP_002873428.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297319265|gb|EFH49687.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  662 bits (1707), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/596 (62%), Positives = 423/596 (70%), Gaps = 81/596 (13%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEE----EEKS 56
           MEFDEYEYLEKTVEE       D S+  K++   EKSERSYRKRE  E  +E    EE+ 
Sbjct: 1   MEFDEYEYLEKTVEE------GDGSNKNKESSGNEKSERSYRKREGGERHDEEGGDEERG 54

Query: 57  RSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERR 116
            S  +  R + EENG R           ERHR  RD+DR+  R++ RE  RD+E  RER 
Sbjct: 55  SSRSKKSRGDGEENGKR-----------ERHRSSRDKDRE--RDKVREGSRDKESDRERS 101

Query: 117 EKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSR-SRRERERESERERE 175
            KE     R+R DR+K R+RER    R SS   R   + R    R SRR ++++ E    
Sbjct: 102 SKE-----RDRSDRDKTRDRERRERERRSSSRSRREEREREVVERGSRRHKDKKDE---- 152

Query: 176 LELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATER 235
                                               PEADPERDQRTVFAYQMPLKATER
Sbjct: 153 ------------------------------------PEADPERDQRTVFAYQMPLKATER 176

Query: 236 DVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP 295
           DVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQ  LGQPVMVKP
Sbjct: 177 DVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQPFLGQPVMVKP 236

Query: 296 SEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPL 355
           SEAEKNL QSNT+ GGT     G +DRKLYVGNLHFNMTE QLR++FE FGPVELVQLPL
Sbjct: 237 SEAEKNLAQSNTTPGGT-----GPVDRKLYVGNLHFNMTELQLRQIFEAFGPVELVQLPL 291

Query: 356 DIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADF 415
           D ETGQCKGFGF+QFAQLEH+KAAQ +LNGKLEI GRT+KVSSV+DH+GTQD A KSADF
Sbjct: 292 DPETGQCKGFGFIQFAQLEHSKAAQISLNGKLEIAGRTIKVSSVSDHIGTQDAAPKSADF 351

Query: 416 DDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPA 475
           DDDDGGGLALNAQSRALLMQKLDR+GIATSI GSLGV P +NG+A NQ  ++      P+
Sbjct: 352 DDDDGGGLALNAQSRALLMQKLDRSGIATSIVGSLGV-PGLNGAAFNQPGMN------PS 404

Query: 476 VPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRV 535
            P P +    IP+   E +G PSECLLLKNMFDPA ET+ DFD EI+ DV +ECSKYG V
Sbjct: 405 FPTPVLPTTAIPSFVNEPVGQPSECLLLKNMFDPATETERDFDFEIREDVADECSKYGEV 464

Query: 536 KHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS 591
            HIYVDK SAGFVYLRF+S EAA +AQRAMHMRWFA+++ISA FM P +YEAK K+
Sbjct: 465 NHIYVDKNSAGFVYLRFQSVEAAVAAQRAMHMRWFAQKMISATFMPPHEYEAKAKA 520

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296082546|emb|CBI21551.3| unnamed protein product [Vitis vinifera]

 Score =  635 bits (1637), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 329/430 (76%), Positives = 367/430 (85%), Gaps = 26/430 (6%)

Query: 165 ERERES-ERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTV 223
           +R+RE  ER RE+E                    RESRR+K+KKE VEPEADPERDQRTV
Sbjct: 94  DRDRELRERSREIE-------------------PRESRRFKDKKEAVEPEADPERDQRTV 134

Query: 224 FAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSG 283
           FAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD MSVPMAIALSG
Sbjct: 135 FAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDAMSVPMAIALSG 194

Query: 284 QLLLGQPVMVKPSEAEKNLVQSNTS---AGGTATGPYGAIDRKLYVGNLHFNMTETQLRK 340
            LL GQPVMVKPSEAEKNLVQSN S   +GG A GPYGA+DRKLYVGNLHFNMTE QLR+
Sbjct: 195 HLLHGQPVMVKPSEAEKNLVQSNASGAVSGGIA-GPYGAVDRKLYVGNLHFNMTELQLRQ 253

Query: 341 LFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT 400
           +FEPFG VELVQLPLD+ETGQCKGFGFVQFA+LEHAKAAQ+ LNGKL+I GR +KVSSVT
Sbjct: 254 IFEPFGRVELVQLPLDLETGQCKGFGFVQFAELEHAKAAQN-LNGKLDIAGRIIKVSSVT 312

Query: 401 DHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSA 460
           DH+G QD  AK+ADFDDDDGGGL+LNAQSRALLMQKLDRTGIA+SIAGSLGV P +NGSA
Sbjct: 313 DHIGVQDAGAKAADFDDDDGGGLSLNAQSRALLMQKLDRTGIASSIAGSLGV-PMLNGSA 371

Query: 461 VNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLE 520
            NQQAISL + GQ AV  PA+   V+ + A+E +G+P+ECLLLKNMFDPA E DPDFDL+
Sbjct: 372 PNQQAISLSINGQAAVSAPALPTQVVTSPASEPVGTPTECLLLKNMFDPATEIDPDFDLD 431

Query: 521 IQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFM 580
           I+ +V+EECS +GRVKHIYV+K SAG+VYLRFE+ EAA +AQRAMHMRWFARRLISAIF+
Sbjct: 432 IKEEVQEECSNFGRVKHIYVEKHSAGYVYLRFETVEAAVTAQRAMHMRWFARRLISAIFL 491

Query: 581 KPEDYEAKFK 590
           +P DYEAKFK
Sbjct: 492 QPRDYEAKFK 501

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|28059803|gb|AAO30095.1| splicing factor-like protein [Arabidopsis thaliana]

 Score =  632 bits (1629), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 372/596 (62%), Positives = 429/596 (71%), Gaps = 74/596 (12%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGK 60
           MEFDEYEYLEKTVEE         S+ KK+    E+SERSYRKRE  E + EE       
Sbjct: 1   MEFDEYEYLEKTVEEGA------GSNKKKEESGNERSERSYRKREGVERQGEEGGEEERV 54

Query: 61  RSR----RDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERR 116
            SR    R + EENG  +   RDR+R++ R  RD+DR+RD+ RE               R
Sbjct: 55  SSRSKKSRGDGEENGGGK---RDRERERHRSSRDKDRERDKVREGS-------------R 98

Query: 117 EKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESEREREL 176
           +KE +RER  +         ERD                     RS R++ R+ ER    
Sbjct: 99  DKESDRERSSK---------ERD---------------------RSDRDKPRDRERRER- 127

Query: 177 ELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERD 236
             E+         E+E ++  R SRR+++KK+  EPEADPERDQRTVFAYQMPLKATERD
Sbjct: 128 --EKRSSSRSRREEKEPEVVERGSRRHRDKKD--EPEADPERDQRTVFAYQMPLKATERD 183

Query: 237 VYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS 296
           VYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQL LGQPVMVKPS
Sbjct: 184 VYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLFLGQPVMVKPS 243

Query: 297 EAEKNLVQSN-TSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPL 355
           EAEKNL QSN T+ GGT     G  DRKLYVGNLHFNM+E QLR++FE FGPVELVQLPL
Sbjct: 244 EAEKNLAQSNSTTVGGT-----GPADRKLYVGNLHFNMSELQLRQIFEAFGPVELVQLPL 298

Query: 356 DIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADF 415
           D ETGQCKGFGF+QF QLEH+KAAQ ALNGKLEI GRT+KVSSV+DH+GTQD+A KSADF
Sbjct: 299 DPETGQCKGFGFIQFVQLEHSKAAQIALNGKLEIAGRTIKVSSVSDHIGTQDSAPKSADF 358

Query: 416 DDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPA 475
           DDDDGGGLALNAQSRA+LMQKLDR+GIATSI GSLGV P +NG+A NQ  ++      P+
Sbjct: 359 DDDDGGGLALNAQSRAMLMQKLDRSGIATSIVGSLGV-PGLNGAAFNQPGMN------PS 411

Query: 476 VPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRV 535
            P   +    IP+   E +G PSECLLLKNMFDPA ET+P+FDLEI+ DV +ECSKYG V
Sbjct: 412 FPTSVLPTTAIPSFVNEHVGLPSECLLLKNMFDPATETEPNFDLEIRDDVADECSKYGPV 471

Query: 536 KHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS 591
            HIYVDK SAGFVYLRF+S EAAA+AQRAMHMRWFA+++ISA FM P +YEAK K+
Sbjct: 472 NHIYVDKNSAGFVYLRFQSVEAAAAAQRAMHMRWFAQKMISATFMPPHEYEAKAKA 527

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512787|ref|XP_003525097.1| PREDICTED: RNA-binding protein 39-like [Glycine max]

 Score =  630 bits (1625), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 380/597 (63%), Positives = 443/597 (74%), Gaps = 53/597 (8%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGK 60
           M+FDEYEYLEKTVEE   +       SKKK    +KSERSYRK     +++ +   R  K
Sbjct: 1   MDFDEYEYLEKTVEEDIDKDS-----SKKKKDITDKSERSYRKPR-DVDDDLDADDRKSK 54

Query: 61  RSRRDEDEENGSRRDRDRDRDRDKE------RHRRDRDRDRDRGRERERETERDRERSRE 114
           RSR D DE  GS++DRDRDR+RD++      RHR +R+RD +R    +    RD+++ ++
Sbjct: 55  RSRGD-DENGGSKKDRDRDRERDRDRERSSGRHRSERERDGERKDRDKDRERRDKDKDKD 113

Query: 115 RREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERER 174
           R      R+R    DREKERER RD                        +++ERE E+E 
Sbjct: 114 RDRDRDRRDRDRDGDREKERER-RD------------------------KDKEREGEKEA 148

Query: 175 ELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATE 234
                R R R    R+RERD EMR+ RR++ KKE  EPEADPERDQRTVFAYQMPLKATE
Sbjct: 149 RERSTRSRSRSERDRDRERDFEMRDGRRFRVKKEASEPEADPERDQRTVFAYQMPLKATE 208

Query: 235 RDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK 294
           RDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD MSVPMAIALSGQLLLGQPVMVK
Sbjct: 209 RDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDAMSVPMAIALSGQLLLGQPVMVK 268

Query: 295 PSEAEKNLVQSN-TSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQL 353
           PSEAEKNLVQSN +       GPYGA+DRKLYVGNLHFNMTE+QLR++FEPFGPVE+VQL
Sbjct: 269 PSEAEKNLVQSNASGGAAGVAGPYGAVDRKLYVGNLHFNMTESQLREIFEPFGPVEVVQL 328

Query: 354 PLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSA 413
           PLD+ETG CKGFGFVQF  LEHAKAAQS LNGKLEI GRT+KVS VTDHV +QD  AKSA
Sbjct: 329 PLDLETGHCKGFGFVQFTHLEHAKAAQS-LNGKLEIAGRTIKVSCVTDHVASQDATAKSA 387

Query: 414 DFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQ 473
           D DDD+ GGL LNA SRALLMQ+L     A +   S+G+ P VNGS   QQAISLP +G 
Sbjct: 388 DLDDDE-GGLTLNAHSRALLMQRL-----AGADPASIGL-PVVNGSVPAQQAISLP-IGA 439

Query: 474 PAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYG 533
           P +P       V+PN   E +G+PSECLLLKNMFDP+ ET+PDFD++I+ DVEEECSKYG
Sbjct: 440 PVLP-----TLVMPNPVVEPVGNPSECLLLKNMFDPSTETEPDFDIDIKEDVEEECSKYG 494

Query: 534 RVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFK 590
           RVKHI+VDK+SAGFVYLRF++ EAA++AQ AMH+RWFARRLISA+FM+PE YEAKFK
Sbjct: 495 RVKHIFVDKKSAGFVYLRFDTVEAASAAQHAMHLRWFARRLISAVFMQPELYEAKFK 551

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18416114|ref|NP_568220.1| RNA-binding protein 39 [Arabidopsis thaliana] gi|15451046|gb|AAK96794.1| splicing factor-like protein [Arabidopsis thaliana] gi|332004077|gb|AED91460.1| RNA-binding protein 39 [Arabidopsis thaliana]

 Score =  629 bits (1622), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 372/597 (62%), Positives = 430/597 (72%), Gaps = 76/597 (12%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEK----- 55
           MEFDEYEYLEKTVEE         S+ KK+    E+SERSYRKRE  E + EE       
Sbjct: 1   MEFDEYEYLEKTVEEGA------GSNKKKEESGNERSERSYRKREGGERQGEEGGEEERV 54

Query: 56  SRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRER 115
           S   K+SR D +E  G +RDR+R+    + R  RD+DR+RD+ RE               
Sbjct: 55  SSRSKKSRGDGEENGGGKRDRERE----RHRSSRDKDRERDKVREGS------------- 97

Query: 116 REKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERE 175
           R+KE +RER  +         ERD                     RS R++ R+ ER   
Sbjct: 98  RDKESDRERSSK---------ERD---------------------RSDRDKPRDRERRER 127

Query: 176 LELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATER 235
              E+         E+E ++  R SRR+++KK+  EPEADPERDQRTVFAYQMPLKATER
Sbjct: 128 ---EKRSSSRSRREEKEPEVVERGSRRHRDKKD--EPEADPERDQRTVFAYQMPLKATER 182

Query: 236 DVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP 295
           DVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQL LGQPVMVKP
Sbjct: 183 DVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLFLGQPVMVKP 242

Query: 296 SEAEKNLVQSN-TSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLP 354
           SEAEKNL QSN T+ GGT     G  DRKLYVGNLHFNM+E QLR++FE FGPVELVQLP
Sbjct: 243 SEAEKNLAQSNSTTVGGT-----GPADRKLYVGNLHFNMSELQLRQIFEAFGPVELVQLP 297

Query: 355 LDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAD 414
           LD ETGQCKGFGF+QF QLEH+KAAQ ALNGKLEI GRT+KVSSV+DH+GTQD+A KSAD
Sbjct: 298 LDPETGQCKGFGFIQFVQLEHSKAAQIALNGKLEIAGRTIKVSSVSDHIGTQDSAPKSAD 357

Query: 415 FDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQP 474
           FDDDDGGGLALNAQSRA+LMQKLDR+GIATSI GSLGV P +NG+A NQ  ++      P
Sbjct: 358 FDDDDGGGLALNAQSRAMLMQKLDRSGIATSIVGSLGV-PGLNGAAFNQPGMN------P 410

Query: 475 AVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGR 534
           + P   +    IP+   E +G PSECLLLKNMFDPA ET+P+FDLEI+ DV +ECSKYG 
Sbjct: 411 SFPTSVLPTTAIPSFVNEHVGLPSECLLLKNMFDPATETEPNFDLEIRDDVADECSKYGP 470

Query: 535 VKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS 591
           V HIYVDK SAGFVYLRF+S EAAA+AQRAMHMRWFA+++ISA FM P +YEAK K+
Sbjct: 471 VNHIYVDKNSAGFVYLRFQSVEAAAAAQRAMHMRWFAQKMISATFMPPHEYEAKAKA 527

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147856399|emb|CAN82467.1| hypothetical protein VITISV_002664 [Vitis vinifera]

 Score =  621 bits (1602), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 335/474 (70%), Positives = 379/474 (79%), Gaps = 22/474 (4%)

Query: 121 ERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELER 180
           E E  E+   E E  +++DG  +S  RS R            R E  R   RER      
Sbjct: 5   EYEYLEKAVEEPENRKKKDGGEKSE-RSYRKREGGEEDDDDERGEGRRSKRRERH----- 58

Query: 181 ERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEF 240
           E++R R  R+ ER+    + RR+K+KKE VEPEADPERDQRTVFAYQMPLKATERDVYEF
Sbjct: 59  EKDRRRSGRDGERE---SKGRRFKDKKEAVEPEADPERDQRTVFAYQMPLKATERDVYEF 115

Query: 241 FSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEK 300
           FSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD MSVPMAIALSG LL GQPVMVKPSEAEK
Sbjct: 116 FSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDAMSVPMAIALSGHLLHGQPVMVKPSEAEK 175

Query: 301 NLVQSNTS---AGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDI 357
           NLVQSN S   +GG A GPYGA+DRKLYVGNLHFNMTE QLR++FEPFG VELVQLPLD+
Sbjct: 176 NLVQSNASGAVSGGIA-GPYGAVDRKLYVGNLHFNMTELQLRQIFEPFGRVELVQLPLDL 234

Query: 358 ETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDD 417
           ETGQCKGFGFVQFA+LEHAKAAQ+ LNGKL+I GR +KVSSVTDH+G QD  AK+ADFDD
Sbjct: 235 ETGQCKGFGFVQFAELEHAKAAQN-LNGKLDIAGRIIKVSSVTDHIGVQDAGAKAADFDD 293

Query: 418 DDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVP 477
           DDGGGL+LNAQSRALLMQKLDRT       GSLGV P +NGSA NQQAISL + GQ AV 
Sbjct: 294 DDGGGLSLNAQSRALLMQKLDRT-------GSLGV-PMLNGSAPNQQAISLSINGQAAVS 345

Query: 478 VPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKH 537
            PA+   V+ + A+E +G+P+ECLLLKNMFDPA E DPDFDL+I+ +V+EECS +GRVKH
Sbjct: 346 APALPTQVVTSPASEPVGTPTECLLLKNMFDPATEIDPDFDLDIKEEVQEECSNFGRVKH 405

Query: 538 IYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS 591
           IYV+K SAG+VYLRFE+ EAA +AQRAMHMRWFARRLISAIF++P DYEAKFK 
Sbjct: 406 IYVEKHSAGYVYLRFETVEAAVTAQRAMHMRWFARRLISAIFLQPRDYEAKFKG 459

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|9758966|dbj|BAB09409.1| splicing factor-like protein [Arabidopsis thaliana]

 Score =  616 bits (1588), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 366/586 (62%), Positives = 422/586 (72%), Gaps = 76/586 (12%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEK----- 55
           MEFDEYEYLEKTVEE         S+ KK+    E+SERSYRKRE  E + EE       
Sbjct: 1   MEFDEYEYLEKTVEE------GAGSNKKKEESGNERSERSYRKREGGERQGEEGGEEERV 54

Query: 56  SRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRER 115
           S   K+SR D +E  G +RDR+R+    + R  RD+DR+RD+ RE               
Sbjct: 55  SSRSKKSRGDGEENGGGKRDRERE----RHRSSRDKDRERDKVREGS------------- 97

Query: 116 REKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERE 175
           R+KE +RER  +         ERD                     RS R++ R+ ER   
Sbjct: 98  RDKESDRERSSK---------ERD---------------------RSDRDKPRDRERRER 127

Query: 176 LELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATER 235
              E+         E+E ++  R SRR+++KK+  EPEADPERDQRTVFAYQMPLKATER
Sbjct: 128 ---EKRSSSRSRREEKEPEVVERGSRRHRDKKD--EPEADPERDQRTVFAYQMPLKATER 182

Query: 236 DVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP 295
           DVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQL LGQPVMVKP
Sbjct: 183 DVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLFLGQPVMVKP 242

Query: 296 SEAEKNLVQSN-TSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLP 354
           SEAEKNL QSN T+ GGT     G  DRKLYVGNLHFNM+E QLR++FE FGPVELVQLP
Sbjct: 243 SEAEKNLAQSNSTTVGGT-----GPADRKLYVGNLHFNMSELQLRQIFEAFGPVELVQLP 297

Query: 355 LDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAD 414
           LD ETGQCKGFGF+QF QLEH+KAAQ ALNGKLEI GRT+KVSSV+DH+GTQD+A KSAD
Sbjct: 298 LDPETGQCKGFGFIQFVQLEHSKAAQIALNGKLEIAGRTIKVSSVSDHIGTQDSAPKSAD 357

Query: 415 FDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQP 474
           FDDDDGGGLALNAQSRA+LMQKLDR+GIATSI GSLGV P +NG+A NQ  ++      P
Sbjct: 358 FDDDDGGGLALNAQSRAMLMQKLDRSGIATSIVGSLGV-PGLNGAAFNQPGMN------P 410

Query: 475 AVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGR 534
           + P   +    IP+   E +G PSECLLLKNMFDPA ET+P+FDLEI+ DV +ECSKYG 
Sbjct: 411 SFPTSVLPTTAIPSFVNEHVGLPSECLLLKNMFDPATETEPNFDLEIRDDVADECSKYGP 470

Query: 535 VKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFM 580
           V HIYVDK SAGFVYLRF+S EAAA+AQRAMHMRWFA+++ISA FM
Sbjct: 471 VNHIYVDKNSAGFVYLRFQSVEAAAAAQRAMHMRWFAQKMISATFM 516

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	591
TAIR|locus:2178198	527	AT5G09880 [Arabidopsis thalian	0.634	0.711	0.735	9.5e-150
UNIPROTKB|E2R4L0	530	RBM39 "Uncharacterized protein	0.641	0.715	0.412	3.1e-67
UNIPROTKB|Q14498	530	RBM39 "RNA-binding protein 39"	0.641	0.715	0.412	3.1e-67
MGI|MGI:2157953	530	Rbm39 "RNA binding motif prote	0.641	0.715	0.412	3.1e-67
UNIPROTKB|F1MA64	530	Rbm39 "Protein Rbm39" [Rattus	0.641	0.715	0.412	3.1e-67
RGD|1310071	524	Rbm39 "RNA binding motif prote	0.626	0.706	0.419	5.1e-67
UNIPROTKB|E1BRU3	529	LOC100858247 "Uncharacterized	0.639	0.714	0.415	6.5e-67
ZFIN|ZDB-GENE-040426-2852	523	rbm39a "RNA binding motif prot	0.636	0.718	0.415	6.5e-67
UNIPROTKB|F6QIA5	525	RBM39 "Uncharacterized protein	0.626	0.704	0.418	3.6e-66
UNIPROTKB|F2Z5I2	525	RBM39 "Uncharacterized protein	0.626	0.704	0.418	3.6e-66

TAIR|locus:2178198 AT5G09880 [Arabidopsis thaliana (taxid:3702)]

 Score = 1414 (502.8 bits), Expect = 9.5e-150, Sum P(2) = 9.5e-150
 Identities = 287/390 (73%), Positives = 320/390 (82%)

Query:   203 YKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSK 262
             +++KK+  EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSK
Sbjct:   152 HRDKKD--EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSK 209

Query:   263 GVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSN-TSAGGTATGPYGAID 321
             GVGYIEFYDVMSVPMAIALSGQL LGQPVMVKPSEAEKNL QSN T+ GGT  GP    D
Sbjct:   210 GVGYIEFYDVMSVPMAIALSGQLFLGQPVMVKPSEAEKNLAQSNSTTVGGT--GP---AD 264

Query:   322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             RKLYVGNLHFNM+E QLR++FE FGPVELVQLPLD ETGQCKGFGF+QF QLEH+KAAQ 
Sbjct:   265 RKLYVGNLHFNMSELQLRQIFEAFGPVELVQLPLDPETGQCKGFGFIQFVQLEHSKAAQI 324

Query:   382 ALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAXXXXXXXXXLALNAQSRALLMQKLDRTG 441
             ALNGKLEI GRT+KVSSV+DH+GTQD+A KSA         LALNAQSRA+LMQKLDR+G
Sbjct:   325 ALNGKLEIAGRTIKVSSVSDHIGTQDSAPKSADFDDDDGGGLALNAQSRAMLMQKLDRSG 384

Query:   442 IATSIAGSLGVAPAVNGSAVNQQAISLXXXXXXXXXXXXXXXXXXXNMAAEFIGSPSECL 501
             IATSI GSLGV P +NG+A NQ  ++                    +   E +G PSECL
Sbjct:   385 IATSIVGSLGV-PGLNGAAFNQPGMN------PSFPTSVLPTTAIPSFVNEHVGLPSECL 437

Query:   502 LLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASA 561
             LLKNMFDPA ET+P+FDLEI+ DV +ECSKYG V HIYVDK SAGFVYLRF+S EAAA+A
Sbjct:   438 LLKNMFDPATETEPNFDLEIRDDVADECSKYGPVNHIYVDKNSAGFVYLRFQSVEAAAAA 497

Query:   562 QRAMHMRWFARRLISAIFMKPEDYEAKFKS 591
             QRAMHMRWFA+++ISA FM P +YEAK K+
Sbjct:   498 QRAMHMRWFAQKMISATFMPPHEYEAKAKA 527

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|E2R4L0 RBM39 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 683 (245.5 bits), Expect = 3.1e-67, P = 3.1e-67
 Identities = 161/390 (41%), Positives = 216/390 (55%)

Query:   204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
             K+K  V EP     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct:   133 KDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRR 192

Query:   261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI 320
             SKG+ Y+EF DV SVP+AI L+GQ +LG P++V+ S+AEKN  ++   A     G  G +
Sbjct:   193 SKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKN--RAAAMANNLQKGSAGPM 250

Query:   321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
               +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK A 
Sbjct:   251 --RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 308

Query:   381 SALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAXXXXXXXXXLALNAQSRALLMQKLDRT 440
               LNG  E+ GR +KV  VT+      +A+            + L    R  LM +L   
Sbjct:   309 EQLNG-FELAGRPMKVGHVTERTDAS-SASSFLDSDELERTGIDLGTTGRLQLMARLAE- 365

Query:   441 GIATSIAGSLGVAPAVNGSAVNQQAISLXXXXXXXXXXXXXXXXXXXNMAAEFIGSPSEC 500
             G    I  +   A  ++GS                              AA      ++C
Sbjct:   366 GTGLQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAAASVQPLATQC 425

Query:   501 LLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTEAAA 559
               L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S  AA 
Sbjct:   426 FQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAI 485

Query:   560 SAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
             +A  A+H RWFA ++I+A ++    Y   F
Sbjct:   486 AAVNALHGRWFAGKMITAAYVPLPTYHNLF 515

GO:0005813 "centrosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q14498 RBM39 "RNA-binding protein 39" [Homo sapiens (taxid:9606)]

 Score = 683 (245.5 bits), Expect = 3.1e-67, P = 3.1e-67
 Identities = 161/390 (41%), Positives = 216/390 (55%)

Query:   204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
             K+K  V EP     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct:   133 KDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRR 192

Query:   261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI 320
             SKG+ Y+EF DV SVP+AI L+GQ +LG P++V+ S+AEKN  ++   A     G  G +
Sbjct:   193 SKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKN--RAAAMANNLQKGSAGPM 250

Query:   321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
               +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK A 
Sbjct:   251 --RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 308

Query:   381 SALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAXXXXXXXXXLALNAQSRALLMQKLDRT 440
               LNG  E+ GR +KV  VT+      +A+            + L    R  LM +L   
Sbjct:   309 EQLNG-FELAGRPMKVGHVTERTDAS-SASSFLDSDELERTGIDLGTTGRLQLMARLAE- 365

Query:   441 GIATSIAGSLGVAPAVNGSAVNQQAISLXXXXXXXXXXXXXXXXXXXNMAAEFIGSPSEC 500
             G    I  +   A  ++GS                              AA      ++C
Sbjct:   366 GTGLQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAAASVQPLATQC 425

Query:   501 LLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTEAAA 559
               L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S  AA 
Sbjct:   426 FQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAI 485

Query:   560 SAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
             +A  A+H RWFA ++I+A ++    Y   F
Sbjct:   486 AAVNALHGRWFAGKMITAAYVPLPTYHNLF 515

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006396 "RNA processing" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005813 "centrosome" evidence=IDA

GO:0015630 "microtubule cytoskeleton" evidence=IDA

MGI|MGI:2157953 Rbm39 "RNA binding motif protein 39" [Mus musculus (taxid:10090)]

 Score = 683 (245.5 bits), Expect = 3.1e-67, P = 3.1e-67
 Identities = 161/390 (41%), Positives = 216/390 (55%)

Query:   204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
             K+K  V EP     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct:   133 KDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRR 192

Query:   261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI 320
             SKG+ Y+EF DV SVP+AI L+GQ +LG P++V+ S+AEKN  ++   A     G  G +
Sbjct:   193 SKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKN--RAAAMANNLQKGSAGPM 250

Query:   321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
               +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK A 
Sbjct:   251 --RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 308

Query:   381 SALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAXXXXXXXXXLALNAQSRALLMQKLDRT 440
               LNG  E+ GR +KV  VT+      +A+            + L    R  LM +L   
Sbjct:   309 EQLNG-FELAGRPMKVGHVTERTDAS-SASSFLDSDELERTGIDLGTTGRLQLMARLAE- 365

Query:   441 GIATSIAGSLGVAPAVNGSAVNQQAISLXXXXXXXXXXXXXXXXXXXNMAAEFIGSPSEC 500
             G    I  +   A  ++GS                              AA      ++C
Sbjct:   366 GTGLQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAAASVQPLATQC 425

Query:   501 LLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTEAAA 559
               L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S  AA 
Sbjct:   426 FQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAI 485

Query:   560 SAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
             +A  A+H RWFA ++I+A ++    Y   F
Sbjct:   486 AAVNALHGRWFAGKMITAAYVPLPTYHNLF 515

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=TAS

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=TAS

GO:0006351 "transcription, DNA-dependent" evidence=TAS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

UNIPROTKB|F1MA64 Rbm39 "Protein Rbm39" [Rattus norvegicus (taxid:10116)]

 Score = 683 (245.5 bits), Expect = 3.1e-67, P = 3.1e-67
 Identities = 161/390 (41%), Positives = 216/390 (55%)

Query:   204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
             K+K  V EP     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct:   133 KDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRR 192

Query:   261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI 320
             SKG+ Y+EF DV SVP+AI L+GQ +LG P++V+ S+AEKN  ++   A     G  G +
Sbjct:   193 SKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKN--RAAAMANNLQKGSAGPM 250

Query:   321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
               +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK A 
Sbjct:   251 --RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 308

Query:   381 SALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAXXXXXXXXXLALNAQSRALLMQKLDRT 440
               LNG  E+ GR +KV  VT+      +A+            + L    R  LM +L   
Sbjct:   309 EQLNG-FELAGRPMKVGHVTERTDAS-SASSFLDSDELERTGIDLGTTGRLQLMARLAE- 365

Query:   441 GIATSIAGSLGVAPAVNGSAVNQQAISLXXXXXXXXXXXXXXXXXXXNMAAEFIGSPSEC 500
             G    I  +   A  ++GS                              AA      ++C
Sbjct:   366 GTGLQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAAASVQPLATQC 425

Query:   501 LLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTEAAA 559
               L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S  AA 
Sbjct:   426 FQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAI 485

Query:   560 SAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
             +A  A+H RWFA ++I+A ++    Y   F
Sbjct:   486 AAVNALHGRWFAGKMITAAYVPLPTYHNLF 515

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

RGD|1310071 Rbm39 "RNA binding motif protein 39" [Rattus norvegicus (taxid:10116)]

 Score = 681 (244.8 bits), Expect = 5.1e-67, P = 5.1e-67
 Identities = 165/393 (41%), Positives = 222/393 (56%)

Query:   204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
             K+K  V EP     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct:   133 KDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRR 192

Query:   261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI 320
             SKG+ Y+EF DV SVP+AI L+GQ +LG P++V+ S+AEKN  ++   A     G  G +
Sbjct:   193 SKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKN--RAAAMANNLQKGSAGPM 250

Query:   321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
               +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK A 
Sbjct:   251 --RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 308

Query:   381 SALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAXXXXXXXXXLALNAQSRALLMQKL-DR 439
               LNG  E+ GR +KV  VT+      +A+            + L    R  LM +L + 
Sbjct:   309 EQLNG-FELAGRPMKVGHVTERTDAS-SASSFLDSDELERTGIDLGTTGRLQLMARLAEG 366

Query:   440 TGIATSIAGSLGVAPAVNGSAVNQQAISLXXXXXXXXXXXXXXXXXXXNMAAEFIGSP-- 497
             TG        L + PA   +   Q + SL                    +AA     P  
Sbjct:   367 TG--------LQIPPAAQQAL--QMSGSLAFGAVADLQTRLSQQTEASALAAAASVQPLA 416

Query:   498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTE 556
             ++C  L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S  
Sbjct:   417 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIA 476

Query:   557 AAASAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
             AA +A  A+H RWFA ++I+A ++    Y   F
Sbjct:   477 AAIAAVNALHGRWFAGKMITAAYVPLPTYHNLF 509

GO:0005634 "nucleus" evidence=ISO

GO:0005813 "centrosome" evidence=ISO

GO:0015630 "microtubule cytoskeleton" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|E1BRU3 LOC100858247 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 680 (244.4 bits), Expect = 6.5e-67, P = 6.5e-67
 Identities = 162/390 (41%), Positives = 218/390 (55%)

Query:   204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
             K+K  V EP     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct:   133 KDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRR 192

Query:   261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI 320
             SKG+ Y+EF DV SVP+AI L+GQ +LG P++V+ S+AEKN  ++   A     G  G +
Sbjct:   193 SKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKN--RAAAMANNLQKGSAGPM 250

Query:   321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
               +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK A 
Sbjct:   251 --RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 308

Query:   381 SALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAXXXXXXXXXLALNAQSRALLMQKLDRT 440
               LNG  E+ GR +KV  VT+      +A+            + L    R  LM +L   
Sbjct:   309 EQLNG-FELAGRPMKVGHVTERTDAS-SASSFLDSDELERTGIDLGTTGRLQLMARLAE- 365

Query:   441 GIATSIAGSLGVAPAVNGSAVNQQAISLXXXXXXXXXXXXXXXXXXXNMAAEFIGSPSEC 500
             G    I  +   A  ++GS        L                     AA      ++C
Sbjct:   366 GTGLQIPPAAQQALQMSGSLAFGAVADLQTRLSQQNEVFFPIKTVLA-AAASVQPLATQC 424

Query:   501 LLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTEAAA 559
               L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S  AA 
Sbjct:   425 FQLSNMFNPQTEEEAGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAI 484

Query:   560 SAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
             +A  A+H RWFA ++I+A ++    Y + F
Sbjct:   485 AAVNALHGRWFAGKMITAAYVPLPTYHSLF 514

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

ZFIN|ZDB-GENE-040426-2852 rbm39a "RNA binding motif protein 39a" [Danio rerio (taxid:7955)]

 Score = 680 (244.4 bits), Expect = 6.5e-67, P = 6.5e-67
 Identities = 162/390 (41%), Positives = 221/390 (56%)

Query:   204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
             K++  V +P     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct:   129 KDRSPVRQPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSAVGKVRDVRIISDRNSRR 188

Query:   261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI 320
             SKG+ YIEF D  SVP+AI LSGQ LLG P++V+ S+AEKN  ++   A     G  G +
Sbjct:   189 SKGIAYIEFVDSTSVPLAIGLSGQRLLGVPIIVQASQAEKN--RAAALANNLQKGSAGPM 246

Query:   321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
               +LYVG+LHFN+TE  LR +FEPFG ++ +QL +D ETG+ KG+GF+ F+  E AK A 
Sbjct:   247 --RLYVGSLHFNITEDMLRGIFEPFGRIDSIQLMMDSETGRSKGYGFITFSDAECAKKAL 304

Query:   381 SALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAXXXXXXXXXLALNAQSRALLMQKLDRT 440
               LNG  E+ GR +KV  VT+      TA+            + L    R  LM +L   
Sbjct:   305 EQLNG-FELAGRPMKVGHVTERTDAS-TASSFLDNDELERTGIDLGTTGRLQLMARLAE- 361

Query:   441 GIATSIAGSLGVAPAVNGSAVNQQAISLXXXXXXXXXXXXXXXXXXXNMAAEFIGSPSEC 500
             G    I  +   A  ++GS V   A +                    N+ ++ I +   C
Sbjct:   362 GTGLQIPPAAQQALQMSGSMV-AMAAATAAMNPGLSFNINVPTNQALNLPSQPIAT--HC 418

Query:   501 LLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTEAAA 559
               L NMF+P  E D  +++EIQ DV EEC+K+G V HIYVDK+SA G VY++  +  AA 
Sbjct:   419 FQLSNMFNPNSENDHGWEIEIQDDVIEECNKHGGVIHIYVDKKSAEGNVYVKCPTIPAAM 478

Query:   560 SAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
             +A  A+H RWF  ++I+A ++    Y   F
Sbjct:   479 AAVSALHGRWFGGKMITAAYVPLPTYHNLF 508

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F6QIA5 RBM39 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 673 (242.0 bits), Expect = 3.6e-66, P = 3.6e-66
 Identities = 165/394 (41%), Positives = 222/394 (56%)

Query:   204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
             K+K  V EP     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct:   133 KDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRR 192

Query:   261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI 320
             SKG+ Y+EF DV SVP+AI L+GQ +LG P++V+ S+AEKN  ++   A     G  G +
Sbjct:   193 SKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKN--RAAAMANNLQKGSAGPM 250

Query:   321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
               +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK A 
Sbjct:   251 --RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 308

Query:   381 SALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAXXXXXXXXXLALNAQSRALLMQKL-DR 439
               LNG  E+ GR +KV  VT+      +A+            + L    R  LM +L + 
Sbjct:   309 EQLNG-FELAGRPMKVGHVTERTDAS-SASSFLDSDELERTGIDLGTTGRLQLMARLAEG 366

Query:   440 TGIATSIAGSLGVAPAVNGSAVNQQAISLXXXXXXXXXXXXXXXXXXXNMAAEFIGSP-- 497
             TG        L + PA   +   Q + SL                    +AA     P  
Sbjct:   367 TG--------LQIPPAAQQAL--QMSGSLAFGAVADLQTRLSQQTEASALAAAASVQPLA 416

Query:   498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTE 556
             ++C  L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S  
Sbjct:   417 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIA 476

Query:   557 AAASAQRAMHMRWFAR-RLISAIFMKPEDYEAKF 589
             AA +A  A+H RWFA  ++I+A ++    Y   F
Sbjct:   477 AAIAAVNALHGRWFAAGKMITAAYVPLPTYHNLF 510

GO:0005813 "centrosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F2Z5I2 RBM39 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 673 (242.0 bits), Expect = 3.6e-66, P = 3.6e-66
 Identities = 165/394 (41%), Positives = 222/394 (56%)

Query:   204 KEKKEVVEP--EADPE-RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR 260
             K+K  V EP     PE RD RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRR
Sbjct:   133 KDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRR 192

Query:   261 SKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI 320
             SKG+ Y+EF DV SVP+AI L+GQ +LG P++V+ S+AEKN  ++   A     G  G +
Sbjct:   193 SKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKN--RAAAMANNLQKGSAGPM 250

Query:   321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
               +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK A 
Sbjct:   251 --RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 308

Query:   381 SALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSAXXXXXXXXXLALNAQSRALLMQKL-DR 439
               LNG  E+ GR +KV  VT+      +A+            + L    R  LM +L + 
Sbjct:   309 EQLNG-FELAGRPMKVGHVTERTDAS-SASSFLDSDELERTGIDLGTTGRLQLMARLAEG 366

Query:   440 TGIATSIAGSLGVAPAVNGSAVNQQAISLXXXXXXXXXXXXXXXXXXXNMAAEFIGSP-- 497
             TG        L + PA   +   Q + SL                    +AA     P  
Sbjct:   367 TG--------LQIPPAAQQAL--QMSGSLAFGAVADLQTRLSQQTEASALAAAASVQPLA 416

Query:   498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTE 556
             ++C  L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S  
Sbjct:   417 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIA 476

Query:   557 AAASAQRAMHMRWFAR-RLISAIFMKPEDYEAKF 589
             AA +A  A+H RWFA  ++I+A ++    Y   F
Sbjct:   477 AAIAAVNALHGRWFAAGKMITAAYVPLPTYHNLF 510

GO:0005813 "centrosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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

Your Input: GSVIVG00019345001 SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (539 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	591
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-150
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-40
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	7e-34
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-31
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	5e-27
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	2e-24
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	4e-24
smart00360	73	smart00360, RRM, RNA recognition motif	7e-23
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-20
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-20
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-19
cd12286	92	cd12286, RRM_Man1, RNA recognition motif in inner	1e-18
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-17
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-17
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-17
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-16
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-15
smart00360	73	smart00360, RRM, RNA recognition motif	1e-14
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	1e-14
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-14
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-14
cd12282	91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	5e-14
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	6e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	8e-14
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-13
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-13
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-13
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-13
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-13
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	5e-13
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	5e-13
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	8e-13
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-12
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-12
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-12
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-12
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-12
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	2e-12
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-12
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-12
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-12
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-12
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-12
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-11
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-11
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-11
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-11
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	3e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-11
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-11
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	4e-11
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-11
PRK12678	672	PRK12678, PRK12678, transcription termination fact	6e-11
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-11
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-11
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-11
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	8e-11
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	9e-11
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-10
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-10
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-10
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	2e-10
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	2e-10
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-10
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-10
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-10
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	3e-10
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-10
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-10
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-10
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-10
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	4e-10
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-10
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	4e-10
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	4e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-10
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-10
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	7e-10
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	8e-10
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	8e-10
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	8e-10
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-09
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	1e-09
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	1e-09
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-09
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-09
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-09
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-09
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-09
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	2e-09
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-09
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-09
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	3e-09
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	3e-09
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-09
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-09
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	4e-09
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	4e-09
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	6e-09
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	6e-09
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	6e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	7e-09
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	8e-09
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	9e-09
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-08
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-08
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-08
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	1e-08
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-08
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-08
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-08
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	1e-08
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-08
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	2e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-08
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-08
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	3e-08
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	3e-08
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-08
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	3e-08
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	3e-08
PRK12678	672	PRK12678, PRK12678, transcription termination fact	4e-08
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-08
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-08
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	6e-08
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	6e-08
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	7e-08
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	9e-08
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-07
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-07
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	1e-07
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	1e-07
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	1e-07
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-07
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-07
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-07
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	2e-07
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	2e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-07
cd12648	98	cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 i	2e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	3e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	3e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-07
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-07
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	4e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-07
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	5e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	5e-07
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-07
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	6e-07
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	6e-07
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	6e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	7e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	8e-07
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	8e-07
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-06
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-06
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	1e-06
cd12274	71	cd12274, RRM2_NEFsp, RNA recognition motif 2 in ve	1e-06
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	1e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-06
cd12647	96	cd12647, RRM_UHM_SPF45, RNA recognition motif in U	1e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-06
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	1e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-06
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-06
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	2e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-06
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	2e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-06
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	2e-06
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-06
cd12287	102	cd12287, RRM_U2AF35_like, RNA recognition motif in	2e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	3e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-06
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	3e-06
PLN03121	243	PLN03121, PLN03121, nucleic acid binding protein;	3e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	3e-06
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	3e-06
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	3e-06
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	3e-06
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-06
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	4e-06
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	4e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	4e-06
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	4e-06
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	4e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	4e-06
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	4e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-06
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	5e-06
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	5e-06
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	6e-06
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	7e-06
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	7e-06
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	7e-06
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	7e-06
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	7e-06
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	8e-06
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	8e-06
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	8e-06
cd12269	69	cd12269, RRM_Vip1_like, RNA recognition motif in a	8e-06
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-06
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	9e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-05
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	1e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	1e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-05
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	1e-05
PLN03120	260	PLN03120, PLN03120, nucleic acid binding protein;	1e-05
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	1e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-05
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-05
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	2e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	2e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	2e-05
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	2e-05
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	2e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-05
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-05
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	2e-05
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	2e-05
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	2e-05
pfam02724	583	pfam02724, CDC45, CDC45-like protein	2e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-05
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	2e-05
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	3e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-05
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	3e-05
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	3e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	3e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	3e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-05
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	3e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	4e-05
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	4e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	4e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	4e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	4e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	4e-05
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	4e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	5e-05
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	5e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-05
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	5e-05
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	5e-05
pfam02029	431	pfam02029, Caldesmon, Caldesmon	5e-05
cd12460	82	cd12460, RRM2_CID8_like, RNA recognition motif 2 i	5e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	6e-05
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	6e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	6e-05
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	6e-05
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	6e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	7e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	7e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	7e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	7e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	7e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	7e-05
pfam06495	182	pfam06495, Transformer, Fruit fly transformer prot	7e-05
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	7e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	8e-05
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	8e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	8e-05
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	8e-05
smart00360	73	smart00360, RRM, RNA recognition motif	9e-05
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	9e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	9e-05
cd12540	105	cd12540, RRM_U2AFBPL, RNA recognition motif in U2	9e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-04
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	1e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	1e-04
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	1e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-04
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	1e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-04
cd12432	90	cd12432, RRM_ACINU, RNA recognition motif in apopt	1e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	1e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	1e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-04
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	1e-04
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	1e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	2e-04
pfam02029	431	pfam02029, Caldesmon, Caldesmon	2e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-04
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	2e-04
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	2e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-04
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	2e-04
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	2e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-04
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	2e-04
cd12539	103	cd12539, RRM_U2AF35B, RNA recognition motif in spl	2e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	2e-04
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	2e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	2e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-04
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	3e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	3e-04
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	3e-04
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	3e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	3e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	3e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	3e-04
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	3e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	3e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	4e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	4e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	4e-04
cd12511	73	cd12511, RRM2_RBM12_like, RNA recognition motif 2	4e-04
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	4e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	4e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	4e-04
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-04
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	5e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	5e-04
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	5e-04
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	5e-04
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	5e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	5e-04
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	5e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	5e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	5e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	6e-04
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	6e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	6e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	6e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	6e-04
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	6e-04
cd12626	77	cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in	6e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	6e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	7e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	7e-04
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	7e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	7e-04
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	7e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	8e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	8e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	8e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	8e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	8e-04
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	8e-04
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	8e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	9e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.001
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	0.001
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.001
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.001
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	0.001
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.001
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.001
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	0.001
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.001
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	0.001
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	0.001
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.001
COG5296	521	COG5296, COG5296, Transcription factor involved in	0.001
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	0.001
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	0.001
cd12259	76	cd12259, RRM_SRSF11_SREK1, RNA recognition motif i	0.001
TIGR02680	1353	TIGR02680, TIGR02680, TIGR02680 family protein	0.001
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.001
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.002
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.002
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	0.002
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	0.002
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.002
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	0.002
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.002
COG4942	420	COG4942, COG4942, Membrane-bound metallopeptidase	0.002
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.002
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	0.002
TIGR00934	800	TIGR00934, 2a38euk, potassium uptake protein, Trk	0.002
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.002
pfam04502	321	pfam04502, DUF572, Family of unknown function (DUF	0.002
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	0.002
pfam03064	238	pfam03064, U79_P34, HSV U79 / HCMV P34	0.002
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.003
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	0.003
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.003
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.003
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.003
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	0.003
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	0.003
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.003
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	0.003
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	0.003
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.003
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.004
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	0.004
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	0.004
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.004
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	0.004
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.004
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.004
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.004
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	0.004
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	0.004
cd12465	88	cd12465, RRM_UHMK1, RNA recognition motif found in	0.004
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	0.004
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.004
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	0.004
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	0.004

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

 Score =  441 bits (1135), Expect = e-150
 Identities = 209/509 (41%), Positives = 269/509 (52%), Gaps = 70/509 (13%)

Query: 78  RDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERE 137
           R RDR++ R R +  R  D+GRER R   R R+RSR RR+++  R RR R          
Sbjct: 1   RYRDRERGRLR-NDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGR---------- 49

Query: 138 RDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEM 197
                          S+SR  +   R   +R   R+                        
Sbjct: 50  ---------------SRSRSPNRYYRPRGDRSYRRD------------------------ 70

Query: 198 RESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRN 257
              RR        EP  + ERD RTVF  Q+ LKA ERD+YEFFSK GKVRDV+ I DRN
Sbjct: 71  --DRRSGRNT--KEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRN 126

Query: 258 SRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPY 317
           SRRSKGV Y+EFYDV SV  A+AL+GQ+LLG+P++V+ S+AEKN          T     
Sbjct: 127 SRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAA----THQPGD 182

Query: 318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
                KLYVGNLHFN+TE +LR++FEPFG +E VQL  D ETG+ KGFGF+QF   E AK
Sbjct: 183 IPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAK 242

Query: 378 AAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKL 437
            A   +NG  E+ GR +KV    D     D A    D D     G  LN + R  LM+KL
Sbjct: 243 EALEVMNG-FELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKL 301

Query: 438 DRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFI--- 494
           DR        G L +           Q +    +  P +P    T  +       F+   
Sbjct: 302 DRDD----GDGGLLIPGT-GSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPST 356

Query: 495 --GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVD-KRSAGFVYLR 551
                + CL+L NMFDPA E +P+FD EI  DV+EECSKYG V HIYVD K SAG +YL+
Sbjct: 357 NNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLK 416

Query: 552 FESTEAAASAQRAMHMRWFARRLISAIFM 580
           F S +AA +A +A++ R+F  ++I+A F+
Sbjct: 417 FSSVDAALAAFQALNGRYFGGKMITAAFV 445

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

 Score =  141 bits (357), Expect = 1e-40
 Identities = 53/73 (72%), Positives = 62/73 (84%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
           TVF  Q+ LK  ERD+YEFFSKAGKVRDVR+I DRNSRRSKGV Y+EFYD  SVP+A+ L
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 282 SGQLLLGQPVMVK 294
           +GQ LLGQP+MV+
Sbjct: 61  TGQRLLGQPIMVQ 73

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

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

 Score =  123 bits (311), Expect = 7e-34
 Identities = 44/84 (52%), Positives = 62/84 (73%), Gaps = 1/84 (1%)

Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRS-AGFVYLRFESTE 556
           S C++LKNMFDPA ET+ ++D EI+ DV EECSK+G V+HI VDK S  G VY++F++ E
Sbjct: 1   SRCVILKNMFDPAEETEDEWDDEIKEDVLEECSKFGPVEHIKVDKNSPEGVVYVKFKTVE 60

Query: 557 AAASAQRAMHMRWFARRLISAIFM 580
           AA    +A++ RWF  R I+A ++
Sbjct: 61  AAQKCIQALNGRWFDGRQITAEYV 84

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

 Score =  115 bits (290), Expect = 3e-31
 Identities = 45/74 (60%), Positives = 53/74 (71%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVGNLHFN+TE  LR +FEPFG +E VQL  D ETG+ KG+GF+QFA  E AK A   L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 384 NGKLEIVGRTLKVS 397
           NG  E+ GR +KV 
Sbjct: 61  NG-FELAGRPIKVG 73

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

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

 Score =  114 bits (287), Expect = 5e-27
 Identities = 93/365 (25%), Positives = 145/365 (39%), Gaps = 57/365 (15%)

Query: 74  RDRDRDRDRDKERHR-RDRDRDRDRGRERERETERDRER-SRERREKEKERERRERR-DR 130
           RD + DR+R+K R R RDR  +R R R R+R   RDR R SRER  +E  R R  RR D 
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 131 EKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRE 190
              R       RRS  R RR S   R      RR R+R    +      R+ +++R L +
Sbjct: 61  RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQ-----WRKDDKKRSLWD 115

Query: 191 RER-DLEMRESRRYKEKK-----------------------------EVVEPEADPERDQ 220
            +    E+  + + K  +                              V+  +    R  
Sbjct: 116 IKPPGYELVTADQAKASQVFSVPGTAPRPAMTDPEKLLAEGSIITPLPVLPYQQQATRQA 175

Query: 221 RTVFAYQMPLKATERDVYEFFSKA------GKVRDVRLIMDRNSRRSKGVGYIEFYDVMS 274
           R ++   +P +  E  V +FF+         K  D + +   N  + K   ++EF  V  
Sbjct: 176 RRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEE 235

Query: 275 VPMAIALSGQLLLGQPVMVK-------PSEAEKNLVQSNTS----AGGTATGPYGAIDR- 322
              A+AL   +     + ++         +    + Q N                 +D  
Sbjct: 236 ATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSK 295

Query: 323 -KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            ++Y+GNL   + E Q+++L E FG ++   L  DI TG  KG+ F ++        A +
Sbjct: 296 DRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIA 355

Query: 382 ALNGK 386
           ALNGK
Sbjct: 356 ALNGK 360

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

>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 96.7 bits (240), Expect = 2e-24
 Identities = 50/81 (61%), Positives = 63/81 (77%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           RTVF  Q+  +   RD+ EFFS  GKVRDVR+I DRNSRRSKG+ Y+EF DV SVP+AI 
Sbjct: 2   RTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIG 61

Query: 281 LSGQLLLGQPVMVKPSEAEKN 301
           L+GQ +LG P++V+ S+AEKN
Sbjct: 62  LTGQRVLGVPIIVQASQAEKN 82

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor 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. 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|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 95.9 bits (238), Expect = 4e-24
 Identities = 48/81 (59%), Positives = 63/81 (77%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           RTVF  Q+  +   RD+ +FFS  GKVRDVR+I DRNSRRSKG+ Y+EF ++ SVP+AI 
Sbjct: 2   RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 61

Query: 281 LSGQLLLGQPVMVKPSEAEKN 301
           L+GQ LLG P++V+ S+AEKN
Sbjct: 62  LTGQRLLGVPIIVQASQAEKN 82

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or 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). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

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

 Score = 91.9 bits (229), Expect = 7e-23
 Identities = 41/74 (55%), Positives = 50/74 (67%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L+VGNL  + TE +LR+LF  FG VE V+L  D ETG+ KGF FV+F   E A+ A  A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 383 LNGKLEIVGRTLKV 396
           LNGK E+ GR LKV
Sbjct: 61  LNGK-ELDGRPLKV 73

Length = 73

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 94.6 bits (236), Expect = 3e-20
 Identities = 41/205 (20%), Positives = 72/205 (35%), Gaps = 7/205 (3%)

Query: 10  EKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEE 69
            K       +     ++    A    ++     +RE  E        ++G+   +   E 
Sbjct: 100 AKAEAAPAARAAAAAAAEAASAPEAAQARE---RRERGEAARRGAARKAGEGGEQPATEA 156

Query: 70  NGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRD 129
                +R  + +RD+ R R DR+  +      ER    +R R  + R++   RE+ +RR+
Sbjct: 157 RADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRRE 216

Query: 130 REKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELR 189
               R+      RR     R +     R     R   + E    R     R R+R+R  R
Sbjct: 217 ERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGR--RGRRFRDRDRRGR 274

Query: 190 ERERDLEMRESRRYKEKKEVVEPEA 214
                   RE      + +V+ P A
Sbjct: 275 RGGDGGNEREPEL--REDDVLVPVA 297

Length = 672

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

 Score = 83.8 bits (208), Expect = 6e-20
 Identities = 36/75 (48%), Positives = 46/75 (61%), Gaps = 1/75 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            LYVGNL +N+TE  L+ LF  FG V   ++  D ETG+ +GFGFV+    E A AA   
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 383 LNGKLEIVGRTLKVS 397
           LNG  +  GRTL V+
Sbjct: 61  LNGT-DFGGRTLTVN 74

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 81.9 bits (203), Expect = 2e-19
 Identities = 36/72 (50%), Positives = 48/72 (66%), Gaps = 2/72 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+VGNL  + TE  L+ LF  FGP+E +++  D ETG+ KGF FV+F   E A+ A  AL
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 384 NGKLEIVGRTLK 395
           NGK E+ GR L+
Sbjct: 60  NGK-ELGGRELR 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 80.4 bits (199), Expect = 9e-19
 Identities = 38/74 (51%), Positives = 49/74 (66%), Gaps = 2/74 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+VGNL  + TE  LR+LF  FG +E V++  D + G+ KGF FV+F   E A+ A  AL
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 384 NGKLEIVGRTLKVS 397
           NGK E+ GR LKVS
Sbjct: 60  NGK-ELDGRKLKVS 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|240732 cd12286, RRM_Man1, RNA recognition motif in inner nuclear membrane protein Man1 (Man1) and similar proteins

 Score = 80.8 bits (200), Expect = 1e-18
 Identities = 35/92 (38%), Positives = 54/92 (58%), Gaps = 1/92 (1%)

Query: 500 CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTEAA 558
           CL ++NMFDP +E   D+ + IQ  + E+C     + HI VDK S  G VY++  S E A
Sbjct: 1   CLKIRNMFDPEVERGEDWHVRIQDAILEKCGDNNGIVHIQVDKASREGCVYIKCSSPEDA 60

Query: 559 ASAQRAMHMRWFARRLISAIFMKPEDYEAKFK 590
             A +A+H  WF  RL++  +++ E Y ++F 
Sbjct: 61  GKAFKALHGWWFDGRLVTVKYLRLERYHSRFP 92

This subfamily corresponds to the RRM of Man1, also termed LEM domain-containing protein 3 (LEMD3), an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. It is part of a protein complex essential for chromatin organization and cell division. It also functions as an important negative regulator for the transforming growth factor (TGF) beta/activin/Nodal signaling pathway by directly interacting with chromatin-associated proteins and transcriptional regulators, including the R-Smads, Smad1, Smad2, and Smad3. Moreover, Man1 is a unique type of left-right (LR) signaling regulator that acts on the inner nuclear membrane. Man1 plays a crucial role in angiogenesis. The vascular remodeling can be regulated at the inner nuclear membrane through the interaction between Man1 and Smads. Man1 contains an N-terminal LEM domain, two putative transmembrane domains, a MAN1-Src1p C-terminal (MSC) domain, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The LEM domain interacts with the DNA and chromatin-binding protein Barrier-to-Autointegration Factor, and is also necessary for efficient localization of MAN1 in the inner nuclear membrane. Research has indicated that C-terminal nucleoplasmic region of Man1 exhibits a DNA binding winged helix domain and is responsible for both DNA- and Smad-binding. . Length = 92

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 76.6 bits (189), Expect = 2e-17
 Identities = 38/74 (51%), Positives = 46/74 (62%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +L+V NL F  TE +LR+LFE FG +  V LPLD ET + KGF FV F   EHA  A S 
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 383 LNGKLEIVGRTLKV 396
           L+G +   GR L V
Sbjct: 61  LDGSI-FQGRLLHV 73

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

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 85.0 bits (211), Expect = 3e-17
 Identities = 45/214 (21%), Positives = 76/214 (35%), Gaps = 9/214 (4%)

Query: 10  EKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEE 69
                    ++ +  ++    AK E            +E     E +++ +R  R E   
Sbjct: 79  RAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAAR 138

Query: 70  NGSRRDRDRDRDRDKER---HRRDRDRDRDRGRERERETERDRERSRERREKEKERERRE 126
            G+ R      ++          +R  + +R   R R    DR+   ER E+   RE R 
Sbjct: 139 RGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERG-RREERG 197

Query: 127 RRDREKERERERDGERRSSSRSR-----RSSSQSRRSSSRSRRERERESERERELELERE 181
           R   +++R   R+   R   R R     R   + RR    +R +  RE   +R+ +    
Sbjct: 198 RDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEG 257

Query: 182 RERERELRERERDLEMRESRRYKEKKEVVEPEAD 215
           R   R  R R+RD   R       ++E    E D
Sbjct: 258 RGGRRGRRFRDRDRRGRRGGDGGNEREPELREDD 291

Length = 672

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

 Score = 75.3 bits (186), Expect = 5e-17
 Identities = 32/74 (43%), Positives = 46/74 (62%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVG L   + E  L   F PFG ++ +Q+PLD ET + +GF FV+F + E A AA   +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 384 NGKLEIVGRTLKVS 397
           N   E+ GRT++V+
Sbjct: 61  NES-ELFGRTIRVN 73

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

>gnl|CDD|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 = 75.3 bits (186), Expect = 6e-17
 Identities = 38/74 (51%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL+V  L    TE +L  LF  FG VE V L  D ETG+ +GFGFV F  +E A AA   
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 383 LNGKLEIVGRTLKV 396
           LNGK E+ GR +KV
Sbjct: 63  LNGK-ELEGRVIKV 75

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

 Score = 73.5 bits (181), Expect = 3e-16
 Identities = 32/75 (42%), Positives = 47/75 (62%), Gaps = 3/75 (4%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++V NL  +  E+ L +LF PFG V  V++  D+ T +CKG+GFV     E A +A ++L
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 384 NG-KLEIVGRTLKVS 397
           NG +L   GR L+VS
Sbjct: 64  NGYRLG--GRVLQVS 76

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

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

 Score = 70.0 bits (172), Expect = 4e-15
 Identities = 23/75 (30%), Positives = 49/75 (65%), Gaps = 1/75 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           ++YV ++H +++E  ++ +FE FG ++   L  D ETG+ KG+GF+++   + A+ A ++
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 383 LNGKLEIVGRTLKVS 397
           +N   ++ G+ L+V 
Sbjct: 62  MNL-FDLGGQQLRVG 75

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|214636 smart00360, RRM, RNA recognition motif

 Score = 68.4 bits (168), Expect = 1e-14
 Identities = 29/73 (39%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-A 280
           T+F   +P   TE ++ E FSK GKV  VRL+ D+ + +SKG  ++EF        A+ A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 281 LSGQLLLGQPVMV 293
           L+G+ L G+P+ V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 69.5 bits (171), Expect = 1e-14
 Identities = 31/88 (35%), Positives = 41/88 (46%), Gaps = 8/88 (9%)

Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA--------GFVY 549
           S  L L NM  P    D +   EI  DV+EEC KYG+V  + + +  A        G V+
Sbjct: 1   SRVLCLLNMVTPEELEDDEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVF 60

Query: 550 LRFESTEAAASAQRAMHMRWFARRLISA 577
           + F   E A  AQ A+  R F  R + A
Sbjct: 61  VEFADVEDAQKAQLALAGRKFDGRTVVA 88

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

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

 Score = 68.0 bits (167), Expect = 2e-14
 Identities = 26/65 (40%), Positives = 36/65 (55%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             +Y+  L  N T+  L KL +PFG +   +  LD +T +CKG+GFV F   E A  A  
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 382 ALNGK 386
            LNG+
Sbjct: 61  GLNGR 65

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 73.1 bits (178), Expect = 5e-14
 Identities = 64/275 (23%), Positives = 99/275 (36%), Gaps = 13/275 (4%)

Query: 109 RERSRERREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERER 168
              S     K ++ E  +  +   + E     E  S   +   +S+   S      ++  
Sbjct: 8   GPHSSFESVKPEDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISPPSKKRL 67

Query: 169 ESERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQM 228
            S   +E       E+       ER              E  +     + +  T+F   +
Sbjct: 68  LSSERKEENEREMEEQNDG----ERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNL 123

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL 287
           P   TE D+ E F K G V+ VRL+ DR + +S+G  ++EF    S   AI  L+G+ L 
Sbjct: 124 PYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELE 183

Query: 288 GQPVMVKP--------SEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLR 339
           G+P+ V+         SE   NL  S                  LYVGNL     E +L 
Sbjct: 184 GRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELA 243

Query: 340 KLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
            LF+  G +    LP   +    K   FV     +
Sbjct: 244 DLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASK 278

Length = 306

>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 67.2 bits (165), Expect = 5e-14
 Identities = 30/81 (37%), Positives = 46/81 (56%), Gaps = 2/81 (2%)

Query: 501 LLLKNMFDPA-METDPDFDLEIQGDVEEECSKYGRVKHIYV-DKRSAGFVYLRFESTEAA 558
           ++LKN+F P   E DP    E++ D+ EEC K+G+VK + V D+   G   ++F+  E A
Sbjct: 4   VILKNLFSPEEFEEDPTLINELRDDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEA 63

Query: 559 ASAQRAMHMRWFARRLISAIF 579
                A++ RWFA R + A  
Sbjct: 64  DRCIEALNGRWFAGRQLEAER 84

This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 91

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

 Score = 66.6 bits (163), Expect = 6e-14
 Identities = 25/64 (39%), Positives = 37/64 (57%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +L+V NL ++  E  L KLF  FG +  V + +D ++G+ KGF +V F   E A  A   
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 383 LNGK 386
           L+GK
Sbjct: 64  LDGK 67

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

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

 Score = 66.1 bits (162), Expect = 8e-14
 Identities = 34/74 (45%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +L V NL F  TE  L+KLF PFG V  V +P     G+ KGF FVQF     A+ A   
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRK-PDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 383 LNGKLEIVGRTLKV 396
           +NGK +I GR + V
Sbjct: 60  VNGK-KIKGRPVAV 72

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|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 = 66.0 bits (162), Expect = 1e-13
 Identities = 33/76 (43%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL+VG L    TE  +R LFE +G +E V +  D +TGQ KG  FV+F+  E A+ A  A
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 383 LNGK--LEIVGRTLKV 396
           L+GK  +    R L+V
Sbjct: 61  LHGKVTMPGASRPLQV 76

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

>gnl|CDD|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 = 65.3 bits (160), Expect = 2e-13
 Identities = 31/74 (41%), Positives = 44/74 (59%), Gaps = 7/74 (9%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +YVGNL   +TE +L++ F PFG +E V++  D      KG+ FV+F   E A  A  A+
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAV 56

Query: 384 NGKLEIVGRTLKVS 397
           NG   I G+T+K S
Sbjct: 57  NGT-SINGQTVKCS 69

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

 Score = 65.3 bits (160), Expect = 2e-13
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K+++G L   ++E Q+++L E FG ++   L  D  TG  KG+ F ++        A + 
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 383 LNGKLEIVGRTLKV 396
           LNG +++  + L V
Sbjct: 62  LNG-MQLGDKKLTV 74

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

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

 Score = 65.4 bits (160), Expect = 2e-13
 Identities = 32/76 (42%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             L V  L  +MT+ +LR LFE  GP+E  ++  D  TGQ  G+GFV +     A+ A +
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 382 ALNGKLEIVGRTLKVS 397
            LNG  EI  + LKVS
Sbjct: 61  TLNG-FEIRNKRLKVS 75

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|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 72.6 bits (179), Expect = 3e-13
 Identities = 33/195 (16%), Positives = 62/195 (31%), Gaps = 2/195 (1%)

Query: 10  EKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEE 69
                     ++   +++  +   +  +E +  K E +        + +   S  +  + 
Sbjct: 68  ATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQA 127

Query: 70  NGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKE--RERRER 127
              R   +  R     +     ++     R    E   + ER   RR  ++E  +   ER
Sbjct: 128 RERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAER 187

Query: 128 RDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERE 187
            +R +  ER RDG+ R     R    +      R   +R     R    +   +  RE  
Sbjct: 188 GERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDR 247

Query: 188 LRERERDLEMRESRR 202
                 D E R  RR
Sbjct: 248 GDRDGDDGEGRGGRR 262

Length = 672

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

 Score = 63.9 bits (156), Expect = 5e-13
 Identities = 29/73 (39%), Positives = 49/73 (67%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+VGNL F+  E  + + F  +G +  V+LP D ++G+ KGFG+V+F+  E A+AA  AL
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 384 NGKLEIVGRTLKV 396
            G  +++GR +++
Sbjct: 61  GGT-DLLGRPVRL 72

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

>gnl|CDD|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 = 64.2 bits (157), Expect = 5e-13
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
           VF   +P  ATE  + E FS+ G V   RL+ DR++ + KG G+ EF D+ +   AI  L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 282 SGQLLLGQPVMVKPS 296
           +G    G+ + V  +
Sbjct: 61  NGYEFNGRALRVDFA 75

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

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

 Score = 63.5 bits (155), Expect = 8e-13
 Identities = 32/74 (43%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +YV NL F++T   L K+F  +G V  V +  D ET + KG  F+ F   E A     AL
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 384 NGKLEIVGRTLKVS 397
           N K E+ GRTLK S
Sbjct: 64  NNK-ELFGRTLKCS 76

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

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

 Score = 63.4 bits (155), Expect = 1e-12
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            K++VG L ++ T+  LRK F  FG +E   +  D +TG+ +G+GFV F   E A+ A  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 382 ALNGKLEIVGRTLKV 396
             N  ++  GR   V
Sbjct: 61  DPNPIID--GRKANV 73

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

 Score = 63.2 bits (154), Expect = 1e-12
 Identities = 30/74 (40%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +L++ NL +  TE  L KLF  +GP+  V LP+D  T + KGF FV +   EHA  A + 
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 383 LNGKLEIVGRTLKV 396
           L+G +   GR L +
Sbjct: 64  LDGTV-FQGRLLHL 76

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 29/73 (39%), Positives = 44/73 (60%), Gaps = 2/73 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +YV NL  +M + +L++LF  +G +   ++  D + G+ KGFGFV F   E A+ A   L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 384 NGKLEIVGRTLKV 396
           NGK E+ G+ L V
Sbjct: 63  NGK-EVNGKKLYV 74

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

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

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 33/73 (45%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L VGNL    T+ Q R+L  PFG VE   L     TG+ KG+GFV++A    A  A++ L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 384 NGKLEIVGRTLKV 396
           +GK +I GR L+V
Sbjct: 62  DGK-QIGGRKLQV 73

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

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

 Score = 62.8 bits (153), Expect = 2e-12
 Identities = 28/70 (40%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
           +F   +   A E  +YE F + G++  VRL  D +S R KG GY+EF    +   A+ AL
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 282 SGQLLLGQPV 291
            G  LLG+PV
Sbjct: 61  GGTDLLGRPV 70

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

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

 Score = 62.2 bits (152), Expect = 2e-12
 Identities = 34/72 (47%), Positives = 46/72 (63%), Gaps = 3/72 (4%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYV NL  ++TE  LR+ F P+G VE V+L  +    + +GF FV+FA  E A+AA   L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58

Query: 384 NGKLEIVGRTLK 395
           NG L + GRTL+
Sbjct: 59  NG-LVLDGRTLR 69

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

>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 62.6 bits (153), Expect = 2e-12
 Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 11/88 (12%)

Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVK--HIYVDKRSAGF----VYLR 551
           S+ L+L+NM  P      + D +++ ++EEEC KYG+V    ++    S       +++ 
Sbjct: 1   SKILVLRNMVTPG-----EIDEDLKDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVE 55

Query: 552 FESTEAAASAQRAMHMRWFARRLISAIF 579
           F   + A  A RA++ R+F  R ++A F
Sbjct: 56  FSDADEAIKAVRALNGRFFGGRKVTARF 83

This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. 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 RRMs and a C-terminal UHM domain. . Length = 85

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

 Score = 62.1 bits (151), Expect = 2e-12
 Identities = 27/74 (36%), Positives = 46/74 (62%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           ++YVG++ F + E  +R+ F PFGP++ + +  D  T + KGF FV++   E A+ A   
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 383 LNGKLEIVGRTLKV 396
           +NG + + GR +KV
Sbjct: 62  MNGVM-LGGRNIKV 74

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

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

 Score = 62.2 bits (152), Expect = 3e-12
 Identities = 30/73 (41%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 325 YVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
           +VGNL F++ E +LRK FE  G VE V++  D +TG  KGFG+V F   +    A     
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62

Query: 385 GKLEIVGRTLKVS 397
            KL+  GR ++V 
Sbjct: 63  IKLK--GRKIRVK 73

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

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

 Score = 61.8 bits (151), Expect = 3e-12
 Identities = 30/80 (37%), Positives = 46/80 (57%), Gaps = 4/80 (5%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHA----K 377
           R +++ NL F+ TE +L++LF  FG V+  ++  D  TG  KG  FV+F   E A    +
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 378 AAQSALNGKLEIVGRTLKVS 397
           AA +A +  L + GR L V+
Sbjct: 61  AADNAEDSGLSLDGRRLIVT 80

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|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 = 61.5 bits (150), Expect = 4e-12
 Identities = 31/74 (41%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 325 YVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
           +VGN+ ++ TE QL ++F   GPV   +L  D +TG+ KG+GF +F  +E A +A   LN
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 385 GKLEIVGRTLKVSS 398
           G  E  GR L+V  
Sbjct: 62  GY-EFNGRALRVDF 74

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

 Score = 66.9 bits (163), Expect = 6e-12
 Identities = 44/159 (27%), Positives = 74/159 (46%), Gaps = 17/159 (10%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +P   T+ ++   F+  G++   +L+ D+ + +S G G++ +        A+ +L+G  L
Sbjct: 11  LPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRL 70

Query: 287 LGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG 346
             Q   +K S A      S+ S  G            LYV  L   MT+ +L  +F PFG
Sbjct: 71  --QNKTIKVSYARP----SSDSIKGA----------NLYVSGLPKTMTQHELESIFSPFG 114

Query: 347 PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
            +   ++  D  TG  KG GF++F + + A  A   LNG
Sbjct: 115 QIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNG 153

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

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

 Score = 60.5 bits (147), Expect = 9e-12
 Identities = 31/74 (41%), Positives = 46/74 (62%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L+VGNL +++ +  L+  FE FG V   ++  D ETG+ +GFG+V F   E AK A  A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 383 LNGKLEIVGRTLKV 396
           ++GK E+ GR + V
Sbjct: 61  MDGK-ELDGRPINV 73

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

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

 Score = 60.4 bits (147), Expect = 1e-11
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVGNL   +TE  L +LF   GP++  +L   I       + FV++     A AA   +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKL---IREHGNDPYAFVEYYDHRSAAAALQTM 57

Query: 384 NGKLEIVGRTLKV 396
           NG+L I+G+ +KV
Sbjct: 58  NGRL-ILGQEIKV 69

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

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 4/75 (5%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL+VGNL + +   +L++ F  FG V+   +P D ETG  KG+GFV F+  +     ++A
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRD---GLENA 57

Query: 383 LNGKLEIV-GRTLKV 396
           L  +  I+ G  L+V
Sbjct: 58  LQKQKHILEGNKLQV 72

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

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

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
           T+F   +   A + D+ EFF + G+V DVR+  D +  RSKG G++EF        A+  
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDG-RSKGFGHVEFATEEGAQKALEK 59

Query: 282 SGQLLLGQPVMV 293
           SG+ LLG+ + V
Sbjct: 60  SGEELLGREIRV 71

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

>gnl|CDD|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 = 59.4 bits (144), Expect = 2e-11
 Identities = 31/75 (41%), Positives = 46/75 (61%), Gaps = 1/75 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++VGN+ +  TE QL+ +F   GPV   +L  D ETG+ KG+GF ++   E A +A   L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 384 NGKLEIVGRTLKVSS 398
           NG  E+ GR L+V +
Sbjct: 61  NGY-ELNGRQLRVDN 74

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|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 59.6 bits (145), Expect = 3e-11
 Identities = 30/77 (38%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 322 RKLYVGNLHFNMTE-TQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           R L+V  L     + + LRKLF   G     QL +    GQ +GF FV++A  E A+ AQ
Sbjct: 3   RCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIA-PNGQPRGFAFVEYATAEDAEEAQ 61

Query: 381 SALNGKLEIVGRTLKVS 397
            ALNG   + G  ++VS
Sbjct: 62  QALNGHS-LQGSPIRVS 77

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 59.1 bits (143), Expect = 3e-11
 Identities = 31/82 (37%), Positives = 46/82 (56%), Gaps = 5/82 (6%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL++G L F+  E  L ++F  +G +  V +  D ET + +GFGFV F   + AK A  A
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 383 LNGKLEIVGRTLKVSSVTDHVG 404
           +NGK  + GR ++V    D  G
Sbjct: 62  MNGK-SVDGRQIRV----DQAG 78

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

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

 Score = 58.7 bits (143), Expect = 4e-11
 Identities = 30/60 (50%), Positives = 35/60 (58%)

Query: 326 VGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
           V NL  +  E  LR+LF PFGP+  V L  D ETGQ +GF FV F   E A+ A   LNG
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

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

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

 Score = 58.9 bits (143), Expect = 4e-11
 Identities = 31/77 (40%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           DR L+VGNL   +TE  L +LF   GP+E V++P D   G+ K F FV F        A 
Sbjct: 1   DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAI 59

Query: 381 SALNGKLEIVGRTLKVS 397
             LNG + + GR L++ 
Sbjct: 60  QLLNG-IRLFGRELRIK 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 64.5 bits (157), Expect = 5e-11
 Identities = 61/263 (23%), Positives = 105/263 (39%), Gaps = 29/263 (11%)

Query: 55  KSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRE 114
           + R   R R D    +  R +R R R R ++R RR RDRD  RGR   R   R       
Sbjct: 3   RDRERGRLRNDTRRSDKGR-ERSRRRSRSRDRSRRRRDRDYYRGRRG-RSRSR-SPNRYY 59

Query: 115 RREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERER 174
           R   ++   R +RR     +E   + ER    R+      + ++  R   E   +  + R
Sbjct: 60  RPRGDRSYRRDDRRSGRNTKEPLTEAER--DDRTVFVLQLALKARERDLYEFFSKVGKVR 117

Query: 175 ELELERERERERELRERERDLEMRES---------RRYKEKKEVVEP-EADPERDQRTVF 224
           +++  ++R   R       +    ES         +    +  +V+  +A+  R  +   
Sbjct: 118 DVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAAT 177

Query: 225 AYQMPLKA-------------TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
                +               TE+++ + F   G + DV+L  D  + RSKG G+I+F+D
Sbjct: 178 HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHD 237

Query: 272 VMSVPMA-IALSGQLLLGQPVMV 293
                 A   ++G  L G+P+ V
Sbjct: 238 AEEAKEALEVMNGFELAGRPIKV 260

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|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 64.9 bits (159), Expect = 6e-11
 Identities = 33/202 (16%), Positives = 60/202 (29%), Gaps = 6/202 (2%)

Query: 25  SSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDK 84
            ++   A     +  + R    +    + E+  +   + + E                  
Sbjct: 62  GAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASA 121

Query: 85  ERHRRDRDRDRDRGRERERETERDRERSRERREKE-----KERERRERRDREKERERERD 139
               + R+R R+RG    R   R      E+   E      ER   E RD  + R    D
Sbjct: 122 PEAAQARER-RERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDRED 180

Query: 140 GERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEMRE 199
            +  +    R    +  R      R   RE    RE    R+    R  R R    + R 
Sbjct: 181 RQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARG 240

Query: 200 SRRYKEKKEVVEPEADPERDQR 221
               +++ +    + +    +R
Sbjct: 241 DDNREDRGDRDGDDGEGRGGRR 262

Length = 672

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

 Score = 58.4 bits (142), Expect = 6e-11
 Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 2/74 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            LYV NL  ++ + +LR+ F PFG +   ++  D E G+ KGFGFV F+  E A  A + 
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTE 61

Query: 383 LNGKLEIVGRTLKV 396
           +NG++ I G+ L V
Sbjct: 62  MNGRI-IGGKPLYV 74

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

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

 Score = 63.8 bits (155), Expect = 7e-11
 Identities = 36/116 (31%), Positives = 54/116 (46%), Gaps = 5/116 (4%)

Query: 286 LLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGA----IDRKLYVGNLHFNMTETQLRKL 341
                V  + +    +   ++    G A G   A        ++V NL  +  ET L +L
Sbjct: 230 QQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQL 289

Query: 342 FEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           F PFG V+ V++  D+ T QCKG+GFV     + A  A  +LNG   +  R L+VS
Sbjct: 290 FGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNG-YTLGNRVLQVS 344

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

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

 Score = 58.0 bits (141), Expect = 8e-11
 Identities = 31/79 (39%), Positives = 43/79 (54%), Gaps = 5/79 (6%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK---GFGFVQFAQLEHAKA 378
           R++YV NL F + E  LR +F  FG VE +++P   +  Q +   GF FV F     A+ 
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 379 AQSALNGKLEIVGRTLKVS 397
           A   LNG  E+ GR + VS
Sbjct: 61  ALQ-LNGT-ELGGRKISVS 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|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 57.8 bits (140), Expect = 8e-11
 Identities = 31/74 (41%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L  NMT+ ++R LF   G +E  +L  D  TGQ  G+GFV +   E A+ A + L
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 384 NGKLEIVGRTLKVS 397
           NG L +  +T+KVS
Sbjct: 64  NG-LRLQNKTIKVS 76

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

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

 Score = 64.1 bits (156), Expect = 9e-11
 Identities = 52/208 (25%), Positives = 89/208 (42%), Gaps = 25/208 (12%)

Query: 202 RYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRS 261
           R+ +K E    EA P +    ++   +     E  + E F+K G++    ++ D  S RS
Sbjct: 163 RFIKKHE---REAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRS 218

Query: 262 KGVGYIEFYDVMSVPMA-----------IALSGQLLLG--QPVMVKPSEAEKNLVQSNTS 308
           +G  ++ F        A                +L +G  Q    + +E  +   +    
Sbjct: 219 RGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQE 278

Query: 309 AGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFV 368
               A G        LYV NL   +T+ +LR+LF   G +   ++ LD E G  +GFGFV
Sbjct: 279 RKMKAQGV------NLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFV 331

Query: 369 QFAQLEHAKAAQSALNGKLEIVGRTLKV 396
            F+  E A  A + ++G++ + G+ L V
Sbjct: 332 CFSNPEEANRAVTEMHGRM-LGGKPLYV 358

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

 Score = 57.5 bits (140), Expect = 1e-10
 Identities = 23/61 (37%), Positives = 36/61 (59%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVG+LH ++TE  L ++F P GPV  +++  D+ T +  G+ +V F     A+ A   L
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 384 N 384
           N
Sbjct: 62  N 62

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

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

 Score = 57.2 bits (138), Expect = 1e-10
 Identities = 27/69 (39%), Positives = 42/69 (60%), Gaps = 1/69 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL+VG L+   TE ++ ++F P+G VE + +  D E  Q +G  FV+++  E A+AA  A
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59

Query: 383 LNGKLEIVG 391
           LNG   + G
Sbjct: 60  LNGVYTMRG 68

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

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+V NL ++ T+ QL + F   GP++   +  D  + +C+GFG+V FA  E AK A    
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 384 NGKLEIVGRTLKV 396
               +  GR + V
Sbjct: 62  KKT-KFGGRKIHV 73

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

 Score = 57.4 bits (138), Expect = 2e-10
 Identities = 31/78 (39%), Positives = 45/78 (57%), Gaps = 1/78 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++V NL  +  E+ L +LF PFG V  V++  D  T +CKGFGFV     + A  A ++L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 384 NGKLEIVGRTLKVSSVTD 401
           NG   +  R L+VS  T+
Sbjct: 66  NG-YRLGDRVLQVSFKTN 82

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 56.7 bits (137), Expect = 2e-10
 Identities = 34/87 (39%), Positives = 48/87 (55%), Gaps = 6/87 (6%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           DRKL+VG L    TE  +R+LFEPFG +E   + L    G  KG  FV+F+    A+AA 
Sbjct: 1   DRKLFVGMLSKQQTEDDVRRLFEPFGTIEECTI-LRGPDGNSKGCAFVKFSSHAEAQAAI 59

Query: 381 SALNGKLEIVGRTLKVSSVTDHVGTQD 407
           +AL+G      +T+  +S +  V   D
Sbjct: 60  NALHGS-----QTMPGASSSLVVKFAD 81

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

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

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +P   TE D+ + F + G+V   R+I DR + RS+G G++E         AI  L+G   
Sbjct: 7   LPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDF 66

Query: 287 LGQPVMVKPSEAEK 300
            G+ + V  +EA  
Sbjct: 67  GGRTLTV--NEARP 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 56.2 bits (136), Expect = 3e-10
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
           +F   +P   TE D+ E FSK G++  VR++ D++  +SKG  ++EF        A+ AL
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEAL 59

Query: 282 SGQLLLGQPVMVK 294
           +G+ L G+ + V 
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 61.1 bits (147), Expect = 3e-10
 Identities = 49/176 (27%), Positives = 79/176 (44%), Gaps = 1/176 (0%)

Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQP 290
           K TE  + E +    +     L ++ NSR+ +          +        + + +  Q 
Sbjct: 25  KLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQN 84

Query: 291 VMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVEL 350
              +    E       +S    +       +  L+VGNL +++TE  LR+LF+ FGPV+ 
Sbjct: 85  DGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKR 144

Query: 351 VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQ 406
           V+L  D ETG+ +GF FV+F   E A+ A   LNGK E+ GR L+V         +
Sbjct: 145 VRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGK-ELEGRPLRVQKAQPASQPR 199

Length = 306

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

 Score = 56.3 bits (136), Expect = 3e-10
 Identities = 29/79 (36%), Positives = 47/79 (59%), Gaps = 3/79 (3%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           ++L+V N+ F   +  LR++F  FGP+  V++  + E G  KGFGFV FA    A  A+ 
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFN-ERGS-KGFGFVTFANSADADRARE 58

Query: 382 ALNGKLEIVGRTLKVSSVT 400
            L+G   + GR ++V++ T
Sbjct: 59  KLHGT-VVEGRKIEVNNAT 76

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

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

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 26/74 (35%), Positives = 44/74 (59%), Gaps = 7/74 (9%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +L+VGNL  ++TE + ++LF  +G V  V L  +      KGFGF++     +A+ A++ 
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAE 56

Query: 383 LNGKLEIVGRTLKV 396
           L+G +   GR L+V
Sbjct: 57  LDGIM-RKGRQLRV 69

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

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

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 26/72 (36%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
           TVF   +     E ++ + FSK G++ DVRL+ +    +SKG  Y+EF +  SV  A+ L
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKG-KSKGYAYVEFENEESVQEALKL 59

Query: 282 SGQLLLGQPVMV 293
             +L+ G+P+ V
Sbjct: 60  DRELIKGRPMFV 71

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

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 30/74 (40%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L++ +L    T+  L +LF PFG V   ++ +D  TGQ K FGFV +   E A+AA  A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 384 NGKLEIVGRTLKVS 397
           NG  ++ G+ LKV 
Sbjct: 61  NG-FQVGGKRLKVQ 73

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

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

 Score = 58.1 bits (140), Expect = 3e-10
 Identities = 35/122 (28%), Positives = 56/122 (45%), Gaps = 1/122 (0%)

Query: 300 KNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIET 359
           +N+  +      +  G    +  KL++G L +   +  LR  F  FG V   ++ +D ET
Sbjct: 13  QNISSNGNVPVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRET 72

Query: 360 GQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDD 419
           G+ +GFGFV F     A AA S ++GK E+ GR ++V+   D             +    
Sbjct: 73  GRSRGFGFVNFNDEGAATAAISEMDGK-ELNGRHIRVNPANDRPSAPRAYGGGGGYSGGG 131

Query: 420 GG 421
           GG
Sbjct: 132 GG 133

Length = 144

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

 Score = 55.6 bits (135), Expect = 4e-10
 Identities = 25/73 (34%), Positives = 39/73 (53%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
           +VF   +P    E ++ + F   G V  VR++ DR +   KG GY+ F    SV +A+ L
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60

Query: 282 SGQLLLGQPVMVK 294
           +G  L G+ + VK
Sbjct: 61  NGIKLKGRKIRVK 73

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

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

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 29/74 (39%), Positives = 38/74 (51%), Gaps = 9/74 (12%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL+VGNL    T  +LR LFE +G V         E    K +GFV   + E A+ A  A
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTV--------TECDVVKNYGFVHMEEEEDAEDAIKA 52

Query: 383 LNGKLEIVGRTLKV 396
           LNG  E +G+ + V
Sbjct: 53  LNGY-EFMGKRINV 65

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

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

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 9/74 (12%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYV NL  + TE QLR+LF  +G VE V+   D        + FV F + + A  A   +
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 384 NGKLEIVGRTLKVS 397
           NGK E+ G  ++VS
Sbjct: 56  NGK-ELEGSPIEVS 68

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

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 34/73 (46%), Positives = 47/73 (64%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L    TE  LR++F  +GP+E VQ+  D +TG+ +GFGFV F  +E AK A+  L
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 384 NGKLEIVGRTLKV 396
           NG +EI GR ++V
Sbjct: 62  NG-MEIDGRRIRV 73

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

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

 Score = 56.1 bits (136), Expect = 4e-10
 Identities = 26/81 (32%), Positives = 45/81 (55%), Gaps = 5/81 (6%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +Y+G L + +TE  +  +F  +G +  + L  D +TG+ KGF F+ +        A   L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 384 NGKLEIVGRTLKVSSVTDHVG 404
           NG ++++GRT++V    DHV 
Sbjct: 72  NG-IKLLGRTIRV----DHVR 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 62.1 bits (151), Expect = 5e-10
 Identities = 44/165 (26%), Positives = 72/165 (43%), Gaps = 14/165 (8%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
           +F   +      + +++ FSK G +   ++  D N + S+G G++ F    S   AI  +
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGK-SRGYGFVHFEKEESAKAAIQKV 149

Query: 282 SGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKL 341
           +G LL  + V V                       +      LYV NL  ++ E +LR+L
Sbjct: 150 NGMLLNDKEVYVGR-------FIKKHEREAAPLKKF----TNLYVKNLDPSVNEDKLREL 198

Query: 342 FEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK 386
           F  FG +    +  D  +G+ +GF FV F + E A  A   +NGK
Sbjct: 199 FAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMNGK 242

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

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

 Score = 61.7 bits (150), Expect = 6e-10
 Identities = 46/158 (29%), Positives = 75/158 (47%), Gaps = 16/158 (10%)

Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQ 289
             TE  +Y+ F   G V  VR+  D  +RRS G GY+ F +      A+  ++ + L G+
Sbjct: 11  DVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGK 70

Query: 290 PVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVE 349
           P+ +  S+ + +L +S                  ++V NL  ++    L   F  FG + 
Sbjct: 71  PIRIMWSQRDPSLRRSGVG--------------NIFVKNLDKSVDNKALFDTFSKFGNIL 116

Query: 350 LVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKL 387
             ++  D E G+ +G+GFV F + E AKAA   +NG L
Sbjct: 117 SCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGML 153

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

 Score = 61.4 bits (149), Expect = 7e-10
 Identities = 34/115 (29%), Positives = 49/115 (42%), Gaps = 6/115 (5%)

Query: 33  REEKSERSYRKREDSEEEEEEEKSRSGKRSR---RDEDEENGSRRDRDRDRDRDKERHRR 89
           R+E+ +R   K    + +   E+ R   R R   RD    +  R  R+  R RD+ R   
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDR-RRYD 59

Query: 90  DRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERERDGERRS 144
            R     R     R  +R R RSR  R  E+ R R   RDR    +  +D ++RS
Sbjct: 60  SRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRR--LRDRSPSNQWRKDDKKRS 112

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

>gnl|CDD|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 = 55.0 bits (133), Expect = 7e-10
 Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 7/74 (9%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++VG L   +TE +LR LF PFG +  V++P        KG GFVQF     A+AA   L
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPG------KGCGFVQFVHRAAAEAAIQQL 57

Query: 384 NGKLEIVGRTLKVS 397
            G + I G  +++S
Sbjct: 58  QGTI-IGGSRIRLS 70

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

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

 Score = 55.2 bits (133), Expect = 8e-10
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +Y+G+L     E +L+K F  FG V+ V++    +TG  K +GF+QF   E A  A  ++
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 384 NGKLEIVGRTLKV 396
           N  L ++G+ L+V
Sbjct: 62  NNYL-LMGKVLQV 73

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

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

 Score = 55.5 bits (133), Expect = 8e-10
 Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++V NL  +  E+ L ++F PFG V  V++  D  T +CKGFGFV     + A  A ++L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 384 NGKLEIVGRTLKVS 397
           NG   +  R L+VS
Sbjct: 66  NG-YRLGDRVLQVS 78

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 55.3 bits (134), Expect = 8e-10
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++V  +H    E  +   F  FG ++ + L LD  TG  KG+  +++   + A+AA   L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 384 NGKLEIVGRTLKVS 397
           NGK E++G+T+ V 
Sbjct: 69  NGK-ELLGQTISVD 81

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

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 60.7 bits (147), Expect = 1e-09
 Identities = 42/203 (20%), Positives = 90/203 (44%), Gaps = 11/203 (5%)

Query: 10  EKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEE 69
            K    + +  ++  + S K+ ++E++ +    K++  E+ +EE K R  K   +++   
Sbjct: 85  SKGPAAKTKPAKEPKNESGKEEEKEKE-QVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPP 143

Query: 70  NGSRRDRDRDRDRDKERHR-RDRDRDRDRGRERERETERDRERSRERREKEKERER---- 124
               +++++  +  ++R   + R+R R + R ++   ++   + +E  E+EK+R+     
Sbjct: 144 KEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREA 203

Query: 125 ----RERRDREKERERERD-GERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELE 179
                E  D  +ERE+E D G+ R ++ S     +SR+SS  SRR      + +    + 
Sbjct: 204 VKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISRRSSSSLKKPDPSPSMA 263

Query: 180 RERERERELRERERDLEMRESRR 202
               RE   R   R         
Sbjct: 264 SPETRESSKRTETRPRTSLRPPS 286

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 54.7 bits (132), Expect = 1e-09
 Identities = 26/64 (40%), Positives = 36/64 (56%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL+VG +  N+ E  LR LFE FG +  + +  D  TG  KG  F+ +   E A  AQSA
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 383 LNGK 386
           L+ +
Sbjct: 67  LHEQ 70

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 60.8 bits (148), Expect = 1e-09
 Identities = 48/226 (21%), Positives = 93/226 (41%), Gaps = 17/226 (7%)

Query: 45  EDSEEEEEEEKSRSGKRSRRDEDEEN---GSRRDRDRDRDRDKERHRRDRDRDRDRGRER 101
            +  + +E+   ++  +  R +D       +RRDR+  RD    R RR+   +R+  R  
Sbjct: 583 GEETKPQEQPAPKAEAKPERQQDRRKPRQNNRRDRNERRDTRDNRTRREGRENREENRRN 642

Query: 102 ERETERDRERSRERR---EKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRS 158
            R+ ++    +RE +     EK R + E++ +   RER+R   RR+    +R + Q  ++
Sbjct: 643 RRQAQQQTAETRESQQAEVTEKARTQDEQQ-QAPRRERQR---RRND--EKRQAQQEAKA 696

Query: 159 SSRSRRERERESERERELELERERERERELRERER---DLEMRESRRYKEKKEVVEPEAD 215
            +   +  +   + ER  +++  R++ R+L ++ R    +         E+    EP   
Sbjct: 697 LNVEEQSVQETEQEERVQQVQPRRKQ-RQLNQKVRIEQSVAEEAVAPVVEETVAAEPVVQ 755

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRS 261
                RT           +    +      + RD    M R SRRS
Sbjct: 756 EVPAPRTELVKVPLPVVAQTAPEQDEENNAENRDNN-GMPRRSRRS 800

Length = 1068

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

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 24/64 (37%), Positives = 36/64 (56%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYV  L   MT+ +L  LF P+G +   ++  D  TG  +G GF++F +   A+ A  AL
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 384 NGKL 387
           NG +
Sbjct: 63  NGTI 66

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

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

 Score = 54.1 bits (131), Expect = 2e-09
 Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +Y+G+L     E +LRK F  FG V  ++L    +TG+ KG+ FV+F   E AK     +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 384 NGKLEIVGRTLKVS 397
           N  L +  R LK  
Sbjct: 62  NNYL-LFERLLKCK 74

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 60.1 bits (145), Expect = 2e-09
 Identities = 30/78 (38%), Positives = 51/78 (65%), Gaps = 1/78 (1%)

Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
           AI  ++YVG++ F + E  +R+ F+PFGP++ + +  D  TG+ KGF FV++   E A+ 
Sbjct: 105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQL 164

Query: 379 AQSALNGKLEIVGRTLKV 396
           A   +NG++ + GR +KV
Sbjct: 165 ALEQMNGQM-LGGRNIKV 181

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

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

 Score = 53.7 bits (130), Expect = 2e-09
 Identities = 30/74 (40%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVGNL F  TE Q+ +LF   G ++ + + LD  T    GF FV++   E A+ A   L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 384 NG-KLEIVGRTLKV 396
           NG KL+   R ++V
Sbjct: 61  NGTKLD--DRIIRV 72

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

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

 Score = 53.9 bits (129), Expect = 2e-09
 Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +++ NL  +  E  L ++F PFG V  V++  D  T +CKGFGFV     E A  A ++L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 384 NGKLEIVGRTLKVSSVTD 401
           NG   +  + L+VS  T 
Sbjct: 64  NG-YRLGDKILQVSFKTS 80

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

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

 Score = 53.9 bits (129), Expect = 2e-09
 Identities = 30/74 (40%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++V NL     E+ L +LF PFG V  V++  D  T +CKGFGFV     + A  A ++L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 384 NGKLEIVGRTLKVS 397
           NG   +  R L+VS
Sbjct: 64  NG-YRLGDRVLQVS 76

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGP-VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           L++GNL   + E  L   F  FG  ++  ++  D +TG  KGF F+ +   E + AA  A
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 383 LNGKLEIVGRTLKVS 397
           +NG+  +  R + VS
Sbjct: 64  MNGQY-LCNRPITVS 77

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

 Score = 58.4 bits (141), Expect = 3e-09
 Identities = 30/74 (40%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L   MT+ ++R LF   G +E  +L  D  TGQ  G+GFV + + E A+ A ++L
Sbjct: 6   LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSL 65

Query: 384 NGKLEIVGRTLKVS 397
           NG L +  +T+KVS
Sbjct: 66  NG-LRLQNKTIKVS 78

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

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

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 24/64 (37%), Positives = 37/64 (57%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L++G+L   M E  +   F   G V  V++  + +TG+  G+GFV+FA  E A+ A  +L
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 384 NGKL 387
           NGK 
Sbjct: 62  NGKP 65

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

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

 Score = 53.3 bits (129), Expect = 3e-09
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +++ NL  ++    L   F  FG +   ++  D E G  KG+GFV F   E A  A   +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 384 NGKLEIVGRTLKV 396
           NG L +  + + V
Sbjct: 64  NGML-LNDKKVFV 75

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

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

 Score = 53.2 bits (128), Expect = 3e-09
 Identities = 27/65 (41%), Positives = 38/65 (58%), Gaps = 3/65 (4%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+VGNL F  TE +LR  F   G +  V++    ++G+CKGF FV F ++E    A +AL
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIE---FATNAL 57

Query: 384 NGKLE 388
            GK  
Sbjct: 58  KGKHL 62

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 53.3 bits (129), Expect = 3e-09
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+VG L  N+ +  L+++F  +G V+ V LP+D E    +G+ +V+F   E A+ A   +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 384 NGKLEIVGRTLKVS 397
           +G  +I G+ + V 
Sbjct: 61  DGG-QIDGQEVTVE 73

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

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 58.7 bits (142), Expect = 4e-09
 Identities = 40/227 (17%), Positives = 88/227 (38%), Gaps = 4/227 (1%)

Query: 9   LEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDE 68
           L      +R +K      + K    +E    S ++ E  +E+ +EEK +  ++ + +  +
Sbjct: 71  LSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKD 130

Query: 69  ENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERR 128
                  +++   ++KE   +++++  +  R+RE E +R+R R++ R +K  +++   ++
Sbjct: 131 RKPKEEAKEKRPPKEKE---KEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKK 187

Query: 129 DREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELEREREREREL 188
               E E++R   R +          +          ++RE+      E E  +  E   
Sbjct: 188 KEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISR 247

Query: 189 RERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATER 235
           R     L+  +        E  E     E   RT         A+ R
Sbjct: 248 RSSS-SLKKPDPSPSMASPETRESSKRTETRPRTSLRPPSARPASAR 293

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

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

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
           TV+   +    TE DV EFF K  ++  VRL  D+ +   KG G+++F D  S+  A+ L
Sbjct: 1   TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59

Query: 282 SGQLLLGQPVMV 293
            G +L G+P+ +
Sbjct: 60  DGTVLCGRPIRI 71

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

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

 Score = 52.4 bits (126), Expect = 6e-09
 Identities = 25/72 (34%), Positives = 44/72 (61%), Gaps = 1/72 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++VG+L   +    LR  F PFG +   ++  D++TG+ KG+GFV F + E A+ A  ++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 384 NGKLEIVGRTLK 395
           NG+  + GR ++
Sbjct: 62  NGQ-WLGGRAIR 72

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

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

 Score = 52.6 bits (127), Expect = 6e-09
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +YVGNL   +TE  L +LF   GPV  V +P D  T   +G+GFV+F   E A  A   +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 384 NGKLEIVGRTLKVS 397
           N  +++ G+ ++V+
Sbjct: 61  NM-IKLYGKPIRVN 73

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

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

 Score = 52.6 bits (127), Expect = 6e-09
 Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLP--LDIETGQCK---GFGFVQFAQLEHAKA 378
           L+V NL+F  TE  L+K FE  G V  V +    D +        G+GFV+F   E A+ 
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 379 AQSALNGKL 387
           A   L G +
Sbjct: 63  ALKRLQGTV 71

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

 Score = 52.5 bits (126), Expect = 7e-09
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+V NL F++T+  L   F    P++   +  D ETG+ +G+GFV FA LE A+ A + L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 384 NGKLEIVGRTLKV 396
             K  + GR L++
Sbjct: 62  KNKK-LHGRILRL 73

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 52.2 bits (126), Expect = 8e-09
 Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +L V NLH+++TE  L +LF   G V+ V++  D  +G+ +G   V F + E A+ A   
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIKQ 60

Query: 383 LNGKLEIVGRTLKVS 397
            NG L + G+ ++V 
Sbjct: 61  FNGVL-LDGQPMQVE 74

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

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

 Score = 52.3 bits (126), Expect = 9e-09
 Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQ-LPLDI--ETGQCKGFGFVQFAQLEHAKAA 379
           +L++GNL   +TE  L KLF  +G ++    L        GQ +G+ FV F   E A+ A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 380 QSALNGKLEIVGRTLKVS 397
             +LNGK   +G+ L V 
Sbjct: 61  LKSLNGKT-ALGKKLVVR 77

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

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

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-A 280
           TV+   +P   T  D+++ FSK GKV  V ++ D+ +R+SKGV +I F D       + A
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 281 LSGQLLLGQPVMVK 294
           L+ + L G+ +   
Sbjct: 63  LNNKELFGRTLKCS 76

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

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
            RT+F   +  + TE  +YE F +AG +  V++  D N  + K   ++ F   +SVP AI
Sbjct: 1   DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAI 59

Query: 280 AL-SGQLLLGQPVMVK 294
            L +G  L G+ + +K
Sbjct: 60  QLLNGIRLFGRELRIK 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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 57.0 bits (137), Expect = 1e-08
 Identities = 46/158 (29%), Positives = 71/158 (44%), Gaps = 17/158 (10%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +P   T+R++Y  F   G +   R++ D  +  S G  +++F        AI  L+G   
Sbjct: 115 LPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNG--- 171

Query: 287 LGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG 346
               + V+     K L  S    GG +       D  LYV NL   +T+ QL  +F  +G
Sbjct: 172 ----ITVR----NKRLKVSYARPGGESIK-----DTNLYVTNLPRTITDDQLDTIFGKYG 218

Query: 347 PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
            +    +  D  TG  +G  FV+F + E A+ A SALN
Sbjct: 219 QIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALN 256

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 30/76 (39%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           DR L+VGNL   +TE  + +LF   GPV  V++P D + G+ K F FV F        A 
Sbjct: 1   DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNFKHEVSVPYAM 59

Query: 381 SALNGKLEIVGRTLKV 396
           + LNG +++ GR L +
Sbjct: 60  NLLNG-IKLYGRPLNI 74

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

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 19/71 (26%), Positives = 34/71 (47%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F   +    T  ++ E F   G +  + ++ D+ + + KG  YIEF D  SV  A+ L+
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLN 61

Query: 283 GQLLLGQPVMV 293
                G+ + V
Sbjct: 62  ESEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

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

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 23/48 (47%), Positives = 32/48 (66%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
           KL+VG L  ++TE  LR+ F  +G VE V++  D ETG+ +GF FV F
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

>gnl|CDD|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 = 51.8 bits (125), Expect = 1e-08
 Identities = 27/63 (42%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL V N+ F  T+ +LR+LF PFG V+ V+LP   + G  +GF FV+F   + A+ A  A
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFD-GSHRGFAFVEFVTKQEAQNAMEA 60

Query: 383 LNG 385
           L  
Sbjct: 61  LKS 63

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

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

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 26/51 (50%), Positives = 34/51 (66%), Gaps = 3/51 (5%)

Query: 338 LRKLFEPFGPVELV--QLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK 386
           LRK+F  FG  ++V   +P+D ETG+ KG+ FV+FA  E AK A  ALNG 
Sbjct: 24  LRKIFSKFGVGKIVGIYMPVD-ETGKTKGYAFVEFATPEEAKEAVKALNGY 73

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

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 2/62 (3%)

Query: 232 ATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQP 290
            TE D+ + FSK G +  +R++ D  + RSKG  ++EF D      A+ AL+G+ L G+ 
Sbjct: 10  TTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRE 68

Query: 291 VM 292
           + 
Sbjct: 69  LR 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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 57.8 bits (139), Expect = 2e-08
 Identities = 42/219 (19%), Positives = 110/219 (50%), Gaps = 21/219 (9%)

Query: 11   KTVEEQRQQKQDDDSSSKKKAKREE--KSERSYRKREDSEEEEEEEKSRSGKRSRRDEDE 68
            K  EE R ++       +KK K EE  K+E +  K E+ ++ EEE+K     + +  E++
Sbjct: 1587 KKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEK 1646

Query: 69   ENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRE-RREKEKERERRER 127
                         +  E  ++  + ++ +  E  ++ E D++++ E ++ +E E++  E 
Sbjct: 1647 -------------KKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEA 1693

Query: 128  RDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRE-----RERESERERELELERER 182
              +E E  ++ +  ++  +  ++ + + +++   ++ +     +E E ++++  E +++ 
Sbjct: 1694 LKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDE 1753

Query: 183  ERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQR 221
            E ++++   +++ E +     KEK+ V+E E D E ++R
Sbjct: 1754 EEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKR 1792

Length = 2084

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

 Score = 51.0 bits (123), Expect = 2e-08
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L++G L ++ TE  LR+ F  +G V    +  D  TG+ +GFGFV FA      +    L
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFA---DPSSVDKVL 57

Query: 384 NGKLEIV-GRT 393
             K  ++ GR 
Sbjct: 58  AAKPHVLDGRE 68

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

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

 Score = 51.2 bits (122), Expect = 2e-08
 Identities = 27/74 (36%), Positives = 47/74 (63%), Gaps = 3/74 (4%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVGNL  ++TE  + +LF   GP +  ++ +D  T     + FV+F +  HA A+ +A+
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59

Query: 384 NGKLEIVGRTLKVS 397
           NG+ +I+G+ +KV+
Sbjct: 60  NGR-KIMGKEVKVN 72

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

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

 Score = 51.0 bits (122), Expect = 2e-08
 Identities = 28/62 (45%), Positives = 39/62 (62%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYV NL   +TE +LRK+FE +G +    L  D  TG  +G  FV++ + E A+AA S+L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 384 NG 385
           NG
Sbjct: 63  NG 64

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

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

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 5/73 (6%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +Y G    +   + +++LFE  GPV  V +             F+ F  LE A+ A   L
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQ----PHAFITFENLEAAQLAIETL 57

Query: 384 NGKLEIVGRTLKV 396
           NG   + G  +KV
Sbjct: 58  NGA-SVDGNCIKV 69

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

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

 Score = 56.1 bits (135), Expect = 3e-08
 Identities = 26/108 (24%), Positives = 44/108 (40%), Gaps = 2/108 (1%)

Query: 20  KQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRD 79
           ++ D    K + +  ++S    R+R        +   RS +RS R++      RR   R 
Sbjct: 3   EEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRS 62

Query: 80  RDRDK-ERHRRDRDRDRDRGRERER-ETERDRERSRERREKEKERERR 125
               +    RR RDR R R R     E  R R R R    + ++ +++
Sbjct: 63  PRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKK 110

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

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 56.0 bits (135), Expect = 3e-08
 Identities = 34/218 (15%), Positives = 81/218 (37%), Gaps = 9/218 (4%)

Query: 19  QKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSR-RDRD 77
            K   D + K+  K   K   +  K     + E  ++    K   ++E ++   + ++  
Sbjct: 69  SKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEP 128

Query: 78  RDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERE 137
           +DR   +E   +   +++++ +E++ E  RDRE  + +RE+ + + R ++  ++K   ++
Sbjct: 129 KDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEK-KRERVRAKSRPKKPPKKKPPNKK 187

Query: 138 RDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEM 197
           ++       R     +   +         E +   ERE E +  ++RE      E D   
Sbjct: 188 KEPPEEEKQRQAAREAVKGK-------PEEPDVNEEREKEEDDGKDRETTTSPMEEDESR 240

Query: 198 RESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATER 235
           + S   +     ++                     T  
Sbjct: 241 QSSEISRRSSSSLKKPDPSPSMASPETRESSKRTETRP 278

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

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

 Score = 50.7 bits (121), Expect = 3e-08
 Identities = 32/77 (41%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           DR L+VGNL   + E  L +LF   GP+  V +  D E G+ K FGFV F   E    A 
Sbjct: 1   DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAI 59

Query: 381 SALNGKLEIVGRTLKVS 397
           + LNG + + GR +KV 
Sbjct: 60  ALLNG-IRLYGRPIKVH 75

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

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 50.8 bits (122), Expect = 3e-08
 Identities = 29/74 (39%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L V  L +  TE  L+  F  FG + +VQ+  D +TGQ KGFGFV+FA  E        
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYE---DQVKV 57

Query: 383 LNGKLEIVGRTLKV 396
           L+ +  I GR   V
Sbjct: 58  LSQRHMIDGRWCDV 71

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 50.5 bits (121), Expect = 3e-08
 Identities = 30/73 (41%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDI-ETGQCKGFGFVQFAQLEHAKAAQS 381
           K+ V N+ F  T  +LR+LF  FG ++ V+LP  +  TG  +GFGFV F   + AK A  
Sbjct: 2   KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61

Query: 382 ALNGKLEIVGRTL 394
           AL     + GR L
Sbjct: 62  ALCHSTHLYGRRL 74

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 55.7 bits (135), Expect = 4e-08
 Identities = 31/179 (17%), Positives = 57/179 (31%), Gaps = 12/179 (6%)

Query: 44  REDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERER 103
           R           +     +RR       +R+      +    +               E 
Sbjct: 59  RGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEA 118

Query: 104 ETERDRERSRERREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSR 163
            +  +  ++RERRE+ +   R   R   +  E+     R  ++       +  R     R
Sbjct: 119 ASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDR 178

Query: 164 RERERESERERELELERERERERELRERE-RDLEMRESRRYKEKKEVVEPEADPERDQR 221
            +R+ E+ER            ER  RE   RD + R+ R  +E+ +  E     +   R
Sbjct: 179 EDRQAEAER-----------GERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDR 226

Length = 672

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

 Score = 50.4 bits (121), Expect = 4e-08
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 325 YVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
           +VGN+ +  T  +L++ F+  G +  + +  D  TGQ KGF +++F      + A   LN
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLN 61

Query: 385 GKLEIVGRTLKVS 397
              E  GR +KV+
Sbjct: 62  ES-EFRGRQIKVT 73

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

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

 Score = 50.4 bits (121), Expect = 4e-08
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
            +F   +P   T  D+   F  AG    VRL+ D+ + +SKG  ++EF    +  M  AL
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDT--AEAMTKAL 59

Query: 282 S 282
            
Sbjct: 60  K 60

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

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

 Score = 50.3 bits (121), Expect = 5e-08
 Identities = 19/49 (38%), Positives = 32/49 (65%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
           RTVF   +P  ATE ++ E FS+ G+V+  R++ D+ +  SKG  +++F
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKF 49

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

 Score = 49.6 bits (119), Expect = 6e-08
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 5/75 (6%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++V NL +++ E +LRKLF   G +  V+L  +   G+ KG+ +V+F   E+ ++ Q AL
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKN-YKGKSKGYAYVEF---ENEESVQEAL 57

Query: 384 NGKLEIV-GRTLKVS 397
               E++ GR + VS
Sbjct: 58  KLDRELIKGRPMFVS 72

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

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

 Score = 49.5 bits (118), Expect = 6e-08
 Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 9/74 (12%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K++VGN+    T  +LR LFE FG V        +E  + K + FV   + E A AA  A
Sbjct: 2   KIFVGNVSATCTSDELRGLFEEFGRV--------VECDKVKDYAFVHMEREEEALAAIEA 53

Query: 383 LNGKLEIVGRTLKV 396
           LNGK E+ GR + V
Sbjct: 54  LNGK-EVKGRRINV 66

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

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

 Score = 49.6 bits (119), Expect = 7e-08
 Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
           I  +++VG +  + TE +LR  F  FG V+ V++  D   G  KG+GFV F   E A+  
Sbjct: 1   IPNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKI 59

Query: 380 QSALNGKLEIVGRTLKVS 397
            +   G L   G+ L + 
Sbjct: 60  LA--MGNLNFRGKKLNIG 75

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

 Score = 49.2 bits (118), Expect = 9e-08
 Identities = 30/73 (41%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V NL +  T   LR++FE +G V  V +P D  T + +GF FV+F     A+ A  A+
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 384 NGKLEIVGRTLKV 396
           +GK E+ GR L+V
Sbjct: 61  DGK-ELDGRELRV 72

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

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

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 10/77 (12%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK--GFGFVQFAQLEHAKAA 379
           R L+V N++ N+ + +LR LFE FG +  +          CK  GF  V +  +  A+ A
Sbjct: 2   RTLFVRNINSNVEDEELRALFEQFGDIRTLY-------TACKHRGFIMVSYYDIRAARRA 54

Query: 380 QSALNGKLEIVGRTLKV 396
           + AL G  E+ GR L +
Sbjct: 55  KRALQGT-ELGGRKLDI 70

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

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 4/75 (5%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K++VG L  ++TE + ++ F  FG V   QL  D +TG+ +GFGFV F   +   A +  
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF---DSESAVERV 57

Query: 383 L-NGKLEIVGRTLKV 396
              G LE+ G+ ++V
Sbjct: 58  FSAGMLELGGKQVEV 72

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

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           ++L+V  +  ++T+ QL +LF+    +E   L  D  TG+ KGF +V ++    A  A+ 
Sbjct: 1   QRLFV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKE 59

Query: 382 ALNGKLEIVGRTLKVS 397
            LNG     G  LKV 
Sbjct: 60  KLNGFEYPPGNRLKVK 75

This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAAQ 380
           K++VG +  + +E  LR+LFE +G V  + +  D      Q KG  FV F   + A  AQ
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62

Query: 381 SAL 383
           +AL
Sbjct: 63  NAL 65

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

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

 Score = 49.1 bits (117), Expect = 1e-07
 Identities = 30/82 (36%), Positives = 44/82 (53%), Gaps = 4/82 (4%)

Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
           GP G     L++ +L     + +L ++F PFG V   ++ +D  T Q K FGFV F    
Sbjct: 1   GPEGC---NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPA 57

Query: 375 HAKAAQSALNGKLEIVGRTLKV 396
            A+AA  A+NG  +I  + LKV
Sbjct: 58  SAQAAIQAMNG-FQIGMKRLKV 78

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

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

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L +  L   +T+ + R LF   GPV+  ++  D  TG   GFGFV +   E A+ A   L
Sbjct: 3   LIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTL 62

Query: 384 NGKLEIVGRTLKVS 397
           NG L++  + +KV+
Sbjct: 63  NG-LQLQNKRIKVA 75

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

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 25/63 (39%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +L V NL   + E +LRKLFE FG +  VQL    + G+ + FGFV +   E A+ A   
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYT-KDGKFRKFGFVGYKTEEEAQKALKH 60

Query: 383 LNG 385
            N 
Sbjct: 61  FNN 63

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYV N+        LR+LF  +GP+  V +PLD  T + +GF +VQF  +  A+ A   L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 384 NGKLEIVGRTLKV 396
           +     +GR +++
Sbjct: 63  DRT-RFLGREIEI 74

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 54.0 bits (129), Expect = 2e-07
 Identities = 42/221 (19%), Positives = 92/221 (41%), Gaps = 4/221 (1%)

Query: 29   KKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHR 88
            K + ++   +     R D   EE   K+   K++   + EE   + +  + +  D  +  
Sbjct: 1073 KPSYKDFDFDAKEDNRADEATEEAFGKAEEAKKTETGKAEE-ARKAEEAKKKAEDARKAE 1131

Query: 89   RDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKER-ERERDGERRSSSR 147
              R  +  R  E  R+ E  +     R+ ++  +    R+  + ++ E  R  E    + 
Sbjct: 1132 EARKAEDARKAEEARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAE 1191

Query: 148  SRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEMRESRRYKEKK 207
              R +  +R++ +  + E ER++E  R+ E  ++ E  ++  E ++D E  E+++ +E++
Sbjct: 1192 ELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAE--EAKKAEEER 1249

Query: 208  EVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVR 248
               E     E         Q  +KA E    +   KA + +
Sbjct: 1250 NNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKK 1290

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 54.0 bits (129), Expect = 2e-07
 Identities = 39/224 (17%), Positives = 106/224 (47%), Gaps = 10/224 (4%)

Query: 2    EFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKR 61
            E  + +  +K  EE ++  +     +KKKA+  +K+E + +K E++++ +E +K     +
Sbjct: 1429 EKKKADEAKKKAEEAKKADE-----AKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAK 1483

Query: 62   SRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKE 121
             + DE ++      +  D  +     ++  D  +     ++ +  +  E +++  E +K 
Sbjct: 1484 -KADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKA 1542

Query: 122  RERRERRDREKERERERDGERRSSSRSRRSSSQS----RRSSSRSRRERERESERERELE 177
             E+++  + +K  E ++  E++ +  ++++        R++    + E  R  E  +  E
Sbjct: 1543 EEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYE 1602

Query: 178  LERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQR 221
             E++ + E   +  E  ++  E ++ +E+K+ VE     E +++
Sbjct: 1603 EEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEK 1646

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 54.0 bits (129), Expect = 2e-07
 Identities = 32/200 (16%), Positives = 96/200 (48%), Gaps = 5/200 (2%)

Query: 11   KTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKRE--DSEEEEEEEKSRSGKRSRRDEDE 68
            K  EE ++  +   +   KKA   +K+E   +  E   +EE ++ E+ +  + +++ E++
Sbjct: 1516 KKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEED 1575

Query: 69   ENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERR 128
            +N + R  +  +  ++ R         +  + +  E ++  E   +  E +K  E +++ 
Sbjct: 1576 KNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKV 1635

Query: 129  DREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELEREREREREL 188
            ++ K++E E   E++ +   +++  +++  ++   ++ E + ++  E +   E E++   
Sbjct: 1636 EQLKKKEAE---EKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAE 1692

Query: 189  RERERDLEMRESRRYKEKKE 208
              ++   E +++   K+K+ 
Sbjct: 1693 ALKKEAEEAKKAEELKKKEA 1712

Length = 2084

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

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 22/48 (45%), Positives = 29/48 (60%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
           K++VG L  N TE  ++K F  FG VE   L  D +T + +GFGFV F
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48

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

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 50.6 bits (121), Expect = 2e-07
 Identities = 29/88 (32%), Positives = 44/88 (50%)

Query: 54  EKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSR 113
            +SRS +RSRR     +  RR+R R+R R +ER RR R R R   R R   + R      
Sbjct: 4   SRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSRS 63

Query: 114 ERREKEKERERRERRDREKERERERDGE 141
               + ++R+R   +D  + ++RER   
Sbjct: 64  RSPSRRRDRKRERDKDAREPKKRERQKL 91

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 30/74 (40%), Positives = 44/74 (59%), Gaps = 9/74 (12%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE---TGQCKGFGFVQFAQLEHAKA 378
           R L+VGNL   +TE +LR+ FE +G VE V    DI+    GQ   + FV+F  L+ A  
Sbjct: 3   RTLFVGNLEITITEEELRRAFERYGVVEDV----DIKRPPRGQGNAYAFVKFLNLDMAHR 58

Query: 379 AQSALNGKLEIVGR 392
           A+ A++G+   +GR
Sbjct: 59  AKVAMSGQ--YIGR 70

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 47.5 bits (114), Expect = 2e-07
 Identities = 26/60 (43%), Positives = 32/60 (53%), Gaps = 6/60 (10%)

Query: 338 LRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           L KLF PFG VE ++L          GF FV+F+  E A+ A   LNG L   GR L+V 
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVL-FGGRPLRVD 54

(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|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 53.9 bits (130), Expect = 2e-07
 Identities = 45/209 (21%), Positives = 80/209 (38%), Gaps = 10/209 (4%)

Query: 9   LEKTVEEQRQQKQD----DDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRR 64
           LEK  EE +  K +    +D   + + + EE   +    + +    EEE +    +    
Sbjct: 683 LEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQL--QSRLE 740

Query: 65  DEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREK----EK 120
           + +EE     +   +     E    + +   +   + + E E   E+ +  +E+    E+
Sbjct: 741 ELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEE 800

Query: 121 ERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELER 180
           E E  ERR    ERE E   +RR          +        + +   E   E E ELE 
Sbjct: 801 ELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEE 860

Query: 181 ERERERELRERERDLEMRESRRYKEKKEV 209
            +E   EL   + +LE       +EK+E+
Sbjct: 861 LKEELEELEAEKEELEDELKELEEEKEEL 889

Length = 1163

>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 14/89 (15%)

Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKH--IYVDKRSAG-------FV 548
           S  ++L+NM  P      D D +++G+V EEC K+G V    IY +K+           +
Sbjct: 1   SRVMVLRNMVGPE-----DLDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 55

Query: 549 YLRFESTEAAASAQRAMHMRWFARRLISA 577
           ++ F     A  A +A++ RWF  R + A
Sbjct: 56  FVEFSLPSEAEKAIQALNGRWFGGRKVKA 84

This subgroup corresponds to the RRM3 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), 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. The research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 98

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

 Score = 47.9 bits (115), Expect = 3e-07
 Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 7/66 (10%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF----AQLEHAKAA 379
           L+VG L  ++TE+ L + F  FG V  V++    + G  +GF ++      AQL+  K  
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCK-- 59

Query: 380 QSALNG 385
            S LNG
Sbjct: 60  -STLNG 64

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

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

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 332 NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK-LEIV 390
           ++TE  LR+ F PFG ++ + +  D +T + KG  +V+FA+   A  A   +NGK L   
Sbjct: 13  SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

Query: 391 GRTLKV 396
            + LKV
Sbjct: 73  TKPLKV 78

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 47.2 bits (113), Expect = 4e-07
 Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           ++   +P   TE D+ EFFS  GKV  VRL+  RN  R +G  ++EF        A+   
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLV--RNKDRPRGFAFVEFASPEDAEAALKKL 58

Query: 283 GQLLLG 288
             L+L 
Sbjct: 59  NGLVLD 64

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

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

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
            +F   +P   TE ++ +FFS+ G V+DV++I DR    SKG G++ F         +A+
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAG-VSKGYGFVTFETQEDAEKILAM 62

Query: 282 S 282
            
Sbjct: 63  G 63

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

 Score = 47.4 bits (113), Expect = 4e-07
 Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL++G L +  T+  L+  F  +G +    +  D  T + +GFGFV FA      AA +A
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 383 LNGKLEIVGRT 393
              K++  GR 
Sbjct: 61  RPHKVD--GRE 69

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

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

 Score = 47.3 bits (113), Expect = 5e-07
 Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 3/77 (3%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+VGNL ++  +  L + F+  G V  V++  D + G+ KGFG V+FA  E A+ A    
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKA-LEK 59

Query: 384 NGKLEIVGRTLKVSSVT 400
           +G+ E++GR ++V   T
Sbjct: 60  SGE-ELLGREIRVDLAT 75

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

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 52.8 bits (126), Expect = 5e-07
 Identities = 28/210 (13%), Positives = 99/210 (47%), Gaps = 8/210 (3%)

Query: 7    EYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDE 66
            +  +K  EE    K+  +++  +     +++E +  K E +E+++EE K ++    ++ E
Sbjct: 1332 DAAKKKAEEA---KKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAE 1388

Query: 67   DEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDR-----ERSRERREKEKE 121
            +++      +  + D+ K    +     + +  E +++ E  +     ++  E  +K  E
Sbjct: 1389 EKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADE 1448

Query: 122  RERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERE 181
             +++    ++ E  +++  E + +  +++ + +++++    ++  E + + +   +    
Sbjct: 1449 AKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEA 1508

Query: 182  RERERELRERERDLEMRESRRYKEKKEVVE 211
            +++  E ++ E   +  E+++ +E K+  E
Sbjct: 1509 KKKADEAKKAEEAKKADEAKKAEEAKKADE 1538

Length = 2084

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

 Score = 48.0 bits (114), Expect = 5e-07
 Identities = 27/90 (30%), Positives = 34/90 (37%), Gaps = 7/90 (7%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  L+V NL ++ TE  L   F  FG V      +D  TG+ KG GFV F       A  
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

Query: 381 SALNGKLEIVGRTLKVSSVTDHVGTQDTAA 410
                     G T   S ++    T D   
Sbjct: 61  K----NAPAAGST---SLLSGSSLTADIGD 83

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

 Score = 47.3 bits (112), Expect = 5e-07
 Identities = 30/82 (36%), Positives = 45/82 (54%), Gaps = 4/82 (4%)

Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
           GP G     L++ +L    T+T L + F PFG V   ++ +D +T   K FGFV +   +
Sbjct: 1   GPEGC---NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPD 57

Query: 375 HAKAAQSALNGKLEIVGRTLKV 396
            A+AA  A+NG  +I  + LKV
Sbjct: 58  SAQAAIQAMNG-FQIGTKRLKV 78

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

>gnl|CDD|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 = 46.8 bits (112), Expect = 6e-07
 Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
           +F  Q+P  ATE DV   F + G + +V +I D+++ +SKG  +++F        AI AL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 282 SGQLLL---GQPVMVK 294
            G++ +    +P+ VK
Sbjct: 62  HGKVTMPGASRPLQVK 77

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

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 52.5 bits (125), Expect = 6e-07
 Identities = 31/220 (14%), Positives = 99/220 (45%), Gaps = 8/220 (3%)

Query: 7    EYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDE 66
            +  +K  E +++  +   +   KKA   +K+E     ++  E ++ EEK ++ +  + +E
Sbjct: 1500 DEAKKAAEAKKKADEAKKAEEAKKADEAKKAEE---AKKADEAKKAEEKKKADELKKAEE 1556

Query: 67   DEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRE 126
             ++   ++  +  +  +++++   R  +  +  E  R  E  +    E++ K +E ++ E
Sbjct: 1557 LKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAE 1616

Query: 127  RRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERE-----RESERERELELERE 181
                + E  ++ + E++   + ++  ++ ++ +   ++  E        E ++  E +++
Sbjct: 1617 EAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKK 1676

Query: 182  RERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQR 221
             E  ++  E E+       +  +E K+  E +     +++
Sbjct: 1677 AEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKK 1716

Length = 2084

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

 Score = 47.1 bits (111), Expect = 6e-07
 Identities = 24/60 (40%), Positives = 34/60 (56%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LY+  LH   T+  L KL +P+G +   +  LD  T +CKG+GFV F     A+ A +AL
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63

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

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 52.0 bits (125), Expect = 6e-07
 Identities = 52/204 (25%), Positives = 88/204 (43%), Gaps = 12/204 (5%)

Query: 9   LEKTVEEQRQQKQD-DDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDED 67
            E  +E   ++++D ++  ++++   EEK ER+   RE + E E E + +    +  +E+
Sbjct: 507 AEDRIERLEERREDLEELIAERRETIEEKRERAEELRERAAELEAEAEEKREAAAEAEEE 566

Query: 68  EENGSRRDRDRDRDRDKERHRRDR-DRDRDRGRERERETERDRERSRERREK--EKERER 124
            E       + +    + + R +  +R R        + E + ER RE+RE   E   ER
Sbjct: 567 AEEAREEVAELNSKLAELKERIESLERIRTLLAAIA-DAEDEIERLREKREALAELNDER 625

Query: 125 RER----RDREKERERERDGERRSSSRSRRS---SSQSRRSSSRSRRERERESERERELE 177
           RER    R+R++E E E D  R   +R  +        +          ER+  +     
Sbjct: 626 RERLAEKRERKRELEAEFDEARIEEAREDKERAEEYLEQVEEKLDELREERDDLQAEIGA 685

Query: 178 LERERERERELRERERDLEMRESR 201
           +E E E   ELRER   LE R   
Sbjct: 686 VENELEELEELRERREALENRVEA 709

Length = 880

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

 Score = 47.0 bits (111), Expect = 6e-07
 Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L  NMT+ + + LF   G +E  +L  D  TGQ  G+GFV +     A  A + L
Sbjct: 6   LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 384 NGKLEIVGRTLKVS 397
           NG L++  +T+KVS
Sbjct: 66  NG-LKLQTKTIKVS 78

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

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

 Score = 46.8 bits (112), Expect = 7e-07
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
           TE  +YE FS AG V  +R+  D  +RRS G  Y+ F +      A+  L+  ++ G+P+
Sbjct: 12  TEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKGKPI 71

Query: 292 MVKPS 296
            +  S
Sbjct: 72  RIMWS 76

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

 Score = 46.6 bits (110), Expect = 8e-07
 Identities = 30/74 (40%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L  NMT+ +LR LF   G VE  +L  D   G   G+GFV +   + A+ A + L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 384 NGKLEIVGRTLKVS 397
           NG L +  +T+KVS
Sbjct: 64  NG-LRLQSKTIKVS 76

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

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

 Score = 46.6 bits (110), Expect = 8e-07
 Identities = 30/74 (40%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L  NMT+ + R LF   G +E  +L  D  TGQ  G+GFV +   + A+ A + L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 384 NGKLEIVGRTLKVS 397
           NG L +  +T+KVS
Sbjct: 65  NG-LRLQTKTIKVS 77

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

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

 Score = 50.8 bits (121), Expect = 1e-06
 Identities = 40/197 (20%), Positives = 77/197 (39%), Gaps = 42/197 (21%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           ++YV ++H +++ET ++ +FE FG +   QL         KG+GF+++  L+    A ++
Sbjct: 206 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS 265

Query: 383 LN-----GKLEIVGRTLK---------------------VSSVTDHVGTQDTAAKSADFD 416
           +N     G+   VG+ +                       ++ T  +   +  A +A   
Sbjct: 266 MNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGAAV-- 323

Query: 417 DDDGGGLALNAQSRAL----LMQKLDRTGI---ATSIAGSLGVAPAVNGSAVNQQAISLP 469
                 L   AQS A     L   +    +   A   A  +   P    + V    + +P
Sbjct: 324 ------LGPRAQSPATPSSSLPTDIGNKAVVSSAKKEAEEVPPLPQAAPAVVKPGPMEIP 377

Query: 470 V-VGQPAVPVPAVTAPV 485
             V  P + +P++ AP 
Sbjct: 378 TPVPPPGLAIPSLVAPP 394

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

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

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 24/73 (32%), Positives = 39/73 (53%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F   +P   TE +  E+FS+ GKV D +L+ D ++ RS+G G++ F    +V    +  
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 283 GQLLLGQPVMVKP 295
              L G+ V VK 
Sbjct: 62  MLELGGKQVEVKR 74

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

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

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
           +RT++   +    T   + EFFS+AG+V+ VR+  D    +     ++EF +  SV  A+
Sbjct: 4   RRTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDET--QPTRYAFVEFAEQTSVINAL 61

Query: 280 ALSGQLLLGQPVMVKPS 296
            L+G +  G+P+ V  S
Sbjct: 62  KLNGAMFGGRPLKVNHS 78

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative RNA exonuclease NEF-sp

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 21/71 (29%), Positives = 38/71 (53%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +YV     ++TE  L++ F     +E + LP D+ +G+   + F++F Q + A AA   +
Sbjct: 1   IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60

Query: 384 NGKLEIVGRTL 394
            G+ E+ GR  
Sbjct: 61  TGEWELKGRRA 71

This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

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

 Score = 46.1 bits (109), Expect = 1e-06
 Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L + NL    T+ Q  +L  PFG +E   L     TG  KG+GFV++ + + A  A+S L
Sbjct: 2   LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61

Query: 384 NGKLEIVGRTLKV 396
            GK ++  RTL V
Sbjct: 62  LGK-QLGSRTLYV 73

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

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

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 23/50 (46%), Positives = 31/50 (62%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFA 371
           +K++VG L  N+TET LRK F  FG V  V +  D E  + +GFGF+ F 
Sbjct: 3   KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFE 52

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 30/98 (30%), Positives = 50/98 (51%), Gaps = 12/98 (12%)

Query: 497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKH--IY-----VDKRSAGFVY 549
           PS+ +LL+NM  P      + D +++ +V+EECSKYG+V    I+          A  ++
Sbjct: 1   PSKVVLLRNMVGPG-----EVDEDLEPEVKEECSKYGKVTKVLIFEIPGASPDDEAVRIF 55

Query: 550 LRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEA 587
           + FE  E+A  A   ++ R+F  R + A F   E +  
Sbjct: 56  VEFERVESAIKAVVDLNGRFFGGRTVKASFYDEERFRR 93

This subgroup corresponds to the RRM of SPF45, also termed RNA-binding motif protein 17 (RBM17), an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. . Length = 96

>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 = 46.3 bits (110), Expect = 1e-06
 Identities = 25/75 (33%), Positives = 44/75 (58%), Gaps = 2/75 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL+V  L F++T+ +L KLF+  G V+ V+L +   +G+ KG  +V++     A  A   
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRL-VTNRSGKPKGLAYVEYENESSASQAVLK 62

Query: 383 LNGKLEIVGRTLKVS 397
           ++G  EI  +T+ V+
Sbjct: 63  MDG-TEIKEKTISVA 76

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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 28/73 (38%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVG L   +TE  LR  F  FG +  + +   +   QC    FV F   E A+ A   L
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITV---VPRQQC---AFVTFTTREAAEKAAERL 57

Query: 384 NGKLEIVGRTLKV 396
             KL I GR LK+
Sbjct: 58  FNKLIINGRRLKL 70

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|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 = 45.7 bits (109), Expect = 1e-06
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE--TGQCKGFGFVQFAQLEHAKAAQS 381
           LYVGNL +  T+  L       G V++  +        G+ KGF +V+FA    A A + 
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 382 ALNGKLEIVGRTLKVS 397
            L G+ E  G+   V+
Sbjct: 61  KLEGR-EFNGKKCVVT 75

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

 Score = 50.6 bits (121), Expect = 2e-06
 Identities = 26/64 (40%), Positives = 38/64 (59%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVG+L  ++TE +L  LF+PFGPV  V++  D  T +  G+G+V F     A+ A   +
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 384 NGKL 387
           N K 
Sbjct: 63  NFKR 66

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

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 28/73 (38%), Positives = 45/73 (61%), Gaps = 3/73 (4%)

Query: 325 YVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
           Y+GNL +++TE  +R+ F+    +  V+L  D ETG+ KGFG V FA  E   AA   L+
Sbjct: 3   YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KLD 60

Query: 385 GKLEIVGRTLKVS 397
           G + + GR ++++
Sbjct: 61  GTV-LCGRPIRIA 72

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

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 18/62 (29%), Positives = 31/62 (50%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           TE D+ E+FS+ G V  V ++ D+ + + +G  ++ F D   V   +      + G  V 
Sbjct: 12  TEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQKYHTINGHRVE 71

Query: 293 VK 294
           VK
Sbjct: 72  VK 73

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 50.9 bits (121), Expect = 2e-06
 Identities = 31/223 (13%), Positives = 106/223 (47%), Gaps = 4/223 (1%)

Query: 2    EFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREE---KSERSYRKREDSEEEEEEEKSRS 58
            E  + +  +K  EE +++  +   ++  K K +E   K+E   +  E  ++ EE +K+  
Sbjct: 1389 EKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADE 1448

Query: 59   GKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREK 118
             K+   +  +   +++  +  +  D+ + + +  +  D  +++  E ++  + +++  E 
Sbjct: 1449 AKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEA 1508

Query: 119  EKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELEL 178
            +K+ +  ++ +  K+ +  +  E    +   + + + +++    + E  +++E +++ E 
Sbjct: 1509 KKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEE 1568

Query: 179  ERERERERELRERERD-LEMRESRRYKEKKEVVEPEADPERDQ 220
             ++ E ++ +  R+ +  +  E  R +E  ++ E E   + ++
Sbjct: 1569 AKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEE 1611

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 50.5 bits (120), Expect = 2e-06
 Identities = 31/216 (14%), Positives = 114/216 (52%), Gaps = 6/216 (2%)

Query: 11   KTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEEN 70
            +  E+++++ +    ++KKKA+ ++K++ + +K E+ +++ +E K  +  + + DE ++ 
Sbjct: 1367 EAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKK 1426

Query: 71   GSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETE-----RDRERSRERREKEKERERR 125
               + +  D  + K    +  D  + +  E ++  E      + +++ E ++K +E ++ 
Sbjct: 1427 AEEK-KKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKA 1485

Query: 126  ERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERE 185
            +   ++ E  +++  E + ++ +++ + +++++    + +  +++E  ++ +  ++ E +
Sbjct: 1486 DEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEK 1545

Query: 186  RELRERERDLEMRESRRYKEKKEVVEPEADPERDQR 221
            ++  E ++  E++++   K+ +E  + E D     R
Sbjct: 1546 KKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALR 1581

Length = 2084

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 47.9 bits (114), Expect = 2e-06
 Identities = 41/99 (41%), Positives = 51/99 (51%), Gaps = 2/99 (2%)

Query: 98  GRERERETERDRERSRERREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRR 157
           GR R R   R R R R R      RERR  R R +ER+R R    RS  RSRRS S  R 
Sbjct: 2   GRSRSRSPRRSRRRGRSR--SRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRH 59

Query: 158 SSSRSRRERERESERERELELERERERERELRERERDLE 196
            S      R R+ +RER+ +    ++RER+   +E DLE
Sbjct: 60  RSRSRSPSRRRDRKRERDKDAREPKKRERQKLIKEEDLE 98

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>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 = 45.5 bits (108), Expect = 2e-06
 Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
           ++  +F   +P   T+ ++ + F K G V+ VRL+ +R+  + KG+ Y+E+ +  S   A
Sbjct: 1   EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSG-KPKGLAYVEYENESSASQA 59

Query: 279 I 279
           +
Sbjct: 60  V 60

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

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 31/76 (40%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           RT+    +    +E D+ EFFS  G+V  VRL  DR    S    ++EF D  S   A+ 
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEFADAESALSALN 58

Query: 281 LSGQLLLGQPVMVKPS 296
           LSG LL G P+ V PS
Sbjct: 59  LSGTLLGGHPLRVSPS 74

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

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 10/77 (12%)

Query: 322 RKLYVGNLH-FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
            +++VGNL+   +++  L ++F  +G +  + L         KG+GFVQF   E A+AA 
Sbjct: 1   SRVFVGNLNTDKVSKEDLEEIFSKYGKILGISLH--------KGYGFVQFDNEEDARAAV 52

Query: 381 SALNGKLEIVGRTLKVS 397
           +  NG+ EI G+ L ++
Sbjct: 53  AGENGR-EIAGQKLDIN 68

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

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 50.7 bits (121), Expect = 2e-06
 Identities = 42/210 (20%), Positives = 86/210 (40%), Gaps = 2/210 (0%)

Query: 3   FDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRS 62
           + +Y  L +   +  Q+   D+    + +K+E + E     +   E +EEE++ +  +  
Sbjct: 229 YLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEE 288

Query: 63  RRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKER 122
            +   +E    +      +R K              ++ E+E ++++E   E  EKE + 
Sbjct: 289 LKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKE-EIEELEKELKE 347

Query: 123 ERRERRDREKERERERDGERRSSS-RSRRSSSQSRRSSSRSRRERERESERERELELERE 181
              +R   E+E E+    + +         + +   S   S   + +E E E + E E+E
Sbjct: 348 LEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKE 407

Query: 182 RERERELRERERDLEMRESRRYKEKKEVVE 211
            +   EL E+E DL   E +   +  E +E
Sbjct: 408 AKLLLELSEQEEDLLKEEKKEELKIVEELE 437

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 50.1 bits (119), Expect = 2e-06
 Identities = 37/206 (17%), Positives = 83/206 (40%), Gaps = 11/206 (5%)

Query: 13  VEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGS 72
           +EE+R+ +Q  +   ++K K+ EK +R  R+      E +E+ + +       E+    +
Sbjct: 84  LEEERRHRQRLEKDKREK-KKREKEKRGRRRHHSLGTESDEDIAPAQMVDIVTEEMPENA 142

Query: 73  RRDRDRDRDRDKERHRRDRDRDR----------DRGRERERETERDRERSRERREKEKER 122
               + D+D +      D D D+           + R  E     ++       +K K+ 
Sbjct: 143 LPSDEDDKDPNDPYRALDIDLDKPLADSEKLPVQKHRNAETSKSPEKGDVPAVEKKSKKP 202

Query: 123 ERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERER 182
           +++E++++EKER++++  E         +   S  S++      E               
Sbjct: 203 KKKEKKEKEKERDKDKKKEVEGFKSLLLALDDSPASAASVAEADEASLANTVSGTAPDSE 262

Query: 183 ERERELRERERDLEMRESRRYKEKKE 208
             E +  E E   +  + ++ K++KE
Sbjct: 263 PDEPKDAEAEETKKSPKHKKKKQRKE 288

This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown. Length = 561

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 29/76 (38%), Positives = 41/76 (53%), Gaps = 8/76 (10%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIET---GQCKGFGFVQFAQLEHAKAAQ 380
           ++V NL F++T   L+ LF   G V    L  D++T   G+ KGFG V F   E A+ A 
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNV----LRADVKTDNDGRSKGFGTVLFESPEDAQRAI 56

Query: 381 SALNGKLEIVGRTLKV 396
              NG  ++ GR L+V
Sbjct: 57  EMFNG-YDLEGRELEV 71

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

>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 26/96 (27%), Positives = 44/96 (45%), Gaps = 20/96 (20%)

Query: 500 CLLLKNMFD-PAMETDPDFDL--------EIQGDVEE-------ECSKYGRVKHIYVDKR 543
            +LLKNM+  P                  EIQ   +E       E S++G ++ + V   
Sbjct: 1   TILLKNMYPNPDNAIASLDGQGVLTLSEEEIQEHFDEFYEDVFLELSRFGEIEDLVVCDN 60

Query: 544 SA----GFVYLRFESTEAAASAQRAMHMRWFARRLI 575
                 G VY++FE+ E A +A +A++ R++A R +
Sbjct: 61  LGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPL 96

This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants. . Length = 102

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

 Score = 49.5 bits (118), Expect = 3e-06
 Identities = 32/121 (26%), Positives = 47/121 (38%), Gaps = 11/121 (9%)

Query: 3   FDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRS 62
            DE    E+   E+ + +  D SS + + +  ++S    R R  S E    E SR   R 
Sbjct: 1   RDEEPDRER---EKSRGRDRDRSSERPRRRSRDRSRFRDRHRR-SRERSYREDSRPRDRR 56

Query: 63  RRDEDEENGSRRDRDRDRDRDKERHRRDRD-RDRDRGRERERETERDRERSRERREKEKE 121
           R D            R     + R R  R  R      E+ R   RDR  S + R+ +K+
Sbjct: 57  RYDSRS-----PRSLRYSSVRRSRDRPRRRSRSVRSI-EQHRRRLRDRSPSNQWRKDDKK 110

Query: 122 R 122
           R
Sbjct: 111 R 111

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

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 50.1 bits (119), Expect = 3e-06
 Identities = 34/216 (15%), Positives = 110/216 (50%), Gaps = 13/216 (6%)

Query: 11   KTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKRED-------SEEEEEEEKSRSGKRSR 63
            K  EE+++  +   +   KKA+ ++K+E + +  ED       +EE ++ E++R  +  +
Sbjct: 1540 KKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMK 1599

Query: 64   RDEDEENGSRRD-RDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKER 122
              E+E+     + +  +  + K    +  + ++ +  + +++   +++++ E ++ E+E 
Sbjct: 1600 LYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEEN 1659

Query: 123  ERRERRDREKERERERDGE--RRSSSRSRRSSSQSRRSSSRSRRE---RERESERERELE 177
            + +   + +K  E ++  E  +++    ++++   ++ +  +++    +++E+E +++ E
Sbjct: 1660 KIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAE 1719

Query: 178  LERERERERELRERERDLEMRESRRYKEKKEVVEPE 213
              ++ E E +++  E   E  E ++  E+ +  E E
Sbjct: 1720 ELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEE 1755

Length = 2084

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

 Score = 44.4 bits (106), Expect = 3e-06
 Identities = 13/44 (29%), Positives = 24/44 (54%)

Query: 527 EECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWF 570
           +  S +G V+ I + K+  GF ++ F + EAA  A + ++   F
Sbjct: 3   KLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLF 46

(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|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 50.5 bits (121), Expect = 3e-06
 Identities = 43/231 (18%), Positives = 90/231 (38%), Gaps = 4/231 (1%)

Query: 9   LEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEE--EKSRSGKRSRRDE 66
           LE+  EE  + +++ +   ++  + E++ E    + E+  EE EE  E+    K    + 
Sbjct: 241 LEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEEL 300

Query: 67  DEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRE 126
           + E    R+R  + + + E      +  +++    + E E       E  +   E E  +
Sbjct: 301 EGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAK 360

Query: 127 RRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERER 186
               E++     +         R   ++     +  R E E        LE   ER  ER
Sbjct: 361 EE-LEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSER 419

Query: 187 ELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDV 237
            L + + +L+  E+   + + E+ E   + E  +  +   +  LK  ER++
Sbjct: 420 -LEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKELEREL 469

Length = 1163

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 20/55 (36%), Positives = 35/55 (63%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
           K++VG L  + TE Q+++ F  FG +E ++LP+D +T + +GF FV +   E  +
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQ 55

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|215589 PLN03121, PLN03121, nucleic acid binding protein; Provisional

 Score = 48.7 bits (116), Expect = 3e-06
 Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 9/64 (14%)

Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG---YIEFYDVMSVPMAIALSGQLLL 287
           KATE+DVY+FFS  G +  V +I      RS       Y+ F D  ++  A+ LSG  ++
Sbjct: 16  KATEKDVYDFFSHCGAIEHVEII------RSGEYACTAYVTFKDAYALETAVLLSGATIV 69

Query: 288 GQPV 291
            Q V
Sbjct: 70  DQRV 73

Length = 243

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

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 24/63 (38%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVGNL   +TE  L+++F+  GPV+ V++  D +  +   +GFV++ Q   A+ A   L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 384 NGK 386
           NG+
Sbjct: 60  NGR 62

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

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 26/92 (28%)

Query: 300 KNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIET 359
           ++LV +N   GG   G                 ++  +L ++FE +G VE + +P     
Sbjct: 2   QHLVVAN---GGLGNG-----------------VSREELLRVFEKYGTVEDLVMPPG--- 38

Query: 360 GQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG 391
              K + FV ++ +E A AA  ALNGK   + 
Sbjct: 39  ---KPYCFVSYSSIEDAAAAYDALNGKELELP 67

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

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFG-PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           L++G+L   M E  +++ F   G  V  V++  +  TG   G+ FV+FA    A+     
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 383 LNGKL 387
           LNGK 
Sbjct: 62  LNGKP 66

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

>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
           +RTV+   +  + TE  +   FS  G+V D R+  D NS       +IEF D      A+
Sbjct: 2   RRTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNS--VLRFAFIEFTDEEGARAAL 59

Query: 280 ALSGQLLLGQPVMVKPS 296
           +LSG +L   PV V PS
Sbjct: 60  SLSGTMLGFYPVRVLPS 76

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

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

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 22/62 (35%), Positives = 34/62 (54%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYV  L   MT+ +L +LF  +G +   ++  D  TG  +G GF++F +   A+ A   L
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 384 NG 385
           NG
Sbjct: 63  NG 64

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

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-A 280
            +F   +  + TE+++   FSK G+V +V L+ D  +  S+G G++ F  V     AI  
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 281 LSGQLLLGQPVMV 293
           L+G+ L G+ + V
Sbjct: 63  LNGKELEGRVIKV 75

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

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 23/77 (29%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPM 277
           +D   ++   +P + TE D+   FS+ G++ D+ L+ D+ + +SKG  ++ + D  S  +
Sbjct: 7   KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTIL 66

Query: 278 AI-ALSGQLLLGQPVMV 293
           A+  L+G  LLG+ + V
Sbjct: 67  AVDNLNGIKLLGRTIRV 83

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

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 46.8 bits (111), Expect = 4e-06
 Identities = 29/73 (39%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 73  RRDRDRDRDRDKERHRRDRDRDRDRGRER-ERETERDRERSRERREKEKERERRERRDRE 131
           RR R R R R ++R  R R+R R R R+R  R   R   RSR  R   + R R     R 
Sbjct: 10  RRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSRSRSPSRR 69

Query: 132 KERERERDGERRS 144
           ++R+RERD + R 
Sbjct: 70  RDRKRERDKDARE 82

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

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

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 23/75 (30%), Positives = 39/75 (52%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F   +P   TE D+ ++FS+ G V +V ++ D   +R +G G+I F    SV   +   
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEH 64

Query: 283 GQLLLGQPVMVKPSE 297
              + G+ V VK +E
Sbjct: 65  FHDINGKKVEVKRAE 79

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

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

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 8/66 (12%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +LYV     + +E+ +R++F P+G V+ V++           F FV+F  LE A  A+ +
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKM--------ISNFAFVEFESLESAIRAKDS 52

Query: 383 LNGKLE 388
           ++GK+ 
Sbjct: 53  VHGKVL 58

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 45.0 bits (106), Expect = 4e-06
 Identities = 22/66 (33%), Positives = 41/66 (62%), Gaps = 1/66 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R L++GNL  N++E +LR+ F+ +G +E V +      GQ   + F++F  L+ A  A+ 
Sbjct: 9   RNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPAR-GQGGAYAFLKFQNLDMAHRAKV 67

Query: 382 ALNGKL 387
           A++G++
Sbjct: 68  AMSGRV 73

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B 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. RBM15B belongs 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 = 85

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

 Score = 44.5 bits (106), Expect = 4e-06
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+V N   +  ++ +R LFE +G +  ++ P  +   + + F +VQF   E A AA + L
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILSIRFP-SLRFNKTRRFCYVQFTSPESAAAAVALL 61

Query: 384 NGKLE 388
           NGKL 
Sbjct: 62  NGKLG 66

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

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 44.6 bits (105), Expect = 4e-06
 Identities = 20/56 (35%), Positives = 37/56 (66%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
           +K++VG L+   TE ++R+ F  FG +E ++LP+D +T + +GF F+ F + +  K
Sbjct: 5   KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVK 60

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 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 = 44.5 bits (106), Expect = 4e-06
 Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 2/48 (4%)

Query: 228 MPLKATERDVYEFFSKAGK--VRDVRLIMDRNSRRSKGVGYIEFYDVM 273
           + L  TE D+ +  S      ++DVRLI D+ +  S+G  ++EF  + 
Sbjct: 10  LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLE 57

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

 Score = 44.7 bits (105), Expect = 4e-06
 Identities = 30/74 (40%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L  NMT+ +L+ LF   G +E  +L  D  TGQ  G+GFV +   + A+ A + L
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 384 NGKLEIVGRTLKVS 397
           NG L +  +T+KVS
Sbjct: 67  NG-LRLQTKTIKVS 79

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

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 49.4 bits (117), Expect = 5e-06
 Identities = 46/204 (22%), Positives = 94/204 (46%), Gaps = 7/204 (3%)

Query: 10   EKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEE 69
            ++  EE   + ++   +   KA+   K+E + +K ED+ + EE  K+   +++      E
Sbjct: 1090 DEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARKAEEARKAEDARKAEEARKAE 1149

Query: 70   NGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRD 129
            +  R +  R +  D  +    R  +  +  E  R+ E  R ++ E R+ E  R+    R 
Sbjct: 1150 DAKRVEIAR-KAEDARKAEEARKAEDAKKAEAARKAEEVR-KAEELRKAEDARKAEAARK 1207

Query: 130  REKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERER--E 187
             E+ER+ E   E R +  ++++ +  +   ++   E  +++E ER  E  R+ E  R   
Sbjct: 1208 AEEERKAE---EARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAH 1264

Query: 188  LRERERDLEMRESRRYKEKKEVVE 211
               R+  ++  E+R+  E K+  E
Sbjct: 1265 FARRQAAIKAEEARKADELKKAEE 1288

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 49.4 bits (117), Expect = 5e-06
 Identities = 31/189 (16%), Positives = 87/189 (46%), Gaps = 4/189 (2%)

Query: 7    EYLEKTVEEQRQQKQ--DDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRR 64
            E  +K  E + + ++    +   KK  + ++K     +K E+ ++ EEE K ++ + +++
Sbjct: 1610 EEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKK 1669

Query: 65   DEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRER-REKEKERE 123
             E+++  +   +  + D  K      ++ +  +  E  ++ E + ++  E  ++ E+E +
Sbjct: 1670 AEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENK 1729

Query: 124  RRERRDREKERERERDGER-RSSSRSRRSSSQSRRSSSRSRRERERESERERELELERER 182
             +    +++  E ++  E  +     ++  +  ++   +   E  +E E   E EL+ E 
Sbjct: 1730 IKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEED 1789

Query: 183  ERERELRER 191
            E+ R   ++
Sbjct: 1790 EKRRMEVDK 1798

Length = 2084

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

 Score = 44.9 bits (107), Expect = 5e-06
 Identities = 27/75 (36%), Positives = 49/75 (65%), Gaps = 1/75 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + L+V  L+++ TE++LR+ FE +GP++ ++L  D +TG+ +G+ F++F      KAA  
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 382 ALNGKLEIVGRTLKV 396
             +GK +I GR + V
Sbjct: 62  YADGK-KIDGRRVLV 75

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 44.2 bits (105), Expect = 5e-06
 Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 8/81 (9%)

Query: 316 PYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH 375
           P+ A     +VGNL FN  +  L  +F+    V+ V+L  D ET + KGF +V+F  +E 
Sbjct: 1   PFTA-----FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVES 54

Query: 376 AKAAQSALNGKLEIVGRTLKV 396
            K A    +G L    R+L+V
Sbjct: 55  LKEAL-EYDGALFD-DRSLRV 73

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 44.2 bits (105), Expect = 5e-06
 Identities = 25/81 (30%), Positives = 44/81 (54%), Gaps = 2/81 (2%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGP-VELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
           D  ++VG+L  ++T+  L++ F    P V   ++ +D  TG+ KG+GFV+F   +    A
Sbjct: 1   DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60

Query: 380 QSALNGKLEIVGRTLKVSSVT 400
            + +NG      R ++VS  T
Sbjct: 61  LTEMNGVY-CSSRPMRVSPAT 80

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

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

 Score = 44.1 bits (105), Expect = 6e-06
 Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             ++VGN+   +++  +RKL E  G V   +   D  TG+ K FGF +F   E A  A  
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 382 ALNGKLEIVGRTLKVS 397
            LNG LE+ G+ L V 
Sbjct: 61  LLNG-LELGGKKLLVK 75

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

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 44.1 bits (104), Expect = 7e-06
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++VGNL F   E  L ++F   G +E V++  D +T   KGF +VQF      + A   L
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL-LL 60

Query: 384 NGKLE--IVGRTLKVS 397
           N K    ++ R L+VS
Sbjct: 61  NEKKFPPMLPRELRVS 76

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 44.2 bits (104), Expect = 7e-06
 Identities = 27/70 (38%), Positives = 43/70 (61%), Gaps = 7/70 (10%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE---TGQCKGFGFVQFAQLEHAK 377
           +R L++GNL   +TET LR+ F+ FG +  V    DI+    GQ   +GF++F  L+ A 
Sbjct: 7   NRTLFLGNLDITVTETDLRRAFDRFGVITEV----DIKRPGRGQTSTYGFLKFENLDMAH 62

Query: 378 AAQSALNGKL 387
            A+ A++GK+
Sbjct: 63  RAKLAMSGKV 72

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

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 48.7 bits (117), Expect = 7e-06
 Identities = 25/161 (15%), Positives = 61/161 (37%), Gaps = 6/161 (3%)

Query: 9   LEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDE 68
           LEK  E   + K    +  +++A++EE       KRE  EE + E +  +   +  +   
Sbjct: 21  LEKLKELGIEVKSHSSTVEEEEARKEEA------KREAEEEAKAEAEEAAAAEAEEEAKA 74

Query: 69  ENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERR 128
           E  +    +   +         R  + +  R  E    R + +   +++K  + ++++ +
Sbjct: 75  EAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPK 134

Query: 129 DREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERE 169
            +     +   G +    R  R   + ++   +   +  RE
Sbjct: 135 RKAARGGKRGKGGKGRRRRRGRRRRRKKKKKQKPTEKIPRE 175

Length = 746

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

 Score = 44.1 bits (104), Expect = 7e-06
 Identities = 24/57 (42%), Positives = 34/57 (59%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
           KL+VG L  ++ E  L + F  FGPVE  ++  D +TG+ +GFGFV F   + A  A
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57

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

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

 Score = 44.0 bits (104), Expect = 7e-06
 Identities = 19/47 (40%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
           ++VG +   M ET++R  F  +G V+ V++  D  TG  KG+GFV F
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSF 53

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

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 43.9 bits (104), Expect = 8e-06
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
           T F   +P    + D+   F     V+ VRL+ D+ + + KG  Y+EF DV S+  A+  
Sbjct: 3   TAFVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEY 61

Query: 282 SGQLLLGQPVMV 293
            G L   + + V
Sbjct: 62  DGALFDDRSLRV 73

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 44.0 bits (104), Expect = 8e-06
 Identities = 21/54 (38%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
           TVF   + ++  E ++  FF+K G V++V++I DR    SKG G++ FYD + V
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTG-VSKGYGFVSFYDDVDV 59

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

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

 Score = 44.0 bits (104), Expect = 8e-06
 Identities = 19/61 (31%), Positives = 34/61 (55%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            KL+VG L+   +++ LR+ F  +G +    + +D  T + +GFGF+ F+  + A  A  
Sbjct: 3   CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

Query: 382 A 382
           A
Sbjct: 63  A 63

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

>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of uncharacterized plant proteins similar to fission yeast Vip1

 Score = 43.6 bits (103), Expect = 8e-06
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 230 LKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQ 289
            KATERD+Y+FFS +G +  V +       +     Y+ F D  +   A+ LSG  ++ Q
Sbjct: 8   PKATERDIYDFFSFSGDIEYVEIQRSGEQSQ---TAYVTFKDPQAQETALLLSGATIVDQ 64

Query: 290 PVMV 293
            V +
Sbjct: 65  SVTI 68

This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 69

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

 Score = 43.4 bits (103), Expect = 9e-06
 Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 4/58 (6%)

Query: 524 DVEEECSKYGRVKHIYV----DKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISA 577
           D+ E  SK+G ++ + +    D +S GF ++ FES E A  A  A++ +    R +  
Sbjct: 14  DLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKV 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|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 43.5 bits (103), Expect = 9e-06
 Identities = 18/48 (37%), Positives = 31/48 (64%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
           K++VG L    TE ++R+ F  FG +  ++LP+D +T + +GF F+ F
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF 48

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

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 15/46 (32%), Positives = 27/46 (58%)

Query: 224 FAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
           F   +P   TE ++ E F   G++ +V L +D+ ++RSKG  ++ F
Sbjct: 3   FVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSF 48

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

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 16/40 (40%), Positives = 27/40 (67%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
           TERD+ E FS+ G +  V+++ D+ + RS+G G++ F  V
Sbjct: 12  TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESV 51

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

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

 Score = 47.3 bits (112), Expect = 1e-05
 Identities = 30/103 (29%), Positives = 45/103 (43%), Gaps = 2/103 (1%)

Query: 295 PSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLP 354
            + A  N + S  S G             L V  L  +MT+ +L  LF   GP+   ++ 
Sbjct: 82  ANMASTNSLNSLGSGGSDDNDT-NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIM 140

Query: 355 LDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
            D +TG   G+ FV F     ++ A   LNG + +  + LKVS
Sbjct: 141 RDYKTGYSFGYAFVDFGSEADSQRAIKNLNG-ITVRNKRLKVS 182

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 48.2 bits (114), Expect = 1e-05
 Identities = 31/219 (14%), Positives = 94/219 (42%), Gaps = 17/219 (7%)

Query: 7    EYLEKTVEEQRQ--QKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRR 64
            +  +K  EE ++  + +     +KKKA   +K+  + +K +++++ EE +K+   K++  
Sbjct: 1473 DEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEE 1532

Query: 65   DEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERER 124
             +  +   + +  +  D  K+     +  ++ +  E ++  E      R+  E +K  E 
Sbjct: 1533 AKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEA 1592

Query: 125  RERRD---------------REKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERE 169
            R                   ++ E  + +  E + +   ++   Q ++  +  +++ E  
Sbjct: 1593 RIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEEL 1652

Query: 170  SERERELELERERERERELRERERDLEMRESRRYKEKKE 208
             + E E +++   E ++   ++++  E +++   ++K  
Sbjct: 1653 KKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAA 1691

Length = 2084

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 28/79 (35%), Positives = 38/79 (48%), Gaps = 8/79 (10%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RK++VG L  +MTE  LR+ F  FG V  V +P        + F FV FA     + AQS
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFAD---PEVAQS 52

Query: 382 ALNGKLEIVGRTLKVSSVT 400
                  I G ++ VS+  
Sbjct: 53  LCGEDHIIKGVSVHVSNAE 71

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

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

 Score = 43.3 bits (103), Expect = 1e-05
 Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAG-KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
            V    +P  ATE D+ +FFS        + ++ D + R + G  Y+EF        A+ 
Sbjct: 1   VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPT-GEAYVEFASPEDARRALR 59

Query: 281 LSGQLLLGQPV 291
                + G+ +
Sbjct: 60  KHNNKMGGRYI 70

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

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

 Score = 43.5 bits (102), Expect = 1e-05
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++VG+L   +T   ++  F PFG +   ++  D+ TG+ KG+GFV F     A+ A   +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 384 NGKLEIVGRTLKVSSVT 400
            G+  + GR ++ +  T
Sbjct: 64  GGQW-LGGRQIRTNWAT 79

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

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

 Score = 43.6 bits (102), Expect = 1e-05
 Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 3/77 (3%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVGNL  ++TE  + +LF   GP +  ++    E      + FV+F +   A AA +A+
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMI--TEHTSNDPYCFVEFYEHRDAAAALAAM 59

Query: 384 NGKLEIVGRTLKVSSVT 400
           NG+ +I+G+ +KV+  T
Sbjct: 60  NGR-KILGKEVKVNWAT 75

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional

 Score = 46.6 bits (111), Expect = 1e-05
 Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 3/77 (3%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           RTV    + LKATERD+ EFFS +G +  V   M   + RS+ + Y+ F D      A+ 
Sbjct: 5   RTVKVSNVSLKATERDIKEFFSFSGDIEYVE--MQSENERSQ-IAYVTFKDPQGAETALL 61

Query: 281 LSGQLLLGQPVMVKPSE 297
           LSG  ++ Q V + P+E
Sbjct: 62  LSGATIVDQSVTITPAE 78

Length = 260

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

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 19/63 (30%), Positives = 36/63 (57%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++VG+L   +T+  L   F  F      ++  D+++G+ +G+GFV F   + A+ A + +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 384 NGK 386
           NGK
Sbjct: 62  NGK 64

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

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

 Score = 43.3 bits (101), Expect = 1e-05
 Identities = 25/60 (41%), Positives = 34/60 (56%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LY+  L  N T+  L KL +P+G +   +  LD  T +CKG+GFV F     A+ A SAL
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

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

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+VG L    TE  LR++F  +G +  ++L  DI TG  KG+ FV++     A  A    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 384 NGKLEIVGRTLKV 396
           + KL I G  + V
Sbjct: 66  H-KLVIDGSEIFV 77

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

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

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA- 280
            +F Y +P  A E  +++ FS  G V +V++I D  + + KG G++   +      AIA 
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 281 LSGQLLLGQPVMV 293
           L+G  L G+ + V
Sbjct: 63  LNGYRLGGRVLQV 75

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

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

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 17/49 (34%), Positives = 29/49 (59%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           +F   +P    E D+ + FSK G++ +V + +D+ S +SKG  Y+ F D
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLD 53

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

 Score = 42.8 bits (100), Expect = 2e-05
 Identities = 21/70 (30%), Positives = 35/70 (50%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F Y +   A E  +++ F   G V +V++I D N+ + KG G++   +     MAIA  
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 283 GQLLLGQPVM 292
               LG  V+
Sbjct: 66  NGYRLGDRVL 75

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 47.8 bits (113), Expect = 2e-05
 Identities = 24/210 (11%), Positives = 101/210 (48%), Gaps = 5/210 (2%)

Query: 2    EFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKR 61
            E  + E  +K  E ++ +++     +KKKA+  +K++ + +K E+++++ +  K ++ + 
Sbjct: 1282 ELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEA 1341

Query: 62   SRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKE 121
             +  E     + +        + E      +    +  E +++ +  ++++ E+++ ++ 
Sbjct: 1342 KKAAE-----AAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEA 1396

Query: 122  RERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERE 181
            +++ E   ++ +  ++    ++ +  +++ + + +++    ++  E +   E + + E  
Sbjct: 1397 KKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEA 1456

Query: 182  RERERELRERERDLEMRESRRYKEKKEVVE 211
            ++ E   ++ E   +  E+++  E+ +  +
Sbjct: 1457 KKAEEAKKKAEEAKKADEAKKKAEEAKKAD 1486

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 47.1 bits (111), Expect = 2e-05
 Identities = 20/204 (9%), Positives = 101/204 (49%)

Query: 10   EKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEE 69
             +   ++ +  ++   +++KK +  +K   + +K+ + +++ +E K ++ +  ++ ++ +
Sbjct: 1352 AEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELK 1411

Query: 70   NGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRD 129
              +   +  D  + K   ++  D  + +  E ++  E  ++    ++ +E +++  E + 
Sbjct: 1412 KAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKK 1471

Query: 130  REKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELR 189
             ++ +++  + ++   ++ +   ++ +   ++   E +++++  ++ E  ++ +  ++  
Sbjct: 1472 ADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAE 1531

Query: 190  ERERDLEMRESRRYKEKKEVVEPE 213
            E ++  E +++   K+  E+ + E
Sbjct: 1532 EAKKADEAKKAEEKKKADELKKAE 1555

Length = 2084

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

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           RT+F   +  +  E  +YE F +AG +  V +  D+   + K  G++ F    SVP AIA
Sbjct: 2   RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEG-KPKSFGFVCFKHSESVPYAIA 60

Query: 281 -LSGQLLLGQPVMVK 294
            L+G  L G+P+ V 
Sbjct: 61  LLNGIRLYGRPIKVH 75

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

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.4 bits (113), Expect = 2e-05
 Identities = 32/181 (17%), Positives = 58/181 (32%), Gaps = 1/181 (0%)

Query: 29  KKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHR 88
           +    + + E    K E    E+  E+ R        + EE         +     +   
Sbjct: 680 EAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRL 739

Query: 89  RDRDRDRDRGRERERETERDRERSRERREK-EKERERRERRDREKERERERDGERRSSSR 147
            + + + +   E   E +   E   E  E  E+   + +    E E +R+   E      
Sbjct: 740 EELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELE 799

Query: 148 SRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEMRESRRYKEKK 207
                ++ R  +     E   +     E E+E   E   EL E+  +LE       KE +
Sbjct: 800 EELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELE 859

Query: 208 E 208
           E
Sbjct: 860 E 860

Length = 1163

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

 Score = 43.8 bits (103), Expect = 2e-05
 Identities = 19/59 (32%), Positives = 32/59 (54%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           T+F   +P  ATE  +   FSK G VR    ++D+++ R+KG G++ F D  +    + 
Sbjct: 3   TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 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|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 43.1 bits (101), Expect = 2e-05
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L 281
           VF   +  + T  D+   F+  GK+ D R++ D  + +SKG G++ FY+ +    AI  +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 282 SGQLLLGQPV 291
            GQ L G+ +
Sbjct: 64  GGQWLGGRQI 73

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

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 47.7 bits (114), Expect = 2e-05
 Identities = 45/246 (18%), Positives = 82/246 (33%), Gaps = 9/246 (3%)

Query: 2   EFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEE--EEEKSRSG 59
           E +E E   + + ++ ++     S+ +K   R E       +R     +E  E E     
Sbjct: 706 ELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEE 765

Query: 60  KRSRRDEDEENGSRRDRDR-DRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREK 118
              R +E EE  +  + +  + +   E+ + +    R+   E   E     E +   RE+
Sbjct: 766 LEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRER 825

Query: 119 EKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELEL 178
               E  ERR    ER  E   E+         S  +         E   E E E E  L
Sbjct: 826 ---LESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELE---ELIEELESELEALL 879

Query: 179 ERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVY 238
                 E  L     +LE       + + +  E   + E  +  +   ++ L+  E  + 
Sbjct: 880 NERASLEEALALLRSELEELSEELRELESKRSELRRELEELREKLAQLELRLEGLEVRID 939

Query: 239 EFFSKA 244
               + 
Sbjct: 940 NLQERL 945

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 47.8 bits (113), Expect = 2e-05
 Identities = 23/53 (43%), Positives = 38/53 (71%), Gaps = 1/53 (1%)

Query: 107 RDRERSRERREKEKERERRERRDREKERERERDGER-RSSSRSRRSSSQSRRS 158
           + RE + E+ ++E E++ RE R+REKE+E+ER+ ER R + R+ ++SS S  S
Sbjct: 579 KKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAKASSSSHES 631

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +YVG + +  TE ++R  F   G +E + L    +TG+ +G  F+ F   E AK A  AL
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRA-LAL 59

Query: 384 NGKLEIVGRTLKV 396
           +G+ ++ GR LKV
Sbjct: 60  DGE-DMGGRFLKV 71

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
           ++R LYV NL F ++  +L  LF  +G +  +++     T + +G  FV +  +  AK A
Sbjct: 1   VNRILYVRNLPFKISSEELYDLFGKYGAIRQIRIG---NTKETRGTAFVVYEDIYDAKNA 57

Query: 380 QSALNGKLEIVGRTLKV 396
              L+G   +  R L V
Sbjct: 58  CDHLSG-FNVANRYLVV 73

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

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

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 25/64 (39%), Positives = 34/64 (53%), Gaps = 7/64 (10%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           +RKL+VG L     E  +R +F PFG +E   +  D + GQ +G  FV FA      + Q
Sbjct: 1   ERKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFA------SRQ 53

Query: 381 SALN 384
            ALN
Sbjct: 54  CALN 57

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

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 47.1 bits (112), Expect = 2e-05
 Identities = 39/209 (18%), Positives = 73/209 (34%), Gaps = 15/209 (7%)

Query: 10  EKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEE 69
           E+  E ++ ++  ++   ++  +  E  E    + E+ +E  EE K+R       + +  
Sbjct: 210 EELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKAR-----LLEIESL 264

Query: 70  NGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRD 129
                    +  R+ ER   + +   +R  E ERE E   E     R   +E E    + 
Sbjct: 265 ELEALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKL 324

Query: 130 REKERERERDGERRSSSRSR----------RSSSQSRRSSSRSRRERERESERERELELE 179
           +  E   E+  E+     S            +     R      R  E E E E+ LE  
Sbjct: 325 KSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERL 384

Query: 180 RERERERELRERERDLEMRESRRYKEKKE 208
           ++ E   +  + E           +E+ E
Sbjct: 385 KQLEEAIQELKEELAELSAALEEIQEELE 413

Length = 908

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR-NSRRSKGVGYIEFYDVMSVPMAIA 280
           T +   +P   TE D+ EFF +   V  VRL  +  +  R +G GY EF D  S+  A++
Sbjct: 3   TAYLGNLPYDVTEEDIKEFF-RGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALS 61

Query: 281 LSGQLLLGQPVMV 293
           L+ + L  + + V
Sbjct: 62  LNDESLKNRRIRV 74

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

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

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 7/73 (9%)

Query: 325 YVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
           YVGN+    T+  L  LF+ FG +   +   D      +GF FV+    E A  A   L 
Sbjct: 4   YVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQLQ 57

Query: 385 GKLEIVGRTLKVS 397
           G   + GR L+  
Sbjct: 58  GFP-VHGRPLRCG 69

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

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 21/55 (38%), Positives = 35/55 (63%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
           K++VG L  +  E ++R+ F  FG VE ++LP+D +T + +GF F+ F + E  K
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 55

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 46.9 bits (112), Expect = 2e-05
 Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 5/84 (5%)

Query: 44  REDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERER 103
             + E ++E     + +    D+D++  S  + +     +      D D D D   +   
Sbjct: 105 DIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSED-----DEDDDDDDDDDDIA 159

Query: 104 ETERDRERSRERREKEKERERRER 127
             ER  ER R RRE E++R   E 
Sbjct: 160 TRERSLERRRRRREWEEKRAELEF 183

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 24/61 (39%), Positives = 31/61 (50%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +YV  L  N T   L+ +F  +G V  V LP    TG  KGF F++F   E A+ A   L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 384 N 384
           N
Sbjct: 62  N 62

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

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 25/74 (33%), Positives = 36/74 (48%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
           +V+   +   AT  ++   F   G V  V ++ D+ S   KG  YIEF D  SV  A+AL
Sbjct: 1   SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALAL 60

Query: 282 SGQLLLGQPVMVKP 295
              L  G+ + V P
Sbjct: 61  DESLFRGRQIKVMP 74

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 46.4 bits (111), Expect = 3e-05
 Identities = 19/143 (13%), Positives = 31/143 (21%)

Query: 80  RDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERERD 139
                      R   R     R+ E       + +       R                 
Sbjct: 67  AATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQ 126

Query: 140 GERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEMRE 199
              R           +R++     +          E   E ER+  R   +RE      E
Sbjct: 127 ARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAE 186

Query: 200 SRRYKEKKEVVEPEADPERDQRT 222
                 ++E      D +R  R 
Sbjct: 187 RGERGRREERGRDGDDRDRRDRR 209

Length = 672

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 16/44 (36%), Positives = 29/44 (65%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           +P K TE+D+ ++FS  G++  V++  D  + +SKG G++ F D
Sbjct: 7   LPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFAD 50

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 42/196 (21%), Positives = 71/196 (36%), Gaps = 12/196 (6%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGK 60
           +E    E   +    + + +Q      + + + EE  E     +E  EE EEE +S    
Sbjct: 714 LERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEA 773

Query: 61  RSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEK 120
            ++  E+ E    + +    + ++     +    R    ERE E+   R   RER E+E 
Sbjct: 774 LAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQR---RERLEQEI 830

Query: 121 ERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELER 180
           E    E  + E         E+           +      +   E     + E E EL+ 
Sbjct: 831 EELEEEIEELE---------EKLDELEEELEELEKELEELKEELEELEAEKEELEDELKE 881

Query: 181 ERERERELRERERDLE 196
             E + EL E  R+LE
Sbjct: 882 LEEEKEELEEELRELE 897

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 38/231 (16%), Positives = 82/231 (35%), Gaps = 17/231 (7%)

Query: 11  KTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEEN 70
             + E+ ++ +++    +++ +  ++   + ++  +  E   EE  +        ++E  
Sbjct: 305 SLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELE 364

Query: 71  GSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDR 130
                   + +   E               RE   E + E +  R E E+ +   E  + 
Sbjct: 365 EKLSALLEELEELFEAL-------------REELAELEAELAEIRNELEELKREIESLEE 411

Query: 131 EKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRE 190
             ER  ER  +     +      ++     ++  E   E   E E +LE  R+R +EL  
Sbjct: 412 RLERLSERLEDL----KEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKELER 467

Query: 191 RERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFF 241
              +L+    R  KE   +       E +QR     +  L+A E  +   +
Sbjct: 468 ELAELQEELQRLEKELSSLEARLDRLEAEQRASQGVRAVLEALESGLPGVY 518

Length = 1163

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 42/192 (21%), Positives = 77/192 (40%), Gaps = 9/192 (4%)

Query: 5   EYEYLEKTVEEQRQQKQD-DDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSR 63
           E E L +T+ E  +++++  +     + + EE  E       ++  ++ + ++   +R  
Sbjct: 259 EIEDLRETIAETEREREELAEEVRDLRERLEELEEERDDLLAEAGLDDADAEAVEARREE 318

Query: 64  RDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERE 123
            ++ +E    RDR  +     + H  + +  R+   + E   E  RE + E  E E E  
Sbjct: 319 LEDRDE--ELRDRLEECRVAAQAHNEEAESLREDADDLEERAEELREEAAE-LESELEEA 375

Query: 124 RRERRDREKERERERD-----GERRSSSRSRRSSSQSRRSSSRSRRERERESERERELEL 178
           R    DR +E E   +      ER   +     +++      R  R+  RE E E E  L
Sbjct: 376 REAVEDRREEIEELEEEIEELRERFGDAPVDLGNAEDFLEELREERDELREREAELEATL 435

Query: 179 ERERERERELRE 190
              RER  E   
Sbjct: 436 RTARERVEEAEA 447

Length = 880

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

 Score = 42.5 bits (99), Expect = 3e-05
 Identities = 23/60 (38%), Positives = 33/60 (55%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LY+  L    T+  L KL +P+G +   +  LD  T QCKG+GFV F     A+ A ++L
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 22/58 (37%), Positives = 30/58 (51%)

Query: 239 EFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS 296
           E FS  G++  V +  DR +  SKG  YIEF  V  V  A+ L G  L G  ++V  +
Sbjct: 22  EHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALELDGSDLGGGNLVVDEA 79

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 42.3 bits (99), Expect = 3e-05
 Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 326 VGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
           V  L    TE  LR++F  +GP+  V +  D  TG+ +GF FV F +++ +K A    NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 386 KLEIVGRTLKV 396
            +E+ GR ++V
Sbjct: 64  -MELDGRRIRV 73

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

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

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +L+VGNL  ++TE +L++ F+ FG V  V++      G+   FGFV F   +  +A Q  
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVF---DDPEAVQKI 61

Query: 383 LNGK 386
           L  K
Sbjct: 62  LANK 65

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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 42.1 bits (99), Expect = 3e-05
 Identities = 19/49 (38%), Positives = 28/49 (57%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFA 371
           KL+VG L +  T+  LR+ F  +G V    +  D  T + +GFGFV+F 
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFK 49

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

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

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++VG+L   +T   ++  F PFG +   ++  D+ TG+ KG+GFV F     A+ A   +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 384 NGKLEIVGRTLKVSSVT 400
            G+  + GR ++ +  T
Sbjct: 64  GGQW-LGGRQIRTNWAT 79

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

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

 Score = 42.0 bits (98), Expect = 4e-05
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F Y +   + E  +++ F   G V +V++I D N+ + KG G++   +     MAIA  
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 283 GQLLLGQPVM---VKPSEAEK 300
               LG  V+    K ++  K
Sbjct: 66  NGYRLGDRVLQVSFKTNKTHK 86

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 41.5 bits (98), Expect = 4e-05
 Identities = 17/57 (29%), Positives = 35/57 (61%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
           +F Y +P + T++D+Y+ F+  G V   ++ +D+N+ +SK  G++ + +  S   AI
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAI 57

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

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

 Score = 42.0 bits (98), Expect = 4e-05
 Identities = 20/70 (28%), Positives = 35/70 (50%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F Y +   A E  +++ F   G V +V++I D N+ + KG G++   +     MAIA  
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 283 GQLLLGQPVM 292
               LG  ++
Sbjct: 64  NGYRLGDKIL 73

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

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 46.2 bits (110), Expect = 4e-05
 Identities = 47/209 (22%), Positives = 75/209 (35%), Gaps = 7/209 (3%)

Query: 10  EKTVEEQRQQKQDDDSSSKKKAKREEKS---ERSYRKREDSEEEEEEEKSRSGKRSRRDE 66
           E   E +  Q++  +   + +    E S   ER      + EE EE  +    K     E
Sbjct: 278 ELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKE 337

Query: 67  DEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRER-REKEKERERR 125
           + E   R     + ++        ++   ++      E E   E  RE   E E E    
Sbjct: 338 ELE--ERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEI 395

Query: 126 ERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERE 185
                E +RE E   ER      R    +       +  E  +    E   ELE   E+ 
Sbjct: 396 RNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQL 455

Query: 186 RELRERERDLEMRESRRYKEKKEVVEPEA 214
            ELR+R ++LE RE    +E+ + +E E 
Sbjct: 456 EELRDRLKELE-RELAELQEELQRLEKEL 483

Length = 1163

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

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 20/47 (42%), Positives = 28/47 (59%)

Query: 333 MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
            TE  LR+ F+ FG +E V +  D  TG+ KGFG+V+F +   A  A
Sbjct: 12  YTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVA 58

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 24/74 (32%), Positives = 40/74 (54%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL+VG++   +TE ++R +FE  G V  V +  D  TG  +G  FV+++  + A  A  A
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 383 LNGKLEIVGRTLKV 396
           L+ +  + G    V
Sbjct: 61  LHNQRTLPGGASPV 74

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 46.6 bits (111), Expect = 4e-05
 Identities = 36/133 (27%), Positives = 52/133 (39%), Gaps = 2/133 (1%)

Query: 71  GSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRE--RR 128
           GSR  R        E     R R+R  G +RE  + +   R  E R  E  +E  +  R+
Sbjct: 658 GSRAPRGGILFSRSEPAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRK 717

Query: 129 DREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELEREREREREL 188
             E E+E E+  +     + R    +   SS     E  +   +E E  +E   E   +L
Sbjct: 718 IGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKL 777

Query: 189 RERERDLEMRESR 201
            E   DLE R S 
Sbjct: 778 EEALNDLEARLSH 790

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

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

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 4/68 (5%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA---- 379
           +++G L ++ T+  L+  F  FG V    L LD  TG+ +GFGFV F + E         
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 380 QSALNGKL 387
           +  LNGK+
Sbjct: 61  EHKLNGKV 68

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

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 42.0 bits (98), Expect = 4e-05
 Identities = 25/67 (37%), Positives = 40/67 (59%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL++G L F  T+  LR+ FE +G +    +  D +T + +GFGFV ++ +E   AA S
Sbjct: 3   RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMS 62

Query: 382 ALNGKLE 388
           A   K++
Sbjct: 63  ARPHKVD 69

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 46.0 bits (109), Expect = 4e-05
 Identities = 79/372 (21%), Positives = 132/372 (35%), Gaps = 63/372 (16%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI--ALSGQL 285
           +P    E D+ E     G V  V ++        K    +EF D  S    +  A S  +
Sbjct: 10  LPQDVVEADLVEALIPFGPVSYVMML------PGKRQALVEFEDEESAKACVNFATSVPI 63

Query: 286 LL-GQPVMVKPS---EAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKL 341
            + GQP     S   E +++      SAG            ++ V N  + +T   L ++
Sbjct: 64  YIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKV-------LRVIVENPMYPITLDVLYQI 116

Query: 342 FEPFGPVELVQLPLDIETGQCKGF--GFVQFAQLEHAKAAQSALNGKLEIVG-RTLKVS- 397
           F P+G V      L I T          V+F  +  A+ A++ALNG     G  TLK+  
Sbjct: 117 FNPYGKV------LRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEY 170

Query: 398 SVTDHVGTQDTAAKSADFDDDD--GGGLALNAQSRALLMQKLDRTGIATSIAGSLGV--- 452
           +    +  +     S D+ + D  G       Q+       L     ++           
Sbjct: 171 AKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGG 230

Query: 453 --APAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEF---IGSPSECLLLKNMF 507
             AP   G  +       P  G P+   PA  A  +    + +    G P   L++  + 
Sbjct: 231 PLAPLAGGDRMG------PPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLH 284

Query: 508 DPAMETDPDFDLEIQ-GDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAM- 565
              +  D  F+L    G+VE       RVK +  +K+    + +   +      AQ A+ 
Sbjct: 285 QEKVNCDRLFNLFCVYGNVE-------RVKFMK-NKKETALIEM---ADPYQ--AQLALT 331

Query: 566 HM---RWFARRL 574
           H+   + F + L
Sbjct: 332 HLNGVKLFGKPL 343

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|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 = 41.3 bits (97), Expect = 5e-05
 Identities = 19/49 (38%), Positives = 29/49 (59%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           VF   +P +ATE  + + FS+ G V   RL+ DR + + KG G+ E+ D
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKD 49

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

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 232 ATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQP 290
           A E DV++ F++ G+++++ L +DR +   KG   IE+        AI  L+G+ LLGQ 
Sbjct: 18  AQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQT 77

Query: 291 VMV 293
           + V
Sbjct: 78  ISV 80

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

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 46.3 bits (109), Expect = 5e-05
 Identities = 31/209 (14%), Positives = 103/209 (49%), Gaps = 4/209 (1%)

Query: 11   KTVEEQRQQKQDDDSSSKKKAKREEKSE---RSYRKREDSEEEEEEEKSRSGKRSRRDED 67
            +  E  R+ +++  +   +KA+  +K+E   ++   ++D+EE ++ E+ R+ +  R+ E+
Sbjct: 1200 RKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEE 1259

Query: 68   EENGSRRDRDRDRDRDKERHRRD-RDRDRDRGRERERETERDRERSRERREKEKERERRE 126
                    R      ++ R   + +  +  +  +  ++ E  ++    +++ E+ ++  E
Sbjct: 1260 ARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADE 1319

Query: 127  RRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERER 186
             + + +E +++ D  ++ +  +++++  ++  +  +  E E   E+    E ++E  +++
Sbjct: 1320 AKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKK 1379

Query: 187  ELRERERDLEMRESRRYKEKKEVVEPEAD 215
                +++  E +++   K+K E  + +AD
Sbjct: 1380 ADAAKKKAEEKKKADEAKKKAEEDKKKAD 1408

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 46.3 bits (109), Expect = 5e-05
 Identities = 32/194 (16%), Positives = 82/194 (42%), Gaps = 2/194 (1%)

Query: 28   KKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERH 87
            K +A R+ + ER   +   +E+ ++ E  +  + +++D +E   +  +R+ +  R  E  
Sbjct: 1201 KAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEA 1260

Query: 88   RRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERERDGERRSSSR 147
            R      R    + E    R  +  ++  EK+K  E ++  +++K  E ++  E    + 
Sbjct: 1261 RMAHFARRQAAIKAEEA--RKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKAD 1318

Query: 148  SRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEMRESRRYKEKK 207
              +  ++  +  + + +++  E+++  E           E    E   E  E ++ + KK
Sbjct: 1319 EAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKK 1378

Query: 208  EVVEPEADPERDQR 221
            +    +   E  ++
Sbjct: 1379 KADAAKKKAEEKKK 1392

Length = 2084

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 45.8 bits (108), Expect = 5e-05
 Identities = 18/53 (33%), Positives = 35/53 (66%)

Query: 99  RERERETERDRERSRERREKEKERERRERRDREKERERERDGERRSSSRSRRS 151
           ++RE   E+ +  + ++  +E+ERE+ + ++RE+ERERE +   ++SS S  S
Sbjct: 579 KKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAKASSSSHES 631

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 45.1 bits (107), Expect = 5e-05
 Identities = 26/121 (21%), Positives = 59/121 (48%), Gaps = 2/121 (1%)

Query: 80  RDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERE-- 137
             + + + +  +  +  + +ERE+E E    R R  +EK +E  R++ +   K+R  +  
Sbjct: 95  AKQAQRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQAAKQRTPKHK 154

Query: 138 RDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEM 197
           ++    +SS    S+   R  S    ++R +E E ++  + +++RE ER  + +++  E 
Sbjct: 155 KEAAESASSSLSGSAKPERNVSQEEAKKRLQEWELKKLKQQQQKREEERRKQRKKQQEEE 214

Query: 198 R 198
            
Sbjct: 215 E 215

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 45.8 bits (108), Expect = 5e-05
 Identities = 43/209 (20%), Positives = 96/209 (45%), Gaps = 3/209 (1%)

Query: 14  EEQRQQKQDDDSSSKKKAKREEKSERSYRK-REDSEEEEEEEKSRSGKRSRRDEDEENGS 72
           EE +    D+ +  ++ A+REE+ +  + +  E  +E +     +S     R   E++G+
Sbjct: 47  EESKTSTDDEAALLERLARREERRDERFSEALERQKEFKPTSTDQSLSEPSRRMQEDSGA 106

Query: 73  RRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREK 132
             +   + +  KE  R +R+   +     + E + D   + E +++EKE E  E    ++
Sbjct: 107 ENETVEEEE--KEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKR 164

Query: 133 ERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERE 192
               E +GE  +       ++ SR  +  ++ E  +E E+ ++ + E   E E   ++RE
Sbjct: 165 GSLEENNGEFMTHKLKHTENTFSRGGAEGAQVEAGKEFEKLKQKQQEAALELEELKKKRE 224

Query: 193 RDLEMRESRRYKEKKEVVEPEADPERDQR 221
              ++ E    + K+E  + ++  E ++R
Sbjct: 225 ERRKVLEEEEQRRKQEEADRKSREEEEKR 253

Length = 431

>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 41.7 bits (98), Expect = 5e-05
 Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 217 ERDQRTVFAYQMPLKATERDVYEFF-SKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
           E   RT++   +  K T+ DV  FF S  G+V  +RL+ D +   S  + ++EF    S 
Sbjct: 1   EMCARTIYCTNIDKKVTQSDVKLFFESLCGEVSRLRLLGDYH--HSTRIAFVEFAMAESA 58

Query: 276 PMAIALSGQLLLGQPVMVKPSEA 298
             A+  SG +L   P+ V PS+ 
Sbjct: 59  IAALNCSGAVLGSLPIRVSPSKT 81

This subgroup corresponds to the RRM2 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 82

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

 Score = 41.2 bits (97), Expect = 6e-05
 Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 241 FSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
           F K G V   R+I DR + RS+G GY++F        AI A+ G+ L G+P+ V
Sbjct: 20  FEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINV 73

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

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

 Score = 41.4 bits (98), Expect = 6e-05
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIM--DRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQ 284
           +    TE  +YE FS+ G ++  R+IM  DR ++   G  ++E+Y       A+  L+G 
Sbjct: 6   LSFYTTEEQIYELFSRCGDIK--RIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGT 63

Query: 285 LLLGQPVMV 293
            L  + + V
Sbjct: 64  KLDDRIIRV 72

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

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 45.8 bits (109), Expect = 6e-05
 Identities = 33/204 (16%), Positives = 74/204 (36%), Gaps = 9/204 (4%)

Query: 9   LEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDE 68
           LE+  +  R++  + +   ++   + E+ E          +E  EE +   ++    ++E
Sbjct: 300 LEQQKQILRERLANLERQLEELEAQLEELESK-------LDELAEELAELEEKLEELKEE 352

Query: 69  ENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERR 128
                 + +      +E   R  + +      R +  + + + +    E E+   R ER 
Sbjct: 353 LESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERL 412

Query: 129 DREKERER-ERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERE 187
           +  +ER + E +   +    +     Q+         E  +E     E  LE  RE   E
Sbjct: 413 EDRRERLQQEIEELLKKLEEAELKELQAELEELEEELEELQEELERLEEALEELREELEE 472

Query: 188 LRERERDLEMRESRRYKEKKEVVE 211
             +     E RE  + + + + +E
Sbjct: 473 AEQALDAAE-RELAQLQARLDSLE 495

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

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

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 25/67 (37%), Positives = 37/67 (55%), Gaps = 7/67 (10%)

Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV 390
           + +TE  L+K F PFG +  + + ++ E    K  GFV F ++E A  A + LNG   + 
Sbjct: 12  YGLTEEILKKAFSPFGNI--INISMEKE----KNCGFVTFEKMESADRAIAELNGTT-VQ 64

Query: 391 GRTLKVS 397
           G  LKVS
Sbjct: 65  GVQLKVS 71

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 41.5 bits (98), Expect = 6e-05
 Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 19/92 (20%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQ---LPLDIETGQCKGF------------- 365
           R ++VGNL     +  L+KLF+ FGP+E V+   +P+  +    K               
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 366 -GFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
             +V F + E A+ A   LNG  E  G  ++V
Sbjct: 61  NAYVVFKEEESAEKA-LKLNGT-EFEGHHIRV 90

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 45.9 bits (108), Expect = 7e-05
 Identities = 39/227 (17%), Positives = 101/227 (44%), Gaps = 4/227 (1%)

Query: 11   KTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEEN 70
            +  EE R+ +        +KA+   K+E + RK ED+++ E   K+   +++      E+
Sbjct: 1140 RKAEEARKAEDAKRVEIARKAEDARKAEEA-RKAEDAKKAEAARKAEEVRKAEELRKAED 1198

Query: 71   GSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDR 130
              + +  R +  ++ +    R  +  +  E  ++ E  ++ + E ++ E+ER   E R  
Sbjct: 1199 ARKAEAAR-KAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKF 1257

Query: 131  EKERERERDGERRS-SSRSRRSSSQSRRSSSRSRRERERESEREREL-ELEREREREREL 188
            E+ R       + +  +   R + + +++  + + +  +++E +++  E +++ E  ++ 
Sbjct: 1258 EEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKA 1317

Query: 189  RERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATER 235
             E ++  E  + +    KK+  E +   E  +    A     +A E 
Sbjct: 1318 DEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEE 1364

Length = 2084

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

 Score = 41.0 bits (97), Expect = 7e-05
 Identities = 21/59 (35%), Positives = 34/59 (57%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPV 291
           TE  + E+FSK G+V D  ++ D  + RS+G G++ F D  SV   +A    +L G+ +
Sbjct: 11  TEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLDGREI 69

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

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

 Score = 41.4 bits (98), Expect = 7e-05
 Identities = 26/78 (33%), Positives = 35/78 (44%), Gaps = 4/78 (5%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVEL--VQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           L +  L    TE  + +       V +  V+L  D  TG  +GF FV+F  LE A     
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 382 ALNGKLEIV--GRTLKVS 397
           ALN     V  GR ++VS
Sbjct: 65  ALNNLDPFVIDGRVVRVS 82

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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 41.0 bits (96), Expect = 7e-05
 Identities = 17/62 (27%), Positives = 31/62 (50%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           VF   +  +  E  ++  F K G +  VR++ D  +   KG  Y++F D  +V  A+ L+
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLN 61

Query: 283 GQ 284
            +
Sbjct: 62  EK 63

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 41.5 bits (98), Expect = 7e-05
 Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 4/76 (5%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQL--PLDIETGQCKGF-GFVQFAQLEHAKAAQ 380
           LYVGNL+  +TE  L + F  FGP+  V++  P   E  +     GFV F     A+ A 
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 381 SALNGKLEIVGRTLKV 396
             L+GK +++G  LK+
Sbjct: 64  DELDGK-DVMGYELKL 78

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

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

 Score = 41.2 bits (97), Expect = 7e-05
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L 281
           +F   +  K   + + E F  AGKV    +  D+   +S+G+G ++F   +    AI+  
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEG-KSRGMGVVQFEHPIEAVQAISMF 59

Query: 282 SGQLLLGQPVMVK 294
           +GQ+L  +P+ VK
Sbjct: 60  NGQMLFDRPMRVK 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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 41.6 bits (97), Expect = 7e-05
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L    TE  LR++F  +GP+  V +  D ++ + +GF FV F  ++ AK A+   
Sbjct: 12  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 71

Query: 384 NGKLEIVGRTLKV 396
           NG +E+ GR ++V
Sbjct: 72  NG-MELDGRRIRV 83

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

>gnl|CDD|219061 pfam06495, Transformer, Fruit fly transformer protein

 Score = 43.5 bits (102), Expect = 7e-05
 Identities = 44/114 (38%), Positives = 57/114 (50%), Gaps = 15/114 (13%)

Query: 65  DEDEENGSRRDRDRD-RDRDKERHRRDRDRDRDRGRE-RERETERDR-------ERSRER 115
           D D  + S RD  RD R ++K  +  D  R+RDR R  R+R+T+  R        R+R R
Sbjct: 2   DADSSSRSPRDTRRDSRKKEKIPYFADEVRERDRVRNLRQRKTQSTRPTTSHRGRRTRSR 61

Query: 116 -REKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERER 168
            R +  ER   +RR R + R R      RS SR R +SS  RR  SRSR    R
Sbjct: 62  SRSQSAERNSCQRRHRSRSRSR-----NRSDSRHRSTSSTERRRRSRSRSRYSR 110

This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster. Length = 182

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 45.3 bits (108), Expect = 7e-05
 Identities = 30/116 (25%), Positives = 53/116 (45%), Gaps = 2/116 (1%)

Query: 100 ERERETERDRERSRERREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSS 159
           ERE +  R+  +  ERR  ++E E  +R+  E   ++E + E++    S +  +   +  
Sbjct: 68  ERELKERRNELQRLERRLLQRE-ETLDRKM-ESLDKKEENLEKKEKELSNKEKNLDEKEE 125

Query: 160 SRSRRERERESERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEAD 215
                  E+  E ER   L +E  +E  L E E +     ++  KE +E  + EAD
Sbjct: 126 ELEELIAEQREELERISGLTQEEAKEILLEEVEEEARHEAAKLIKEIEEEAKEEAD 181

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

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

 Score = 40.8 bits (96), Expect = 8e-05
 Identities = 12/53 (22%), Positives = 26/53 (49%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           +P   T+ ++   F   G +   +++ DR + +S G G++++ D      AI 
Sbjct: 8   LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

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|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 40.9 bits (96), Expect = 8e-05
 Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +YVGN+ +  T  +L   F   G V  V +  D  +G  KGF +++F+  E  + A  AL
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-AL 60

Query: 384 NGKLEIVGRTLKVSS 398
           +  L   GR +KV  
Sbjct: 61  DESL-FRGRQIKVMP 74

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

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

 Score = 41.2 bits (96), Expect = 8e-05
 Identities = 24/67 (35%), Positives = 38/67 (56%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL++G L F  T+  LR  FE +G +    +  D  T + +GFGFV ++ +E   AA +
Sbjct: 3   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

Query: 382 ALNGKLE 388
           A   K++
Sbjct: 63  ARPHKVD 69

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

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 41.1 bits (96), Expect = 8e-05
 Identities = 17/49 (34%), Positives = 31/49 (63%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
           +K++VG +  +  E  LR  FE +G +E++++  D  +G+ +GF FV F
Sbjct: 1   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

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

 Score = 40.7 bits (96), Expect = 9e-05
 Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 5/57 (8%)

Query: 524 DVEEECSKYGRVKHIYV-----DKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI 575
           ++ E  SK+G+V+ + +       +S GF ++ FES E A  A  A++ +    R +
Sbjct: 15  ELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPL 71

Length = 73

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

 Score = 41.2 bits (96), Expect = 9e-05
 Identities = 20/70 (28%), Positives = 35/70 (50%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F Y +  +A E  +++ F   G V +V++I D  + + KG G++   +     MAIA  
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 283 GQLLLGQPVM 292
               LG  V+
Sbjct: 64  NGYRLGDRVL 73

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

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

 Score = 41.0 bits (96), Expect = 9e-05
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 323 KLYVGNLHFNMTE-TQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           KL + NL +++ +  +L+K+F  +G V    +P     G+  GF FV   + ++A+ A  
Sbjct: 2   KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRK-RGGKLCGFAFVTMKKRKNAEIALE 60

Query: 382 ALNGKLEIVGRTLKV 396
             NG LEI GR + V
Sbjct: 61  NTNG-LEIDGRPVAV 74

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins

 Score = 41.5 bits (98), Expect = 9e-05
 Identities = 28/102 (27%), Positives = 42/102 (41%), Gaps = 23/102 (22%)

Query: 501 LLLKNMF-DPAME------TDPDFDLEIQ------------GDVEEECSKYGRVKHIYVD 541
           LL+ NMF    +E       D D  LE               DV  E  K+G V    V 
Sbjct: 2   LLIPNMFTHFGLEQTQRDEYDTDEGLEYDEEDLYSDFEEFYDDVLPEFEKFGEVVQFKVC 61

Query: 542 KRSA----GFVYLRFESTEAAASAQRAMHMRWFARRLISAIF 579
                   G VY++++S E A +A +  + RW+A + ++  F
Sbjct: 62  CNYEPHLRGNVYVQYQSEEEALAAFKMFNGRWYAGKQLTCEF 103

This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. . Length = 105

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

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 4/62 (6%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
           TE  + E FS+ G ++  +LI +  +       ++E+YD  S   A+  ++G+L+LGQ +
Sbjct: 11  TEDLLAELFSQIGPIKSCKLIREHGN---DPYAFVEYYDHRSAAAALQTMNGRLILGQEI 67

Query: 292 MV 293
            V
Sbjct: 68  KV 69

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

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 12/38 (31%), Positives = 23/38 (60%)

Query: 234 ERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           E ++ ++FS+ G V  +RL   + + +SKG  ++EF  
Sbjct: 13  EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFES 50

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 45.1 bits (106), Expect = 1e-04
 Identities = 40/231 (17%), Positives = 103/231 (44%), Gaps = 12/231 (5%)

Query: 2    EFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSE-----RSYRKREDS---EEEEEE 53
            E  +   + +  E+ R+ ++   +   KKA+   K+E        RK ED+   E   + 
Sbjct: 1149 EDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKA 1208

Query: 54   EKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRR---DRDRDRDRGRERERETERDRE 110
            E+ R  + +R+ ED +      +  +  +D E  ++   +R+ +  R  E  R     R 
Sbjct: 1209 EEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARR 1268

Query: 111  RSRER-REKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERE 169
            ++  +  E  K  E ++  +++K  E ++  E++ +  +++ + +++++    ++  E +
Sbjct: 1269 QAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAK 1328

Query: 170  SERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQ 220
             + +   +   E ++  E  + E +    E+   +EK E  E + +  + +
Sbjct: 1329 KKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKK 1379

Length = 2084

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 62/264 (23%), Positives = 94/264 (35%), Gaps = 44/264 (16%)

Query: 4   DEYEYLEKTVEEQRQQKQDDDSSSKKKAKR-EEKSERSYRKREDSEEEEEE-EKSRSGKR 61
           D  E L   +EE R   Q  +  ++   +  ++  ER+   RE++ E E E E++R    
Sbjct: 321 DRDEELRDRLEECRVAAQAHNEEAESLREDADDLEERAEELREEAAELESELEEAREAVE 380

Query: 62  SRRDEDEENGSRRDRDRDR------DRDK-ERHRRDRDRDRDRGRERERETERDRERSRE 114
            RR+E EE     +  R+R      D    E    +   +RD  RERE E E     +RE
Sbjct: 381 DRREEIEELEEEIEELRERFGDAPVDLGNAEDFLEELREERDELREREAELEATLRTARE 440

Query: 115 RREKEKE-----------------------RERRERRD---------REKERERERDGER 142
           R E+ +                         E RER +          E+  E E   ER
Sbjct: 441 RVEEAEALLEAGKCPECGQPVEGSPHVETIEEDRERVEELEAELEDLEEEVEEVEERLER 500

Query: 143 RSS---SRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEMRE 199
                 +  R    + RR          RE+  E+    E  RER  EL     +     
Sbjct: 501 AEDLVEAEDRIERLEERREDLEELIAERRETIEEKRERAEELRERAAELEAEAEEKREAA 560

Query: 200 SRRYKEKKEVVEPEADPERDQRTV 223
           +   +E +E  E  A+       +
Sbjct: 561 AEAEEEAEEAREEVAELNSKLAEL 584

Length = 880

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

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 4/76 (5%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R ++VG +  +++E  L++ F   G V   ++ L  +      F FV+FA  E A +A +
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFSNCGEV--TRVRLCGDRQHSARFAFVEFADAESALSALN 58

Query: 382 ALNGKLEIVGRTLKVS 397
            L+G L + G  L+VS
Sbjct: 59  -LSGTL-LGGHPLRVS 72

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

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 44.8 bits (107), Expect = 1e-04
 Identities = 30/162 (18%), Positives = 62/162 (38%), Gaps = 8/162 (4%)

Query: 75  DRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKER 134
           +  ++  + +       + +     E E E + +   +    E  +     E   R  E 
Sbjct: 42  EARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARPAED 101

Query: 135 ERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERD 194
           E  R  E  +     + +++ ++     +++ +R++ R  +     +  R R  R R R 
Sbjct: 102 EAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKRKAARGGKRGKGGKGRRRRRGRRRRRK 161

Query: 195 LEMRESRRYKEKKEVVEPEADPERDQRTV--FAYQMPLKATE 234
            + ++    K  +EVV PE        TV   A +M +KA E
Sbjct: 162 KKKKQKPTEKIPREVVIPETI------TVAELAEKMAVKAAE 197

Length = 746

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

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 17/76 (22%), Positives = 38/76 (50%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
             +F   + LK ++  +   F++ GK+ +  +++D N++RS+G G+I F        A+ 
Sbjct: 3   CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

Query: 281 LSGQLLLGQPVMVKPS 296
                + G  + +K +
Sbjct: 63  AQPHSIDGNQIELKRA 78

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

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 26/127 (20%), Positives = 60/127 (47%), Gaps = 12/127 (9%)

Query: 97  RGRERERETERDRERSRERREKEKERERRERRDREKE---------RERERDGERRSSSR 147
             + + ++  +     ++++E+EKERE  E R R  +         + ++   +R    +
Sbjct: 95  AKQAQRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQAAKQRTPKHK 154

Query: 148 SRRSSSQSRRSSSRSRRERER--ESERERELELERE-RERERELRERERDLEMRESRRYK 204
              + S S   S  ++ ER    E  ++R  E E +  +++++ RE ER  + ++ +  +
Sbjct: 155 KEAAESASSSLSGSAKPERNVSQEEAKKRLQEWELKKLKQQQQKREEERRKQRKKQQEEE 214

Query: 205 EKKEVVE 211
           E+K+  E
Sbjct: 215 ERKQKAE 221

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

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

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 4/68 (5%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA---- 379
           ++VG L ++ T+  L++ F  FG V    + +D  TG+ +GFGFV F      +      
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 380 QSALNGKL 387
           +  L+G++
Sbjct: 61  EHKLDGRV 68

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

>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 8/83 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLD-IETGQCKGFGFVQFAQLEHAKAAQ 380
           R L++ NL    T  QL++L    G   +    +D I++  C    +V ++ +E A A +
Sbjct: 2   RALHIDNLVRPFTLNQLKELLSETGTGVIEGFWMDKIKS-HC----YVTYSTVEEAVATR 56

Query: 381 SALNGKL--EIVGRTLKVSSVTD 401
            AL+G        + LKV  V  
Sbjct: 57  EALHGLQWPSSNPKRLKVDFVPQ 79

This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity. . Length = 90

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 40.5 bits (94), Expect = 1e-04
 Identities = 22/61 (36%), Positives = 34/61 (55%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL++G L F  TE  LR  +E +G +    +  D  + + +GFGFV F+ +    AA +
Sbjct: 3   RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62

Query: 382 A 382
           A
Sbjct: 63  A 63

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 40.5 bits (94), Expect = 1e-04
 Identities = 23/66 (34%), Positives = 37/66 (56%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  LYV  L   MT+ +L +LF  +G +   ++ +D  TG  +G GF++F +   A+ A 
Sbjct: 2   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61

Query: 381 SALNGK 386
             LNG+
Sbjct: 62  KGLNGQ 67

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

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+VG L    +  +L + F+ FG +        I+    + + ++++  +E A+AA+ AL
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIR------RIDYDPGRNYAYIEYESIEAAQAAKEAL 54

Query: 384 NGK-LEIVGRTLKV 396
            G  L   GR L+V
Sbjct: 55  RGFPLGGPGRRLRV 68

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 6/76 (7%)

Query: 220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
           Q T+  + +    +++++   FS+ G+V+D+R    R S++     ++EFYD+ +   A+
Sbjct: 1   QGTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQK-----FVEFYDIRAAEAAL 55

Query: 280 -ALSGQLLLGQPVMVK 294
            AL+G+  LG  + VK
Sbjct: 56  DALNGRPFLGGRLKVK 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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 40.5 bits (94), Expect = 1e-04
 Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LY+ NL  +M E +L  + +PFG V   ++  D  +G  +G GF +    E  +A  S  
Sbjct: 3   LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISHF 61

Query: 384 NGKL 387
           NGK 
Sbjct: 62  NGKF 65

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

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 6/60 (10%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA------LSGQLL 286
           +E D+   F   GK++   L  D  + + KG G+IE+ +  S   AIA      L GQ L
Sbjct: 13  SEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQL 72

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

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

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           RT+F   +  K TE  ++E F +AG V  V++  D++  + K   ++ F   +SVP A+ 
Sbjct: 2   RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDG-KPKQFAFVNFKHEVSVPYAMN 60

Query: 281 -LSGQLLLGQPVMVK 294
            L+G  L G+P+ ++
Sbjct: 61  LLNGIKLYGRPLNIQ 75

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

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 44.7 bits (105), Expect = 2e-04
 Identities = 28/216 (12%), Positives = 107/216 (49%), Gaps = 13/216 (6%)

Query: 7    EYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDE 66
            +  +K  EE+++  +     +KKKA+ ++K     +K   ++++ +E K ++ ++ + DE
Sbjct: 1381 DAAKKKAEEKKKADE-----AKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADE 1435

Query: 67   DEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRE 126
             ++      +  +  +  E  ++  +  +    E  ++ +  ++++ E ++ ++ +++ E
Sbjct: 1436 AKKKAEEAKKADEAKKKAEEAKKAEEAKKKA--EEAKKADEAKKKAEEAKKADEAKKKAE 1493

Query: 127  RRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERER----ESERERELELERER 182
               ++ +  ++    ++ +  ++++  +  + +  +++  E     E+++  E +   E 
Sbjct: 1494 EAKKKADEAKKAAEAKKKADEAKKA--EEAKKADEAKKAEEAKKADEAKKAEEKKKADEL 1551

Query: 183  ERERELRERERDLEMRESRRYKEKKEVVEPEADPER 218
            ++  EL++ E   +  E+++ +E K +   +A+  +
Sbjct: 1552 KKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAK 1587

Length = 2084

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

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 4/67 (5%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA---- 379
           L+VGNL ++ T   L   F+  G    V+L  D +TG+ KG  FV+F   E    A    
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 380 QSALNGK 386
            + L G+
Sbjct: 63  HTLLKGR 69

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

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 16/37 (43%), Positives = 25/37 (67%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
           TE DV ++FS+ GKV D  L+ D+ + R +G G++ F
Sbjct: 12  TEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48

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

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 19/60 (31%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 232 ATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQP 290
            TE D+ E F+  G+++D+ ++ D+ ++ SKGV Y++F    S   A+  ++G+ L G  
Sbjct: 14  VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 44.6 bits (105), Expect = 2e-04
 Identities = 42/218 (19%), Positives = 94/218 (43%), Gaps = 15/218 (6%)

Query: 5   EYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRR 64
           + + +++ +++ + +K++  +   ++A+ +   E    +++  E+EEEEEKSR  K    
Sbjct: 705 KEQRIKEELKKLKLEKEELLADKVQEAQDKINEELKLLEQKIKEKEEEEEKSRLKKEEEE 764

Query: 65  DEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERER 124
           +E  E   +     + +   E+            +  E + E+ + +  E R  E+E + 
Sbjct: 765 EEKSELSLKEKELAEEEEKTEKL-----------KVEEEKEEKLKAQEEELRALEEELKE 813

Query: 125 RERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERER 184
                 E++   E++ + +           +       + E+  E E ER  E   + E 
Sbjct: 814 EAELLEEEQLLIEQEEKIKEEELEE----LALELKEEQKLEKLAEEELERLEEEITKEEL 869

Query: 185 ERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRT 222
            +EL  +E +LE ++ +   E KE  E E   E ++ +
Sbjct: 870 LQELLLKEEELEEQKLKDELESKEEKEKEEKKELEEES 907

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 44.3 bits (104), Expect = 2e-04
 Identities = 21/59 (35%), Positives = 32/59 (54%)

Query: 97  RGRERERETERDRERSRERREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQS 155
           + RE   E  +     + R E+E+E+E+ + R+RE+ERE ER  +  SSS   R S   
Sbjct: 579 KKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAKASSSSHESRMSEPQ 637

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 41/232 (17%), Positives = 80/232 (34%), Gaps = 6/232 (2%)

Query: 6   YEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRD 65
            E L++ ++E + + ++ +    +  +  E    +  +     ++ EE +    +     
Sbjct: 173 SELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQ 232

Query: 66  EDEENGSRRDRDRDRDRDKERHR-RDRDRDRDRGRERERETERDRERSRERREKEKERER 124
           E E    R     +     E  + R  + +       +   E  RE  R   E E++ ER
Sbjct: 233 EIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIER 292

Query: 125 RERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERER 184
            E  +RE E   E     R+         +      +S  ER  + E + E       E 
Sbjct: 293 LEELEREIEELEEELEGLRALLEEL----EELLEKLKSLEERLEKLEEKLEKLESELEEL 348

Query: 185 ERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERD 236
             E  E  + LE R  +  +E+ E +E E +   ++       +     E  
Sbjct: 349 AEEKNELAKLLEERL-KELEERLEELEKELEKALERLKQLEEAIQELKEELA 399

Length = 908

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 4/61 (6%)

Query: 337 QLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQL-EHAKAAQSALNGKLEIVGRTLK 395
            L + F   G +  V +P D ETG  KGF +++F  +    KA +  L+G  ++ G  L 
Sbjct: 19  SLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE--LDGS-DLGGGNLV 75

Query: 396 V 396
           V
Sbjct: 76  V 76

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 43.9 bits (103), Expect = 2e-04
 Identities = 38/170 (22%), Positives = 74/170 (43%), Gaps = 9/170 (5%)

Query: 14  EEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSR 73
            E+R++ ++ +  +K + K + +     +K E   E EEEEK + G       +E NG  
Sbjct: 120 REEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGS-----LEENNGEF 174

Query: 74  RDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKE 133
                    +            + G+E E+  ++ +E + E  E +K+RE R +   E+E
Sbjct: 175 MTHKLKHTENTFSRGGAEGAQVEAGKEFEKLKQKQQEAALELEELKKKREERRKVLEEEE 234

Query: 134 RERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERE 183
           + R+++   R S    R   + RR      R R   +E+ +++  +   E
Sbjct: 235 QRRKQEEADRKS----REEEEKRRLKEEIERRRAEAAEKRQKVPEDGLSE 280

Length = 431

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

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 20/47 (42%), Positives = 31/47 (65%)

Query: 226 YQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
           + + L  TERD+ E FSK G + DV ++ D+ SRRS+G  ++ F +V
Sbjct: 15  FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 61

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

>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 31/88 (35%), Positives = 42/88 (47%), Gaps = 19/88 (21%)

Query: 321 DRKLYVGNLHFNMTETQLRKLF-----------EPFGPVELVQLPLDIETGQCKGFGFVQ 369
            R+LYVGNL   +TE +L   F            P  PV  VQ+  +      K F FV+
Sbjct: 1   ARRLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPE------KNFAFVE 54

Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           F  +E A AA  AL+G +   G+ LK+ 
Sbjct: 55  FRTVEEATAAL-ALDG-IIFKGQPLKIR 80

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

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

 Score = 40.5 bits (94), Expect = 2e-04
 Identities = 23/66 (34%), Positives = 37/66 (56%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  LYV  L   MT+ +L +LF  +G +   ++ +D  TG  +G GF++F +   A+ A 
Sbjct: 5   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64

Query: 381 SALNGK 386
             LNG+
Sbjct: 65  KGLNGQ 70

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K+ V NL F  T+  +R LF  +G ++ V++P   +    +GF FV+F+  + A  A +A
Sbjct: 2   KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQ-SARGFAFVEFSTAKEALNAMNA 60

Query: 383 LNGKLEIVGRTL 394
           L     ++GR L
Sbjct: 61  LKD-THLLGRRL 71

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

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 29/82 (35%), Positives = 44/82 (53%), Gaps = 4/82 (4%)

Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
           GP GA    L++ +L     +  L ++F PFG V   ++ +D +T   K FGFV +    
Sbjct: 4   GPEGA---NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 60

Query: 375 HAKAAQSALNGKLEIVGRTLKV 396
            A+AA  A+NG  +I  + LKV
Sbjct: 61  SAQAAIQAMNG-FQIGMKRLKV 81

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

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 27/78 (34%), Positives = 33/78 (42%), Gaps = 10/78 (12%)

Query: 324 LYVGNLH-FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           L+V         E  + KLFEPFGP+    +         K F FV+F   E A  A  A
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIR--------KTFAFVEFEDSEDATKALEA 53

Query: 383 LNGKLEIVGRTLKVSSVT 400
           L+G   I G  L V  V 
Sbjct: 54  LHGS-RIDGSVLTVEFVK 70

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

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

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 20/48 (41%), Positives = 28/48 (58%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
           K++VG L  N T   +++ FE FG V+   L  D  T + +GFGFV F
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48

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

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++VG +  ++ E +L  LFE  GP+  ++L +D  +G  +G+ FV +   E A+ A   L
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDF-SGLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 384 NGKLEI-VGRTLKVS 397
           +   EI  G+ L V 
Sbjct: 63  HNY-EIRPGKRLGVC 76

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 26/78 (33%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 324 LYVGNLHFNMTETQ----LRKLFEPFGPVELVQLPLDIETGQCKGF-GFVQFAQLEHAKA 378
           LYV  +   +TE +    L   F  FG +  V++          GF  FV+F     A  
Sbjct: 3   LYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKV-FPNAAVATPGFYAFVKFYSARAASR 61

Query: 379 AQSALNGKLEIVGRTLKV 396
           AQ A NGK    G  LKV
Sbjct: 62  AQKACNGKWLFQGSPLKV 79

This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. . Length = 81

>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF 35 kDa subunit B (U2AF35B)

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 29/99 (29%), Positives = 42/99 (42%), Gaps = 20/99 (20%)

Query: 501 LLLKNMF-DPAMET--DPDFD------LEIQGDVE-------EECSKYGRVKHIYV---- 540
           +LL NM+  P       P          E+Q   E       EE SK+G V+ + V    
Sbjct: 3   ILLSNMYQSPIAGAPGGPRGQGQSLDPRELQEHFEDFYEDIFEELSKFGEVEALNVCDNL 62

Query: 541 DKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIF 579
                G VY++F   E AA+A +A+  R++  R I   F
Sbjct: 63  GDHMVGNVYVKFRDEEHAAAALKALQGRFYDGRPIIVEF 101

This subgroup corresponds to the RRM of U2AF35B, also termed zinc finger CCCH domain-containing protein 60 (C3H60), which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. Members in this family are mainly found in plant. They show high sequence homology to vertebrates U2AF35 that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. U2AF35B contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants. . Length = 103

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 7/65 (10%)

Query: 332 NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG 391
           ++TE  L + F  +GPV  V   +D + GQ      V F ++E A+AA + + G+ ++ G
Sbjct: 18  SVTEQYLTRHFSRYGPVVHVV--IDRQRGQA----LVFFDKVEAAQAAVNEMKGR-KLGG 70

Query: 392 RTLKV 396
           R L+V
Sbjct: 71  RKLQV 75

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

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

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 11/72 (15%)

Query: 320 IDRKLYVGNLHF-----NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
             R +Y+GN+       N+ E +LRK  E +G +E +++  +      K   F+ F  + 
Sbjct: 1   ASRNVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILRE------KACAFINFMNIP 54

Query: 375 HAKAAQSALNGK 386
           +A AA   LNGK
Sbjct: 55  NAIAALQTLNGK 66

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|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 6/75 (8%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + L V NL ++ +E  L+++FE    + + Q       G+ KG+ FV+F   E AK A +
Sbjct: 2   KVLVVNNLSYSASEDSLQEVFEKATSIRIPQ-----NNGRPKGYAFVEFESAEDAKEALN 56

Query: 382 ALNGKLEIVGRTLKV 396
           + N   EI GR++++
Sbjct: 57  SCN-NTEIEGRSIRL 70

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

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

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPV 291
           TE D+   F   G++  V+L  D  + RSKG G+I+F D      A+  L+G  L G+P+
Sbjct: 11  TEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPI 70

Query: 292 MV 293
            V
Sbjct: 71  KV 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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 40.8 bits (95), Expect = 3e-04
 Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 241 FSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKPSEAE 299
           F+  G V D ++I+DR + RS+G G++ F D  +   AI+ + G+ L G+ + V P+   
Sbjct: 55  FAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDR 114

Query: 300 KNLVQSNTSAGGTATGPYG 318
            +  ++    GG + G  G
Sbjct: 115 PSAPRAYGGGGGYSGGGGG 133

Length = 144

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.5 bits (103), Expect = 3e-04
 Identities = 40/178 (22%), Positives = 62/178 (34%), Gaps = 7/178 (3%)

Query: 35  EKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRD 94
            K     +KRE  E EEE  +  +      +E +   +      D   +  R   + +R 
Sbjct: 658 NKRSSLAQKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQ 717

Query: 95  RDRGRER----ERETERDRERSRERREKEKERERRERRDREKERERERDGERRSSSRSRR 150
            +  +      E E E+ + R     E E+E E  E    E +   E   E   S     
Sbjct: 718 LEELKRELAALEEELEQLQSR---LEELEEELEELEEELEELQERLEELEEELESLEEAL 774

Query: 151 SSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEMRESRRYKEKKE 208
           +  +        +R+  +E   E E ELE    R   L      LE R  R  +E +E
Sbjct: 775 AKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEE 832

Length = 1163

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 47/212 (22%), Positives = 88/212 (41%), Gaps = 8/212 (3%)

Query: 12  TVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENG 71
           T+EE R++ ++ ++   +    EE+ E    + E +E+  E E        RR++ EE  
Sbjct: 469 TIEEDRERVEELEA---ELEDLEEEVEEVEERLERAEDLVEAEDRIERLEERREDLEELI 525

Query: 72  SRRDRDRDRDRDK-ERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDR 130
           + R    +  R++ E  R           E+        E + E RE+  E   +   + 
Sbjct: 526 AERRETIEEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREEVAELNSK-LAEL 584

Query: 131 EKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRE 190
           ++  E     ER  +  +  + ++      R +RE   E   ER   L  +RER+REL  
Sbjct: 585 KERIESL---ERIRTLLAAIADAEDEIERLREKREALAELNDERRERLAEKRERKRELEA 641

Query: 191 RERDLEMRESRRYKEKKEVVEPEADPERDQRT 222
              +  + E+R  KE+ E    + + + D+  
Sbjct: 642 EFDEARIEEAREDKERAEEYLEQVEEKLDELR 673

Length = 880

>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 = 39.5 bits (93), Expect = 3e-04
 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMS 274
           DP     T+F  ++ L+ TE  + E FS+ G +R +RL+ D  +  SKG  ++E+     
Sbjct: 1   DPYL---TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERD 57

Query: 275 VPMA 278
              A
Sbjct: 58  ALRA 61

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

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           ++V NL + +   +L+++F+  G V    +  D E G+ +G G VQF     A  A S  
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 384 NGKLEIVGRTLKV 396
           NG++ +  R ++V
Sbjct: 60  NGQM-LFDRPMRV 71

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

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

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 27/78 (34%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQL---PLDIETGQ--CKGFGFVQFAQLEHAKA 378
           L+V NL+F+ T   L   F+        ++   P     GQ    GFGFV F   E A+A
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 379 AQSALNGKLEIVGRTLKV 396
           A  A++G   + G TL V
Sbjct: 63  ALKAMDGF-VLDGHTLVV 79

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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 3/67 (4%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ---LEHAKAAQ 380
           +++G L++  T+  LR+ F  FG V    +  D  TG+ +GFGF+ F +   +      +
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 381 SALNGKL 387
             L+GK+
Sbjct: 61  HILDGKI 67

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

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

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
           I  +++VG + F   E  LRK F  +G V+ V++  D   G  KG+GFV F   E A+
Sbjct: 1   IPNRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQ 57

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 6/55 (10%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHA 376
           R +Y+GNL  + +E +LR+  E FGP++ +++  +      K   FV F  + +A
Sbjct: 4   RNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFLSIANA 52

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 43.4 bits (102), Expect = 3e-04
 Identities = 43/246 (17%), Positives = 90/246 (36%), Gaps = 24/246 (9%)

Query: 9   LEKTVEEQRQQKQDDDSSSKKKAKREEKSE-RSYRKREDSEEEEEEEKSRSGKRSRRDED 67
            E   E + + + + +  +++K ++E + E  +       E E EE +      +   ED
Sbjct: 669 QEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTED 728

Query: 68  EENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRER 127
           E      +   + + + E     +      G  +E E E + E   +  E E E +  E 
Sbjct: 729 EGEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGED 788

Query: 128 RDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELER------- 180
            + + +   E   E    + +        +S +++     ++   E+EL  E        
Sbjct: 789 GEMKGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQD 848

Query: 181 -------------ERERERELRERERDLEMRESRRYKEKKEVVEP---EADPERDQRTVF 224
                        + E E E  E E + E  E    +E++E  EP   E    R ++ ++
Sbjct: 849 EKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETRQKQAIY 908

Query: 225 AYQMPL 230
            + +P+
Sbjct: 909 LFLLPI 914

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

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

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LY+ NL  +M E +L  + +PFG V   ++  D  +G  +G GF +    E  +A  +  
Sbjct: 3   LYISNLPLSMDEQELESMLKPFGQVISTRILRD-ASGTSRGVGFARMESTEKCEAIITHF 61

Query: 384 NGK 386
           NGK
Sbjct: 62  NGK 64

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 20/66 (30%), Positives = 35/66 (53%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D +++VG+L   +T+  L + F  +   +  ++  D  TG+ KG+GFV F+       A 
Sbjct: 6   DFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAM 65

Query: 381 SALNGK 386
             +NGK
Sbjct: 66  KEMNGK 71

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

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 43.1 bits (102), Expect = 3e-04
 Identities = 42/212 (19%), Positives = 74/212 (34%), Gaps = 28/212 (13%)

Query: 20  KQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRD 79
           K+ ++     K K +E  E      E S E  E  +          E EE        ++
Sbjct: 186 KRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEEL-------KE 238

Query: 80  RDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRE------------- 126
              + E+     +  + +  E+ RE E   E  ++  E+ +E+ +               
Sbjct: 239 EIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKL 298

Query: 127 RRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERER 186
               E+  +  R+ E+R S      +    R      +E   E  +++  ELE+  E   
Sbjct: 299 SEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLE--- 355

Query: 187 ELRERERDLE-----MRESRRYKEKKEVVEPE 213
           EL ER    E       E  R K++   + PE
Sbjct: 356 ELEERHELYEEAKAKKEELERLKKRLTGLTPE 387

Length = 880

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 43.1 bits (102), Expect = 4e-04
 Identities = 61/291 (20%), Positives = 113/291 (38%), Gaps = 35/291 (12%)

Query: 4   DEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSR----SG 59
           +E E L++ ++E  ++    +  + +  + EEK E    +  + EEE EE +      + 
Sbjct: 239 EELEELQEELKEAEEEL---EELTAELQELEEKLEELRLEVSELEEEIEELQKELYALAN 295

Query: 60  KRSRRDEDEENGSRRDRDRDRDRDK-----ERHRRDRDRDRDRGRERERETERDRERSRE 114
           + SR ++ ++    R  + +R  ++     E      D   +   E E + E  +E    
Sbjct: 296 EISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELES 355

Query: 115 RREK--EKERERRERRDREKERERERDGERR---------SSSRSRRSSSQSRRSSSRSR 163
              +  E E E  E   R +E E + +  R          +S  +     ++R      R
Sbjct: 356 LEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDR 415

Query: 164 RERERESERERELELERER---------ERERELRERERDLEMRESRRYKEKKEVVEPEA 214
           RER ++   E   +LE            E E EL E + +LE  E    + ++E+ E E 
Sbjct: 416 RERLQQEIEELLKKLEEAELKELQAELEELEEELEELQEELERLEEALEELREELEEAEQ 475

Query: 215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
             +  +R +   Q  L + ER         G    V+ ++   S  S  +G
Sbjct: 476 ALDAAERELAQLQARLDSLERLQENL---EGFSEGVKALLKNQSGLSGILG 523

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 43.2 bits (102), Expect = 4e-04
 Identities = 50/253 (19%), Positives = 85/253 (33%), Gaps = 17/253 (6%)

Query: 9   LEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEE----EEEEKSRSGKRSRR 64
           L    + ++  +   +   + KAK EE   +     ED E+     EEE K        +
Sbjct: 163 LFGLEKYEKLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQ 222

Query: 65  DEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERR-------- 116
           +E EE    ++ +   +R  E        +  + R  E E+                   
Sbjct: 223 EEQEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERL 282

Query: 117 --EKEKERERRERRDREKERERERDGERRS--SSRSRRSSSQSRRSSSRSRRERERESER 172
             E E++ ER E  +RE E   E     R+                    + E + E   
Sbjct: 283 LEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLE 342

Query: 173 ERELEL-ERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLK 231
               EL E + E  + L ER ++LE R     KE ++ +E     E   + +      L 
Sbjct: 343 SELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAIQELKEELAELS 402

Query: 232 ATERDVYEFFSKA 244
           A   ++ E   + 
Sbjct: 403 AALEEIQEELEEL 415

Length = 908

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

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L 281
           VF   +  + T  D+   F+  G++ D R++ D  + +SKG G++ F++      AI  +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 282 SGQLLLGQPV 291
            GQ L G+ +
Sbjct: 64  GGQWLGGRQI 73

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

>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding protein RBM12, RBM12B and similar proteins

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           VF + +P  A E DV EFF     V DV  +   N R + G   ++F        A+   
Sbjct: 2   VFLHGLPYTADEHDVKEFFHGL-DVEDVIFLKRHNGRNN-GNAIVKFATFQDAKEALKRH 59

Query: 283 GQLLLGQPVMVKPS 296
            +L+  + + +  S
Sbjct: 60  RELMGSRYIELMLS 73

This subfamily corresponds to the RRM2 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B shows high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. . Length = 73

>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 = 39.5 bits (93), Expect = 4e-04
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 4/58 (6%)

Query: 328 NLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
           NL + +T   L ++F P+G VE + +       Q      VQF  +E A+ A+ ALNG
Sbjct: 8   NLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQA----LVQFDSVESAENAKKALNG 61

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|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 323 KLYVGNLHFNMTETQLRKLF-EPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           ++++ N+ +++    L+ LF E  G V  V+L  D E G+ +G G V+F   E  + A  
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKD-EEGKSRGCGVVEFKDKESVQKALE 59

Query: 382 ALNGKLEIVGRTLKV 396
            +N + E+ GR L V
Sbjct: 60  TMN-RYELKGRKLVV 73

This subfamily corresponds to the RRM1 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. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 21/66 (31%), Positives = 37/66 (56%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  LYV  L   M++ ++ +LF  +G +   ++ +D  TG  +G GF++F +   A+ A 
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60

Query: 381 SALNGK 386
             LNG+
Sbjct: 61  KGLNGQ 66

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFE-PFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           ++VG+L   + E+ L  LF+  F   +  ++  D  TG  +G+GFV+F+     + A   
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 383 LNGKLEIVGRTLKVSSVT 400
           + G     GR +++S+ T
Sbjct: 64  MQGVY-CGGRPMRISTAT 80

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

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

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 4/56 (7%)

Query: 524 DVEEECSKYGRVKHIYV----DKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI 575
           D+++  SK+G ++ I +      RS GF ++ FE  E A  A  A++ +    R +
Sbjct: 14  DLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 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|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 42.7 bits (100), Expect = 5e-04
 Identities = 22/89 (24%), Positives = 41/89 (46%), Gaps = 14/89 (15%)

Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGF---------V 548
           S  ++L+NM  P      D D  ++G++ EEC K+G V  + ++    G          +
Sbjct: 514 SNVIVLRNMVTPQ-----DIDEFLEGEIREECGKFGVVDRVIINFEKQGEEEDAEIIVKI 568

Query: 549 YLRFESTEAAASAQRAMHMRWFARRLISA 577
           ++ F  +     A+ A+  R+F  R + A
Sbjct: 569 FVEFSDSMEVDRAKAALDGRFFGGRTVVA 597

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

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

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQ 289
           K TE  ++E F +AG V +V +  DR ++  +G G++EF        AI  ++   L G+
Sbjct: 9   KVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGK 68

Query: 290 PVMVK 294
           P+ V 
Sbjct: 69  PIRVN 73

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

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 40.6 bits (95), Expect = 5e-04
 Identities = 31/99 (31%), Positives = 46/99 (46%), Gaps = 3/99 (3%)

Query: 46  DSEEEEEEEKSRSGKRSRRDEDEENGSRRDRD---RDRDRDKERHRRDRDRDRDRGRERE 102
                    + RS  R RR+   E    R+RD   R R R   R RR R   R R R R 
Sbjct: 6   SRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSRSRS 65

Query: 103 RETERDRERSRERREKEKERERRERRDREKERERERDGE 141
               RDR+R R++  +E ++  R++  +E++ E + D E
Sbjct: 66  PSRRRDRKRERDKDAREPKKRERQKLIKEEDLEGKSDEE 104

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 38.7 bits (90), Expect = 5e-04
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 7/74 (9%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +L+VGNL  ++TE + +KLF  +G       P ++   + KGFGF++      A+ A++ 
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGE------PGEVFINKGKGFGFIKLESRALAEIAKAE 56

Query: 383 LNGKLEIVGRTLKV 396
           L+    + GR L+V
Sbjct: 57  LD-DTPMRGRQLRV 69

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 38.5 bits (89), Expect = 5e-04
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +Y G +   +TE  +R+ F PFG +      ++I     KG+ F++F+  E A  A  ++
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQI------MEIRVFPEKGYSFIRFSTHESAAHAIVSV 56

Query: 384 NGKLEIVGRTLK 395
           NG   I G  +K
Sbjct: 57  NGT-TIEGHVVK 67

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 38.7 bits (90), Expect = 5e-04
 Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 4/52 (7%)

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
           RD RT+F   +P   T  ++ E F  A    D+RL   ++   SKG+ YIEF
Sbjct: 1   RDARTLFVKNLPYNITVDELKEVFEDA---VDIRLPSGKDG-SSKGIAYIEF 48

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

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

 Score = 38.9 bits (91), Expect = 5e-04
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LY+ NL  +M E  L  + +P+G V   ++  D   GQ +G GF +    E  +   S  
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRD-SKGQSRGVGFARMESREKCEDIISKF 61

Query: 384 NGK 386
           NGK
Sbjct: 62  NGK 64

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

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 19/57 (33%), Positives = 35/57 (61%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
           +++VG +  ++ E +L  LFE  GP+  ++L +D  +GQ +G+ F+ F   E A+ A
Sbjct: 3   EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEA 59

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

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

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 2/66 (3%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           +++D+ ++F+K G+V D  + MD N+ RS+G G+I F D  SV   +      L G+  +
Sbjct: 12  SKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQKEHRLDGR--L 69

Query: 293 VKPSEA 298
           + P +A
Sbjct: 70  IDPKKA 75

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.4 bits (100), Expect = 6e-04
 Identities = 39/196 (19%), Positives = 68/196 (34%), Gaps = 17/196 (8%)

Query: 4   DEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSR 63
           ++ E L++ +EE+    ++ +    +  + +E+ E       +  EE  E         R
Sbjct: 330 EKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEAL-------R 382

Query: 64  RDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERE 123
            +  E      +   + +  K       +R        ER +ER  +   E +E E E E
Sbjct: 383 EELAELEAELAEIRNELEELKREIESLEER-------LERLSERLEDLKEELKELEAELE 435

Query: 124 RRERRDREKERERERDGERRSSSRSRRS---SSQSRRSSSRSRRERERESERERELELER 180
             +    E   E E   E+    R R        +       R E+E  S   R   LE 
Sbjct: 436 ELQTELEELNEELEELEEQLEELRDRLKELERELAELQEELQRLEKELSSLEARLDRLEA 495

Query: 181 ERERERELRERERDLE 196
           E+   + +R     LE
Sbjct: 496 EQRASQGVRAVLEALE 511

Length = 1163

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 42.5 bits (101), Expect = 6e-04
 Identities = 24/165 (14%), Positives = 58/165 (35%)

Query: 26  SSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKE 85
           SSK+  ++ ++     +    + EEEE  K  + + +  +   E       + + +   E
Sbjct: 16  SSKELLEKLKELGIEVKSHSSTVEEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAE 75

Query: 86  RHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERERDGERRSS 145
                   +            R  E    R  +   R  + ++  +K++  +   ++   
Sbjct: 76  AAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKR 135

Query: 146 SRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRE 190
             +R           R RR R R  +++++ +   +  RE  + E
Sbjct: 136 KAARGGKRGKGGKGRRRRRGRRRRRKKKKKQKPTEKIPREVVIPE 180

Length = 746

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

 Score = 38.7 bits (90), Expect = 6e-04
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V NL  + T  +  +L   +G +E   L     TG  KG+GFV++ + + A  A    
Sbjct: 2   LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKA---- 57

Query: 384 NGKLEIVGRTL 394
             +LE++G+ L
Sbjct: 58  --RLELLGKQL 66

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

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 42.7 bits (101), Expect = 6e-04
 Identities = 29/234 (12%), Positives = 85/234 (36%), Gaps = 15/234 (6%)

Query: 4    DEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSR 63
            ++ E  EK + ++++ K      + K  K + K +   +K+  +++ ++     + KR  
Sbjct: 1143 EQEEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVD 1202

Query: 64   RDEDEENGSRRDR------DRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERRE 117
             DE  +   + D         D++ D+E+  + +     R + ++  + +  E + E   
Sbjct: 1203 SDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSS 1262

Query: 118  KEKERERRERRDRE---------KERERERDGERRSSSRSRRSSSQSRRSSSRSRRERER 168
             +  +E + +   +             +  DGE    S+    + +  +          +
Sbjct: 1263 DDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALK 1322

Query: 169  ESERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRT 222
            + ++  +    +++ + R  +           R  K+K +    + D      +
Sbjct: 1323 KKKKSEKKTARKKKSKTRVKQASASQSSRLLRRPRKKKSDSSSEDDDDSEVDDS 1376

Length = 1388

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 38.3 bits (89), Expect = 6e-04
 Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 11/61 (18%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL+VGNL    TE ++R LFE +G V    L  DI     K +GFV    ++   AA  A
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKV----LECDI----IKNYGFV---HMDDKTAADEA 50

Query: 383 L 383
           +
Sbjct: 51  I 51

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 38.5 bits (89), Expect = 6e-04
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 6/62 (9%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +Y G +   +TE  +R+ F PFG +  V++  D      KG+ FV+F   E A  A  ++
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSV 56

Query: 384 NG 385
           NG
Sbjct: 57  NG 58

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)

 Score = 38.4 bits (89), Expect = 6e-04
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KLY+GNL   +T   LR+LF         +LPL  +     G+ FV +     A  A   
Sbjct: 3   KLYIGNLSPAVTAEDLRQLFGD------RKLPLTGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 383 LNGKLEIVGRTLKV 396
           L+GK+E+ G+ ++V
Sbjct: 57  LSGKVELHGKVMEV 70

This subgroup corresponds to the RRM1 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, which is a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 38.3 bits (89), Expect = 6e-04
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +YVGN+ +  T  +L   F   GP+  V +  D  +G  KG+ +++FA  +  +AA  AL
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAA-VAL 60

Query: 384 NGKLEIVGRTLKV 396
           +      GR +KV
Sbjct: 61  DESS-FRGRVIKV 72

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

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

 Score = 38.8 bits (91), Expect = 7e-04
 Identities = 14/58 (24%), Positives = 30/58 (51%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
           +T+F  ++    TE  +   F + G ++ +RL+ D+ + + +G  +IEF     +  A
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

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

 Score = 38.3 bits (89), Expect = 7e-04
 Identities = 18/43 (41%), Positives = 29/43 (67%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
           T++D+ E+FSK G+V D  + +D  + RS+G G++ F D  SV
Sbjct: 11  TKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASV 53

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

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

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL V NL F +++  +++LF  FG ++   +  D  +G+  G   V F +   A  A   
Sbjct: 2   KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYD-RSGRSLGTADVVFERRADALKAMKQ 60

Query: 383 LNG-KLEIVGRTLKV 396
            NG  L+  GR +K+
Sbjct: 61  YNGVPLD--GRPMKI 73

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

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 38.1 bits (89), Expect = 7e-04
 Identities = 25/81 (30%), Positives = 37/81 (45%), Gaps = 6/81 (7%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELV-QLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           RK+ + N+  ++    L  L   +G V+   Q+P   ET        V +   E A+ A 
Sbjct: 1   RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVN----VTYESPEQAQQAV 56

Query: 381 SALNGKLEIVGRTLKVSSVTD 401
           + LNG  E  G  LKVS + D
Sbjct: 57  NKLNGH-EYEGSKLKVSYIPD 76

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

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

 Score = 38.1 bits (88), Expect = 7e-04
 Identities = 20/49 (40%), Positives = 28/49 (57%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
           +K++VG L  N     +++ FE FG VE   L  D  T + +GFGFV F
Sbjct: 4   KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF 52

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 38.0 bits (89), Expect = 8e-04
 Identities = 16/60 (26%), Positives = 32/60 (53%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
             +F   +P   T+  + ++FS+ G++ +  +I DR + +S+G G++ F D  S   A  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 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|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 14/48 (29%), Positives = 27/48 (56%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
            +F   +P     +++ E+FS+ GKV+   +  D+ +  SKG G++ F
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSF 48

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.4 bits (99), Expect = 8e-04
 Identities = 38/207 (18%), Positives = 90/207 (43%), Gaps = 11/207 (5%)

Query: 11   KTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEEN 70
            + +EE  +   +DD   +K    E+       K E      ++E  +   +     D + 
Sbjct: 1027 EKIEELTEYGNNDDVLKEKDIIDEDIDGNHEGKAEAKAHVGQDEGLKPSYK-----DFDF 1081

Query: 71   GSRRDRDRDRDRDKERHRRDRDRDRDRGR-ERERETERDRERSRERREKEKERERRERRD 129
             ++ D   D   ++   + +  +  + G+ E  R+ E  ++++ + R+ E+ R+  + R 
Sbjct: 1082 DAKEDNRADEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARKAEEARKAEDARK 1141

Query: 130  REKERERERDGERRSSSRSR--RSSSQSRRSSSRSRRERERESERERELELERERERERE 187
             E+ R+ E       + ++   R + ++R++    + E  R++E  R+ E  R+ E  R+
Sbjct: 1142 AEEARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARK 1201

Query: 188  LRERERDLEMR---ESRRYKEKKEVVE 211
                 +  E R   E+R+ ++ K+   
Sbjct: 1202 AEAARKAEEERKAEEARKAEDAKKAEA 1228

Length = 2084

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 42.4 bits (100), Expect = 8e-04
 Identities = 47/240 (19%), Positives = 77/240 (32%), Gaps = 14/240 (5%)

Query: 4   DEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEE-----EEEEEKSRS 58
           +    L K + E   + +      ++  + EE+   +  + E+ E      +EE +  R 
Sbjct: 747 ERIAQLSKELTELEAEIE---ELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALRE 803

Query: 59  GKRSRRDE-DEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERRE 117
                R E    N    +     +  + R      R  D   + E  +E     + E  E
Sbjct: 804 ALDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEE 863

Query: 118 KEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELE 177
            E+  E  E        ER    E  +  RS             S+R   R    E   +
Sbjct: 864 LEELIEELESELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELREK 923

Query: 178 LERERERERELRERERDLEMRESRRYKEKKEVVEP-----EADPERDQRTVFAYQMPLKA 232
           L +   R   L  R  +L+ R S  Y    E  E      E D E  +R +   +  +K 
Sbjct: 924 LAQLELRLEGLEVRIDNLQERLSEEYSLTLEEAEALENKIEDDEEEARRRLKRLENKIKE 983

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

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

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 17/51 (33%), Positives = 29/51 (56%)

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
           P   TE D+ E F + G +  V ++ D+N+  SKG GY++F+      +A+
Sbjct: 9   PKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 42.3 bits (99), Expect = 8e-04
 Identities = 38/222 (17%), Positives = 76/222 (34%), Gaps = 14/222 (6%)

Query: 10   EKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEE 69
              T++E  QQ    D +   +   E+  E     +E+ E  E+  KS          +++
Sbjct: 4040 NNTLDEDIQQDDFSDLAEDDEKMNEDGFEE--NVQENEESTEDGVKSDEELEQGEVPEDQ 4097

Query: 70   NGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRD 129
                  +   +         + + D+    E E   E D  R     + E E+ + +   
Sbjct: 4098 AIDNHPKMDAKSTFASAEADEENTDKGIVGENEELGEEDGVRGNGTADGEFEQVQEDTST 4157

Query: 130  REKERERERDGERRSSSRSRRSSSQSRR-SSSRSRRERERESERERELELERERERE--- 185
             ++    E D + +S     R   Q+ R        E + ++  + E    +E E E   
Sbjct: 4158 PKEAMS-EADRQYQSLGDHLREWQQANRIHEWEDLTESQSQAFDDSEFMHVKEDEEEDLQ 4216

Query: 186  -------RELRERERDLEMRESRRYKEKKEVVEPEADPERDQ 220
                    +++  +RD    ++        + E EAD   D+
Sbjct: 4217 ALGNAEKDQIKSIDRDESANQNPDSMNSTNIAEDEADEVGDK 4258

Length = 4600

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 41.9 bits (98), Expect = 8e-04
 Identities = 32/159 (20%), Positives = 75/159 (47%), Gaps = 3/159 (1%)

Query: 22  DDDSSSKKK--AKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRD 79
           D DS S KK      E +E+    R D  + +E E     KR+++ ++E +  + D D+ 
Sbjct: 173 DTDSISDKKVVEALREDNEKGVNFRRDMTDLKERESQEDAKRAQQLKEELDKKQIDADKA 232

Query: 80  RDR-DKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERER 138
           + + D  +   D+ RD  R +++E +       +   +E ++  E ++R   + + E ++
Sbjct: 233 QQKADFAQDNADKQRDEVRQKQQEAKNLPKPADTSSPKEDKQVAENQKREIEKAQIEIKK 292

Query: 139 DGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELE 177
           + E    ++  ++    + S +  +   ++E E +++ E
Sbjct: 293 NDEEALKAKDHKAFDLKQESKASEKEAEDKELEAQKKRE 331

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 42.0 bits (98), Expect = 9e-04
 Identities = 19/50 (38%), Positives = 27/50 (54%)

Query: 140 GERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELR 189
             + +  R        R +  ++R ERERE E+E+E E ERERE ER  +
Sbjct: 574 SSKLAKKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

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

 Score = 41.4 bits (97), Expect = 0.001
 Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 8/101 (7%)

Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRS--------AG 546
           G P++ + L N+       D +   EI  DV+ E SKYG + +I + + +         G
Sbjct: 406 GKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVG 465

Query: 547 FVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEA 587
            V+L +    +A  A   M+ R F  R++ A F   + Y+A
Sbjct: 466 KVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGEDCYKA 506

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

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 5/57 (8%)

Query: 524 DVEEECSKYGRVK--HIYVD---KRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI 575
           ++ E    +G +   H+ +D   KRS GF ++ F   E A  A   +    F  RL+
Sbjct: 15  ELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLL 71

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

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

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 13/47 (27%), Positives = 27/47 (57%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
           +F   +    TE D+ + FSK G + +V L +D+ +++ KG  ++ +
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 14/37 (37%), Positives = 20/37 (54%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
            +  + E FS  G V+DV L +DR     +G  Y+EF
Sbjct: 11  NKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEF 47

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

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

 Score = 36.7 bits (86), Expect = 0.001
 Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 6/61 (9%)

Query: 237 VYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP 295
           +Y+ FS  G V  ++L      ++  G  ++EF    +   A+  L+G L  G+P+ V  
Sbjct: 1   LYKLFSPFGNVEKIKL-----LKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 296 S 296
           S
Sbjct: 56  S 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|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 43/241 (17%), Positives = 76/241 (31%), Gaps = 25/241 (10%)

Query: 4   DEYEYLEKTVEE-QRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSG--- 59
            + E LE+  E+ +R Q+   +    + A    K +   ++ E+ EEE    +       
Sbjct: 200 KQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEELSRLEEELEELQ 259

Query: 60  -------------KRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETE 106
                        K    +  EE    ++   +   + E    +    R+R  E E E E
Sbjct: 260 EELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELE 319

Query: 107 RDRERSRERREKEKERER--------RERRDREKERERERDGERRSSSRSRRSSSQSRRS 158
              ER  E +EK +  +          E  ++      E   E      +     +    
Sbjct: 320 ELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFE 379

Query: 159 SSRSRRERERESERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPER 218
           + R           E   ELE  +     L ER   L  R     +E KE+     + + 
Sbjct: 380 ALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQT 439

Query: 219 D 219
           +
Sbjct: 440 E 440

Length = 1163

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

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
           +F Y +P + T+ D+ + F   G V   ++ +D+ +  SK  G++ + +  S   AI A+
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 282 SG 283
           +G
Sbjct: 67  NG 68

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

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 29/77 (37%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
           I R +YVGNL    T  QL + F   G V+ V++  D    Q   + FV+FA+      A
Sbjct: 3   IRRTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGD--ETQPTRYAFVEFAEQTSVINA 60

Query: 380 QSALNGKLEIVGRTLKV 396
              LNG     GR LKV
Sbjct: 61  L-KLNGA-MFGGRPLKV 75

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 30/133 (22%), Positives = 48/133 (36%), Gaps = 9/133 (6%)

Query: 108 DRERSRERREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERE 167
              R      + +  E +  R+R +  +RE      SS +S     ++R           
Sbjct: 660 RAPRGGILFSRSEPAELQRLRERLEGLKREL-----SSLQSELRRIENRLDELSQELSDA 714

Query: 168 RESERERELELERERERERELRER----ERDLEMRESRRYKEKKEVVEPEADPERDQRTV 223
                E E E+E+  + E +L+ER    E DL   E      K E+ E EA  E  +  +
Sbjct: 715 SRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDL 774

Query: 224 FAYQMPLKATERD 236
              +  L   E  
Sbjct: 775 HKLEEALNDLEAR 787

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

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

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 15/47 (31%), Positives = 27/47 (57%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
           +F   + +  T  DV ++F + GKV D  L+ D+ + R +G G++ F
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48

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

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

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 17/48 (35%), Positives = 29/48 (60%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
           K++VG L ++ ++  L+  F  FG V    + +D  TG+ +GFGF+ F
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILF 48

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 18/49 (36%), Positives = 32/49 (65%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
           +KL+VG +  +  E  LR  FE +G ++ +++  D ++G+ +GFGFV F
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 28/154 (18%), Positives = 61/154 (39%), Gaps = 2/154 (1%)

Query: 48  EEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETER 107
            + +EEE+ R  + +  +E  E      R +  +   ER   +    +    E +RE E+
Sbjct: 395 SKVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEK 454

Query: 108 DRERSRERREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERE 167
                   R + +++ R++R  R ++R  ER    +     ++   +  R  +  R+ R+
Sbjct: 455 LESELERFRREVRDKVRKDREIRARDRRIER--LEKELEEKKKRVEELERKLAELRKMRK 512

Query: 168 RESERERELELERERERERELRERERDLEMRESR 201
            E   +       E+     + E E +  ++E  
Sbjct: 513 LELSGKGTPVKVVEKLTLEAIEEAEEEYGIKEGD 546

Length = 652

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 34/163 (20%), Positives = 69/163 (42%), Gaps = 2/163 (1%)

Query: 72  SRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDRE 131
           ++      ++  KE   +      +      RE  + R+ +R  RE+ +  E R  +  E
Sbjct: 32  AKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEERLVQKEE 91

Query: 132 KERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRER 191
           +   R    +   +    R  + S R       E++ ++E  R   L  E+ R+  L+  
Sbjct: 92  QLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNELYRVAGLTPEQARKLLLKLL 151

Query: 192 ERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATE 234
           + +LE  +++R K+ +E  E + + ER  + + A  M   A+E
Sbjct: 152 DAELEEEKAQRVKKIEE--EADLEAERKAQNILAQAMQRIASE 192

Length = 508

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 19/159 (11%), Positives = 73/159 (45%)

Query: 60  KRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKE 119
            R +  +       + R +  ++  E  +  +  +++R ++ E+E  + +E+ ++  E E
Sbjct: 65  GRIQSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAE 124

Query: 120 KERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELE 179
           K+ +  +++  E+ R+   + ++++ +   ++++++ +  + +  +++ E   +   E +
Sbjct: 125 KQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAK 184

Query: 180 RERERERELRERERDLEMRESRRYKEKKEVVEPEADPER 218
            + E     ++ E + +    +   E +   + E   E 
Sbjct: 185 AKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEA 223

Length = 387

>gnl|CDD|227615 COG5296, COG5296, Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]

 Score = 41.2 bits (96), Expect = 0.001
 Identities = 47/203 (23%), Positives = 86/203 (42%), Gaps = 14/203 (6%)

Query: 21  QDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDR 80
             D +S++K+A  +     S    ED+ E  +  +   G+ + + E+E+        ++ 
Sbjct: 16  DSDVASNRKRAHDDLDDVLSSSSDEDNNENVDYAEESGGEGNEKSEEEK-------FKNP 68

Query: 81  DRDKERHRRDRDRDRDRG-RERERET---ERDRERSRERREKEKERERRERRDREKERER 136
            R + + + + DR +     E ERE+   ER+ E S+   E+ +   R E++ R      
Sbjct: 69  YRLEGKFKDEADRAKIMAMTEIERESILFEREEEISK-LMERRELAIRMEQQHRSSGCTD 127

Query: 137 ERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLE 196
            R   R     S     + +    +  RERE     ER +EL+R ++ + EL E E+ L+
Sbjct: 128 TRRSTRYEPLTSAAEEKKKKLLELKKTREREERLYSERHIELQRFKDYK-ELEESEQGLQ 186

Query: 197 MRESRRYK-EKKEVVEPEADPER 218
              +  Y  E  E +    D   
Sbjct: 187 EEYTPSYAEEAVEDISRTDDFAE 209

Length = 521

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 7/73 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE-TGQCKGFGFVQFAQLEHAKAAQ 380
           R L++GNL    T + LR+ FE FG +    + +DI+  G    + F+Q+A +     A 
Sbjct: 3   RTLFIGNLEKTTTYSDLREAFERFGEI----IDIDIKKQGGNPAYAFIQYADIASVVKAM 58

Query: 381 SALNGKLEIVGRT 393
             ++G  E +G  
Sbjct: 59  RKMDG--EYLGNN 69

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|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 28/72 (38%), Positives = 35/72 (48%), Gaps = 9/72 (12%)

Query: 333 MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQL--------EHAKAAQSALN 384
            T  Q+R  F PFG +E  +L LD  TGQ  G   V F           E AKAA   LN
Sbjct: 10  TTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEAAKAAVDGLN 69

Query: 385 GKLEIVGRTLKV 396
           G+  I G+ ++V
Sbjct: 70  GR-RIGGKRVRV 80

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 4/68 (5%)

Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSR---RSKGVGYIEFYDVMSVPMAIALSGQLLL 287
           +ATE  +   F   GK+ ++RL    +      SK V ++++ D   V +A+ L+  + +
Sbjct: 10  QATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSK-VCFVKYEDPEDVGVALHLTNTVFI 68

Query: 288 GQPVMVKP 295
            + ++V P
Sbjct: 69  DRALIVVP 76

This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable. . Length = 76

>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 27/192 (14%), Positives = 49/192 (25%), Gaps = 18/192 (9%)

Query: 31  AKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRD--RDRDRDKERHR 88
           A+R+ +S      R   +        +  +R    +  +     D D         +R  
Sbjct: 798 AERQAESAERELARAARKAAAAAAAWKQARRELERDAADLDLPTDPDALEAVGLALKRFG 857

Query: 89  RDRDRDRDRGRERERETERDRERSRER-REKEKERERRE----RRDREKERERERDGERR 143
                     RE  R         R R    E +             E E    R     
Sbjct: 858 DHLHTLEVAVREL-RHAATRAAEQRARAARAESDAREAAEDAAEARAEAEEASLRLRTLE 916

Query: 144 SSS-------RSRRSSSQSRRSSSRSRRERERESER---ERELELERERERERELRERER 193
            S        R+R + +++  +S      R  E+     E     E +R       +   
Sbjct: 917 ESVGAMVDEIRARLAETRAALASGGRELPRLAEALATAEEARGRAEEKRAEADATLDERA 976

Query: 194 DLEMRESRRYKE 205
           +       + +E
Sbjct: 977 EARDHAIGQLRE 988

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length [Hypothetical proteins, Conserved]. Length = 1353

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 39/169 (23%), Positives = 74/169 (43%), Gaps = 10/169 (5%)

Query: 28  KKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERH 87
           +++ ++EEK     R R   EE E+E +     R+   ++E     R ++++    + R 
Sbjct: 172 ERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEEAEKRRRQ 231

Query: 88  RRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERERDGERRSSSR 147
           +++  R R          E   E   ER ++E+  E  ER    +++  + + E+ ++ +
Sbjct: 232 KQELQRAR----------EEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEK 281

Query: 148 SRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLE 196
            R    + RR   +   E+E     ERE ELE       E  ER+  +E
Sbjct: 282 RRMKRLEHRRELEQQIEEKEERRAAEREEELEEGERLREEEAERQARIE 330

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +P   T++++   FS  G++   R++ D  +  S+GVG+I F   +    AI AL+G + 
Sbjct: 8   LPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALNGTIP 67

Query: 287 LG--QPVMVK 294
            G  +P+ VK
Sbjct: 68  PGATEPITVK 77

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 40.9 bits (95), Expect = 0.002
 Identities = 28/134 (20%), Positives = 71/134 (52%), Gaps = 17/134 (12%)

Query: 4    DEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSR 63
             E E   K  EE ++ ++D     KKKA+  +K+E   +K  ++ ++E EE  ++ +  +
Sbjct: 1655 AEEENKIKAAEEAKKAEED-----KKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKK 1709

Query: 64   RDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERE 123
            ++ +E+            +  E  ++  + ++ +  E ++E E D++++ E ++ E+E++
Sbjct: 1710 KEAEEK------------KKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKK 1757

Query: 124  RRERRDREKERERE 137
            +     +E+E++ E
Sbjct: 1758 KIAHLKKEEEKKAE 1771

Length = 2084

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 233 TERDVYEFFSKAGK--VRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQ 289
           T+ D+    ++AG   V+ ++    + + +SKG  Y+EF    +       L G+   G+
Sbjct: 11  TDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNGK 70

Query: 290 PVMVKP 295
             +V  
Sbjct: 71  KCVVTY 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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 37/205 (18%), Positives = 85/205 (41%), Gaps = 3/205 (1%)

Query: 7   EYLEKTVEEQRQQKQDDDSSSKKKAKREEKS-ERSYRKREDSEEEEEEEKSRSGKRSRRD 65
              EK  +++R +K  +++ +  +   + +  +    K ++  ++  E      K    +
Sbjct: 165 GSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEE 224

Query: 66  EDEENGSRRDRDRDRDRDKERHRRDR-DRDRDRGRERERETERDRERSRERREKEKERER 124
           E+         + +R    +   RD  +      +E E+E E   +  +E +E+EKE++ 
Sbjct: 225 ENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKL 284

Query: 125 RERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRER-ERESERERELELERERE 183
           +E   +   +E E           R+   + +   S    ++ E+E ++E+E   E E+E
Sbjct: 285 QEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKE 344

Query: 184 RERELRERERDLEMRESRRYKEKKE 208
            +    +RE + E  E     ++K 
Sbjct: 345 LKELEIKREAEEEEEEQLEKLQEKL 369

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

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

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGK-VRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA-I 279
           ++F   +    T+  + E F      VR  +++MD  + RSKG G++ F D      A  
Sbjct: 3   SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62

Query: 280 ALSGQLLLGQPVMVKPS 296
            ++G     +P+ V P+
Sbjct: 63  EMNGVYCSSRPMRVSPA 79

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

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 7/73 (9%)

Query: 316 PYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLD-IETGQCKGFGFVQFAQLE 374
           PY A     Y+GNL +++TE  +++ F     V  V+LP +  + G+ +GFG+ +F   +
Sbjct: 1   PYTA-----YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRD 54

Query: 375 HAKAAQSALNGKL 387
               A S  +  L
Sbjct: 55  SLLQALSLNDESL 67

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

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

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 16/53 (30%), Positives = 25/53 (47%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           D   +F   +P   TE ++ EFF + G V +VR+       R    G++ F D
Sbjct: 2   DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDD 54

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
           +F   +  K  E D+ +FFS+ G V++V+++ DR    SKG G++ F
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAG-VSKGYGFVTF 50

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 21/62 (33%), Positives = 35/62 (56%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +++VG +  ++ E +L  LFE  GP+  ++L +D  TG  +G+ FV F   E A+ A   
Sbjct: 3   EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62

Query: 383 LN 384
            N
Sbjct: 63  YN 64

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 29/211 (13%), Positives = 60/211 (28%), Gaps = 6/211 (2%)

Query: 11  KTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEEN 70
            ++E Q  +  DD    +K+         +   +E  +     E+  + +RS R+     
Sbjct: 76  ASLEAQLIETADDLKKLRKQIADLNARLNALEVQEREQRRRLAEQLAALQRSGRNPPPAL 135

Query: 71  GSRRDRDRDRDRDK--ERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERR 128
               +  +   R             +R    +   +            + E      E+R
Sbjct: 136 LVSPEDAQRSVRLAIYYGALNPARAERIDALKATLKQLAAVRAEIAAEQAELTTLLSEQR 195

Query: 129 DREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELEREREREREL 188
            ++ +  +  + ER+ +     S   + +      R  E   + E     E    + RE 
Sbjct: 196 AQQAKLAQLLE-ERKKTLAQLNSELSADQKKLEELRANESRLKNEIA-SAEAAAAKAREA 253

Query: 189 RERERDLEMRESRRYKEKKEVVEPEADPERD 219
                    R   R  E K   E       +
Sbjct: 254 AAAAEAAAAR--ARAAEAKRTGETYKPTAPE 282

Length = 420

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

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 5/67 (7%)

Query: 320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
           +D K+YVGNL  N  +T+L + F  +GP+  V +  +       GF FV+F     A  A
Sbjct: 3   LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADA 57

Query: 380 QSALNGK 386
              L+G+
Sbjct: 58  VRELDGR 64

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

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 6/61 (9%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           + V NL F  TE +LR+LFE FG +  + LP        +    V+F +   A+ A  +L
Sbjct: 3   ILVKNLPFGTTEEELRELFEKFGSLGRLLLP------PSRTIALVEFLEPSDARKAFKSL 56

Query: 384 N 384
            
Sbjct: 57  A 57

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|130009 TIGR00934, 2a38euk, potassium uptake protein, Trk family

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 45/223 (20%), Positives = 88/223 (39%), Gaps = 17/223 (7%)

Query: 27  SKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKER 86
           S +  KR+E  + S   + D+  +E        K ++R      GSR     D  R    
Sbjct: 188 SGEFVKRDEPDQNSPDVKSDTRADESISDLEFEKFAKR-----RGSRDVDPEDLYRSIMM 242

Query: 87  HRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERERDGERRSSS 146
            +   +R R++     R  ER  E  +E+ E+       ER  +   R R  D     + 
Sbjct: 243 LQGIHERIREKSSANSRSDERSSESIQEQVERRPSTSDIERNSQSLTR-RYDDKSFDKAV 301

Query: 147 RSRRSSSQSRRSSSRSRRERERESERERELE------LERERERERELRERERDLEMRES 200
           R RRS     ++  R+      E +R ++ E       +    +++  R R  +L+ R++
Sbjct: 302 RLRRS-----KTIDRAEACDLEELDRAKDFEKMTYDNWKAHHRKKKNFRPRGWNLKFRKA 356

Query: 201 RRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSK 243
            R+ +  +    +        + F  + P  ++E ++Y  ++K
Sbjct: 357 SRFPKDSDRNYEDNGNHLSASSSFGSEEPSLSSEENLYPTYNK 399

The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system [Transport and binding proteins, Cations and iron carrying compounds]. Length = 800

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 17/49 (34%), Positives = 31/49 (63%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
           +K++VG +  +  E  LR  FE +G +E +++  D ++G+ +GF FV F
Sbjct: 1   KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572)

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 30/153 (19%), Positives = 54/153 (35%), Gaps = 11/153 (7%)

Query: 33  REEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRD 92
             +K +    +R + E EEE       K   R  D +         +  ++ +  R D D
Sbjct: 109 EADKLDEEQEERVEKEREEELAGDAMKKLENRTADSKREMEVLERLEELKELQSRRADVD 168

Query: 93  RD------RDRGRERERETER--DRERSRERREKEKERERRERRDREKERERERDGER-- 142
            +        R ++ E E E   +          E E +RR   D + E + E +     
Sbjct: 169 VNSMLEALFRREKKEEEEEEEEDEALIKSLSFGPETEEDRRRADDEDSEDDEEDNDNTPS 228

Query: 143 -RSSSRSRRSSSQSRRSSSRSRRERERESERER 174
            +S S S    +   + S+  R E    S+ ++
Sbjct: 229 PKSGSSSPAKPTSILKKSAAKRSEAPSSSKAKK 261

Family of eukaryotic proteins with undetermined function. Length = 321

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 15/77 (19%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPF---------GPVELVQLPLDIE------TGQCKGFGF 367
           +L + NL  ++ E +L++LF              ++ V++  D++       G+ KG+GF
Sbjct: 2   RLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGF 61

Query: 368 VQFAQLEHAKAAQSALN 384
           V+F   EHA  A  ALN
Sbjct: 62  VEFTNHEHALKALRALN 78

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

>gnl|CDD|217348 pfam03064, U79_P34, HSV U79 / HCMV P34

 Score = 39.5 bits (92), Expect = 0.002
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 3/78 (3%)

Query: 113 RERREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSS---SRSRRERERE 169
           R+R  K+KE+ R E   + KE  R++  E+R +   +R       S      S ++   +
Sbjct: 160 RKRSGKQKEKRRVEDSQKHKEDRRKKQEEKRRNDEDKRPGGGGGSSGGQSGLSTKDEPPK 219

Query: 170 SERERELELERERERERE 187
            +R++  + ER  E +  
Sbjct: 220 EKRQKHHDPERRLEPQSH 237

This family represents herpes virus protein U79 and cytomegalovirus early phosphoprotein P34 (UL112). Length = 238

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

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 12/50 (24%), Positives = 25/50 (50%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           T+F   +    T+ D+ +FFS    ++   ++ D  +  S+G G++ F  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAM 50

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPV 291
           TE D+ E F + G+V+ V++  DR+  RS+G   + F        AI   +G LL GQP+
Sbjct: 13  TEEDLEELFGRVGEVKKVKINYDRSG-RSEGTADVVFEKREDAERAIKQFNGVLLDGQPM 71

Query: 292 MVK 294
            V+
Sbjct: 72  QVE 74

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

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 40.5 bits (95), Expect = 0.003
 Identities = 36/219 (16%), Positives = 71/219 (32%), Gaps = 11/219 (5%)

Query: 7   EYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDE 66
           +Y E+  E +R+ ++ +++  + +   EE  E+   K E   E+ E  +    +    + 
Sbjct: 169 KYKERKEEAERKLERTEENLERLEDLLEEL-EKQLEKLERQAEKAERYQELKAELRELEL 227

Query: 67  -------DEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKE 119
                   E      + + +  R +E     ++   +  +E E       E   E  E +
Sbjct: 228 ALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQ 287

Query: 120 KERERRERRDREKERERERDGERRSSSRSRRSSSQSR---RSSSRSRRERERESEREREL 176
           +E    +    E E E     ER     +     + R           + E E       
Sbjct: 288 EELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLE 347

Query: 177 ELERERERERELRERERDLEMRESRRYKEKKEVVEPEAD 215
           ELE+      E +E   +         +E  E +  E  
Sbjct: 348 ELEQLLAELEEAKEELEEKLSALLEELEELFEALREELA 386

Length = 1163

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

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 14/50 (28%), Positives = 29/50 (58%)

Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           + T+  +  +FS+ G++ D  ++ D N++RS+G G++ F     V  A+ 
Sbjct: 10  ETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMN 59

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

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 40.3 bits (94), Expect = 0.003
 Identities = 33/201 (16%), Positives = 75/201 (37%), Gaps = 4/201 (1%)

Query: 7   EYLEKTVEEQRQQKQDDDSSSKKKAKREEKS---ERSYRKREDSEEEEEEEKSRSGKRSR 63
           +  EK  E +++ K+ +    K+K + EE     +    KRE  EEEEE+ +    K  +
Sbjct: 312 DDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQ 371

Query: 64  RDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERE 123
            +E+     + + +R     K +      ++ +    +      ++E    + EK++E +
Sbjct: 372 LEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELK 431

Query: 124 RRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERE 183
             E  +   E ++ +  E +     +       +     + E   +  +  +L  + E  
Sbjct: 432 IVEELEESLETKQGKLTEEKEELEKQALKLLKDK-LELKKSEDLLKETKLVKLLEQLELL 490

Query: 184 RERELRERERDLEMRESRRYK 204
             R+  E     E +      
Sbjct: 491 LLRQKLEEASQKESKAREGLA 511

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

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

 Score = 36.8 bits (85), Expect = 0.003
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 234 ERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMV 293
           E D+ E FS+ G V    +I D+ + + +G G++ F +  S   A  +    + G  V V
Sbjct: 13  EGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKFHPINGHRVEV 72

Query: 294 K 294
           K
Sbjct: 73  K 73

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

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 40.4 bits (95), Expect = 0.003
 Identities = 38/221 (17%), Positives = 78/221 (35%), Gaps = 7/221 (3%)

Query: 5   EYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRR 64
           E   LE+++ E+ ++ +D   + ++ AK E + ++   + E+ E E EEE+ R  +    
Sbjct: 302 EIASLERSIAEKERELED---AEERLAKLEAEIDKLLAEIEELEREIEEERKR--RDKLT 356

Query: 65  DEDEENGSRRDRDRDRDRDKE-RHRRDRDRDRDRGRERERETERDRERSRERREKEKERE 123
           +E  E     +  R    + +      RD  +D   + E+      E  RE    ++E +
Sbjct: 357 EEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQ 416

Query: 124 RRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERE 183
           R      +          + +     +            + E+      + E EL   +E
Sbjct: 417 RLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKE 476

Query: 184 RERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVF 224
               + +    L+ RE    + +    E      R    V 
Sbjct: 477 EYDRVEKELSKLQ-RELAEAEAQARASEERVRGGRAVEEVL 516

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

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

 Score = 36.7 bits (86), Expect = 0.003
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 14/80 (17%)

Query: 324 LYVGNLHFNMTETQLRK----LFEPFGPVELVQLPLDI---ETGQCKGFGFVQFAQLEHA 376
           LY+ NL+  + + +L++    LF  FGPV      LDI   +T + +G  FV F  +E A
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPV------LDIVASKTLKMRGQAFVVFKDVESA 55

Query: 377 KAAQSALNGKLEIVGRTLKV 396
             A  AL G      + +++
Sbjct: 56  TNALRALQGF-PFYDKPMRI 74

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

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+V N+        LR+ F  +GP+  V +PLD  T + +GF ++QF  +  A+ A   L
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 384 NGKLEIVGRTLKV 396
           N K  + GR +++
Sbjct: 63  NRKW-VCGRQIEI 74

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

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

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELV---QLPLDIETGQCKGFG--FVQFAQLEHAK 377
           ++Y+ NL ++ +E  L +  + F PV ++   Q      + + +  G  + +F+  E A+
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60

Query: 378 AAQSALNGKLEIVGRTLKV 396
                LNGK     R L V
Sbjct: 61  KVVKDLNGK-VFKNRKLFV 78

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

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 14/37 (37%), Positives = 26/37 (70%)

Query: 239 EFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
           E+FSK G++++  ++ D  ++RS+G G++ F D  SV
Sbjct: 17  EYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASV 53

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 3/76 (3%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
           D+ ++F  Q+    T+ ++ E FS+ GK+ +V LI   N   +    +I+F    +   A
Sbjct: 2   DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARA 59

Query: 279 I-ALSGQLLLGQPVMV 293
           + + +  +L  + + V
Sbjct: 60  VESENHSMLKNKTMHV 75

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 14/78 (17%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELV----QLPLDIETGQCKGFGFVQFAQLEHAKA 378
           K+YVGNL    T+ +L   FE +GP+  V      P         GF FV+F     A+ 
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP---------GFAFVEFEDPRDAED 51

Query: 379 AQSALNGKLEIVGRTLKV 396
           A  AL+G+  I G  ++V
Sbjct: 52  AVRALDGR-RICGNRVRV 68

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

>gnl|CDD|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 = 36.0 bits (84), Expect = 0.004
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 5/58 (8%)

Query: 524 DVEEECSKYGRVKHIYVDK-----RSAGFVYLRFESTEAAASAQRAMHMRWFARRLIS 576
           ++E   SK+GRV+ + + K      S GF ++ FES E A +A R ++ +    R+I 
Sbjct: 17  ELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIK 74

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

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 15/48 (31%), Positives = 29/48 (60%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
           T+F   +P   T+  + EFFS+ G ++   ++ D+ S++ +G GY+ F
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTF 48

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

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 3/70 (4%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +P   T++++ + FS+ G++   R++ D+ +  S+GVG+I F   +    AI  L+GQ  
Sbjct: 8   LPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNGQKP 67

Query: 287 LG--QPVMVK 294
            G  +P+ VK
Sbjct: 68  EGASEPITVK 77

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

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 39/194 (20%), Positives = 68/194 (35%), Gaps = 10/194 (5%)

Query: 11  KTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRD-EDEE 69
           + +EE+ ++ ++  +  +K      K      +  +   +E EE SR     R+D    E
Sbjct: 680 EELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKDLARLE 739

Query: 70  NGSRRDRDRDRDRDKER-----HRRDRDRDRDRGRERERETERDRERSRERREKEKER-E 123
               +  +R     KE         + +   +   E   E E + E    + E+ KE  +
Sbjct: 740 AEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELK 799

Query: 124 RRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSR---RERERESERERELELER 180
                  E   E     E  ++ R R  S + R +++  R    E + E   E    L  
Sbjct: 800 ALREALDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAA 859

Query: 181 ERERERELRERERD 194
           E E   EL E    
Sbjct: 860 EIEELEELIEELES 873

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 18/72 (25%), Positives = 41/72 (56%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           V+   +P  +TE ++  +FS  G++ ++ L+   ++ R +G+ +I F    +   A+AL 
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60

Query: 283 GQLLLGQPVMVK 294
           G+ + G+ + V+
Sbjct: 61  GEDMGGRFLKVE 72

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 19/63 (30%), Positives = 35/63 (55%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           T+  +  +FS+ G+V D  ++ D+ + RS+G G+++F D   V   +A     L G+ + 
Sbjct: 12  TQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGPHTLDGRTID 71

Query: 293 VKP 295
            KP
Sbjct: 72  PKP 74

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

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 39.7 bits (93), Expect = 0.004
 Identities = 53/271 (19%), Positives = 112/271 (41%), Gaps = 27/271 (9%)

Query: 4   DEYEYLEKTVEEQRQQKQDDDSSSKKKAKRE-EKSERSYRKREDSEEEEEEEKSRSGKRS 62
              E +E+ +EE  ++ +D     + + K +  + E      E S  E+E E   + +R 
Sbjct: 265 KRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGELEAEIASLERSIAEKERELEDAEERL 324

Query: 63  RRDEDEENGSRRDRDRDRDRDKERHRRDRDR-------DRDRGRERERETERDRERSRER 115
            + E  E         + +R+ E  R+ RD+        ++   +   E E   +   E 
Sbjct: 325 AKLE-AEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAET 383

Query: 116 REKEKERER------RERRDREKERERERDGERRSSSRSRR-----SSSQSRRSSSRSRR 164
           R++ K+         RE  + ++E +R ++  +R S          +  +++ +     +
Sbjct: 384 RDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEK 443

Query: 165 ERERESERERELELERERER----ERELRERERDLEMRESRRYKEKKEVVEPEAD---PE 217
           E +    +++E +LE+        E+EL + + + +  E    K ++E+ E EA     E
Sbjct: 444 EDKALEIKKQEWKLEQLAADLSKYEQELYDLKEEYDRVEKELSKLQRELAEAEAQARASE 503

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVR 248
              R   A +  LKA+ + V+   ++ G V 
Sbjct: 504 ERVRGGRAVEEVLKASIQGVHGTVAQLGSVG 534

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 17/47 (36%), Positives = 28/47 (59%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
           VF  ++P    E ++   F KAG + D+RL+MD  S +++G  +I F
Sbjct: 4   VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITF 50

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
           TVF   +  K   + + E FS AG V    ++ D++  +S+G+G + F   +    AI++
Sbjct: 2   TVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDG-KSRGIGTVTFEQPIEAVQAISM 60

Query: 282 -SGQLLLGQPVMVK 294
            +GQLL  +P+ VK
Sbjct: 61  FNGQLLFDRPMHVK 74

This subgroup corresponds to the RRM2 of hnRNP M, a 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). . Length = 76

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

 Score = 36.6 bits (84), Expect = 0.004
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LY+ NL  +M E +L  + +PFG V   ++  D   G  +G GF +    E  +      
Sbjct: 4   LYISNLPVSMDEQELENMLKPFGHVISTRILRD-ANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 384 NGK 386
           NGK
Sbjct: 63  NGK 65

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

>gnl|CDD|240911 cd12465, RRM_UHMK1, RNA recognition motif found in U2AF homology motif kinase 1 (UHMK1) and similar proteins

 Score = 36.5 bits (84), Expect = 0.004
 Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGF--VYLRFES 554
           P+  L L N+ D A   + +   +I  D++EEC KYG V  + + K + G   V++ + +
Sbjct: 2   PTPVLRLLNVLDDAHLQNEEEYEDIIEDIKEECQKYGPVVSLLIPKENPGKGQVFVEYAN 61

Query: 555 TEAAASAQRAMHMRWFARRLISAIF 579
              + +AQ+ +  R F  + + A F
Sbjct: 62  AGDSKAAQKLLTGRIFDGKFVVATF 86

This subgroup corresponds to the RRM of UHMK1. UHMK1, also termed kinase interacting with stathmin (KIS) or P-CIP2, is a serine/threonine protein kinase functionally related to RNA metabolism and neurite outgrowth. It contains an N-terminal kinase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), with high homology to the corresponding motif of the mammalian U2 small nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65 or U2AF2). UHMK1 targets two key regulators of cell proliferation and migration, the cyclin-dependent kinase (CDK) inhibitor p27Kip1 and the microtubule-destabilizing protein stathmin. It plays a critical role during vascular wound repair by preventing excessive vascular smooth muscle cell (VSMC) migration into the vascular lesion. Moreover, UHMK1 may control cell migration and neurite outgrowth by interacting with and phosphorylating the splicing factor SF1, thereby probably contributing to the control of protein expression. Furthermore, UHMK1 may be functionally related to microtubule dynamics and axon development. It localizes to RNA granules, interacts with three proteins found in RNA granules (KIF3A, NonO, and eEF1A), and further enhances the local translation. UHMK1 is highly expressed in regions of the brain implicated in schizophrenia and may play a role in susceptibility to schizophrenia. Length = 88

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

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 3/63 (4%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + L+V  L  + TE  L++ F+  G +   ++  D +TG  KGFGFV F+  E AKAA+ 
Sbjct: 1   KTLFVKGLSEDTTEETLKESFD--GSIA-ARIVTDRDTGSSKGFGFVDFSSEEDAKAAKE 57

Query: 382 ALN 384
           A+ 
Sbjct: 58  AME 60

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

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 36.2 bits (83), Expect = 0.004
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           DRKL++G +     E  +R +F PFG +E  ++ L    G  +G  FV F     A+ A 
Sbjct: 1   DRKLFIGMVSKKCNENDIRVMFSPFGQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAI 59

Query: 381 SALN 384
            A++
Sbjct: 60  KAMH 63

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

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

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 25/75 (33%), Positives = 34/75 (45%), Gaps = 8/75 (10%)

Query: 324 LYVGNLHFNMTETQLRKLFEPF-GPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           L++ NL    T+  L  LF  F G  E V+L   +     +G  FV+F   E A  A  A
Sbjct: 5   LFLQNLPEETTKEMLEMLFNQFPGFKE-VRL---VPR---RGIAFVEFETEEQATVALQA 57

Query: 383 LNGKLEIVGRTLKVS 397
           L G     G  +K+S
Sbjct: 58  LQGFKITPGHAMKIS 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|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+V N+  +     LR+ F  +GP+  V +PLD  T + +GF +VQF  +  A+ A   L
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 384 NGKLEIVGRTLKV 396
           + K  I GR +++
Sbjct: 63  DRKW-ICGRQIEI 74

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	591
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	100.0
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	100.0
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.97
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.96
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.96
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.95
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.94
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.94
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.93
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.93
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.93
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.93
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.92
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.9
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.9
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.89
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.89
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.89
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.87
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.87
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.86
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.84
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.84
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.84
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.83
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.81
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.8
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.79
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.79
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.77
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.76
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.76
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.74
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.73
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.72
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.7
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.69
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.69
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.64
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.63
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.61
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.6
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.57
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.57
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.55
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.49
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.47
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.45
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.45
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.44
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.43
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.42
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.4
PLN03120	260	nucleic acid binding protein; Provisional	99.4
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.39
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.39
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.39
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.39
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.38
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.38
KOG0122	270	consensus Translation initiation factor 3, subunit	99.37
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.36
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.35
PLN03121	243	nucleic acid binding protein; Provisional	99.34
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.34
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.33
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.32
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.32
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.32
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.32
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.3
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.29
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.28
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.28
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.28
PLN03213	759	repressor of silencing 3; Provisional	99.27
KOG0122	270	consensus Translation initiation factor 3, subunit	99.27
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.26
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.24
PLN03120	260	nucleic acid binding protein; Provisional	99.23
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.21
smart00362	72	RRM_2 RNA recognition motif.	99.2
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.2
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.19
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.19
smart00360	71	RRM RNA recognition motif.	99.17
PLN03121	243	nucleic acid binding protein; Provisional	99.15
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.13
smart00362	72	RRM_2 RNA recognition motif.	99.12
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.12
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.1
PLN03213	759	repressor of silencing 3; Provisional	99.09
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.08
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.07
smart00360	71	RRM RNA recognition motif.	99.07
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.04
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.01
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.01
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.01
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	99.0
smart00361	70	RRM_1 RNA recognition motif.	99.0
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.97
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.96
smart00361	70	RRM_1 RNA recognition motif.	98.96
KOG4210	285	consensus Nuclear localization sequence binding pr	98.92
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.88
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.86
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.86
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.84
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.81
KOG1996	378	consensus mRNA splicing factor [RNA processing and	98.79
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.76
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.68
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.68
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.6
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.54
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.53
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.53
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.52
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.49
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.44
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.41
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.39
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.39
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.38
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.36
KOG0226	290	consensus RNA-binding proteins [General function p	98.36
KOG0226	290	consensus RNA-binding proteins [General function p	98.3
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.28
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.27
KOG0151	877	consensus Predicted splicing regulator, contains R	98.25
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.24
KOG0151	877	consensus Predicted splicing regulator, contains R	98.24
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.21
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.15
KOG4210	285	consensus Nuclear localization sequence binding pr	98.12
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.12
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	98.09
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.05
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.02
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.81
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.79
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.78
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.72
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.71
KOG2314	698	consensus Translation initiation factor 3, subunit	97.61
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.51
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.48
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.39
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.35
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.32
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.25
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.22
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.16
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.05
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.92
KOG2314	698	consensus Translation initiation factor 3, subunit	96.91
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.91
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.77
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.71
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.62
KOG3152	278	consensus TBP-binding protein, activator of basal	96.42
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.32
KOG3152	278	consensus TBP-binding protein, activator of basal	96.27
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.18
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.74
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.68
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.11
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	94.95
PF15519	73	RBM39linker: linker between RRM2 and RRM3 domains	94.66
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.65
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.37
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.35
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.35
KOG2135	526	consensus Proteins containing the RNA recognition	94.19
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	93.98
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	93.6
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.43
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.32
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	92.98
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	92.67
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	92.66
KOG0670	752	consensus U4/U6-associated splicing factor PRP4 [R	92.52
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	92.04
KOG2135	526	consensus Proteins containing the RNA recognition	91.66
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	91.41
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	90.77
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	90.55
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	90.22
KOG2068	327	consensus MOT2 transcription factor [Transcription	89.84
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	89.53
KOG2591	684	consensus c-Mpl binding protein, contains La domai	88.95
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	88.91
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	88.47
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	88.37
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	86.92
KOG4368	757	consensus Predicted RNA binding protein, contains	86.67
KOG2318	650	consensus Uncharacterized conserved protein [Funct	85.65
KOG2068	327	consensus MOT2 transcription factor [Transcription	83.38
KOG2318	650	consensus Uncharacterized conserved protein [Funct	82.89

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

Probab=100.00  E-value=5.6e-53  Score=446.23  Aligned_cols=368  Identities=47%  Similarity=0.700  Sum_probs=269.3

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEec
Q 007742          215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK  294 (591)
Q Consensus       215 ~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~  294 (591)
                      ..+...++|||+|||+.+|+++|+++|..||.|..|.|+.++.+|.++|||||+|.+.++|.+||.|+|+.|.|++|.|.
T Consensus        84 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~  163 (457)
T TIGR01622        84 EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQ  163 (457)
T ss_pred             ccccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEe
Confidence            34556799999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHH
Q 007742          295 PSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE  374 (591)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~  374 (591)
                      ++...............    ...+...+|||+|||..+++++|.++|++||.|..|.|+.+..++.++|||||+|.+.+
T Consensus       164 ~~~~~~~~~~~~~~~~~----~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e  239 (457)
T TIGR01622       164 SSQAEKNRAAKAATHQP----GDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAE  239 (457)
T ss_pred             ecchhhhhhhhcccccC----CCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHH
Confidence            77554333221111111    11223589999999999999999999999999999999999888899999999999999


Q ss_pred             HHHHHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCC
Q 007742          375 HAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAP  454 (591)
Q Consensus       375 ~a~~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  454 (591)
                      +|..|+..|+|. .|.|+.|.|.++.+....................+..........+...+......    +....++
T Consensus       240 ~A~~A~~~l~g~-~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~  314 (457)
T TIGR01622       240 EAKEALEVMNGF-ELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGD----GGLLIPG  314 (457)
T ss_pred             HHHHHHHhcCCc-EECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCC----ccccCCC
Confidence            999999999995 79999999999886544333322222222222233333333444444433332211    0000000


Q ss_pred             cccCccccccccccCcCC---CCCCCCCCCCCCcccccccc-ccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhc
Q 007742          455 AVNGSAVNQQAISLPVVG---QPAVPVPAVTAPVIPNMAAE-FIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECS  530 (591)
Q Consensus       455 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~-~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~  530 (591)
                      ..................   +.............+..... ....++.||+|.||+++.+..++.++.+|.+||.++|.
T Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~  394 (457)
T TIGR01622       315 TGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECS  394 (457)
T ss_pred             ccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHH
Confidence            000000000000000000   00000000011111111111 13567899999999999999999999999999999999


Q ss_pred             cccceEEEEEe-cCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchhhhhccCC
Q 007742          531 KYGRVKHIYVD-KRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS  591 (591)
Q Consensus       531 ~~G~V~~v~l~-~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~~~~~  591 (591)
                      +||.|+.|.|. ....|++||+|.++++|..|++.|||+.|+|+.|.|.|++++.|.+.|+.
T Consensus       395 k~G~v~~v~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~~~~~~~~  456 (457)
T TIGR01622       395 KYGGVVHIYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVYDMSCLP  456 (457)
T ss_pred             hcCCeeEEEEeCCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHHHHhhcCC
Confidence            99999999886 56789999999999999999999999999999999999999999999874

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.

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

Probab=100.00  E-value=1e-53  Score=418.27  Aligned_cols=369  Identities=50%  Similarity=0.749  Sum_probs=293.7

Q ss_pred             ccCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCC
Q 007742          209 VVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLG  288 (591)
Q Consensus       209 ~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g  288 (591)
                      ....+..+++..+++|+..|+..+++.+|.++|+.+|+|.+|.+|.|.+++.++|.|||+|.+.+.+..||.|.|+.++|
T Consensus       168 ~~~~l~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg  247 (549)
T KOG0147|consen  168 ASRILSPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLG  247 (549)
T ss_pred             ccccCCchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccC
Confidence            33445566778899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEeccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEE
Q 007742          289 QPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFV  368 (591)
Q Consensus       289 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~V  368 (591)
                      .+|.|+.+....+.....++... .....+|..+ |||+||..++++++|..+|++||.|..|.+..+..+|.++||+||
T Consensus       248 ~pv~vq~sEaeknr~a~~s~a~~-~k~~~~p~~r-l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi  325 (549)
T KOG0147|consen  248 VPVIVQLSEAEKNRAANASPALQ-GKGFTGPMRR-LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFI  325 (549)
T ss_pred             ceeEecccHHHHHHHHhcccccc-ccccccchhh-hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceE
Confidence            99999999887776443333222 2222333323 999999999999999999999999999999999889999999999


Q ss_pred             EeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCC
Q 007742          369 QFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAG  448 (591)
Q Consensus       369 ef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  448 (591)
                      +|.+.++|.+|+..||| +++.|+.|+|...++............++...+.+++.++..+.++++.++.......-...
T Consensus       326 ~f~~~~~ar~a~e~lng-felAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~  404 (549)
T KOG0147|consen  326 TFVNKEDARKALEQLNG-FELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPST  404 (549)
T ss_pred             EEecHHHHHHHHHHhcc-ceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccch
Confidence            99999999999999999 89999999999998887766665555566656667776666666666666554332111111


Q ss_pred             cCCCCCcccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHH
Q 007742          449 SLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEE  528 (591)
Q Consensus       449 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~  528 (591)
                      .......     ...........+..  ...    .+.|....+...+++.|++|+||++|.+.|.+.|..+|.+||.+.
T Consensus       405 ~~~~l~~-----~~~~~~~~~~~~~~--~~~----~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Ee  473 (549)
T KOG0147|consen  405 AISALLL-----LAKLASAAQFNGVV--RVR----SVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEE  473 (549)
T ss_pred             hhhHHHh-----ccccchHHhhcCCc--Ccc----ccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHH
Confidence            0000000     00000000000000  000    111221223334899999999999999999999999999999999


Q ss_pred             hccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchhhhhccCC
Q 007742          529 CSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFKS  591 (591)
Q Consensus       529 f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~~~~~  591 (591)
                      |.+||.|..|.|.+++.||+||.|.+.+.|..|+.+|||++|.|+.|.+.|++...|+.+||+
T Consensus       474 c~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~~~Y~~~FP~  536 (549)
T KOG0147|consen  474 CGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPLERYHSKFPD  536 (549)
T ss_pred             HHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeehhhhhhhCCC
Confidence            999999999999999999999999999999999999999999999999999999999999996

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

Probab=100.00  E-value=8.4e-48  Score=412.67  Aligned_cols=304  Identities=25%  Similarity=0.400  Sum_probs=231.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcC------------CCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcC
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKA------------GKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSG  283 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~------------G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g  283 (591)
                      .+...++|||+|||+.+|+++|.++|..+            +.|..+.+      +..+|||||+|.+.++|..||.|+|
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~l~g  244 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMALDS  244 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhcCCC
Confidence            34567999999999999999999999975            23444443      4568999999999999999999999


Q ss_pred             CccCCeeEEeccCccccccccccCC-----CC---C-----CCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeE
Q 007742          284 QLLLGQPVMVKPSEAEKNLVQSNTS-----AG---G-----TATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVEL  350 (591)
Q Consensus       284 ~~i~g~~i~v~~~~~~~~~~~~~~~-----~~---~-----~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~  350 (591)
                      +.|.|..|+|...............     ..   .     ..........++|||+|||..+++++|.++|..||.|..
T Consensus       245 ~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~  324 (509)
T TIGR01642       245 IIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKA  324 (509)
T ss_pred             eEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeE
Confidence            9999999999755433211100000     00   0     000111223579999999999999999999999999999


Q ss_pred             EEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHH
Q 007742          351 VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSR  430 (591)
Q Consensus       351 v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  430 (591)
                      +.|+.+..+|.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.++..........       ....          
T Consensus       325 ~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~-~~~~~~l~v~~a~~~~~~~~~~-------~~~~----------  386 (509)
T TIGR01642       325 FNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGK-DTGDNKLHVQRACVGANQATID-------TSNG----------  386 (509)
T ss_pred             EEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEEECccCCCCCCcc-------cccc----------
Confidence            999998888999999999999999999999999996 7999999999875321100000       0000          


Q ss_pred             HHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCC
Q 007742          431 ALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPA  510 (591)
Q Consensus       431 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~  510 (591)
                                           ..+.         ..               ....+..........++.+|+|.||+.+.
T Consensus       387 ---------------------~~~~---------~~---------------~~~~~~~~~~~~~~~~s~v~~l~N~~~~~  421 (509)
T TIGR01642       387 ---------------------MAPV---------TL---------------LAKALSQSILQIGGKPTKVVQLTNLVTGD  421 (509)
T ss_pred             ---------------------cccc---------cc---------------ccccchhhhccccCCCceEEEeccCCchh
Confidence                                 0000         00               00000000001124577899999999888


Q ss_pred             CCCCchhhhhHHHHHHHHhccccceEEEEEecC--------CCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCc
Q 007742          511 METDPDFDLEIQGDVEEECSKYGRVKHIYVDKR--------SAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKP  582 (591)
Q Consensus       511 ~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~--------~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~  582 (591)
                      .+.++++|.+|.++|.++|++||.|+.|.|+.+        +.|+|||+|.++++|.+|+..|||+.|+|+.|.|.|+++
T Consensus       422 ~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       422 DLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            888889999999999999999999999999753        358999999999999999999999999999999999999


Q ss_pred             hhhhhc
Q 007742          583 EDYEAK  588 (591)
Q Consensus       583 ~~~~~~  588 (591)
                      ..|.+.
T Consensus       502 ~~~~~~  507 (509)
T TIGR01642       502 DCYKAG  507 (509)
T ss_pred             HHhhcc
Confidence            999864

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=1.6e-41  Score=347.04  Aligned_cols=335  Identities=19%  Similarity=0.307  Sum_probs=225.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      ..+|||+|||+.+|+++|+++|..||+|..|.|+.++.+|.++|||||+|.+.++|..|| .|||..|.|+.|.|.++.+
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            478999999999999999999999999999999999999999999999999999999999 6999999999999998754


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA  378 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~  378 (591)
                      ....                .....|||+|||..+++++|..+|.+||.|..+.++.+..++.++|||||+|.+.++|..
T Consensus        83 ~~~~----------------~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~  146 (352)
T TIGR01661        83 SSDS----------------IKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADR  146 (352)
T ss_pred             cccc----------------cccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHH
Confidence            3211                113689999999999999999999999999999999887788899999999999999999


Q ss_pred             HHHHhcCCeeeCC--eEEEEEEecCCCCCCcccccC--CCCCCCCCCCccccH----HHHHHHHHHhhhcCCccccCCcC
Q 007742          379 AQSALNGKLEIVG--RTLKVSSVTDHVGTQDTAAKS--ADFDDDDGGGLALNA----QSRALLMQKLDRTGIATSIAGSL  450 (591)
Q Consensus       379 a~~~l~g~~~~~g--~~l~v~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~  450 (591)
                      |+..|||. .+.|  .+|.|.++.............  ...............    .......................
T Consensus       147 ai~~l~g~-~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  225 (352)
T TIGR01661       147 AIKTLNGT-TPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAV  225 (352)
T ss_pred             HHHHhCCC-ccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhh
Confidence            99999996 5776  567787765432111100000  000000000000000    00000000000000000000000


Q ss_pred             CCCCcccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhc
Q 007742          451 GVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECS  530 (591)
Q Consensus       451 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~  530 (591)
                      ........ ...++.. ....++...  ...................+.+|+|.||  |..++        +++|.++|+
T Consensus       226 ~~~~~~~~-~~~~~~~-~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~lfV~NL--~~~~~--------e~~L~~~F~  291 (352)
T TIGR01661       226 LAHQQQQH-AVAQQHA-AQRASPPAT--DGQTAGLAAGAQIAASDGAGYCIFVYNL--SPDTD--------ETVLWQLFG  291 (352)
T ss_pred             hhhhhhhc-ccccccc-cccCCCccc--cccccccccCCCCCCCCCCCcEEEEeCC--CCCCC--------HHHHHHHHH
Confidence            00000000 0000000 000000000  0000000000001111334558999999  78777        899999999


Q ss_pred             cccceEEEEEecC-----CCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchhh
Q 007742          531 KYGRVKHIYVDKR-----SAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDY  585 (591)
Q Consensus       531 ~~G~V~~v~l~~~-----~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  585 (591)
                      +||.|..|.|..+     ++|||||+|.+.++|..|+..|||..|+|+.|.|.|+..+.+
T Consensus       292 ~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       292 PFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             hCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence            9999999988543     589999999999999999999999999999999999987654

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

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

Probab=100.00  E-value=4.2e-40  Score=341.44  Aligned_cols=177  Identities=20%  Similarity=0.363  Sum_probs=153.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||+.+|+++|+++|..||.|..|.++.++.+|.++|||||+|.+.++|..|| .|||..|.|+.|+|.++.
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            4589999999999999999999999999999999999999999999999999999999999 699999999999998643


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHH
Q 007742          298 AEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK  377 (591)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~  377 (591)
                      .........     ...........+|||+|||+.+++++|+++|+.||.|..|.|..+..++.++|||||+|.+.++|.
T Consensus       186 ~~p~a~~~~-----~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~  260 (612)
T TIGR01645       186 NMPQAQPII-----DMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS  260 (612)
T ss_pred             ccccccccc-----ccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHH
Confidence            321110000     000011122379999999999999999999999999999999999888899999999999999999


Q ss_pred             HHHHHhcCCeeeCCeEEEEEEecC
Q 007742          378 AAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       378 ~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      .|+..||+. .|+|+.|.|.++..
T Consensus       261 kAI~amNg~-elgGr~LrV~kAi~  283 (612)
T TIGR01645       261 EAIASMNLF-DLGGQYLRVGKCVT  283 (612)
T ss_pred             HHHHHhCCC-eeCCeEEEEEecCC
Confidence            999999995 89999999998764

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.

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

Probab=100.00  E-value=4.1e-38  Score=278.81  Aligned_cols=307  Identities=20%  Similarity=0.323  Sum_probs=225.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      ...|+|.-||..+|+++|+.+|...|.|++|++++|+.+|.+-|||||.|.++++|.+|+ .+||..+..++|+|.++.+
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARP  120 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARP  120 (360)
T ss_pred             cceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccC
Confidence            467999999999999999999999999999999999999999999999999999999999 7999999999999999876


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA  378 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~  378 (591)
                      ......                ...|||.+||..+|..+|.++|++||.|..-+|+.+..+|.++|.+||.|....+|..
T Consensus       121 Ss~~Ik----------------~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~  184 (360)
T KOG0145|consen  121 SSDSIK----------------DANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEE  184 (360)
T ss_pred             Chhhhc----------------ccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHH
Confidence            443222                2689999999999999999999999999888999998899999999999999999999


Q ss_pred             HHHHhcCCeeeCC--eEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcc
Q 007742          379 AQSALNGKLEIVG--RTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAV  456 (591)
Q Consensus       379 a~~~l~g~~~~~g--~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  456 (591)
                      ||..|||. .-.|  .+|.|.++....                      ....++.+.+.+.... ....+..+......
T Consensus       185 AIk~lNG~-~P~g~tepItVKFannPs----------------------q~t~~a~ls~ly~sp~-rr~~Gp~hh~~~r~  240 (360)
T KOG0145|consen  185 AIKGLNGQ-KPSGCTEPITVKFANNPS----------------------QKTNQALLSQLYQSPA-RRYGGPMHHQAQRF  240 (360)
T ss_pred             HHHhccCC-CCCCCCCCeEEEecCCcc----------------------cccchhhhHHhhcCcc-ccCCCcccchhhhh
Confidence            99999996 4566  488888874321                      0111111111111111 00000000000000


Q ss_pred             cCccccccccccCcCCCCCCCCCCCCCCcccccc---ccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhcccc
Q 007742          457 NGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMA---AEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYG  533 (591)
Q Consensus       457 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G  533 (591)
                      ......++......+       +++.......+.   .+.......||||.||  ...+.        +.-|.++|..||
T Consensus       241 r~~~~~~~~~~~~rf-------sP~~~d~m~~l~~~~lp~~~~~g~ciFvYNL--spd~d--------e~~LWQlFgpFG  303 (360)
T KOG0145|consen  241 RLDNLLNPHAAQARF-------SPMTIDGMSGLAGVNLPGGPGGGWCIFVYNL--SPDAD--------ESILWQLFGPFG  303 (360)
T ss_pred             ccccccchhhhhccC-------CCccccccceeeeeccCCCCCCeeEEEEEec--CCCch--------HhHHHHHhCccc
Confidence            000000000000000       001100111110   1112334689999999  33332        678999999999


Q ss_pred             ceEEEEEec-----CCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          534 RVKHIYVDK-----RSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       534 ~V~~v~l~~-----~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      .|.+|++.+     ..+||+||.+.+.++|..||..|||..++++.|+|+|-+-+
T Consensus       304 Av~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  304 AVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             ceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            999999854     36899999999999999999999999999999999997654

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

Probab=100.00  E-value=9.6e-37  Score=329.66  Aligned_cols=334  Identities=23%  Similarity=0.304  Sum_probs=229.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcccc
Q 007742          222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEK  300 (591)
Q Consensus       222 ~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~~  300 (591)
                      .|||+|||+.+||++|.++|..||.|.+|+|++|..|+.++|||||+|.+.++|.+|| .+|+..|.|+.|+|.|+....
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            6999999999999999999999999999999999999999999999999999999999 699999999999999875432


Q ss_pred             ccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHH
Q 007742          301 NLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ  380 (591)
Q Consensus       301 ~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~  380 (591)
                      .....              ...+|||+|||..+++++|+++|+.||.|..|.|..+. ++.++|||||+|.+.++|..|+
T Consensus        82 ~~~~~--------------~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai  146 (562)
T TIGR01628        82 SLRRS--------------GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAI  146 (562)
T ss_pred             ccccc--------------CCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHH
Confidence            11110              12579999999999999999999999999999998875 7888999999999999999999


Q ss_pred             HHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCC---cCCC---CC
Q 007742          381 SALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAG---SLGV---AP  454 (591)
Q Consensus       381 ~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~---~~  454 (591)
                      ..|+|. .+.|+.|.|............  ....+...-..++.... ....+...+...+....+..   ..+.   ..
T Consensus       147 ~~lng~-~~~~~~i~v~~~~~~~~~~~~--~~~~~~~l~V~nl~~~~-tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~a  222 (562)
T TIGR01628       147 QKVNGM-LLNDKEVYVGRFIKKHEREAA--PLKKFTNLYVKNLDPSV-NEDKLRELFAKFGEITSAAVMKDGSGRSRGFA  222 (562)
T ss_pred             HHhccc-EecCceEEEeccccccccccc--cccCCCeEEEeCCCCcC-CHHHHHHHHHhcCCEEEEEEEECCCCCcccEE
Confidence            999996 699999999765443322100  00000000001111111 11222222222221111100   0000   01


Q ss_pred             cccCccccccccccCc-CCCC--------CCCCCCCCCC---------ccccc-cccccCCCcceEEEeccCCCCCCCCc
Q 007742          455 AVNGSAVNQQAISLPV-VGQP--------AVPVPAVTAP---------VIPNM-AAEFIGSPSECLLLKNMFDPAMETDP  515 (591)
Q Consensus       455 ~~~~~~~~~~~~~~~~-~~~~--------~~~~~~~~~~---------~~~~~-~~~~~~~~s~~l~v~Nl~~p~~~~~~  515 (591)
                      ++.......+...+.. .+..        ...+......         ..... ..........+|+|+||  +..++  
T Consensus       223 fV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl--~~~~~--  298 (562)
T TIGR01628       223 FVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNL--DDTVT--  298 (562)
T ss_pred             EEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCC--CCccC--
Confidence            1111111111111000 0000        0000000000         00000 00112345667999999  77777  


Q ss_pred             hhhhhHHHHHHHHhccccceEEEEEec----CCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchh
Q 007742          516 DFDLEIQGDVEEECSKYGRVKHIYVDK----RSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPED  584 (591)
Q Consensus       516 ~~~~~~~edl~~~f~~~G~V~~v~l~~----~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~  584 (591)
                            +++|+++|+.||.|.+|.+..    .++|+|||+|.+.++|.+|+..|||+.|+|+.|.|.|+..+.
T Consensus       299 ------~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~  365 (562)
T TIGR01628       299 ------DEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKE  365 (562)
T ss_pred             ------HHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcH
Confidence                  899999999999999998854    357999999999999999999999999999999999988643

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

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

Probab=100.00  E-value=1.7e-35  Score=311.33  Aligned_cols=336  Identities=18%  Similarity=0.160  Sum_probs=216.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH---HcCCccCCeeEEecc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA---LSGQLLLGQPVMVKP  295 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~---l~g~~i~g~~i~v~~  295 (591)
                      ++++|||+|||+.+|+++|.++|..||.|..|.++.      ++|||||+|.+.++|..|+.   +++..|.|++|.|.+
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~------~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP------GKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC------CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            368999999999999999999999999999999985      36899999999999999995   478899999999999


Q ss_pred             CccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHH
Q 007742          296 SEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH  375 (591)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~  375 (591)
                      +............  ...  ........|+|.||++.+++++|+++|++||.|..|.|..+.    ..|+|||+|.+.++
T Consensus        75 s~~~~~~~~~~~~--~~~--~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~----~~~~afVef~~~~~  146 (481)
T TIGR01649        75 STSQEIKRDGNSD--FDS--AGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN----NVFQALVEFESVNS  146 (481)
T ss_pred             cCCcccccCCCCc--ccC--CCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC----CceEEEEEECCHHH
Confidence            8654321111000  000  001112579999999999999999999999999999987653    24689999999999


Q ss_pred             HHHHHHHhcCCeeeC-C-eEEEEEEecCCCCCCccc-ccCCCCCCCCC---CCccccHHHHHHHHHHhhhcCCccccCCc
Q 007742          376 AKAAQSALNGKLEIV-G-RTLKVSSVTDHVGTQDTA-AKSADFDDDDG---GGLALNAQSRALLMQKLDRTGIATSIAGS  449 (591)
Q Consensus       376 a~~a~~~l~g~~~~~-g-~~l~v~~~~~~~~~~~~~-~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  449 (591)
                      |.+|++.|||. .|. | +.|.|.+++...-....+ ....++.....   ....+...... ....+............
T Consensus       147 A~~A~~~Lng~-~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~g  224 (481)
T TIGR01649       147 AQHAKAALNGA-DIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQ-RQPALLGQHPSSYGHDG  224 (481)
T ss_pred             HHHHHHHhcCC-cccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccc-cccccccCCCccCCCcc
Confidence            99999999997 454 3 689999987543211111 11101100000   00000000000 00000000000000000


Q ss_pred             CCCC----C-cccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCC-CCCCchhhhhHHH
Q 007742          450 LGVA----P-AVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPA-METDPDFDLEIQG  523 (591)
Q Consensus       450 ~~~~----~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~-~~~~~~~~~~~~e  523 (591)
                      ++..    . ...+...... ...+..+.+  .......+..+.........++.+|+|+||  +. .++        ++
T Consensus       225 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL--~~~~vt--------~~  291 (481)
T TIGR01649       225 YSSHGGPLAPLAGGDRMGPP-HGPPSRYRP--AYEAAPLAPAISSYGPAGGGPGSVLMVSGL--HQEKVN--------CD  291 (481)
T ss_pred             cccCCCCCCcccccccCCCc-ccCCCCCcc--cccccccCccccccCCCCCCCCCEEEEeCC--CCCCCC--------HH
Confidence            0000    0 0000000000 000000000  000000000011111123467889999999  65 466        89


Q ss_pred             HHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          524 DVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       524 dl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      +|.++|+.||.|..|.|....+|+|||+|.+.++|..|+..|||..|.|+.|.|.++..+
T Consensus       292 ~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       292 RLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             HHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            999999999999999998778899999999999999999999999999999999998654

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=100.00  E-value=5e-36  Score=311.16  Aligned_cols=245  Identities=21%  Similarity=0.340  Sum_probs=204.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccC-CeeEEecc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL-GQPVMVKP  295 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~-g~~i~v~~  295 (591)
                      ...++|||+|||+++++++|.++|.+||.|.+|+|+.| .+|.++|||||+|.+.++|..|| .||+..|. |+.|.|.+
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            35699999999999999999999999999999999999 78999999999999999999999 68998875 77776654


Q ss_pred             CccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEe-ccCCCCCcccEEEEEeCCH
Q 007742          296 SEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGP-VELVQLP-LDIETGQCKGFGFVQFAQL  373 (591)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~v~i~-~~~~~~~~~g~a~Vef~~~  373 (591)
                      +..                      .++|||.|||..+++++|.++|.+++. +..+.+. .....+.++|||||+|.+.
T Consensus       135 S~~----------------------~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~  192 (578)
T TIGR01648       135 SVD----------------------NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESH  192 (578)
T ss_pred             ccc----------------------CceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCH
Confidence            321                      278999999999999999999999963 4444333 3333566799999999999


Q ss_pred             HHHHHHHHHhc-CCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCC
Q 007742          374 EHAKAAQSALN-GKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGV  452 (591)
Q Consensus       374 ~~a~~a~~~l~-g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  452 (591)
                      ++|..|+..|+ +.+.+.|+.|.|.++........                                             
T Consensus       193 edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~---------------------------------------------  227 (578)
T TIGR01648       193 RAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDE---------------------------------------------  227 (578)
T ss_pred             HHHHHHHHHhhccceEecCceEEEEeecccccccc---------------------------------------------
Confidence            99999998876 44678999999998743210000                                             


Q ss_pred             CCcccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccc
Q 007742          453 APAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKY  532 (591)
Q Consensus       453 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~  532 (591)
                                                              ......++|+|.||  +..++        +++|.++|+.|
T Consensus       228 ----------------------------------------~~~~~~k~LfVgNL--~~~~t--------ee~L~~~F~~f  257 (578)
T TIGR01648       228 ----------------------------------------DVMAKVKILYVRNL--MTTTT--------EEIIEKSFSEF  257 (578)
T ss_pred             ----------------------------------------cccccccEEEEeCC--CCCCC--------HHHHHHHHHhc
Confidence                                                    00112357999999  77777        89999999999


Q ss_pred             --cceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          533 --GRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       533 --G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                        |.|..|.+.   ++||||+|.+.++|.+|++.|||..|+|+.|.|.|+++.
T Consensus       258 ~~G~I~rV~~~---rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~  307 (578)
T TIGR01648       258 KPGKVERVKKI---RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPV  307 (578)
T ss_pred             CCCceEEEEee---cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCC
Confidence              999999776   579999999999999999999999999999999999874

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.

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

Probab=100.00  E-value=4.4e-36  Score=286.14  Aligned_cols=251  Identities=20%  Similarity=0.332  Sum_probs=215.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCcc-CCeeEEec
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL-LGQPVMVK  294 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i-~g~~i~v~  294 (591)
                      ...++.|||+.||.++.|++|..+|.+.|+|.+++||.|+.+|.++|||||.|.+.++|+.|+ .||+..| .|+.|.|.
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE
Confidence            356799999999999999999999999999999999999999999999999999999999999 6999987 68888887


Q ss_pred             cCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEeccC-CCCCcccEEEEEeCC
Q 007742          295 PSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGP-VELVQLPLDI-ETGQCKGFGFVQFAQ  372 (591)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~v~i~~~~-~~~~~~g~a~Vef~~  372 (591)
                      .+..                      ++.|||+|||..+++++|++.|.++++ |..|.|.... ...+.+|||||+|.+
T Consensus       160 ~Sva----------------------n~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~  217 (506)
T KOG0117|consen  160 VSVA----------------------NCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYES  217 (506)
T ss_pred             Eeee----------------------cceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeec
Confidence            6543                      279999999999999999999999984 6667666554 245679999999999


Q ss_pred             HHHHHHHHHH-hcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCC
Q 007742          373 LEHAKAAQSA-LNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLG  451 (591)
Q Consensus       373 ~~~a~~a~~~-l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  451 (591)
                      ...|..|-.. +++++.+.|..+.|.|+.+.....-.                        .                  
T Consensus       218 H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded------------------------~------------------  255 (506)
T KOG0117|consen  218 HRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDED------------------------T------------------  255 (506)
T ss_pred             chhHHHHHhhccCCceeecCCcceeeccCcccCCChh------------------------h------------------
Confidence            9999888655 46789999999999998653321100                        0                  


Q ss_pred             CCCcccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhcc
Q 007742          452 VAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSK  531 (591)
Q Consensus       452 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~  531 (591)
                                                                 -..=++|+|+||  +..+|        ++.|..+|+.
T Consensus       256 -------------------------------------------ms~VKvLYVRNL--~~~tT--------eE~lk~~F~~  282 (506)
T KOG0117|consen  256 -------------------------------------------MSKVKVLYVRNL--MESTT--------EETLKKLFNE  282 (506)
T ss_pred             -------------------------------------------hhheeeeeeecc--chhhh--------HHHHHHHHHh
Confidence                                                       001137999999  88888        8999999999


Q ss_pred             ccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchhhhh
Q 007742          532 YGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEA  587 (591)
Q Consensus       532 ~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  587 (591)
                      ||.|..|+.+   +-+|||.|.+.++|.+|++.|||+.|+|..|.|.++++.+-.+
T Consensus       283 ~G~veRVkk~---rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  283 FGKVERVKKP---RDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             ccceEEeecc---cceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhc
Confidence            9999999777   4499999999999999999999999999999999999876443

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

Probab=100.00  E-value=7.7e-35  Score=269.84  Aligned_cols=349  Identities=20%  Similarity=0.376  Sum_probs=234.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      |+||||.|.+.+.|+.|+..|..||+|.+|.+-.|..|++.+|||||+|.-+|.|+.|+ .|||..++|+.|+|..+...
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999 69999999999999744322


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHH
Q 007742          300 KNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA  379 (591)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a  379 (591)
                      ....+...-     ..........|||..+.+++.+++|+.+|+.||+|..|.+-..+..+..+||+|+||.+..+...|
T Consensus       194 pQAQpiID~-----vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eA  268 (544)
T KOG0124|consen  194 PQAQPIIDM-----VQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEA  268 (544)
T ss_pred             cccchHHHH-----HHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHH
Confidence            211100000     000001137899999999999999999999999999999999987778899999999999999999


Q ss_pred             HHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCC--ccccCCcCCCCCccc
Q 007742          380 QSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGI--ATSIAGSLGVAPAVN  457 (591)
Q Consensus       380 ~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~  457 (591)
                      +..||- +-++|+.|+|..+.............       +.-........++...+......  ....-+..|.+..+.
T Consensus       269 iasMNl-FDLGGQyLRVGk~vTPP~aLl~Pat~-------s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vS  340 (544)
T KOG0124|consen  269 IASMNL-FDLGGQYLRVGKCVTPPDALLQPATV-------SAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVS  340 (544)
T ss_pred             hhhcch-hhcccceEecccccCCCchhcCCCCc-------ccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccC
Confidence            999997 57999999998765322211111111       11111111111122222211111  111111122221111


Q ss_pred             Cccccccccc-----------cCcC-CCCCCC--CCC------CCCC------ccc---------------ccccc----
Q 007742          458 GSAVNQQAIS-----------LPVV-GQPAVP--VPA------VTAP------VIP---------------NMAAE----  492 (591)
Q Consensus       458 ~~~~~~~~~~-----------~~~~-~~~~~~--~~~------~~~~------~~~---------------~~~~~----  492 (591)
                      .....++...           ..++ +.++..  +|.      ...|      .+.               .+..+    
T Consensus       341 pA~~aa~p~~~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~  420 (544)
T KOG0124|consen  341 PAPRAAQPLGTLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLS  420 (544)
T ss_pred             ccccccCCCCCccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhh
Confidence            1111100000           0000 000000  000      0000      000               00000    


Q ss_pred             --------------------ccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCC-------
Q 007742          493 --------------------FIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-------  545 (591)
Q Consensus       493 --------------------~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~-------  545 (591)
                                          +-...+++|.+.||++|..     +.+.|+.+|.++|++||.|..|.|-....       
T Consensus       421 ~QE~msI~G~sARhlvMqkLmR~~~S~VivLRNMV~P~D-----iDe~LegEi~EECgKfG~V~rViI~nekq~e~edae  495 (544)
T KOG0124|consen  421 EQEHMSISGSSARHLVMQKLMRKQESTVIVLRNMVDPKD-----IDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAE  495 (544)
T ss_pred             hhhCccccCccHHHHHHHHHhccccCcEEEEeccCChhh-----hhhHHHHHHHHHHhcccceeEEEEEecccccccchh
Confidence                                0034678999999988764     45677899999999999999998843322       


Q ss_pred             --eeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchhhhh
Q 007742          546 --GFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEA  587 (591)
Q Consensus       546 --g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  587 (591)
                        -..||+|....++.+|+.+|+|++|+|++|....+.+..|..
T Consensus       496 iiVKIFVefS~~~e~~rak~ALdGRfFgGr~VvAE~YDQ~~FD~  539 (544)
T KOG0124|consen  496 IIVKIFVEFSIASETHRAKQALDGRFFGGRKVVAEVYDQERFDN  539 (544)
T ss_pred             hhheeeeeechhhHHHHHHHhhccceecCceeehhhhhhhcccc
Confidence              246999999999999999999999999999999998887753

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

Probab=100.00  E-value=3.1e-33  Score=265.30  Aligned_cols=178  Identities=34%  Similarity=0.540  Sum_probs=155.7

Q ss_pred             CCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCc-cCC
Q 007742          211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQL-LLG  288 (591)
Q Consensus       211 ~~~~~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~-i~g  288 (591)
                      ....++....-++||+.||..++|.||+.+|++||.|..|.|++|+.||.++|||||.|.+.++|.+|+ .|+++. |.|
T Consensus        25 ~~~d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG  104 (510)
T KOG0144|consen   25 DHTDNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPG  104 (510)
T ss_pred             CCCCCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCC
Confidence            334445556788999999999999999999999999999999999999999999999999999999999 676655 666


Q ss_pred             --eeEEeccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEE
Q 007742          289 --QPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFG  366 (591)
Q Consensus       289 --~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a  366 (591)
                        .+|.|.++.......               +..+.|||+-|+..++|.+|.++|.+||.|+.|.|.++. .+.++|+|
T Consensus       105 ~~~pvqvk~Ad~E~er~---------------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGca  168 (510)
T KOG0144|consen  105 MHHPVQVKYADGERERI---------------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCA  168 (510)
T ss_pred             CCcceeecccchhhhcc---------------ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-ccccccee
Confidence              578888887655433               113789999999999999999999999999999999987 88999999


Q ss_pred             EEEeCCHHHHHHHHHHhcCCeeeCCe--EEEEEEecCCCC
Q 007742          367 FVQFAQLEHAKAAQSALNGKLEIVGR--TLKVSSVTDHVG  404 (591)
Q Consensus       367 ~Vef~~~~~a~~a~~~l~g~~~~~g~--~l~v~~~~~~~~  404 (591)
                      ||.|.+.+.|..||+.|||...+.|+  +|.|.|+.....
T Consensus       169 FV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  169 FVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKD  208 (510)
T ss_pred             EEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCC
Confidence            99999999999999999998788885  899999876543

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

Probab=100.00  E-value=1e-32  Score=268.93  Aligned_cols=338  Identities=20%  Similarity=0.304  Sum_probs=226.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      +.||||++||+.++.++|.++|+.+|+|..+.++.++.++.++|||||.|.-.++++.|+ ++++..+.|+.|.|.++..
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            389999999999999999999999999999999999999999999999999999999999 6899999999999987765


Q ss_pred             ccccccccCCCCCC------C--C--CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEE
Q 007742          299 EKNLVQSNTSAGGT------A--T--GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFV  368 (591)
Q Consensus       299 ~~~~~~~~~~~~~~------~--~--~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~V  368 (591)
                      ..............      .  .  .-...+--.|+|+|||+.+...+|..+|+.||.|..|.|+... .|...|||||
T Consensus        85 R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV  163 (678)
T KOG0127|consen   85 RARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFV  163 (678)
T ss_pred             cccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEE
Confidence            44433111110000      0  0  0001113589999999999999999999999999999999766 5666699999


Q ss_pred             EeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhh-hcCCccccC
Q 007742          369 QFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLD-RTGIATSIA  447 (591)
Q Consensus       369 ef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  447 (591)
                      +|....+|..||..+|+. +|+|++|.|.|+.+............+.         +....  ....-.. .........
T Consensus       164 ~fk~~~dA~~Al~~~N~~-~i~gR~VAVDWAV~Kd~ye~ta~~~~~s---------~Kk~~--~eEed~e~~~d~~~~~~  231 (678)
T KOG0127|consen  164 QFKEKKDAEKALEFFNGN-KIDGRPVAVDWAVDKDTYEDTAHEEKQS---------LKKAV--KEEEDKEADEDDGKDFD  231 (678)
T ss_pred             EEeeHHHHHHHHHhccCc-eecCceeEEeeecccccccccchhhhhh---------hhhcc--chhhhcccccccccccc
Confidence            999999999999999996 7999999999998765433322100000         00000  0000000 000000000


Q ss_pred             CcCCCCCcc-----cCccccc----cccccC-cCCCCCCCCCCCCCCcccc---ccccccCCCcceEEEeccCCCCCCCC
Q 007742          448 GSLGVAPAV-----NGSAVNQ----QAISLP-VVGQPAVPVPAVTAPVIPN---MAAEFIGSPSECLLLKNMFDPAMETD  514 (591)
Q Consensus       448 ~~~~~~~~~-----~~~~~~~----~~~~~~-~~~~~~~~~~~~~~~~~~~---~~~~~~~~~s~~l~v~Nl~~p~~~~~  514 (591)
                      ...+.....     .++.-..    ...... ..-...  .++. .+..+.   -..........+|||.||  |+.++ 
T Consensus       232 ~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e--~S~~-~~~~k~~q~k~~~en~~~~~tVFvRNL--~fD~t-  305 (678)
T KOG0127|consen  232 EEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEE--SSGK-KESDKKAQNKTTRENITEGKTVFVRNL--PFDTT-  305 (678)
T ss_pred             hhcccccccccccccccchhhhcccccccccccccccc--cccc-CcccchhccccccccccccceEEEecC--Ccccc-
Confidence            000000000     0000000    000000 000000  0000 000000   001112334578999999  99988 


Q ss_pred             chhhhhHHHHHHHHhccccceEEEEEe-----cCCCeeEEEEeCCHHHHHHHHHHh-----cc-cccCCeEEEEEEeCch
Q 007742          515 PDFDLEIQGDVEEECSKYGRVKHIYVD-----KRSAGFVYLRFESTEAAASAQRAM-----HM-RWFARRLISAIFMKPE  583 (591)
Q Consensus       515 ~~~~~~~~edl~~~f~~~G~V~~v~l~-----~~~~g~afV~F~~~e~A~~A~~~l-----~g-~~~~g~~l~v~~~~~~  583 (591)
                             ++.|.++|++||.|.++.|.     ..+.|+|||.|.+..+|+.||...     .| ..|+|+.|.|..+-..
T Consensus       306 -------EEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~R  378 (678)
T KOG0127|consen  306 -------EEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTR  378 (678)
T ss_pred             -------HHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccch
Confidence                   89999999999999999773     357999999999999999999876     24 7799999999987543

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

Probab=100.00  E-value=2.8e-32  Score=286.94  Aligned_cols=290  Identities=22%  Similarity=0.257  Sum_probs=208.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC--eeEEeccCc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG--QPVMVKPSE  297 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g--~~i~v~~~~  297 (591)
                      .+|||+||++.+|+++|.++|..||.|..|.++.+..    .|+|||+|.+.++|.+|+ .|||..|.|  ..|+|.++.
T Consensus        97 ~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk  172 (481)
T TIGR01649        97 LRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAK  172 (481)
T ss_pred             EEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEec
Confidence            5799999999999999999999999999999987643    479999999999999999 699999965  477776654


Q ss_pred             cccccc-----cc----------------------cCCC---------------------C-----C--C----------
Q 007742          298 AEKNLV-----QS----------------------NTSA---------------------G-----G--T----------  312 (591)
Q Consensus       298 ~~~~~~-----~~----------------------~~~~---------------------~-----~--~----------  312 (591)
                      ......     ..                      ....                     .     .  +          
T Consensus       173 ~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  252 (481)
T TIGR01649       173 PTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYR  252 (481)
T ss_pred             CCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCCCc
Confidence            322100     00                      0000                     0     0  0          


Q ss_pred             ------C--------CCCCCCCCceEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHH
Q 007742          313 ------A--------TGPYGAIDRKLYVGNLHF-NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK  377 (591)
Q Consensus       313 ------~--------~~~~~~~~~~l~v~nl~~-~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~  377 (591)
                            .        .....+++.+|||+|||+ .+++++|.++|+.||.|..|.|+.++     +|+|||+|.+.++|.
T Consensus       253 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~  327 (481)
T TIGR01649       253 PAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQ  327 (481)
T ss_pred             ccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHH
Confidence                  0        000123567999999998 69999999999999999999998763     689999999999999


Q ss_pred             HHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCccc
Q 007742          378 AAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVN  457 (591)
Q Consensus       378 ~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  457 (591)
                      .||..|||. .|.|++|.|.+++.........   ......    ..  .         +          ....... . 
T Consensus       328 ~Ai~~lng~-~l~g~~l~v~~s~~~~~~~~~~---~~~~~~----~~--~---------~----------~d~~~~~-~-  376 (481)
T TIGR01649       328 LALTHLNGV-KLFGKPLRVCPSKQQNVQPPRE---GQLDDG----LT--S---------Y----------KDYSSSR-N-  376 (481)
T ss_pred             HHHHHhCCC-EECCceEEEEEcccccccCCCC---CcCcCC----Cc--c---------c----------ccccCCc-c-
Confidence            999999996 7999999999875432111100   000000    00  0         0          0000000 0 


Q ss_pred             CccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccc--e
Q 007742          458 GSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGR--V  535 (591)
Q Consensus       458 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~--V  535 (591)
                                 ..+..     +.      .... ....+++.+|+|.||  |..++        +++|+++|..||.  |
T Consensus       377 -----------~r~~~-----~~------~~~~-~~~~~ps~~L~v~NL--p~~~t--------ee~L~~lF~~~G~~~i  423 (481)
T TIGR01649       377 -----------HRFKK-----PG------SANK-NNIQPPSATLHLSNI--PLSVS--------EEDLKELFAENGVHKV  423 (481)
T ss_pred             -----------ccCCC-----cc------cccc-cccCCCCcEEEEecC--CCCCC--------HHHHHHHHHhcCCccc
Confidence                       00000     00      0000 012457789999999  88888        8999999999998  8


Q ss_pred             EEEEEecC---CCeeEEEEeCCHHHHHHHHHHhcccccCCeE------EEEEEeCch
Q 007742          536 KHIYVDKR---SAGFVYLRFESTEAAASAQRAMHMRWFARRL------ISAIFMKPE  583 (591)
Q Consensus       536 ~~v~l~~~---~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~------l~v~~~~~~  583 (591)
                      ..|.+...   .+|+|||+|.+.++|..|+..|||..|.|+.      |+|+|++..
T Consensus       424 ~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       424 KKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             eEEEEecCCCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            88877433   3689999999999999999999999999984      999998753

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).

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=2.1e-33  Score=280.66  Aligned_cols=301  Identities=27%  Similarity=0.471  Sum_probs=237.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcC-----------C-CeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKA-----------G-KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQ  284 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~-----------G-~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~  284 (591)
                      +.++..+||+++|+.++++.+..+|..-           | .+..+.+..      .+.||||+|.+.++|..|+.+++.
T Consensus       172 t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~------~~nfa~ie~~s~~~at~~~~~~~~  245 (500)
T KOG0120|consen  172 TRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNL------EKNFAFIEFRSISEATEAMALDGI  245 (500)
T ss_pred             hhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecc------cccceeEEecCCCchhhhhcccch
Confidence            4567899999999999999999998763           2 266666644      456999999999999999999999


Q ss_pred             ccCCeeEEeccCccccccccccCCC------CCC-CCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccC
Q 007742          285 LLLGQPVMVKPSEAEKNLVQSNTSA------GGT-ATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDI  357 (591)
Q Consensus       285 ~i~g~~i~v~~~~~~~~~~~~~~~~------~~~-~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~  357 (591)
                      .+.|.++++.-..............      +.. ......-....++|++||..+++.++.+++..||++....++.+.
T Consensus       246 ~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~  325 (500)
T KOG0120|consen  246 IFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDS  325 (500)
T ss_pred             hhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccc
Confidence            9999999986444333222111111      000 111111124789999999999999999999999999999999999


Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHh
Q 007742          358 ETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKL  437 (591)
Q Consensus       358 ~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  437 (591)
                      .+|.++||||.+|.++..+..|+..|||. .+.+.+|.|..+.......+....                          
T Consensus       326 ~~g~skg~af~ey~dpsvtd~A~agLnGm-~lgd~~lvvq~A~~g~~~~~~~~~--------------------------  378 (500)
T KOG0120|consen  326 ATGNSKGFAFCEYCDPSVTDQAIAGLNGM-QLGDKKLVVQRAIVGASNANVNFN--------------------------  378 (500)
T ss_pred             ccccccceeeeeeeCCcchhhhhcccchh-hhcCceeEeehhhccchhccccCC--------------------------
Confidence            88999999999999999999999999995 789999999876432111110000                          


Q ss_pred             hhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchh
Q 007742          438 DRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDF  517 (591)
Q Consensus       438 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~  517 (591)
                                                              ......+.++.......++++.+|++.|+++|..+.+++.
T Consensus       379 ----------------------------------------~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~E  418 (500)
T KOG0120|consen  379 ----------------------------------------ISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEE  418 (500)
T ss_pred             ----------------------------------------ccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHH
Confidence                                                    0000111122222233578899999999999999999999


Q ss_pred             hhhHHHHHHHHhccccceEEEEEecC--------CCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchhhhhcc
Q 007742          518 DLEIQGDVEEECSKYGRVKHIYVDKR--------SAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKF  589 (591)
Q Consensus       518 ~~~~~edl~~~f~~~G~V~~v~l~~~--------~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~~~  589 (591)
                      |++|.++|+..|.+||.|.+|.++.+        +.|++||+|.+.++++.|++.|+|++|+|++|.++|++++.|++..
T Consensus       419 yeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeDkY~~r~  498 (500)
T KOG0120|consen  419 YEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDEDKYHARE  498 (500)
T ss_pred             HHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHHHhhccc
Confidence            99999999999999999999999765        5789999999999999999999999999999999999999999865


Q ss_pred             C
Q 007742          590 K  590 (591)
Q Consensus       590 ~  590 (591)
                      .
T Consensus       499 ~  499 (500)
T KOG0120|consen  499 F  499 (500)
T ss_pred             c
Confidence            3

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

Probab=100.00  E-value=9.6e-32  Score=240.33  Aligned_cols=235  Identities=26%  Similarity=0.425  Sum_probs=188.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~  297 (591)
                      .+.++|||+||...+||+-|..+|+++|.+..++|+.+                                  .|+|.|+.
T Consensus         4 ~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~----------------------------------e~~v~wa~   49 (321)
T KOG0148|consen    4 DEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD----------------------------------ELKVNWAT   49 (321)
T ss_pred             CCCceEEeeccChhhHHHHHHHHHHhccccccceeehh----------------------------------hhcccccc
Confidence            35699999999999999999999999999999998865                                  34455544


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHH
Q 007742          298 AEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK  377 (591)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~  377 (591)
                      .+.+  ++.         +.....-.|+|+.|.+.++-+.|++.|.+||+|..++|++|..|++++||+||.|.+.++|+
T Consensus        50 ~p~n--Qsk---------~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAE  118 (321)
T KOG0148|consen   50 APGN--QSK---------PTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAE  118 (321)
T ss_pred             Cccc--CCC---------CccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHH
Confidence            3311  111         11111368999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCccc
Q 007742          378 AAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVN  457 (591)
Q Consensus       378 ~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  457 (591)
                      +||+.|||+| |.++.|+..+++-+....            +...+.                                 
T Consensus       119 nAI~~MnGqW-lG~R~IRTNWATRKp~e~------------n~~~lt---------------------------------  152 (321)
T KOG0148|consen  119 NAIQQMNGQW-LGRRTIRTNWATRKPSEM------------NGKPLT---------------------------------  152 (321)
T ss_pred             HHHHHhCCee-eccceeeccccccCcccc------------CCCCcc---------------------------------
Confidence            9999999985 999999999986543100            000000                                 


Q ss_pred             CccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEE
Q 007742          458 GSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKH  537 (591)
Q Consensus       458 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~  537 (591)
                                                  +..+.+ ...+..++|+|+||  +..++        +++|++.|+.||.|..
T Consensus       153 ----------------------------fdeV~N-Qssp~NtsVY~G~I--~~~lt--------e~~mr~~Fs~fG~I~E  193 (321)
T KOG0148|consen  153 ----------------------------FDEVYN-QSSPDNTSVYVGNI--ASGLT--------EDLMRQTFSPFGPIQE  193 (321)
T ss_pred             ----------------------------HHHHhc-cCCCCCceEEeCCc--Ccccc--------HHHHHHhcccCCcceE
Confidence                                        000000 02345678999999  55566        8999999999999999


Q ss_pred             EEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          538 IYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       538 v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      |.+-+ .+|++||.|.+.|.|.+||..|||..++|+.|+|.|-++.
T Consensus       194 VRvFk-~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~  238 (321)
T KOG0148|consen  194 VRVFK-DQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEG  238 (321)
T ss_pred             EEEec-ccceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccC
Confidence            98874 5999999999999999999999999999999999997664

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

Probab=99.97  E-value=3.4e-29  Score=224.09  Aligned_cols=178  Identities=26%  Similarity=0.400  Sum_probs=159.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      .-.+||+.|...|+.++|++.|.+||.|.++++++|.+|++++|||||.|.+.++|+.|| .|||+.|+++.|+..|+..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            456899999999999999999999999999999999999999999999999999999999 7999999999999999988


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA  378 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~  378 (591)
                      ++.........-.......++.+++||++||+..+++++|++.|++||+|.+|++.++      +||+||.|.+.|.|..
T Consensus       142 Kp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAah  215 (321)
T KOG0148|consen  142 KPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAH  215 (321)
T ss_pred             CccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHH
Confidence            7744333333333444566777899999999999999999999999999999999987      6899999999999999


Q ss_pred             HHHHhcCCeeeCCeEEEEEEecCCCC
Q 007742          379 AQSALNGKLEIVGRTLKVSSVTDHVG  404 (591)
Q Consensus       379 a~~~l~g~~~~~g~~l~v~~~~~~~~  404 (591)
                      ||..+||. .+.|..|++.+.+....
T Consensus       216 AIv~mNnt-ei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  216 AIVQMNNT-EIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             HHHHhcCc-eeCceEEEEeccccCCC
Confidence            99999997 89999999999876544

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.96  E-value=8.4e-29  Score=245.53  Aligned_cols=169  Identities=27%  Similarity=0.412  Sum_probs=152.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+++|+++|+++|..||.|+.|+|+.+..++.++|||||+|.+.++|..|| .||+..|.+++|+|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            345689999999999999999999999999999999999999999999999999999999999 6999999999999998


Q ss_pred             CccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHH
Q 007742          296 SEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH  375 (591)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~  375 (591)
                      +.+....                ....+|||.|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++
T Consensus       184 a~p~~~~----------------~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~  247 (346)
T TIGR01659       184 ARPGGES----------------IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREE  247 (346)
T ss_pred             ccccccc----------------cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHH
Confidence            7543211                113689999999999999999999999999999999998899999999999999999


Q ss_pred             HHHHHHHhcCCeeeCC--eEEEEEEecCC
Q 007742          376 AKAAQSALNGKLEIVG--RTLKVSSVTDH  402 (591)
Q Consensus       376 a~~a~~~l~g~~~~~g--~~l~v~~~~~~  402 (591)
                      |..||+.||+. .|.|  ++|.|.++...
T Consensus       248 A~~Ai~~lng~-~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       248 AQEAISALNNV-IPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             HHHHHHHhCCC-ccCCCceeEEEEECCcc
Confidence            99999999996 4665  78999887654

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).

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

Probab=99.96  E-value=7.1e-29  Score=247.06  Aligned_cols=322  Identities=22%  Similarity=0.316  Sum_probs=219.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      ..||||   +++|+..|.++|+.+|+|++|++++|. |  +-|||||.|.++.+|.+|| ++|...+.|++|+|.|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            358899   899999999999999999999999998 6  9999999999999999999 79999999999999998654


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHH
Q 007742          300 KNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA  379 (591)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a  379 (591)
                      .                     ..|||.||++.++...|+++|+.||.|.+|.+..+. .| ++|| ||+|.+.++|.+|
T Consensus        76 ~---------------------~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~a  131 (369)
T KOG0123|consen   76 P---------------------SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKA  131 (369)
T ss_pred             C---------------------ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHH
Confidence            3                     239999999999999999999999999999999886 44 8999 9999999999999


Q ss_pred             HHHhcCCeeeCCeEEEEEEecCCCCCCccccc-CCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccC---CcCC---C
Q 007742          380 QSALNGKLEIVGRTLKVSSVTDHVGTQDTAAK-SADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIA---GSLG---V  452 (591)
Q Consensus       380 ~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~---~  452 (591)
                      +..+||. .+.|++|.|............... ...+...-..... .......+...+...+...++.   ...+   .
T Consensus       132 i~~~ng~-ll~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~-~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~  209 (369)
T KOG0123|consen  132 IEKLNGM-LLNGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLE-EDSTDEELKDLFSAYGSITSVAVMRDSIGKSKG  209 (369)
T ss_pred             HHHhcCc-ccCCCeeEEeeccchhhhcccccchhhhhhhhheeccc-cccchHHHHHhhcccCcceEEEEeecCCCCCCC
Confidence            9999997 599999999877655432221111 0000000000000 0000111111111111111110   0001   0


Q ss_pred             CCcccCcccccccccc-----CcCCCCCC-CCCCCCC--------Ccc-ccccccccCCCcceEEEeccCCCCCCCCchh
Q 007742          453 APAVNGSAVNQQAISL-----PVVGQPAV-PVPAVTA--------PVI-PNMAAEFIGSPSECLLLKNMFDPAMETDPDF  517 (591)
Q Consensus       453 ~~~~~~~~~~~~~~~~-----~~~~~~~~-~~~~~~~--------~~~-~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~  517 (591)
                      ..+++...+..+....     ..++.... .......        ... ..........+...|+|.|+  ...++    
T Consensus       210 ~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknl--d~~~~----  283 (369)
T KOG0123|consen  210 FGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNL--DETLS----  283 (369)
T ss_pred             ccceeecChhHHHHHHHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccC--ccccc----
Confidence            0111111110000000     01110000 0011100        000 01112223456678999998  55555    


Q ss_pred             hhhHHHHHHHHhccccceEEEEEe----cCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchh
Q 007742          518 DLEIQGDVEEECSKYGRVKHIYVD----KRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPED  584 (591)
Q Consensus       518 ~~~~~edl~~~f~~~G~V~~v~l~----~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~  584 (591)
                          .+.|..+|+.||.|.++.|.    ..++|++||+|.+.++|..|+..+||..+.|+.|.|.++...+
T Consensus       284 ----~e~L~~~f~~~GeI~s~kv~~~~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~  350 (369)
T KOG0123|consen  284 ----DEKLRKIFSSFGEITSAKVMVDENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKE  350 (369)
T ss_pred             ----hhHHHHHHhcccceeeEEEEeccCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhc
Confidence                78999999999999998874    3478999999999999999999999999999999998866444

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

Probab=99.95  E-value=8.4e-27  Score=250.27  Aligned_cols=182  Identities=20%  Similarity=0.291  Sum_probs=147.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||+.+|+++|.++|..||.|..+.|+.+..+|.++|||||+|.+.++|..|| .|||..|.|+.|.|.++.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            3579999999999999999999999999999999999999999999999999999999999 699999999999998775


Q ss_pred             cccccccccCCC------------CCCCCCCCCCCCceEEEcCCCCCC----------CHHHHHHHhccCCCeeEEEEec
Q 007742          298 AEKNLVQSNTSA------------GGTATGPYGAIDRKLYVGNLHFNM----------TETQLRKLFEPFGPVELVQLPL  355 (591)
Q Consensus       298 ~~~~~~~~~~~~------------~~~~~~~~~~~~~~l~v~nl~~~~----------~~~~l~~~f~~~g~i~~v~i~~  355 (591)
                      ............            ..........++.+|+|.||....          ..++|.++|.+||.|..|.|+.
T Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~  453 (509)
T TIGR01642       374 VGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPR  453 (509)
T ss_pred             cCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeec
Confidence            432211100000            000111223456899999996421          2367999999999999999986


Q ss_pred             cC---CCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          356 DI---ETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       356 ~~---~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      +.   .++.+.|+|||+|.++++|.+|+..|||. .|.|+.|.|.|...
T Consensus       454 ~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr-~~~gr~v~~~~~~~  501 (509)
T TIGR01642       454 PNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGR-KFNDRVVVAAFYGE  501 (509)
T ss_pred             cCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCC-EECCeEEEEEEeCH
Confidence            53   23456799999999999999999999997 69999999999754

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

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

Probab=99.95  E-value=8.6e-27  Score=246.59  Aligned_cols=177  Identities=23%  Similarity=0.377  Sum_probs=142.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      .++|||+|||+.+|+++|.++|..||.|..|.++.+..+|.++|||||+|.+.++|..|+ .|||..|.|++|.|.++..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            589999999999999999999999999999999999999999999999999999999999 6999999999999988432


Q ss_pred             ccccccc--------------------------------c------CCCCC-----------------------------
Q 007742          299 EKNLVQS--------------------------------N------TSAGG-----------------------------  311 (591)
Q Consensus       299 ~~~~~~~--------------------------------~------~~~~~-----------------------------  311 (591)
                      .......                                .      .+...                             
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (457)
T TIGR01622       266 STYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALA  345 (457)
T ss_pred             CCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccc
Confidence            1100000                                0      00000                             


Q ss_pred             ----CCCCC---CCCCCceEEEcCCCCCCC----------HHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHH
Q 007742          312 ----TATGP---YGAIDRKLYVGNLHFNMT----------ETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE  374 (591)
Q Consensus       312 ----~~~~~---~~~~~~~l~v~nl~~~~~----------~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~  374 (591)
                          .....   ...++.+|+|.||....+          .++|+++|.+||.|..|.|..    ....|++||+|.+++
T Consensus       346 ~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~----~~~~G~~fV~F~~~e  421 (457)
T TIGR01622       346 IMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDT----KNSAGKIYLKFSSVD  421 (457)
T ss_pred             cccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeC----CCCceeEEEEECCHH
Confidence                00000   123468899999954433          368999999999999998863    345799999999999


Q ss_pred             HHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          375 HAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       375 ~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      +|..|++.|||. .|+|+.|.|.+...
T Consensus       422 ~A~~A~~~lnGr-~f~gr~i~~~~~~~  447 (457)
T TIGR01622       422 AALAAFQALNGR-YFGGKMITAAFVVN  447 (457)
T ss_pred             HHHHHHHHhcCc-ccCCeEEEEEEEcH
Confidence            999999999998 59999999999754

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.94  E-value=2.8e-25  Score=227.16  Aligned_cols=183  Identities=30%  Similarity=0.449  Sum_probs=150.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC--eeEEecc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG--QPVMVKP  295 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g--~~i~v~~  295 (591)
                      ..++|||+|||..+++++|..+|..||.|..+.++.+..+|.++|||||+|.+.++|..|+ .|||..+.|  .+|.|.+
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF  167 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            4578999999999999999999999999999999999888999999999999999999999 699999877  5677766


Q ss_pred             Cccccccc----cc----------cC-C----------------------------------------------C---C-
Q 007742          296 SEAEKNLV----QS----------NT-S----------------------------------------------A---G-  310 (591)
Q Consensus       296 ~~~~~~~~----~~----------~~-~----------------------------------------------~---~-  310 (591)
                      +.......    ..          .. +                                              .   . 
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            54222000    00          00 0                                              0   0 


Q ss_pred             --CC---------CCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHH
Q 007742          311 --GT---------ATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA  379 (591)
Q Consensus       311 --~~---------~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a  379 (591)
                        ..         ........+.+|||+|||+.+++++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|.+|
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~A  327 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMA  327 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHH
Confidence              00         0000011234799999999999999999999999999999999988999999999999999999999


Q ss_pred             HHHhcCCeeeCCeEEEEEEecCC
Q 007742          380 QSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       380 ~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      |..|||. .|.|+.|.|.|.+..
T Consensus       328 i~~lnG~-~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       328 ILSLNGY-TLGNRVLQVSFKTNK  349 (352)
T ss_pred             HHHhCCC-EECCeEEEEEEccCC
Confidence            9999996 799999999998654

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

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

Probab=99.94  E-value=5.7e-26  Score=221.97  Aligned_cols=182  Identities=25%  Similarity=0.436  Sum_probs=148.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      -.+|+|+||||.+.+.+|..+|+.||.|..|.|.....++.+ |||||.|....+|..|| .+|+..|.|++|-|.|+.+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            478999999999999999999999999999999987775555 99999999999999999 5999999999999988754


Q ss_pred             cccccccc----------------------CCC-----------------CC--------------------CC-CC---
Q 007742          299 EKNLVQSN----------------------TSA-----------------GG--------------------TA-TG---  315 (591)
Q Consensus       299 ~~~~~~~~----------------------~~~-----------------~~--------------------~~-~~---  315 (591)
                      +.......                      ...                 .+                    .. +.   
T Consensus       196 Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~  275 (678)
T KOG0127|consen  196 KDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKE  275 (678)
T ss_pred             cccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCc
Confidence            33211000                      000                 00                    00 00   


Q ss_pred             -----C------CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHh-
Q 007742          316 -----P------YGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL-  383 (591)
Q Consensus       316 -----~------~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l-  383 (591)
                           .      ...-..+|||+|||+++|+++|.+.|++||+|..+.|+.++.|+.+.|.|||.|.+..+|.+||.+. 
T Consensus       276 ~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~As  355 (678)
T KOG0127|consen  276 SDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAAS  355 (678)
T ss_pred             ccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcC
Confidence                 0      0001379999999999999999999999999999999999999999999999999999999999877 


Q ss_pred             ----cCCeeeCCeEEEEEEecCC
Q 007742          384 ----NGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       384 ----~g~~~~~g~~l~v~~~~~~  402 (591)
                          .|.+.|.|+.|.|..+...
T Consensus       356 pa~e~g~~ll~GR~Lkv~~Av~R  378 (678)
T KOG0127|consen  356 PASEDGSVLLDGRLLKVTLAVTR  378 (678)
T ss_pred             ccCCCceEEEeccEEeeeeccch
Confidence                2336799999999987543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.93  E-value=4.7e-25  Score=218.84  Aligned_cols=166  Identities=23%  Similarity=0.359  Sum_probs=144.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ....++|||.|||+.+++++|+++|..||+|..|.|+.+..++.++|||||+|.+.++|..||..|++. .|.+++|.|.
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~-~l~gr~i~V~  182 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGI-TVRNKRLKVS  182 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCC-ccCCceeeee
Confidence            344689999999999999999999999999999999999889999999999999999999999999996 6999999998


Q ss_pred             EecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCC
Q 007742          398 SVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVP  477 (591)
Q Consensus       398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  477 (591)
                      ++.+..                                                                          
T Consensus       183 ~a~p~~--------------------------------------------------------------------------  188 (346)
T TIGR01659       183 YARPGG--------------------------------------------------------------------------  188 (346)
T ss_pred             cccccc--------------------------------------------------------------------------
Confidence            763210                                                                          


Q ss_pred             CCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----CCeeEEEEe
Q 007742          478 VPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----SAGFVYLRF  552 (591)
Q Consensus       478 ~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~~g~afV~F  552 (591)
                                      .......|+|.||  |..++        +++|+++|++||.|..|.|..+     ++|+|||+|
T Consensus       189 ----------------~~~~~~~lfV~nL--p~~vt--------ee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F  242 (346)
T TIGR01659       189 ----------------ESIKDTNLYVTNL--PRTIT--------DDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRF  242 (346)
T ss_pred             ----------------cccccceeEEeCC--CCccc--------HHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEE
Confidence                            0011236999999  88888        8999999999999999987543     469999999


Q ss_pred             CCHHHHHHHHHHhcccccCC--eEEEEEEeCchh
Q 007742          553 ESTEAAASAQRAMHMRWFAR--RLISAIFMKPED  584 (591)
Q Consensus       553 ~~~e~A~~A~~~l~g~~~~g--~~l~v~~~~~~~  584 (591)
                      .+.++|.+||+.||+..|.|  ++|.|.|+.+..
T Consensus       243 ~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       243 NKREEAQEAISALNNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             CCHHHHHHHHHHhCCCccCCCceeEEEEECCccc
Confidence            99999999999999999866  789999988753

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).

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

Probab=99.93  E-value=6.4e-26  Score=223.35  Aligned_cols=176  Identities=23%  Similarity=0.326  Sum_probs=136.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +-..|||+||.+++|+++|+.+|+.||.|..|.++.|..||.++|||||+|.+.++|.+|+ .|||..|.|+.|+|....
T Consensus       277 p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  277 PMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             chhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            3344999999999999999999999999999999999999999999999999999999998 699999999999984211


Q ss_pred             cccccccc--------------------------------cC----------------CC-----CC----------CCC
Q 007742          298 AEKNLVQS--------------------------------NT----------------SA-----GG----------TAT  314 (591)
Q Consensus       298 ~~~~~~~~--------------------------------~~----------------~~-----~~----------~~~  314 (591)
                      ........                                ..                ..     .+          ...
T Consensus       357 ~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~  436 (549)
T KOG0147|consen  357 ERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADAS  436 (549)
T ss_pred             eecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccc
Confidence            11000000                                00                00     00          000


Q ss_pred             CCCCCCCceEEEcCCC--CCCC--------HHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 007742          315 GPYGAIDRKLYVGNLH--FNMT--------ETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN  384 (591)
Q Consensus       315 ~~~~~~~~~l~v~nl~--~~~~--------~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~  384 (591)
                      +....++.|+.|.|+-  ...|        .++|.+.|.+||+|.+|.+-++     +.|++||.|.+++.|..|+.+||
T Consensus       437 p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~alh  511 (549)
T KOG0147|consen  437 PAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKALH  511 (549)
T ss_pred             cccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHHHh
Confidence            0011456788888883  2222        2678899999999999988543     35999999999999999999999


Q ss_pred             CCeeeCCeEEEEEEec
Q 007742          385 GKLEIVGRTLKVSSVT  400 (591)
Q Consensus       385 g~~~~~g~~l~v~~~~  400 (591)
                      |. +|.|+.|++.|..
T Consensus       512 gr-WF~gr~Ita~~~~  526 (549)
T KOG0147|consen  512 GR-WFAGRMITAKYLP  526 (549)
T ss_pred             hh-hhccceeEEEEee
Confidence            97 5999999999874

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

Probab=99.93  E-value=1.3e-24  Score=219.87  Aligned_cols=270  Identities=21%  Similarity=0.324  Sum_probs=206.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      .....|+|+|||..+..++|..+|..||.|..|.+...      --.|+|+|..+.+|..|. .|....+...++.+.|+
T Consensus       383 rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~------G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~a  456 (725)
T KOG0110|consen  383 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPG------GTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWA  456 (725)
T ss_pred             hhcceeeeccCccccccHHHHHHhhcccccceeecCcc------cceeeeeecCccchHHHHHHhchhhhccCccccccC
Confidence            34478999999999999999999999999999855421      124999999999999999 68888888888888766


Q ss_pred             cccccccc--ccC-----CCC----------------CCCCC-------C---CCCCC-ceEEEcCCCCCCCHHHHHHHh
Q 007742          297 EAEKNLVQ--SNT-----SAG----------------GTATG-------P---YGAID-RKLYVGNLHFNMTETQLRKLF  342 (591)
Q Consensus       297 ~~~~~~~~--~~~-----~~~----------------~~~~~-------~---~~~~~-~~l~v~nl~~~~~~~~l~~~f  342 (591)
                      ........  ...     ...                .....       .   ..... +.|||.||++.++.++|...|
T Consensus       457 P~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F  536 (725)
T KOG0110|consen  457 PEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLF  536 (725)
T ss_pred             hhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHH
Confidence            54332200  000     000                00000       0   00011 339999999999999999999


Q ss_pred             ccCCCeeEEEEeccCCC---CCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCC
Q 007742          343 EPFGPVELVQLPLDIET---GQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDD  419 (591)
Q Consensus       343 ~~~g~i~~v~i~~~~~~---~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~  419 (591)
                      .+.|.|..|.|...+..   -.+.|||||+|.++++|..|+..|+|. .++|+.|.|.++........            
T Consensus       537 ~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgt-vldGH~l~lk~S~~k~~~~~------------  603 (725)
T KOG0110|consen  537 SKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGT-VLDGHKLELKISENKPASTV------------  603 (725)
T ss_pred             HhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCc-eecCceEEEEeccCcccccc------------
Confidence            99999999988866522   135699999999999999999999997 59999999998741000000            


Q ss_pred             CCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcc
Q 007742          420 GGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSE  499 (591)
Q Consensus       420 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~  499 (591)
                                                     +                                +..+      ......
T Consensus       604 -------------------------------g--------------------------------K~~~------~kk~~t  614 (725)
T KOG0110|consen  604 -------------------------------G--------------------------------KKKS------KKKKGT  614 (725)
T ss_pred             -------------------------------c--------------------------------cccc------cccccc
Confidence                                           0                                0000      012234


Q ss_pred             eEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----CCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          500 CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----SAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       500 ~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      .|+|.||  |+.++        ..+|+.+|..||.|.+|.|+..     ..|||||+|-++.+|..|+.+|.++.|.|+.
T Consensus       615 KIlVRNi--pFeAt--------~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRr  684 (725)
T KOG0110|consen  615 KILVRNI--PFEAT--------KREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRR  684 (725)
T ss_pred             eeeeecc--chHHH--------HHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechh
Confidence            6999999  99887        8999999999999999999865     4789999999999999999999999999999


Q ss_pred             EEEEEeCchhh
Q 007742          575 ISAIFMKPEDY  585 (591)
Q Consensus       575 l~v~~~~~~~~  585 (591)
                      |.+.|+..+.-
T Consensus       685 LVLEwA~~d~~  695 (725)
T KOG0110|consen  685 LVLEWAKSDNT  695 (725)
T ss_pred             hheehhccchH
Confidence            99999988764

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.93  E-value=1.6e-23  Score=199.39  Aligned_cols=187  Identities=23%  Similarity=0.379  Sum_probs=144.2

Q ss_pred             cccCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHh-cCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCc
Q 007742          208 EVVEPEADPERDQRTVFAYQMPLKATERDVYEFFS-KAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQL  285 (591)
Q Consensus       208 ~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~f~-~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~  285 (591)
                      ..-++...+....+.+||.|||+++.+++|+++|. +.|.|..|.|..|.. |+++|||.|+|.++|.+++|+ .||...
T Consensus        32 ~~gs~~gn~~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~-GK~rGcavVEFk~~E~~qKa~E~lnk~~  110 (608)
T KOG4212|consen   32 GAGSQGGNVAARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDES-GKARGCAVVEFKDPENVQKALEKLNKYE  110 (608)
T ss_pred             cccCCCCCcccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccC-CCcCCceEEEeeCHHHHHHHHHHhhhcc
Confidence            34444555555667899999999999999999996 579999999999965 899999999999999999999 599999


Q ss_pred             cCCeeEEeccCcccccccc-------------------------------------------------ccCCCCC-----
Q 007742          286 LLGQPVMVKPSEAEKNLVQ-------------------------------------------------SNTSAGG-----  311 (591)
Q Consensus       286 i~g~~i~v~~~~~~~~~~~-------------------------------------------------~~~~~~~-----  311 (591)
                      +.|++|.|+-.........                                                 ..+....     
T Consensus       111 ~~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~  190 (608)
T KOG4212|consen  111 VNGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNN  190 (608)
T ss_pred             ccCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCcccccccccc
Confidence            9999999953221110000                                                 0000000     


Q ss_pred             ---------------CCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHH
Q 007742          312 ---------------TATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHA  376 (591)
Q Consensus       312 ---------------~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a  376 (591)
                                     .......|....+||.||.+.+....|++.|.-.|.|..|.+-.++ .+.++|+|.++|..+-+|
T Consensus       191 ~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idK-eG~s~G~~vi~y~hpvea  269 (608)
T KOG4212|consen  191 SSNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDK-EGNSRGFAVIEYDHPVEA  269 (608)
T ss_pred             chhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeecc-ccccCCeeEEEecchHHH
Confidence                           0001233446789999999999999999999999999999998887 778999999999999999


Q ss_pred             HHHHHHhcCCeeeCCeEEEEE
Q 007742          377 KAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       377 ~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      -+||..|++.. +..++..+.
T Consensus       270 vqaIsml~~~g-~~~~~~~~R  289 (608)
T KOG4212|consen  270 VQAISMLDRQG-LFDRRMTVR  289 (608)
T ss_pred             HHHHHhhccCC-Cccccceee
Confidence            99999888642 444444443

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

Probab=99.92  E-value=9.5e-24  Score=219.86  Aligned_cols=172  Identities=20%  Similarity=0.426  Sum_probs=143.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||+.+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|..||..|||. .|.|+.|.|.+...
T Consensus       108 ~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~-~i~GR~IkV~rp~~  186 (612)
T TIGR01645       108 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQ-MLGGRNIKVGRPSN  186 (612)
T ss_pred             CEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCe-EEecceeeeccccc
Confidence            78999999999999999999999999999999999889999999999999999999999999996 69999999974311


Q ss_pred             CCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCC
Q 007742          402 HVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAV  481 (591)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (591)
                      .....                                               +.               .          
T Consensus       187 ~p~a~-----------------------------------------------~~---------------~----------  194 (612)
T TIGR01645       187 MPQAQ-----------------------------------------------PI---------------I----------  194 (612)
T ss_pred             ccccc-----------------------------------------------cc---------------c----------
Confidence            00000                                               00               0          


Q ss_pred             CCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----CCeeEEEEeCCHH
Q 007742          482 TAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----SAGFVYLRFESTE  556 (591)
Q Consensus       482 ~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~~g~afV~F~~~e  556 (591)
                           ....  ........|||.||  +..++        +++|+++|+.||.|.++.|..+     .+|||||+|.+.+
T Consensus       195 -----~~~~--~~~~~~~rLfVgnL--p~~vt--------eedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e  257 (612)
T TIGR01645       195 -----DMVQ--EEAKKFNRIYVASV--HPDLS--------ETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQ  257 (612)
T ss_pred             -----cccc--ccccccceEEeecC--CCCCC--------HHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHH
Confidence                 0000  00112347999999  77777        8999999999999999988643     5899999999999


Q ss_pred             HHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          557 AAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       557 ~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      +|.+|+..|||..|+|+.|.|.++...
T Consensus       258 ~A~kAI~amNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       258 SQSEAIASMNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             HHHHHHHHhCCCeeCCeEEEEEecCCC
Confidence            999999999999999999999997653

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.

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

Probab=99.90  E-value=9.7e-23  Score=192.82  Aligned_cols=317  Identities=20%  Similarity=0.254  Sum_probs=204.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-Hc--CCccCCeeEEecc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LS--GQLLLGQPVMVKP  295 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~--g~~i~g~~i~v~~  295 (591)
                      +++.|.++|||+.+||.+|..++.+||.|..+.+...++      .|||+|.+.+.|...+. ..  -..+.|++|.|++
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~  100 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQY  100 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhheeecccccCccccCcceeehh
Confidence            568999999999999999999999999999998886544      79999999999877552 22  2347888998876


Q ss_pred             Ccccccccccc--------------------CCCCC-CCC-CCCCC--CCceEEEcCCCCCCCHHHHHHHhccCCCeeEE
Q 007742          296 SEAEKNLVQSN--------------------TSAGG-TAT-GPYGA--IDRKLYVGNLHFNMTETQLRKLFEPFGPVELV  351 (591)
Q Consensus       296 ~~~~~~~~~~~--------------------~~~~~-~~~-~~~~~--~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v  351 (591)
                      +........+.                    .+... ... +....  .--.++|.|+-+.++-+.|..+|++||.|..|
T Consensus       101 sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKI  180 (492)
T KOG1190|consen  101 SNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKI  180 (492)
T ss_pred             hhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEE
Confidence            54322110000                    00000 000 01011  12466789999999999999999999999888


Q ss_pred             EEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC-eEEEEEEecCCCCCCc-ccccCCCCCCCCCCCccccHHH
Q 007742          352 QLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG-RTLKVSSVTDHVGTQD-TAAKSADFDDDDGGGLALNAQS  429 (591)
Q Consensus       352 ~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g-~~l~v~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  429 (591)
                      ..+...    ..-.|+|+|.+++.|..|..+|+|+-.++| |.|+|.|++-..-... ...+..++....   ++.+ ..
T Consensus       181 iTF~Kn----n~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~---LP~g-d~  252 (492)
T KOG1190|consen  181 ITFTKN----NGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPD---LPVG-DG  252 (492)
T ss_pred             EEEecc----cchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCC---CCCC-cc
Confidence            765432    223599999999999999999999855777 6889988764332111 111111111110   0000 00


Q ss_pred             HHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCC--cceEEEeccC
Q 007742          430 RALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSP--SECLLLKNMF  507 (591)
Q Consensus       430 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--s~~l~v~Nl~  507 (591)
                      +..+..         .++.+.+..+..              .| .+..++.......-  .......+  +.+|.|.|| 
T Consensus       253 ~p~l~~---------~~~aa~~~~~~~--------------~g-~p~aip~~~~~a~~--a~~~~~~~~~n~vllvsnl-  305 (492)
T KOG1190|consen  253 QPSLDQ---------LMAAAFGSVPAV--------------HG-APLAIPSGAAGANA--ADGKIESPSANVVLLVSNL-  305 (492)
T ss_pred             ccccch---------hhhccccccccc--------------cC-CcccCCccchhhcc--cccccccCCCceEEEEecC-
Confidence            000000         000000000000              00 00000000000000  00111122  578999998 


Q ss_pred             CCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchh
Q 007742          508 DPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPED  584 (591)
Q Consensus       508 ~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~  584 (591)
                      ++..+|        .+-|+.+|+.||.|..|+|..+.+..|+|+|.+...|+.|+.+|+|.+|.|+.|.|.|.+-..
T Consensus       306 n~~~VT--------~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  306 NEEAVT--------PDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             chhccc--------hhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcc
Confidence            566666        789999999999999999987778899999999999999999999999999999999987554

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

Probab=99.90  E-value=1.7e-23  Score=177.01  Aligned_cols=168  Identities=30%  Similarity=0.506  Sum_probs=148.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~~  296 (591)
                      .+..+|||+||+..++++.|.++|-+.|+|+++.+.+|+.+...+|||||+|.+.|+|..|+. ||...+-|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            356899999999999999999999999999999999999999999999999999999999994 8888899999999876


Q ss_pred             ccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEeccCCCCCcccEEEEEeCCHHH
Q 007742          297 EAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELV-QLPLDIETGQCKGFGFVQFAQLEH  375 (591)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v-~i~~~~~~~~~~g~a~Vef~~~~~  375 (591)
                      .......               ..+..|||+||.+.+++..|+..|+.||.|... .+..+..+|.++|++||-|.+.+.
T Consensus        87 s~~~~nl---------------~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfea  151 (203)
T KOG0131|consen   87 SAHQKNL---------------DVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEA  151 (203)
T ss_pred             ccccccc---------------cccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHH
Confidence            5211111               112689999999999999999999999987553 677777789999999999999999


Q ss_pred             HHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          376 AKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       376 a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      +..|+.++||++ +..+++.|.++..
T Consensus       152 sd~ai~s~ngq~-l~nr~itv~ya~k  176 (203)
T KOG0131|consen  152 SDAAIGSMNGQY-LCNRPITVSYAFK  176 (203)
T ss_pred             HHHHHHHhccch-hcCCceEEEEEEe
Confidence            999999999984 8999999998754

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

Probab=99.89  E-value=3.3e-22  Score=216.49  Aligned_cols=182  Identities=24%  Similarity=0.403  Sum_probs=151.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccC----CeeEE
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL----GQPVM  292 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~----g~~i~  292 (591)
                      ...++|||+|||..+|+++|+++|..||.|..+.++.+. +|.++|||||+|.+.++|..|+ .++|..|.    |..|.
T Consensus       176 ~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~  254 (562)
T TIGR01628       176 KKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLY  254 (562)
T ss_pred             cCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeE
Confidence            345789999999999999999999999999999999885 5899999999999999999999 69999999    99999


Q ss_pred             eccCccccccccccCCCC--CCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEe
Q 007742          293 VKPSEAEKNLVQSNTSAG--GTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF  370 (591)
Q Consensus       293 v~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef  370 (591)
                      |.++..............  ............+|||+||+..+++++|+++|+.||.|..|.++.+ .++.++|||||+|
T Consensus       255 v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f  333 (562)
T TIGR01628       255 VGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCF  333 (562)
T ss_pred             eecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEe
Confidence            987654332210000000  0000011223468999999999999999999999999999999988 4899999999999


Q ss_pred             CCHHHHHHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          371 AQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       371 ~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      .+.++|.+|+..|||. .|.|++|.|.++..+
T Consensus       334 ~~~~~A~~A~~~~~g~-~~~gk~l~V~~a~~k  364 (562)
T TIGR01628       334 SNPEEANRAVTEMHGR-MLGGKPLYVALAQRK  364 (562)
T ss_pred             CCHHHHHHHHHHhcCC-eeCCceeEEEeccCc
Confidence            9999999999999996 699999999998754

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=99.89  E-value=4.4e-22  Score=177.21  Aligned_cols=183  Identities=30%  Similarity=0.461  Sum_probs=150.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC--eeEEec
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG--QPVMVK  294 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g--~~i~v~  294 (591)
                      -....|||.+||..+|..+|.++|.+||.|+..+|..|..||.++|.|||.|...++|..|+ .|||+.-.|  -+|.|.
T Consensus       125 Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVK  204 (360)
T KOG0145|consen  125 IKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVK  204 (360)
T ss_pred             hcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEE
Confidence            34578999999999999999999999999999999999999999999999999999999999 699998766  477776


Q ss_pred             cCcccccccc---------cc------------------------------CCCC-CCC------C-CCCCCCCceEEEc
Q 007742          295 PSEAEKNLVQ---------SN------------------------------TSAG-GTA------T-GPYGAIDRKLYVG  327 (591)
Q Consensus       295 ~~~~~~~~~~---------~~------------------------------~~~~-~~~------~-~~~~~~~~~l~v~  327 (591)
                      +++.......         +.                              ++.. +..      . .......-+|||.
T Consensus       205 FannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvY  284 (360)
T KOG0145|consen  205 FANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVY  284 (360)
T ss_pred             ecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEE
Confidence            5443221000         00                              0000 000      0 0111124799999


Q ss_pred             CCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          328 NLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       328 nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ||.+++.+.-|+++|.+||.|..|.|++|..+++.+||+||.+.+-++|..||..|||. .+.++.|.|.+.+.
T Consensus       285 NLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy-~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  285 NLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGY-RLGDRVLQVSFKTN  357 (360)
T ss_pred             ecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCc-cccceEEEEEEecC
Confidence            99999999999999999999999999999988999999999999999999999999995 79999999998653

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

Probab=99.89  E-value=6.7e-22  Score=206.04  Aligned_cols=164  Identities=30%  Similarity=0.434  Sum_probs=134.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCC-eeEEEEee-cCCCCCccceEEEEecCcchHHHHH-HHc-C-CccCCeeEEe
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGK-VRDVRLIM-DRNSRRSKGVGYIEFYDVMSVPMAI-ALS-G-QLLLGQPVMV  293 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~-i~~v~~~~-d~~~g~~~G~afV~F~~~e~A~~Al-~l~-g-~~i~g~~i~v  293 (591)
                      ..++|||+|||+.+|+++|.+.|.+++. ++.+.++. ....+.++|||||+|.+.++|..|+ .|+ + ..+.|+.|.|
T Consensus       137 ~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~V  216 (578)
T TIGR01648       137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV  216 (578)
T ss_pred             cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEE
Confidence            4689999999999999999999999864 44444433 3345678999999999999999999 554 3 3588999999


Q ss_pred             ccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccC--CCeeEEEEeccCCCCCcccEEEEEeC
Q 007742          294 KPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPF--GPVELVQLPLDIETGQCKGFGFVQFA  371 (591)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~--g~i~~v~i~~~~~~~~~~g~a~Vef~  371 (591)
                      .|+.+.......           .....++|||+||+..+++++|+++|+.|  |.|..|.++        ++||||+|.
T Consensus       217 dwA~p~~~~d~~-----------~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~  277 (578)
T TIGR01648       217 DWAEPEEEVDED-----------VMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFE  277 (578)
T ss_pred             Eeeccccccccc-----------ccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeC
Confidence            998654322111           01123789999999999999999999999  999999775        459999999


Q ss_pred             CHHHHHHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          372 QLEHAKAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       372 ~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      +.++|.+||+.||+. .|.|+.|.|.++++.
T Consensus       278 s~e~A~kAi~~lnG~-~i~Gr~I~V~~Akp~  307 (578)
T TIGR01648       278 DREDAVKAMDELNGK-ELEGSEIEVTLAKPV  307 (578)
T ss_pred             CHHHHHHHHHHhCCC-EECCEEEEEEEccCC
Confidence            999999999999997 799999999998654

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

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

Probab=99.87  E-value=5.9e-20  Score=171.90  Aligned_cols=327  Identities=18%  Similarity=0.160  Sum_probs=213.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH---HcCCccCCeeEEec
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA---LSGQLLLGQPVMVK  294 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~---l~g~~i~g~~i~v~  294 (591)
                      ..+-.|.|++|-..++|.+|.+.+..||+|..|.++..      +..|.|+|.+++.|..++.   -+...+.|++..+.
T Consensus        29 ~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~------~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~N  102 (494)
T KOG1456|consen   29 NPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH------KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFN  102 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc------cceeeeeeccccchhhheehhccCcccccCchhhcc
Confidence            34578999999999999999999999999999988754      3479999999999999983   45566899999888


Q ss_pred             cCccccccccccCCCCCCCCCCCCCCCceEEE--cCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCC
Q 007742          295 PSEAEKNLVQSNTSAGGTATGPYGAIDRKLYV--GNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ  372 (591)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v--~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~  372 (591)
                      ++..+........+         ..++..|++  -|--+.+|.+.|+.++.+.|+|..|.|++.  ++   -.|+|||.+
T Consensus       103 yStsq~i~R~g~es---------~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFds  168 (494)
T KOG1456|consen  103 YSTSQCIERPGDES---------ATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDS  168 (494)
T ss_pred             cchhhhhccCCCCC---------CCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeech
Confidence            88654432222111         111244444  344567999999999999999999988764  22   369999999


Q ss_pred             HHHHHHHHHHhcCCeeeCC-eEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCC
Q 007742          373 LEHAKAAQSALNGKLEIVG-RTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLG  451 (591)
Q Consensus       373 ~~~a~~a~~~l~g~~~~~g-~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  451 (591)
                      ++.|+.|..+|||.-.+.| ++|+|.|+++..-....+.+.. |+..............+-    +.....    +..++
T Consensus       169 v~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~Dt-wDyTlp~~~~~~~~g~~~----~~r~~~----p~~~~  239 (494)
T KOG1456|consen  169 VEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDT-WDYTLPDLRGPYDPGRNH----YDRQRQ----PAPLG  239 (494)
T ss_pred             hHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCcc-ccccCCCCCCCCCCCCCC----CccccC----CCccC
Confidence            9999999999999855777 6999999987654444333222 322211100000000000    000000    00000


Q ss_pred             CCCcccCccccccccccCcCCCCCCCCCCCCCCccc---cccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHH
Q 007742          452 VAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIP---NMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEE  528 (591)
Q Consensus       452 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~  528 (591)
                      ..+...+..  +.......+..++.+.|+...+..-   ....+..+.+..++.|.+|.. ....        .+.|+.+
T Consensus       240 ~~pss~~G~--h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh-~k~N--------~drlFNl  308 (494)
T KOG1456|consen  240 YHPSSRGGG--HSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDH-GKMN--------CDRLFNL  308 (494)
T ss_pred             CChhhcCCC--CCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccc-cccc--------hhhhhhh
Confidence            000000000  0000000011111111111000000   011123466788999999933 2222        7899999


Q ss_pred             hccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchh
Q 007742          529 CSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPED  584 (591)
Q Consensus       529 f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~  584 (591)
                      |..||.|..|++++-..|-|+|++.+..+.+.|+..||+..+.|.+|.|.+.++..
T Consensus       309 ~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~  364 (494)
T KOG1456|consen  309 FCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNF  364 (494)
T ss_pred             hhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccc
Confidence            99999999999998889999999999999999999999999999999999877653

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

Probab=99.87  E-value=6.4e-22  Score=188.69  Aligned_cols=165  Identities=25%  Similarity=0.394  Sum_probs=140.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC--eEEEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG--RTLKVSS  398 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g--~~l~v~~  398 (591)
                      .-.+||+-||..|+|.+|+++|++||.|.+|.|++|+.++.++|+|||.|.+.++|..|+.+||+...|-|  .+|.|.|
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~  113 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKY  113 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecc
Confidence            36899999999999999999999999999999999999999999999999999999999999999766777  4677766


Q ss_pred             ecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCC
Q 007742          399 VTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPV  478 (591)
Q Consensus       399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  478 (591)
                      +......                                                                         
T Consensus       114 Ad~E~er-------------------------------------------------------------------------  120 (510)
T KOG0144|consen  114 ADGERER-------------------------------------------------------------------------  120 (510)
T ss_pred             cchhhhc-------------------------------------------------------------------------
Confidence            5311000                                                                         


Q ss_pred             CCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEec----CCCeeEEEEeCC
Q 007742          479 PAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK----RSAGFVYLRFES  554 (591)
Q Consensus       479 ~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~----~~~g~afV~F~~  554 (591)
                                      -.....|||+-|  +..++        +.+|.++|++||.|+.|.|.+    .++|||||+|.+
T Consensus       121 ----------------~~~e~KLFvg~l--sK~~t--------e~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fst  174 (510)
T KOG0144|consen  121 ----------------IVEERKLFVGML--SKQCT--------ENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFST  174 (510)
T ss_pred             ----------------cccchhhhhhhc--ccccc--------HHHHHHHHHhhCccchhhheecccccccceeEEEEeh
Confidence                            012346899988  66666        889999999999999998854    479999999999


Q ss_pred             HHHHHHHHHHhcccc-cCCe--EEEEEEeCchh
Q 007742          555 TEAAASAQRAMHMRW-FARR--LISAIFMKPED  584 (591)
Q Consensus       555 ~e~A~~A~~~l~g~~-~~g~--~l~v~~~~~~~  584 (591)
                      .+-|..||+.|||.. +.|+  +|.|.|++++.
T Consensus       175 ke~A~~Aika~ng~~tmeGcs~PLVVkFADtqk  207 (510)
T KOG0144|consen  175 KEMAVAAIKALNGTQTMEGCSQPLVVKFADTQK  207 (510)
T ss_pred             HHHHHHHHHhhccceeeccCCCceEEEecccCC
Confidence            999999999999998 6665  59999998764

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

Probab=99.86  E-value=7e-21  Score=182.61  Aligned_cols=166  Identities=29%  Similarity=0.435  Sum_probs=140.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCC-eeEEEEeecCC-CCCccceEEEEecCcchHHHHH-H-HcCC-ccCCeeEEe
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGK-VRDVRLIMDRN-SRRSKGVGYIEFYDVMSVPMAI-A-LSGQ-LLLGQPVMV  293 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~-i~~v~~~~d~~-~g~~~G~afV~F~~~e~A~~Al-~-l~g~-~i~g~~i~v  293 (591)
                      .+++|||+|||.+.++++|.+.|++.++ |++|.|..... ..+.+|||||+|.+...|..|- . +++. .+.|+.+.|
T Consensus       163 an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tV  242 (506)
T KOG0117|consen  163 ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITV  242 (506)
T ss_pred             ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCccee
Confidence            4699999999999999999999999985 67777776442 4578999999999999998887 4 4544 489999999


Q ss_pred             ccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCH
Q 007742          294 KPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQL  373 (591)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~  373 (591)
                      .|+.+.........           ..-+.|||.||+..+|++.|+++|+.||.|..|..++|        ||||.|.+-
T Consensus       243 dWAep~~e~ded~m-----------s~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR  303 (506)
T KOG0117|consen  243 DWAEPEEEPDEDTM-----------SKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAER  303 (506)
T ss_pred             eccCcccCCChhhh-----------hheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecch
Confidence            99987554332211           11279999999999999999999999999999988754        899999999


Q ss_pred             HHHHHHHHHhcCCeeeCCeEEEEEEecCCCC
Q 007742          374 EHAKAAQSALNGKLEIVGRTLKVSSVTDHVG  404 (591)
Q Consensus       374 ~~a~~a~~~l~g~~~~~g~~l~v~~~~~~~~  404 (591)
                      ++|.+||+.+||+ +|+|..|.|..+++...
T Consensus       304 ~davkAm~~~ngk-eldG~~iEvtLAKP~~k  333 (506)
T KOG0117|consen  304 EDAVKAMKETNGK-ELDGSPIEVTLAKPVDK  333 (506)
T ss_pred             HHHHHHHHHhcCc-eecCceEEEEecCChhh
Confidence            9999999999997 79999999999987654

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

Probab=99.84  E-value=1.5e-19  Score=168.15  Aligned_cols=210  Identities=25%  Similarity=0.416  Sum_probs=157.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVEL--------VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG  391 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~--------v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g  391 (591)
                      .+..|||.|||..+|.+++.++|++||.|..        |.|..+. .|..+|-|++.|...+++..|++.|++. .|.|
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~-~~rg  210 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDED-ELRG  210 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcc-cccC
Confidence            3578999999999999999999999997754        6777776 5899999999999999999999999996 7999


Q ss_pred             eEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcC
Q 007742          392 RTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVV  471 (591)
Q Consensus       392 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  471 (591)
                      +.|+|..++-............       .+..........+.+++..-.                              
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~-------k~k~~~~kk~~k~q~k~~dw~------------------------------  253 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKE-------KGKCKDKKKLKKQQQKLLDWR------------------------------  253 (382)
T ss_pred             cEEEEehhhhhhccCcCccccc-------ccccccHHHHHHHHHhhcccC------------------------------
Confidence            9999998865443332222111       001111111111111110000                              


Q ss_pred             CCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCC-CchhhhhHHHHHHHHhccccceEEEEE-ecCCCeeEE
Q 007742          472 GQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMET-DPDFDLEIQGDVEEECSKYGRVKHIYV-DKRSAGFVY  549 (591)
Q Consensus       472 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~-~~~~~~~~~edl~~~f~~~G~V~~v~l-~~~~~g~af  549 (591)
                                     |.-..+.-....++|+|+||++|..+. +++++.+|.++|.+.|.+||.|.+|.| ..++.|.+-
T Consensus       254 ---------------pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvt  318 (382)
T KOG1548|consen  254 ---------------PDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVT  318 (382)
T ss_pred             ---------------CCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeE
Confidence                           000011123445689999999998554 448889999999999999999999977 678999999


Q ss_pred             EEeCCHHHHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          550 LRFESTEAAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       550 V~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      |.|.+.++|..||+.|+|+.|+|+.|..+.....
T Consensus       319 V~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  319 VSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             EEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            9999999999999999999999999999875543

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

Probab=99.84  E-value=1.9e-20  Score=158.67  Aligned_cols=162  Identities=27%  Similarity=0.433  Sum_probs=137.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      .+|||+||+..++++.|+++|-+.|+|..+.|+.+..++..+|||||||.+.++|.-|++.||. +.+-|++|+|..+..
T Consensus        10 ~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~-VkLYgrpIrv~kas~   88 (203)
T KOG0131|consen   10 ATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNM-VKLYGRPIRVNKASA   88 (203)
T ss_pred             ceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHH-HHhcCceeEEEeccc
Confidence            7999999999999999999999999999999999999999999999999999999999999996 789999999987631


Q ss_pred             CCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCC
Q 007742          402 HVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAV  481 (591)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (591)
                      ....                                                                            
T Consensus        89 ~~~n----------------------------------------------------------------------------   92 (203)
T KOG0131|consen   89 HQKN----------------------------------------------------------------------------   92 (203)
T ss_pred             cccc----------------------------------------------------------------------------
Confidence            0000                                                                            


Q ss_pred             CCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEE-EE-----ecCCCeeEEEEeCCH
Q 007742          482 TAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHI-YV-----DKRSAGFVYLRFEST  555 (591)
Q Consensus       482 ~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v-~l-----~~~~~g~afV~F~~~  555 (591)
                                   ..-+..|+|+|| +| ...        +..|.+.|+.||.+... .+     .++++||+||.|.+.
T Consensus        93 -------------l~vganlfvgNL-d~-~vD--------e~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sf  149 (203)
T KOG0131|consen   93 -------------LDVGANLFVGNL-DP-EVD--------EKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASF  149 (203)
T ss_pred             -------------cccccccccccc-Cc-chh--------HHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhH
Confidence                         001125999999 33 443        78899999999988763 22     235789999999999


Q ss_pred             HHHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          556 EAAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       556 e~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      +.+.+|+..|||..++.++|.|+|+..+
T Consensus       150 easd~ai~s~ngq~l~nr~itv~ya~k~  177 (203)
T KOG0131|consen  150 EASDAAIGSMNGQYLCNRPITVSYAFKK  177 (203)
T ss_pred             HHHHHHHHHhccchhcCCceEEEEEEec
Confidence            9999999999999999999999997543

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

Probab=99.84  E-value=1.3e-20  Score=170.89  Aligned_cols=148  Identities=29%  Similarity=0.474  Sum_probs=134.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      -+|||+|||..+++.+|+.+|++||+|+.|.|+++        ||||...+...|..|+ .||+..|.|..|+|..+..+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            46999999999999999999999999999999954        9999999999999999 59999999999999877654


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHH
Q 007742          300 KNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA  379 (591)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a  379 (591)
                      .                  ..+.+|+|+||.+.++.++|++.|++||+|..+.|++        +|+||.|.-.++|..|
T Consensus        75 s------------------k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------dy~fvh~d~~eda~~a  128 (346)
T KOG0109|consen   75 S------------------KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------DYAFVHFDRAEDAVEA  128 (346)
T ss_pred             C------------------CCccccccCCCCccccCHHHhhhhcccCCceeeeeec--------ceeEEEEeeccchHHH
Confidence            1                  1237899999999999999999999999999999974        5899999999999999


Q ss_pred             HHHhcCCeeeCCeEEEEEEecCCC
Q 007742          380 QSALNGKLEIVGRTLKVSSVTDHV  403 (591)
Q Consensus       380 ~~~l~g~~~~~g~~l~v~~~~~~~  403 (591)
                      +..|+|+ +|.|+.++|...+...
T Consensus       129 ir~l~~~-~~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen  129 IRGLDNT-EFQGKRMHVQLSTSRL  151 (346)
T ss_pred             Hhccccc-ccccceeeeeeecccc
Confidence            9999997 7999999999877554

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

Probab=99.83  E-value=2.8e-20  Score=188.68  Aligned_cols=174  Identities=30%  Similarity=0.476  Sum_probs=146.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC---CCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS---RRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~---g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ++|||.||++..|.++|..+|...|.|.++.|...+..   -.|.|||||+|.+.++|+.|+ .|+|+.|.|+.|.|..+
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            44999999999999999999999999999988775532   136799999999999999999 68999999999999988


Q ss_pred             ccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHH
Q 007742          297 EAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHA  376 (591)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a  376 (591)
                      ...+..       ..+.........+.|+|.|||+.++..+|+.+|..||.|..|.|+.....+..+|||||+|.++.+|
T Consensus       596 ~~k~~~-------~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea  668 (725)
T KOG0110|consen  596 ENKPAS-------TVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREA  668 (725)
T ss_pred             cCcccc-------ccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHH
Confidence            611110       0111112222257999999999999999999999999999999998755677799999999999999


Q ss_pred             HHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          377 KAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       377 ~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      .+|+.+|.++ .|.|+.|.+.|++..
T Consensus       669 ~nA~~al~ST-HlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  669 KNAFDALGST-HLYGRRLVLEWAKSD  693 (725)
T ss_pred             HHHHHhhccc-ceechhhheehhccc
Confidence            9999999986 599999999998754

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

Probab=99.81  E-value=4.6e-19  Score=158.69  Aligned_cols=252  Identities=25%  Similarity=0.401  Sum_probs=153.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC--eEEEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG--RTLKVSS  398 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g--~~l~v~~  398 (591)
                      .+.|||+-|...-.|++++.+|.+||.|.+|.+.... .|.++|+|||+|.+..+|..||..|||.-.+-|  ..|.|.+
T Consensus        19 drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   19 DRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             chhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            4899999999999999999999999999999999886 889999999999999999999999999644555  5778888


Q ss_pred             ecCCCCCC-----cccccCCCCCCCCCCCccc--cHHHHHHHHHHhh-----------------------------hcCC
Q 007742          399 VTDHVGTQ-----DTAAKSADFDDDDGGGLAL--NAQSRALLMQKLD-----------------------------RTGI  442 (591)
Q Consensus       399 ~~~~~~~~-----~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~-----------------------------~~~~  442 (591)
                      +.......     .....-.-+..   ..+.+  .....+.++++..                             ..+.
T Consensus        98 ADTdkER~lRRMQQma~qlGm~~P---l~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl  174 (371)
T KOG0146|consen   98 ADTDKERTLRRMQQMAGQLGMFNP---LALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGL  174 (371)
T ss_pred             ccchHHHHHHHHHHHHHHhcccCc---cccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhccc
Confidence            75432211     11111111111   11111  1111111111100                             0000


Q ss_pred             c-ccc-CCc-CCCCCcccCccccccccccCcCCCCC---------------------CC--CCCC---------------
Q 007742          443 A-TSI-AGS-LGVAPAVNGSAVNQQAISLPVVGQPA---------------------VP--VPAV---------------  481 (591)
Q Consensus       443 ~-~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------~~--~~~~---------------  481 (591)
                      . ..+ +.. ...++.+.............+.|..+                     ++  .+.+               
T Consensus       175 ~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~  254 (371)
T KOG0146|consen  175 AAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYA  254 (371)
T ss_pred             ccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHh
Confidence            0 000 000 00000000000000000000011000                     00  0000               


Q ss_pred             -CC-----C---ccc---cccc--cccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEE--e---c
Q 007742          482 -TA-----P---VIP---NMAA--EFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYV--D---K  542 (591)
Q Consensus       482 -~~-----~---~~~---~~~~--~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l--~---~  542 (591)
                       ..     +   .+|   ....  ...++..+.|||.+|  |.+..        ..+|..+|-.||.|++.++  +   .
T Consensus       255 Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHL--PQEFg--------DaEliQmF~PFGhivSaKVFvDRATN  324 (371)
T KOG0146|consen  255 AAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHL--PQEFG--------DAELIQMFLPFGHIVSAKVFVDRATN  324 (371)
T ss_pred             hhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeC--chhhc--------cHHHHHHhccccceeeeeeeehhccc
Confidence             00     0   000   0000  114677899999999  77776        5789999999999998765  2   3


Q ss_pred             CCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchhhh
Q 007742          543 RSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYE  586 (591)
Q Consensus       543 ~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~  586 (591)
                      .+++|+||.|.|+.+|+.||.+|||..|+=++|+|.+-.++.-+
T Consensus       325 QSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkdan  368 (371)
T KOG0146|consen  325 QSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDAN  368 (371)
T ss_pred             cccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCccccC
Confidence            47999999999999999999999999999999999998877643

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

Probab=99.80  E-value=2.4e-19  Score=162.75  Aligned_cols=147  Identities=25%  Similarity=0.415  Sum_probs=131.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      -.|||+|||..+++.+|+.+|++||+|..|.|+++        |+||...+...|..||..|||. .|+|..|.|.-++.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgY-tLhg~nInVeaSks   73 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGY-TLHGVNINVEASKS   73 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccc-eecceEEEEEeccc
Confidence            47999999999999999999999999999999854        8999999999999999999995 89999999986643


Q ss_pred             CCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCC
Q 007742          402 HVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAV  481 (591)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (591)
                      +                                                                               
T Consensus        74 K-------------------------------------------------------------------------------   74 (346)
T KOG0109|consen   74 K-------------------------------------------------------------------------------   74 (346)
T ss_pred             c-------------------------------------------------------------------------------
Confidence            1                                                                               


Q ss_pred             CCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHH
Q 007742          482 TAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASA  561 (591)
Q Consensus       482 ~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A  561 (591)
                                   ..++..|+|.||  ..+++        -++|+..|++||.|+.+.|.   ++++||.|.-.++|..|
T Consensus        75 -------------sk~stkl~vgNi--s~tct--------n~ElRa~fe~ygpviecdiv---kdy~fvh~d~~eda~~a  128 (346)
T KOG0109|consen   75 -------------SKASTKLHVGNI--SPTCT--------NQELRAKFEKYGPVIECDIV---KDYAFVHFDRAEDAVEA  128 (346)
T ss_pred             -------------CCCccccccCCC--Ccccc--------CHHHhhhhcccCCceeeeee---cceeEEEEeeccchHHH
Confidence                         234557999999  55666        58899999999999999888   67999999999999999


Q ss_pred             HHHhcccccCCeEEEEEEeCc
Q 007742          562 QRAMHMRWFARRLISAIFMKP  582 (591)
Q Consensus       562 ~~~l~g~~~~g~~l~v~~~~~  582 (591)
                      +..|+|+.|.|++|+|++.+-
T Consensus       129 ir~l~~~~~~gk~m~vq~sts  149 (346)
T KOG0109|consen  129 IRGLDNTEFQGKRMHVQLSTS  149 (346)
T ss_pred             Hhcccccccccceeeeeeecc
Confidence            999999999999999998654

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

Probab=99.79  E-value=2.1e-17  Score=161.30  Aligned_cols=170  Identities=24%  Similarity=0.313  Sum_probs=132.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      ....|-+.+|||.+|+++|.++|..++ |.++.+.  ..+|+..|-|||+|.+.+++.+||+.+...+..+-|.|-.+..
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~--r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIP--RRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEe--ccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCC
Confidence            456788999999999999999999994 6665444  4568899999999999999999999999999999999977654


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEeccCCCCCcccEEEEEeCCHHHHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVEL-VQLPLDIETGQCKGFGFVQFAQLEHAK  377 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~-v~i~~~~~~~~~~g~a~Vef~~~~~a~  377 (591)
                      ............     ......-.|.|++||+.|++++|.++|+..-.+.. |.++.+. .+.+.|.|||+|.+.+.|+
T Consensus        86 ~e~d~~~~~~g~-----~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae  159 (510)
T KOG4211|consen   86 AEADWVMRPGGP-----NSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAE  159 (510)
T ss_pred             ccccccccCCCC-----CCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHH
Confidence            433221111110     11123468999999999999999999999876655 5565554 6779999999999999999


Q ss_pred             HHHHHhcCCeeeCCeEEEEEEe
Q 007742          378 AAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       378 ~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +||+....  .|.-+-|.|-.+
T Consensus       160 ~Al~rhre--~iGhRYIEvF~S  179 (510)
T KOG4211|consen  160 IALGRHRE--NIGHRYIEVFRS  179 (510)
T ss_pred             HHHHHHHH--hhccceEEeehh
Confidence            99965544  477788888654

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

Probab=99.79  E-value=3.7e-17  Score=155.25  Aligned_cols=283  Identities=20%  Similarity=0.241  Sum_probs=195.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCe--eEEeccC-
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQ--PVMVKPS-  296 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~--~i~v~~~-  296 (591)
                      -.++|.|+-+.+|-+-|.++|+.||.|..|..+..-+    .=.|+|+|.+.+.|+.|- .|+|+.|..-  +|+|.++ 
T Consensus       151 Lr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn----~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sk  226 (492)
T KOG1190|consen  151 LRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNN----GFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSK  226 (492)
T ss_pred             EEEEeccceeeeEHHHHHHHHhhcceeEEEEEEeccc----chhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhh
Confidence            4678999999999999999999999999887664322    235899999999999998 7999998653  4444322 


Q ss_pred             ---------ccccccccccCCC-C-----------------------------CC----CC-CCCCC--CCceEEEcCCC
Q 007742          297 ---------EAEKNLVQSNTSA-G-----------------------------GT----AT-GPYGA--IDRKLYVGNLH  330 (591)
Q Consensus       297 ---------~~~~~~~~~~~~~-~-----------------------------~~----~~-~~~~~--~~~~l~v~nl~  330 (591)
                               +.+.........+ +                             +.    .. +....  .+..|.|.||.
T Consensus       227 lt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln  306 (492)
T KOG1190|consen  227 LTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLN  306 (492)
T ss_pred             cccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCc
Confidence                     1110000000000 0                             00    00 00011  14678888885


Q ss_pred             -CCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCCCCCCccc
Q 007742          331 -FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTA  409 (591)
Q Consensus       331 -~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~  409 (591)
                       ..+|.+.|..+|.-||.|..|.|+.++.     -.|+|+|.+...|..|+..|+|. .+.|++|+|.+++-..-.....
T Consensus       307 ~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~-~l~gk~lrvt~SKH~~vqlp~e  380 (492)
T KOG1190|consen  307 EEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGH-KLYGKKLRVTLSKHTNVQLPRE  380 (492)
T ss_pred             hhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcc-eecCceEEEeeccCccccCCCC
Confidence             5689999999999999999999998763     46999999999999999999995 7999999999876432111000


Q ss_pred             -ccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCCCCCcc--
Q 007742          410 -AKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVI--  486 (591)
Q Consensus       410 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  486 (591)
                       ....++                               ...                            ....+...+  
T Consensus       381 gq~d~gl-------------------------------T~d----------------------------y~~spLhrfkk  401 (492)
T KOG1190|consen  381 GQEDQGL-------------------------------TKD----------------------------YGNSPLHRFKK  401 (492)
T ss_pred             CCccccc-------------------------------ccc----------------------------CCCCchhhccC
Confidence             000000                               000                            000000001  


Q ss_pred             ccccccc-cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEE-EecCCCeeEEEEeCCHHHHHHHHHH
Q 007742          487 PNMAAEF-IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIY-VDKRSAGFVYLRFESTEAAASAQRA  564 (591)
Q Consensus       487 ~~~~~~~-~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~-l~~~~~g~afV~F~~~e~A~~A~~~  564 (591)
                      |...+.. ..+|+.+|.+.|+  |...+        +++|+.+|...|.+.+.+ .-......|++++.++|+|..|+-.
T Consensus       402 pgsKN~~ni~PpsatlHlsni--p~svs--------ee~lk~~f~~~g~~vkafkff~kd~kmal~q~~sveeA~~ali~  471 (492)
T KOG1190|consen  402 PGSKNYQNIFPPSATLHLSNI--PPSVS--------EEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEEAIQALID  471 (492)
T ss_pred             cccccccccCCchhheeeccC--Ccccc--------hhHHHHhhhcCCceEEeeeecCCCcceeecccCChhHhhhhccc
Confidence            0011111 3467789999999  88777        899999999999876554 4445567999999999999999999


Q ss_pred             hcccccCCe-EEEEEEeCc
Q 007742          565 MHMRWFARR-LISAIFMKP  582 (591)
Q Consensus       565 l~g~~~~g~-~l~v~~~~~  582 (591)
                      |++..+++. .|+|+|.+-
T Consensus       472 ~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  472 LHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             cccccCCCCceEEEEeecc
Confidence            999999765 799999753

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

Probab=99.77  E-value=2.7e-18  Score=160.29  Aligned_cols=169  Identities=20%  Similarity=0.461  Sum_probs=137.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      +.|||+.|.+.+.++.|+..|.+||+|++|.|.+++.+++.+|||||||.-++.|..|++.|||. .++|+.|+|.....
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~-mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQ-MLGGRNIKVGRPSN  192 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccc-cccCccccccCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999997 59999999974310


Q ss_pred             CCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCC
Q 007742          402 HVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAV  481 (591)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (591)
                                           .+....-...+....                                            
T Consensus       193 ---------------------mpQAQpiID~vqeeA--------------------------------------------  207 (544)
T KOG0124|consen  193 ---------------------MPQAQPIIDMVQEEA--------------------------------------------  207 (544)
T ss_pred             ---------------------CcccchHHHHHHHHH--------------------------------------------
Confidence                                 000000000010000                                            


Q ss_pred             CCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----CCeeEEEEeCCHH
Q 007742          482 TAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----SAGFVYLRFESTE  556 (591)
Q Consensus       482 ~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~~g~afV~F~~~e  556 (591)
                                    ..-+.|+|..+ .|. ++        ++||+.+|.-||.|++|.|.+.     .+||+||+|.+.+
T Consensus       208 --------------k~fnRiYVaSv-HpD-LS--------e~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~q  263 (544)
T KOG0124|consen  208 --------------KKFNRIYVASV-HPD-LS--------ETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQ  263 (544)
T ss_pred             --------------HhhheEEeeec-CCC-cc--------HHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEecccc
Confidence                          01125888887 343 33        7899999999999999999543     4799999999999


Q ss_pred             HHHHHHHHhcccccCCeEEEEEEe
Q 007742          557 AAASAQRAMHMRWFARRLISAIFM  580 (591)
Q Consensus       557 ~A~~A~~~l~g~~~~g~~l~v~~~  580 (591)
                      +...|+..||-.-++|+-|.|.-+
T Consensus       264 s~~eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  264 SQSEAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             chHHHhhhcchhhcccceEecccc
Confidence            999999999999999999998653

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

Probab=99.76  E-value=1.1e-17  Score=167.11  Aligned_cols=151  Identities=24%  Similarity=0.389  Sum_probs=133.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       323 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      .|||+   +.+|+..|+++|+++|+|.+|.+..+. +  +-|||||.|.++++|..||..||.. .+.|++|+|.|... 
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~-~~~~~~~rim~s~r-   74 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFD-VLKGKPIRIMWSQR-   74 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCc-ccCCcEEEeehhcc-
Confidence            58888   899999999999999999999999997 6  9999999999999999999999997 59999999987631 


Q ss_pred             CCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCCC
Q 007742          403 VGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVT  482 (591)
Q Consensus       403 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  482 (591)
                                                                                                      
T Consensus        75 --------------------------------------------------------------------------------   74 (369)
T KOG0123|consen   75 --------------------------------------------------------------------------------   74 (369)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC---CCeeEEEEeCCHHHHH
Q 007742          483 APVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR---SAGFVYLRFESTEAAA  559 (591)
Q Consensus       483 ~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~---~~g~afV~F~~~e~A~  559 (591)
                                    ....|+|+||  +..++        ..+|.++|+.||.|++|++...   ++|+ ||+|.+.++|.
T Consensus        75 --------------d~~~~~i~nl--~~~~~--------~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~  129 (369)
T KOG0123|consen   75 --------------DPSLVFIKNL--DESID--------NKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAK  129 (369)
T ss_pred             --------------CCceeeecCC--CcccC--------cHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHH
Confidence                          0112999999  55555        5899999999999999998543   6788 99999999999


Q ss_pred             HHHHHhcccccCCeEEEEEEeCchhhh
Q 007742          560 SAQRAMHMRWFARRLISAIFMKPEDYE  586 (591)
Q Consensus       560 ~A~~~l~g~~~~g~~l~v~~~~~~~~~  586 (591)
                      +|+..|||..+.|+.|.|..+..+...
T Consensus       130 ~ai~~~ng~ll~~kki~vg~~~~~~er  156 (369)
T KOG0123|consen  130 KAIEKLNGMLLNGKKIYVGLFERKEER  156 (369)
T ss_pred             HHHHHhcCcccCCCeeEEeeccchhhh
Confidence            999999999999999999988776654

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

Probab=99.76  E-value=3.5e-18  Score=164.09  Aligned_cols=178  Identities=25%  Similarity=0.398  Sum_probs=153.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      +.++|||++|+|.+|++.|+..|.+||.|.++.+++|+.+++++||+||+|.+++.+.++|..-.+.|.|+.|.+..+.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            57999999999999999999999999999999999999999999999999999999999998888899999998876654


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA  378 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~  378 (591)
                      ..........          .....|+|++||..+++.++++.|++||.|..+.++.+..+...+||+||.|.+.+.+.+
T Consensus        85 r~~~~~~~~~----------~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdk  154 (311)
T KOG4205|consen   85 REDQTKVGRH----------LRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDK  154 (311)
T ss_pred             cccccccccc----------cceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccce
Confidence            3322221110          134799999999999999999999999999999999999899999999999999999998


Q ss_pred             HHHHhcCCeeeCCeEEEEEEecCCCCCCcc
Q 007742          379 AQSALNGKLEIVGRTLKVSSVTDHVGTQDT  408 (591)
Q Consensus       379 a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~  408 (591)
                      ++ .+.- ..|.|++|.|..+.+.......
T Consensus       155 v~-~~~f-~~~~gk~vevkrA~pk~~~~~~  182 (311)
T KOG4205|consen  155 VT-LQKF-HDFNGKKVEVKRAIPKEVMQST  182 (311)
T ss_pred             ec-ccce-eeecCceeeEeeccchhhcccc
Confidence            87 3444 4699999999998877654443

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

Probab=99.74  E-value=1.1e-17  Score=149.81  Aligned_cols=179  Identities=29%  Similarity=0.464  Sum_probs=141.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCc-cCCe--eEEec
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQL-LLGQ--PVMVK  294 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~-i~g~--~i~v~  294 (591)
                      ..++|||+.|...-.|+|++.+|..||.|.+|.+.+... |.++|||||.|.+.-+|.+|| .|+|.. +.|-  .|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            468999999999999999999999999999999988765 899999999999999999999 688775 5553  44442


Q ss_pred             cCcccccc------------------------------------------------------------------------
Q 007742          295 PSEAEKNL------------------------------------------------------------------------  302 (591)
Q Consensus       295 ~~~~~~~~------------------------------------------------------------------------  302 (591)
                      ++...+..                                                                        
T Consensus        97 ~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A  176 (371)
T KOG0146|consen   97 FADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAA  176 (371)
T ss_pred             eccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhccccc
Confidence            21111100                                                                        


Q ss_pred             ----ccc--cCCCC--------------------------C---------------------------------------
Q 007742          303 ----VQS--NTSAG--------------------------G---------------------------------------  311 (591)
Q Consensus       303 ----~~~--~~~~~--------------------------~---------------------------------------  311 (591)
                          ..+  ..++.                          +                                       
T Consensus       177 ~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aa  256 (371)
T KOG0146|consen  177 APVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAA  256 (371)
T ss_pred             CCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhh
Confidence                000  00000                          0                                       


Q ss_pred             -------------------CCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCC
Q 007742          312 -------------------TATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ  372 (591)
Q Consensus       312 -------------------~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~  372 (591)
                                         ......++..+.|||..||....+.+|.++|-+||.|.+.+++.|..|+.+++|+||.|.+
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDN  336 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDN  336 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCC
Confidence                               0000122335899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          373 LEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       373 ~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +.+|+.||++||| +.|+=+.|+|...
T Consensus       337 p~SaQaAIqAMNG-FQIGMKRLKVQLK  362 (371)
T KOG0146|consen  337 PASAQAAIQAMNG-FQIGMKRLKVQLK  362 (371)
T ss_pred             chhHHHHHHHhcc-hhhhhhhhhhhhc
Confidence            9999999999999 5788888887654

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

Probab=99.73  E-value=1.7e-16  Score=140.78  Aligned_cols=206  Identities=22%  Similarity=0.350  Sum_probs=145.2

Q ss_pred             ceEEEcCCCCCCCHHHHHH----HhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          322 RKLYVGNLHFNMTETQLRK----LFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~----~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      .+|||.||+..+..++|+.    +|+.||.|..|....   +...+|.|||.|.+++.|..|+.+|+| +.|-|++++|.
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~g-fpFygK~mriq   85 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQG-FPFYGKPMRIQ   85 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcC-CcccCchhhee
Confidence            5999999999999988777    999999999988874   667899999999999999999999999 57999999999


Q ss_pred             EecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCC
Q 007742          398 SVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVP  477 (591)
Q Consensus       398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  477 (591)
                      |++...+.......  .+........   ..       .+..          .+.+...++.....             .
T Consensus        86 yA~s~sdii~~~~~--~~v~~~~k~~---~~-------~~~~----------~~~~~~~ng~~~~~-------------~  130 (221)
T KOG4206|consen   86 YAKSDSDIIAQAPG--TFVEKEKKIN---GE-------ILAR----------IKQPLDTNGHFYNM-------------N  130 (221)
T ss_pred             cccCccchhhccCc--eeccccCccc---cc-------cccc----------cCCccccccccccc-------------c
Confidence            99876554333211  0000000000   00       0000          00000000000000             0


Q ss_pred             CCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHH
Q 007742          478 VPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEA  557 (591)
Q Consensus       478 ~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~  557 (591)
                      .....+| .    .....+|..+|++.||  |.+++        .+.|..+|..|.....|.+.....+.|||+|.+...
T Consensus       131 ~~~~p~p-~----~~~~~ppn~ilf~~ni--P~es~--------~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~  195 (221)
T KOG4206|consen  131 RMNLPPP-F----LAQMAPPNNILFLTNI--PSESE--------SEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQ  195 (221)
T ss_pred             cccCCCC-c----cccCCCCceEEEEecC--Ccchh--------HHHHHHHHhhCcccceeEeccCCCceeEEecchhhh
Confidence            0000000 0    1223577889999999  77776        788889999999888888877789999999999999


Q ss_pred             HHHHHHHhcccccC-CeEEEEEEeC
Q 007742          558 AASAQRAMHMRWFA-RRLISAIFMK  581 (591)
Q Consensus       558 A~~A~~~l~g~~~~-g~~l~v~~~~  581 (591)
                      |..|...|.|..+- .+.|.|.|+.
T Consensus       196 a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  196 ASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             hHHHhhhhccceeccCceEEecccC
Confidence            99999999999986 8999998875

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

Probab=99.72  E-value=2.5e-16  Score=139.78  Aligned_cols=173  Identities=21%  Similarity=0.390  Sum_probs=139.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHH----HHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEE
Q 007742          218 RDQRTVFAYQMPLKATERDVYE----FFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVM  292 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~----~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~  292 (591)
                      .++.+|||.||+..+..++|+.    +|++||.|++|....   |.+.+|.|||.|.+++.|..|+ .|+|..+.|++++
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3445999999999999988877    999999999998874   5678999999999999999999 7999999999999


Q ss_pred             eccCccccccccccC--------------------CC--CCC--------C----CCCCCCCCceEEEcCCCCCCCHHHH
Q 007742          293 VKPSEAEKNLVQSNT--------------------SA--GGT--------A----TGPYGAIDRKLYVGNLHFNMTETQL  338 (591)
Q Consensus       293 v~~~~~~~~~~~~~~--------------------~~--~~~--------~----~~~~~~~~~~l~v~nl~~~~~~~~l  338 (591)
                      |+++..+........                    +.  .+.        .    .....+++..+++.|||..++.+.|
T Consensus        84 iqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l  163 (221)
T KOG4206|consen   84 IQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEML  163 (221)
T ss_pred             eecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHH
Confidence            988765443222100                    00  000        0    0223566789999999999999999


Q ss_pred             HHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC-CeEEEEEEe
Q 007742          339 RKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV-GRTLKVSSV  399 (591)
Q Consensus       339 ~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~-g~~l~v~~~  399 (591)
                      ..+|+.|.....|.++...     .++|||+|.+...|..|.+.|+|. .|- ..++.|.++
T Consensus       164 ~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~-~it~~~~m~i~~a  219 (221)
T KOG4206|consen  164 SDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGF-KITKKNTMQITFA  219 (221)
T ss_pred             HHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccc-eeccCceEEeccc
Confidence            9999999999999987654     679999999999999999999994 454 677777665

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.70  E-value=5.8e-17  Score=163.07  Aligned_cols=180  Identities=25%  Similarity=0.336  Sum_probs=144.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      ...++|++||..+++.++.+++..||.+....++.+..+|.++||||.+|.++..+..|+ .|||+.+++.+|.|+.+..
T Consensus       289 ~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~  368 (500)
T KOG0120|consen  289 PNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIV  368 (500)
T ss_pred             cchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhc
Confidence            477999999999999999999999999999999999999999999999999999999999 6999999999999986654


Q ss_pred             ccccccccCC-----CC---CCCCCCCCCCCceEEEcCCCC--CC-CH-------HHHHHHhccCCCeeEEEEeccCC--
Q 007742          299 EKNLVQSNTS-----AG---GTATGPYGAIDRKLYVGNLHF--NM-TE-------TQLRKLFEPFGPVELVQLPLDIE--  358 (591)
Q Consensus       299 ~~~~~~~~~~-----~~---~~~~~~~~~~~~~l~v~nl~~--~~-~~-------~~l~~~f~~~g~i~~v~i~~~~~--  358 (591)
                      .........+     ..   .......+.++..|++.|+-.  .+ .+       ++|+..|.+||.|..|.++.+-.  
T Consensus       369 g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~  448 (500)
T KOG0120|consen  369 GASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDE  448 (500)
T ss_pred             cchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCC
Confidence            4333222222     11   111244566678888888832  11 11       45667788999999999987721  


Q ss_pred             -CCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          359 -TGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       359 -~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                       ...+.|-+||+|.+.++++.|+++|+|. .|.|+.|.+.|..
T Consensus       449 ~~~~G~GkVFVefas~ed~qrA~~~L~Gr-KF~nRtVvtsYyd  490 (500)
T KOG0120|consen  449 NPVPGTGKVFVEFADTEDSQRAMEELTGR-KFANRTVVASYYD  490 (500)
T ss_pred             CcCCCcccEEEEecChHHHHHHHHHccCc-eeCCcEEEEEecC
Confidence             2345788999999999999999999997 7999999998864

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.69  E-value=6.8e-16  Score=145.36  Aligned_cols=296  Identities=20%  Similarity=0.239  Sum_probs=197.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCccc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~~  299 (591)
                      ...|-.++|||..++.+|..+|...........+.....|..-|.|.|.|.+.+.-..|++.+.+.+.++.|.|-.+...
T Consensus        60 ~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~ge  139 (508)
T KOG1365|consen   60 NVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATGE  139 (508)
T ss_pred             ceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCch
Confidence            35566899999999999999998764443333343334578889999999999999999999999999999999766554


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccC----CCeeEEEEeccCCCCCcccEEEEEeCCHHH
Q 007742          300 KNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPF----GPVELVQLPLDIETGQCKGFGFVQFAQLEH  375 (591)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~----g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~  375 (591)
                      ......................-.|.+++||+++++.++.++|.+.    |..+.|.++... .|...|-|||.|...++
T Consensus       140 ~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~  218 (508)
T KOG1365|consen  140 EFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEED  218 (508)
T ss_pred             hheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHH
Confidence            4433332222222222222223578899999999999999999743    234445554443 78889999999999999


Q ss_pred             HHHHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCc
Q 007742          376 AKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPA  455 (591)
Q Consensus       376 a~~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  455 (591)
                      |..|+..-.+  .++.+-|.+-.++                             .+...+.++..... .+....+.+. 
T Consensus       219 aq~aL~khrq--~iGqRYIElFRST-----------------------------aaEvqqvlnr~~s~-pLi~~~~sp~-  265 (508)
T KOG1365|consen  219 AQFALRKHRQ--NIGQRYIELFRST-----------------------------AAEVQQVLNREVSE-PLIPGLTSPL-  265 (508)
T ss_pred             HHHHHHHHHH--HHhHHHHHHHHHh-----------------------------HHHHHHHHHhhccc-cccCCCCCCC-
Confidence            9999965444  2455555443322                             12333333332211 0000000000 


Q ss_pred             ccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccce
Q 007742          456 VNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRV  535 (591)
Q Consensus       456 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V  535 (591)
                                            +++.+....|      ......||.+.+|  |++.+        .++|.++|..|-.-
T Consensus       266 ----------------------~p~~p~~~~p------~~~~kdcvRLRGL--Py~At--------vEdIL~FlgdFa~~  307 (508)
T KOG1365|consen  266 ----------------------LPGGPARLVP------PTRSKDCVRLRGL--PYEAT--------VEDILDFLGDFATD  307 (508)
T ss_pred             ----------------------CCCCccccCC------CCCCCCeeEecCC--Chhhh--------HHHHHHHHHHHhhh
Confidence                                  0000000000      1223679999999  99887        89999999988643


Q ss_pred             EE---EEE----ecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchhhhh
Q 007742          536 KH---IYV----DKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEA  587 (591)
Q Consensus       536 ~~---v~l----~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  587 (591)
                      +.   |.+    .+.+.|.|||+|.+.|.|..|...-+.+...++-|.|--+.-+++++
T Consensus       308 i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~eeln~  366 (508)
T KOG1365|consen  308 IRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEELNE  366 (508)
T ss_pred             cccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHHHHH
Confidence            32   333    34568999999999999999999888888889989888777776663

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

Probab=99.69  E-value=1.4e-15  Score=129.10  Aligned_cols=171  Identities=21%  Similarity=0.314  Sum_probs=132.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ...++|||+|||.+|.+.+|.++|-+||.|..|.|....   ...+||||+|.++-+|..|| ..+|..+.|..|.|..+
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            346899999999999999999999999999999886432   34689999999999999999 69999999999999887


Q ss_pred             ccccccccccCC------CCCCC----CCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEE
Q 007742          297 EAEKNLVQSNTS------AGGTA----TGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFG  366 (591)
Q Consensus       297 ~~~~~~~~~~~~------~~~~~----~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a  366 (591)
                      ............      .+++.    .++..-....|+|.+||+....++|+..+.+.|.|-...+.++       |++
T Consensus        81 rggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~G  153 (241)
T KOG0105|consen   81 RGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVG  153 (241)
T ss_pred             cCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cce
Confidence            654421111110      00111    1122222468999999999999999999999999977777654       479


Q ss_pred             EEEeCCHHHHHHHHHHhcCC-eeeCCeEEEEEE
Q 007742          367 FVQFAQLEHAKAAQSALNGK-LEIVGRTLKVSS  398 (591)
Q Consensus       367 ~Vef~~~~~a~~a~~~l~g~-~~~~g~~l~v~~  398 (591)
                      .|+|...++++-|+..|..+ +.-.|....|..
T Consensus       154 vV~~~r~eDMkYAvr~ld~~~~~seGe~~yirv  186 (241)
T KOG0105|consen  154 VVEYLRKEDMKYAVRKLDDQKFRSEGETAYIRV  186 (241)
T ss_pred             eeeeeehhhHHHHHHhhccccccCcCcEeeEEe
Confidence            99999999999999999875 223455555544

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

Probab=99.64  E-value=2.4e-15  Score=130.44  Aligned_cols=94  Identities=23%  Similarity=0.415  Sum_probs=82.8

Q ss_pred             cccCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCcc
Q 007742          208 EVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL  286 (591)
Q Consensus       208 ~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i  286 (591)
                      .+.+.........++|||+|||+.+|+++|+++|.+||.|..|.++.+..++.++|||||+|.+.++|+.|| .||+..|
T Consensus        22 ~~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i  101 (144)
T PLN03134         22 PVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKEL  101 (144)
T ss_pred             ccccccccccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            333444444445689999999999999999999999999999999999999999999999999999999999 5999999


Q ss_pred             CCeeEEeccCccccc
Q 007742          287 LGQPVMVKPSEAEKN  301 (591)
Q Consensus       287 ~g~~i~v~~~~~~~~  301 (591)
                      .|+.|+|.++.....
T Consensus       102 ~Gr~l~V~~a~~~~~  116 (144)
T PLN03134        102 NGRHIRVNPANDRPS  116 (144)
T ss_pred             CCEEEEEEeCCcCCC
Confidence            999999998865443

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

Probab=99.63  E-value=1.7e-13  Score=129.07  Aligned_cols=296  Identities=19%  Similarity=0.197  Sum_probs=194.7

Q ss_pred             CCCCCCcEEEE--eCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC--e
Q 007742          215 DPERDQRTVFA--YQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG--Q  289 (591)
Q Consensus       215 ~~~~~~~~l~V--~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g--~  289 (591)
                      +....++.|.+  -|--+.||-+-|..+....|+|..|-|++.  +   --.|.|||.+++.|++|- .|||..|-.  -
T Consensus       115 es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--n---gVQAmVEFdsv~~AqrAk~alNGADIYsGCC  189 (494)
T KOG1456|consen  115 ESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--N---GVQAMVEFDSVEVAQRAKAALNGADIYSGCC  189 (494)
T ss_pred             CCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--c---ceeeEEeechhHHHHHHHhhcccccccccce
Confidence            33445555554  444557899999999999999999988865  2   247999999999999999 699998743  4


Q ss_pred             eEEeccCcccccccccc-----------------------------CCC-------CC----------------------
Q 007742          290 PVMVKPSEAEKNLVQSN-----------------------------TSA-------GG----------------------  311 (591)
Q Consensus       290 ~i~v~~~~~~~~~~~~~-----------------------------~~~-------~~----------------------  311 (591)
                      +|+|.++.+........                             ...       .+                      
T Consensus       190 TLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~  269 (494)
T KOG1456|consen  190 TLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYR  269 (494)
T ss_pred             eEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCc
Confidence            66665443322110000                             000       00                      


Q ss_pred             --------CCCCCCCCCCceEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHH
Q 007742          312 --------TATGPYGAIDRKLYVGNLHF-NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA  382 (591)
Q Consensus       312 --------~~~~~~~~~~~~l~v~nl~~-~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~  382 (591)
                              -......+....++|.+|.. .++.+.|..+|..||.|..|.+++.+     .|.|+||+.+....+.|+..
T Consensus       270 ~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~h  344 (494)
T KOG1456|consen  270 DGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTH  344 (494)
T ss_pred             cccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHH
Confidence                    00012233467899999985 47889999999999999999998765     56799999999999999999


Q ss_pred             hcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCcccc
Q 007742          383 LNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVN  462 (591)
Q Consensus       383 l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  462 (591)
                      ||+. .+.|.+|.|..++...-...   ++..+.+                                 +.+.+-..    
T Consensus       345 Lnn~-~lfG~kl~v~~SkQ~~v~~~---~pflLpD---------------------------------gSpSfKdy----  383 (494)
T KOG1456|consen  345 LNNI-PLFGGKLNVCVSKQNFVSPV---QPFLLPD---------------------------------GSPSFKDY----  383 (494)
T ss_pred             hccC-ccccceEEEeeccccccccC---CceecCC---------------------------------CCcchhhc----
Confidence            9995 68999999987653221110   0000000                                 00000000    


Q ss_pred             ccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccce-EEEEE-
Q 007742          463 QQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRV-KHIYV-  540 (591)
Q Consensus       463 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V-~~v~l-  540 (591)
                              .+..     ...-....+...+...+|+++|...|.  |..+|        ++.|..+|...+.. .+|.| 
T Consensus       384 --------s~Sk-----NnRFssp~qAsKNrIq~Ps~vLHffNa--P~~vt--------Ee~l~~i~nek~v~~~svkvF  440 (494)
T KOG1456|consen  384 --------SGSK-----NNRFSSPEQASKNRIQPPSNVLHFFNA--PLGVT--------EEQLIGICNEKDVPPTSVKVF  440 (494)
T ss_pred             --------cccc-----ccccCChhHhhcccccCCcceeEEecC--CCccC--------HHHHHHHhhhcCCCcceEEee
Confidence                    0000     000000011222335789999999999  99888        89999999876643 34443 


Q ss_pred             ecC--CCeeEEEEeCCHHHHHHHHHHhcccccCCe------EEEEEEeCchh
Q 007742          541 DKR--SAGFVYLRFESTEAAASAQRAMHMRWFARR------LISAIFMKPED  584 (591)
Q Consensus       541 ~~~--~~g~afV~F~~~e~A~~A~~~l~g~~~~g~------~l~v~~~~~~~  584 (591)
                      +..  ....+.++|++.++|..||..||...+.+.      +|++.|++.+-
T Consensus       441 p~kserSssGllEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKlcfsts~~  492 (494)
T KOG1456|consen  441 PLKSERSSSGLLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKLCFSTSKH  492 (494)
T ss_pred             cccccccccceeeeehHHHHHHHHHHhccccccCCCCCCCeeeeeeeccccc
Confidence            211  233569999999999999999999998653      57777776554

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

Probab=99.61  E-value=4.2e-14  Score=132.20  Aligned_cols=178  Identities=22%  Similarity=0.272  Sum_probs=136.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeE--------EEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRD--------VRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG  288 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~--------v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g  288 (591)
                      ..+..|||.|||.++|-+++.++|.+||.|..        |+|..+.. |..+|=|.+.|...+++..|+ .|++..+.|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            34577999999999999999999999998853        78888876 999999999999999999999 599999999


Q ss_pred             eeEEeccCcccccccc--------------------ccCC--CCCCCCCCCCCCCceEEEcCCCC----CCC-------H
Q 007742          289 QPVMVKPSEAEKNLVQ--------------------SNTS--AGGTATGPYGAIDRKLYVGNLHF----NMT-------E  335 (591)
Q Consensus       289 ~~i~v~~~~~~~~~~~--------------------~~~~--~~~~~~~~~~~~~~~l~v~nl~~----~~~-------~  335 (591)
                      ..|.|..+.-+.....                    ....  .+.-....-....++|.|.||-.    ..+       .
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlk  290 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLK  290 (382)
T ss_pred             cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHH
Confidence            9999975432221100                    0000  00000111122358999999932    122       3


Q ss_pred             HHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          336 TQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       336 ~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|.+.+.+||.|..|.|.    ..++.|.+.|.|.+.++|..||+.|+|++ |+|++|.......
T Consensus       291 edl~eec~K~G~v~~vvv~----d~hPdGvvtV~f~n~eeA~~ciq~m~GR~-fdgRql~A~i~DG  351 (382)
T KOG1548|consen  291 EDLTEECEKFGQVRKVVVY----DRHPDGVVTVSFRNNEEADQCIQTMDGRW-FDGRQLTASIWDG  351 (382)
T ss_pred             HHHHHHHHHhCCcceEEEe----ccCCCceeEEEeCChHHHHHHHHHhcCee-ecceEEEEEEeCC
Confidence            6777889999999999886    34568899999999999999999999995 9999999986643

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

Probab=99.60  E-value=7.1e-14  Score=118.87  Aligned_cols=182  Identities=18%  Similarity=0.222  Sum_probs=130.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ++.|||+|||.++-+.+|..+|.+||.|..|.|...   ....+||||+|.++-+|..||..-+|. .++|+.|.|.++-
T Consensus         6 ~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGY-dydg~rLRVEfpr   81 (241)
T KOG0105|consen    6 SRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGY-DYDGCRLRVEFPR   81 (241)
T ss_pred             cceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhccccc-ccCcceEEEEecc
Confidence            489999999999999999999999999999988543   224679999999999999999999995 7999999999874


Q ss_pred             CCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCC
Q 007742          401 DHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPA  480 (591)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (591)
                      -..........-   ...                              ..+                    |..   ..+
T Consensus        82 ggr~s~~~~G~y---~gg------------------------------grg--------------------Ggg---~gg  105 (241)
T KOG0105|consen   82 GGRSSSDRRGSY---SGG------------------------------GRG--------------------GGG---GGG  105 (241)
T ss_pred             CCCccccccccc---CCC------------------------------CCC--------------------CCC---CCc
Confidence            322111100000   000                              000                    000   000


Q ss_pred             CCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHH
Q 007742          481 VTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAAS  560 (591)
Q Consensus       481 ~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~  560 (591)
                      ..   .     +..-.....|+|.+|  |...+        |+||+++..+.|.|-...+.+++  .++|+|...|+...
T Consensus       106 ~r---g-----ppsrrSe~RVvVsGL--p~SgS--------WQDLKDHmReaGdvCfadv~rDg--~GvV~~~r~eDMkY  165 (241)
T KOG0105|consen  106 RR---G-----PPSRRSEYRVVVSGL--PPSGS--------WQDLKDHMREAGDVCFADVQRDG--VGVVEYLRKEDMKY  165 (241)
T ss_pred             cc---C-----CcccccceeEEEecC--CCCCc--------hHHHHHHHHhhCCeeeeeeeccc--ceeeeeeehhhHHH
Confidence            00   0     001122346999999  88777        99999999999999888887655  66999999999999


Q ss_pred             HHHHhccccc--CCeEEEEEEeCc
Q 007742          561 AQRAMHMRWF--ARRLISAIFMKP  582 (591)
Q Consensus       561 A~~~l~g~~~--~g~~l~v~~~~~  582 (591)
                      |+.+|....+  .|-+..+.....
T Consensus       166 Avr~ld~~~~~seGe~~yirv~~~  189 (241)
T KOG0105|consen  166 AVRKLDDQKFRSEGETAYIRVRGD  189 (241)
T ss_pred             HHHhhccccccCcCcEeeEEeccc
Confidence            9999988776  466665555443

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

Probab=99.57  E-value=9.1e-14  Score=121.88  Aligned_cols=231  Identities=19%  Similarity=0.234  Sum_probs=130.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecc-CCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC---CeEEEEE
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLD-IETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV---GRTLKVS  397 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~-~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~---g~~l~v~  397 (591)
                      ++|||.+||.++...+|+.+|..|-.-+...|... +.....+-+|||.|.+..+|..|+.+||| +.|+   +..|+|.
T Consensus        35 RTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNG-vrFDpE~~stLhiE  113 (284)
T KOG1457|consen   35 RTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNG-VRFDPETGSTLHIE  113 (284)
T ss_pred             ceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcC-eeeccccCceeEee
Confidence            89999999999999999999999876655555433 22223457999999999999999999999 5787   5789998


Q ss_pred             EecCCCCCCcccccCCCCCCCCCCCccccH--HHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCC
Q 007742          398 SVTDHVGTQDTAAKSADFDDDDGGGLALNA--QSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPA  475 (591)
Q Consensus       398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  475 (591)
                      .++............    ... ....+..  .+..+..............+..+...........++..... ....+.
T Consensus       114 lAKSNtK~kr~k~sg----tP~-~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~-~l~a~~  187 (284)
T KOG1457|consen  114 LAKSNTKRKRRKGSG----TPG-SSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSE-ALSAPD  187 (284)
T ss_pred             ehhcCcccccCCCCC----CCC-CCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchh-hhhhhh
Confidence            887554332211111    111 0111111  11001101111111111111111000000000000000000 000011


Q ss_pred             CCCCCCCCCccccccccc-cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEe-cCCCeeEEEEeC
Q 007742          476 VPVPAVTAPVIPNMAAEF-IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVD-KRSAGFVYLRFE  553 (591)
Q Consensus       476 ~~~~~~~~~~~~~~~~~~-~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~-~~~~g~afV~F~  553 (591)
                      ...|..+. .+....... ......+|||-||  ...++        +++|+.+|+.|-....++|. +.+..+|||+|.
T Consensus       188 ~~~P~a~a-~l~ks~q~~~~~~acstlfianl--~~~~~--------ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~  256 (284)
T KOG1457|consen  188 SKAPSANA-HLEKSSQGGSGARACSTLFIANL--GPNCT--------EDELKQLLSRYPGFHILKIRARGGMPVAFADFE  256 (284)
T ss_pred             hcCCcccc-hhhhhhcccccchhhhhHhhhcc--CCCCC--------HHHHHHHHHhCCCceEEEEecCCCcceEeecHH
Confidence            11111111 111111111 1223346999999  66666        89999999999888777773 456778999999


Q ss_pred             CHHHHHHHHHHhccccc
Q 007742          554 STEAAASAQRAMHMRWF  570 (591)
Q Consensus       554 ~~e~A~~A~~~l~g~~~  570 (591)
                      +.+.|..|+..|+|..+
T Consensus       257 ~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  257 EIEQATDAMNHLQGNLL  273 (284)
T ss_pred             HHHHHHHHHHHhhccee
Confidence            99999999999999876

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

Probab=99.57  E-value=5.6e-15  Score=132.94  Aligned_cols=160  Identities=30%  Similarity=0.501  Sum_probs=130.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      ..+||++||+.+.+.+|..+|..||.|..|.+.        .|||||+|.+.-+|..|+ .+|+..|.|-.+.|.++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            468999999999999999999999999999875        479999999999999999 79999999999888888754


Q ss_pred             cccccccCCC----CCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHH
Q 007742          300 KNLVQSNTSA----GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH  375 (591)
Q Consensus       300 ~~~~~~~~~~----~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~  375 (591)
                      ..........    ......+.......+.|.+++..+..++|...|.++|.+....+        ..+++||+|...++
T Consensus        74 ~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~d  145 (216)
T KOG0106|consen   74 RRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQED  145 (216)
T ss_pred             ccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhh
Confidence            3322111110    01112233444678899999999999999999999999854444        25689999999999


Q ss_pred             HHHHHHHhcCCeeeCCeEEEEE
Q 007742          376 AKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       376 a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      |..|+..|++. .+.|+.|.+.
T Consensus       146 a~ra~~~l~~~-~~~~~~l~~~  166 (216)
T KOG0106|consen  146 AKRALEKLDGK-KLNGRRISVE  166 (216)
T ss_pred             hhhcchhccch-hhcCceeeec
Confidence            99999999996 7999999994

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

Probab=99.55  E-value=7.7e-14  Score=121.11  Aligned_cols=82  Identities=38%  Similarity=0.692  Sum_probs=77.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      .+++|||.|||+.+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|..|+..|++. .|.|+.|.|.++
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~-~i~Gr~l~V~~a  111 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGK-ELNGRHIRVNPA  111 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEeC
Confidence            3579999999999999999999999999999999999889999999999999999999999999996 699999999998


Q ss_pred             cCC
Q 007742          400 TDH  402 (591)
Q Consensus       400 ~~~  402 (591)
                      .+.
T Consensus       112 ~~~  114 (144)
T PLN03134        112 NDR  114 (144)
T ss_pred             CcC
Confidence            654

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

Probab=99.49  E-value=6.4e-13  Score=116.60  Aligned_cols=164  Identities=21%  Similarity=0.346  Sum_probs=116.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEee-cCCCCCccceEEEEecCcchHHHHH-HHcCCccC---CeeEEe
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIM-DRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL---GQPVMV  293 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~-d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~---g~~i~v  293 (591)
                      .-++|||.+||.++...+|..+|..|--.+.+.|.. ++.....+-+|||.|.+..+|.+|| .|||..|.   +..|.|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            369999999999999999999999986555554443 2222235679999999999999999 79999874   677777


Q ss_pred             ccCccccccccccCCC---C----------------------------------C-------------------------
Q 007742          294 KPSEAEKNLVQSNTSA---G----------------------------------G-------------------------  311 (591)
Q Consensus       294 ~~~~~~~~~~~~~~~~---~----------------------------------~-------------------------  311 (591)
                      ..+.............   .                                  +                         
T Consensus       113 ElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~  192 (284)
T KOG1457|consen  113 ELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPS  192 (284)
T ss_pred             eehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCc
Confidence            5332211100000000   0                                  0                         


Q ss_pred             --------CCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHh
Q 007742          312 --------TATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL  383 (591)
Q Consensus       312 --------~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l  383 (591)
                              .........+.+|||.||.+.+++++|+.+|+.|.....++|...  .  .-+.|||+|.+.+.|..||..|
T Consensus       193 a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~--g~~vaf~~~~~~~~at~am~~l  268 (284)
T KOG1457|consen  193 ANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--G--GMPVAFADFEEIEQATDAMNHL  268 (284)
T ss_pred             ccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--C--CcceEeecHHHHHHHHHHHHHh
Confidence                    000011112579999999999999999999999976655555421  2  3457999999999999999999


Q ss_pred             cCC
Q 007742          384 NGK  386 (591)
Q Consensus       384 ~g~  386 (591)
                      +|.
T Consensus       269 qg~  271 (284)
T KOG1457|consen  269 QGN  271 (284)
T ss_pred             hcc
Confidence            985

>PF00076 RRM_1: RNA recognition motif

Probab=99.47  E-value=1.9e-13  Score=104.08  Aligned_cols=69  Identities=26%  Similarity=0.563  Sum_probs=65.5

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEE
Q 007742          223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVM  292 (591)
Q Consensus       223 l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~  292 (591)
                      |||+|||+.+|+++|.++|.+||.|..+.++.+ .++..+|||||+|.+.++|..|+. ++|..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 668899999999999999999995 999999999885

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.45  E-value=2.9e-13  Score=120.48  Aligned_cols=79  Identities=19%  Similarity=0.371  Sum_probs=74.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      -.+||||||||.++.+.|+.+|++||.|++..++.|+.||+++|||||+|.+.+.|..|++-.+..|.|+...++.+.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            4789999999999999999999999999999999999999999999999999999999998888999999988876543

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

Probab=99.45  E-value=2.1e-13  Score=122.92  Aligned_cols=166  Identities=21%  Similarity=0.378  Sum_probs=124.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ..|||++||+.+.+.+|..+|..||.|..|.|.        .||+||+|.+..+|..|+..|++. .|.|..+.|.++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~-~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGK-ELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCc-eecceeeeeecccc
Confidence            468999999999999999999999999998884        568999999999999999999997 68888888877653


Q ss_pred             CCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCC
Q 007742          402 HVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAV  481 (591)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (591)
                      ....+  .                                  .+.++..        .. .......             
T Consensus        73 ~~~~~--g----------------------------------~~~~g~r--------~~-~~~~~~~-------------   94 (216)
T KOG0106|consen   73 KRRGR--G----------------------------------RPRGGDR--------RS-DSRRYRP-------------   94 (216)
T ss_pred             ccccc--C----------------------------------CCCCCCc--------cc-hhhccCC-------------
Confidence            22111  0                                  0000000        00 0000000             


Q ss_pred             CCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHH
Q 007742          482 TAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASA  561 (591)
Q Consensus       482 ~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A  561 (591)
                                  .......|+|.|+  ...+.        +.+|.++|+.+|.+....+   ..+++||+|.+.++|..|
T Consensus        95 ------------p~~s~~r~~~~~~--~~r~~--------~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra  149 (216)
T KOG0106|consen   95 ------------PSRTHFRLIVRNL--SLRVS--------WQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRA  149 (216)
T ss_pred             ------------cccccceeeeccc--hhhhh--------HHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhc
Confidence                        0123346888888  54444        7999999999999965544   577899999999999999


Q ss_pred             HHHhcccccCCeEEEEEE
Q 007742          562 QRAMHMRWFARRLISAIF  579 (591)
Q Consensus       562 ~~~l~g~~~~g~~l~v~~  579 (591)
                      +..|+|..+.|+.|.+.+
T Consensus       150 ~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  150 LEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             chhccchhhcCceeeecc
Confidence            999999999999999943

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.44  E-value=3.9e-12  Score=122.26  Aligned_cols=228  Identities=19%  Similarity=0.269  Sum_probs=141.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhc-cCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFE-PFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~-~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      .+.+||.|||+++..++|+.+|. +.|+|..|.++.+. .++++|+|.|||+++|.+++|++.||. +.+.|++|.|.-.
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk-~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNK-YEVNGRELVVKED  121 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhh-ccccCceEEEecc
Confidence            46799999999999999999996 57899999999996 899999999999999999999999998 5899999999865


Q ss_pred             cCCCCCCccccc---CCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCC--------CC---cccCccccccc
Q 007742          400 TDHVGTQDTAAK---SADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGV--------AP---AVNGSAVNQQA  465 (591)
Q Consensus       400 ~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~---~~~~~~~~~~~  465 (591)
                      .+..-.+....-   ...+...    ...+.     -...+......... ...+.        +.   +..........
T Consensus       122 ~d~q~~~~~~~~r~g~~~f~~~----~~~q~-----G~~~l~~~g~ggG~-~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~  191 (608)
T KOG4212|consen  122 HDEQRDQYGRIVRDGGGGFGGG----GGVQG-----GNGGLNGGGGGGGD-RDRGFSRRDDDRLSRRNNTNTMSNDYNNS  191 (608)
T ss_pred             CchhhhhhhheeeccCcccccC----cceec-----ccccccccCCCCcc-ccCCCCcccccccccccCccccccccccc
Confidence            443221111100   0000000    00000     00000000000000 00000        00   00000000000


Q ss_pred             cccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEE----e
Q 007742          466 ISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYV----D  541 (591)
Q Consensus       466 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l----~  541 (591)
                      ..+..++-+        ..-+..+. .+.++....+||.||  -..+.        ...|.+.|.-.|.|..|.+    .
T Consensus       192 ~~~~lfgl~--------~~Flr~~h-~f~pPl~~k~fvanl--~~~vg--------~~kL~qvfgmAGkv~~vdf~idKe  252 (608)
T KOG4212|consen  192 SNYNLFGLS--------ASFLRSLH-IFSPPLHNKVFVANL--DYKVG--------NKKLKQVFGMAGKVQSVDFSIDKE  252 (608)
T ss_pred             hhhhcccch--------hhhhhhcc-CCCCCccceeeeecc--ccccc--------hHHHHHHhccceeeeeeceeeccc
Confidence            011111110        00011111 123455567999999  55544        5789999999999998865    3


Q ss_pred             cCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEE
Q 007742          542 KRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIF  579 (591)
Q Consensus       542 ~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~  579 (591)
                      ..+.|+|.|+|.++-+|..||..|++.-+..++.++.+
T Consensus       253 G~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  253 GNSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             cccCCeeEEEecchHHHHHHHHhhccCCCccccceeec
Confidence            45789999999999999999999998778888888776

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.43  E-value=2e-14  Score=121.99  Aligned_cols=79  Identities=29%  Similarity=0.521  Sum_probs=74.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      .+.-|||||||+.+||.||..+|++||.|++|.|++|+.||.++||||+.|.+.-+...|+ .|||..|.|+.|+|....
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            4678999999999999999999999999999999999999999999999999999999999 799999999999997553

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

Probab=99.42  E-value=8.2e-13  Score=127.26  Aligned_cols=170  Identities=23%  Similarity=0.416  Sum_probs=140.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ...|+|++|++.++++.|++.|..||.|..|.+..+..++.++||+||+|.+++....+|..-..  .|.|+.|.+..+.
T Consensus         6 ~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h--~~dgr~ve~k~av   83 (311)
T KOG4205|consen    6 SGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTH--KLDGRSVEPKRAV   83 (311)
T ss_pred             CcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeeccccc--ccCCccccceecc
Confidence            37899999999999999999999999999999999999999999999999999999988855443  5899999888765


Q ss_pred             CCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCC
Q 007742          401 DHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPA  480 (591)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (591)
                      .........                                                                       
T Consensus        84 ~r~~~~~~~-----------------------------------------------------------------------   92 (311)
T KOG4205|consen   84 SREDQTKVG-----------------------------------------------------------------------   92 (311)
T ss_pred             Ccccccccc-----------------------------------------------------------------------
Confidence            422111000                                                                       


Q ss_pred             CCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEe-----cCCCeeEEEEeCCH
Q 007742          481 VTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVD-----KRSAGFVYLRFEST  555 (591)
Q Consensus       481 ~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~-----~~~~g~afV~F~~~  555 (591)
                                   ....+..|+|..|  |..++        ++++++.|.+||.|..+.++     ...+||+||.|.+.
T Consensus        93 -------------~~~~tkkiFvGG~--~~~~~--------e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e  149 (311)
T KOG4205|consen   93 -------------RHLRTKKIFVGGL--PPDTT--------EEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSE  149 (311)
T ss_pred             -------------cccceeEEEecCc--CCCCc--------hHHHhhhhhccceeEeeEEeecccccccccceeeEeccc
Confidence                         0114568999999  88877        89999999999988888664     24689999999999


Q ss_pred             HHHHHHHHHhcccccCCeEEEEEEeCchhhhh
Q 007742          556 EAAASAQRAMHMRWFARRLISAIFMKPEDYEA  587 (591)
Q Consensus       556 e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  587 (591)
                      +.+.+++. ..-+.|+|+.|.|--|.+++-..
T Consensus       150 ~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  150 DSVDKVTL-QKFHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             cccceecc-cceeeecCceeeEeeccchhhcc
Confidence            98888876 47778999999999988887554

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.40  E-value=9.1e-12  Score=117.89  Aligned_cols=176  Identities=21%  Similarity=0.265  Sum_probs=128.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcC----CCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKA----GKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~----G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      -.|-+++||+++|+.++..+|..-    |-...|-++... .|+..|-|||.|...++|+.||..|.+.|+.+-|.+-.+
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRS  240 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            456789999999999999999643    344566666554 378999999999999999999998888888887776433


Q ss_pred             ccccc-----------cccc-cCCCCC---CCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCC-eeE--EEEeccCC
Q 007742          297 EAEKN-----------LVQS-NTSAGG---TATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGP-VEL--VQLPLDIE  358 (591)
Q Consensus       297 ~~~~~-----------~~~~-~~~~~~---~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~--v~i~~~~~  358 (591)
                      .....           .... ..+...   ....+......+|.+++||+.++.++|..+|..|.. |..  |.|..+. 
T Consensus       241 TaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-  319 (508)
T KOG1365|consen  241 TAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-  319 (508)
T ss_pred             hHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-
Confidence            22111           0000 000000   011122223579999999999999999999998863 333  6666664 


Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          359 TGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       359 ~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      .|...|.|||+|.+.+.|..|++.+++++ ...+.|.|-.+
T Consensus       320 qGrPSGeAFIqm~nae~a~aaaqk~hk~~-mk~RYiEvfp~  359 (508)
T KOG1365|consen  320 QGRPSGEAFIQMRNAERARAAAQKCHKKL-MKSRYIEVFPC  359 (508)
T ss_pred             CCCcChhhhhhhhhhHHHHHHHHHHHHhh-cccceEEEeec
Confidence            78889999999999999999999999874 56888888655

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.40  E-value=1.7e-12  Score=120.19  Aligned_cols=77  Identities=35%  Similarity=0.534  Sum_probs=71.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCccc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~~  299 (591)
                      .++|||+|||+.+|+++|+++|..||.|..|.|+.+..   .+|||||+|.+.++|..||.|||..|.|+.|.|.++...
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCC
Confidence            57999999999999999999999999999999998864   479999999999999999999999999999999987543

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.39  E-value=8.2e-13  Score=105.58  Aligned_cols=80  Identities=28%  Similarity=0.495  Sum_probs=75.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ..+++|||+||.+.+||++|.++|+.+|.|..|.|-.|+.+...-|||||+|.+.++|..|| -++|+.+..++|.|.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            35799999999999999999999999999999999999999889999999999999999999 59999999999999876


Q ss_pred             c
Q 007742          297 E  297 (591)
Q Consensus       297 ~  297 (591)
                      .
T Consensus       114 ~  114 (153)
T KOG0121|consen  114 A  114 (153)
T ss_pred             c
Confidence            4

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.39  E-value=1.3e-12  Score=99.37  Aligned_cols=69  Identities=32%  Similarity=0.591  Sum_probs=62.5

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEE
Q 007742          223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVM  292 (591)
Q Consensus       223 l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~  292 (591)
                      |||+|||+.+++++|.++|..||.|..+.+..++. |.++|+|||+|.+.++|..|+. +++..|.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999987 8999999999999999999995 566889999874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.39  E-value=4.5e-12  Score=125.73  Aligned_cols=138  Identities=32%  Similarity=0.493  Sum_probs=111.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      .++|||+|||+.+|+++|.++|..||.|..|.+..++.+|.++|||||+|.+.++|..|+ .+++..|.|+.|.|.+...
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            599999999999999999999999999999999999999999999999999999999999 6889999999999998643


Q ss_pred             --cccccccc------CCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccC
Q 007742          299 --EKNLVQSN------TSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDI  357 (591)
Q Consensus       299 --~~~~~~~~------~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~  357 (591)
                        ........      .................+++.+++..++...+..+|..+|.+..+.+....
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSK  261 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCC
Confidence              11111100      000111122233345889999999999999999999999999777665443

>PF00076 RRM_1: RNA recognition motif

Probab=99.39  E-value=2.5e-12  Score=97.85  Aligned_cols=70  Identities=43%  Similarity=0.778  Sum_probs=65.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEE
Q 007742          324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLK  395 (591)
Q Consensus       324 l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~  395 (591)
                      |||+|||..+++++|+++|+.||.|..+.+..+ ..+..+|+|||+|.+.++|..|+..|+|. .+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~-~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGK-KINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTE-EETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCC-EECccCcC
Confidence            799999999999999999999999999999887 57889999999999999999999999995 79999885

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.38  E-value=8.8e-13  Score=105.40  Aligned_cols=78  Identities=28%  Similarity=0.447  Sum_probs=74.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +.+|||+||+..++|++|+++|+.+|+|..|.|-.+..+..+.|||||+|.+.++|..||..++|. .++.++|.|.+.
T Consensus        36 S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryisgt-rLddr~ir~D~D  113 (153)
T KOG0121|consen   36 SCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGT-RLDDRPIRIDWD  113 (153)
T ss_pred             cceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccC-cccccceeeecc
Confidence            379999999999999999999999999999999999888899999999999999999999999996 799999999874

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.38  E-value=1.3e-12  Score=110.59  Aligned_cols=76  Identities=26%  Similarity=0.402  Sum_probs=70.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      .++|||+||+..+++.+|..+|..||+|.+|+|...     ..|||||+|.++-+|..|+ .|+|..|.|..|.|..+..
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            589999999999999999999999999999999875     4689999999999999999 7999999999999988765


Q ss_pred             cc
Q 007742          299 EK  300 (591)
Q Consensus       299 ~~  300 (591)
                      ..
T Consensus        85 ~~   86 (195)
T KOG0107|consen   85 RP   86 (195)
T ss_pred             Cc
Confidence            43

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.37  E-value=1.6e-12  Score=116.07  Aligned_cols=81  Identities=26%  Similarity=0.287  Sum_probs=77.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +..+|-|.||+.+++|.+|+++|.+||.|..|.|.+|+.||.++|||||.|.+-++|.+|| .|||.-+..--|.|.|+.
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            4588999999999999999999999999999999999999999999999999999999999 699999999999999987


Q ss_pred             cc
Q 007742          298 AE  299 (591)
Q Consensus       298 ~~  299 (591)
                      +.
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            64

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.36  E-value=9.2e-13  Score=106.15  Aligned_cols=82  Identities=29%  Similarity=0.424  Sum_probs=77.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ...+..|||.++....||++|.+.|..||+|.+|-|..|..||..+|||+|+|.+.++|++|+ .+||..+.|++|.|.|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            445788999999999999999999999999999999999999999999999999999999999 7999999999999998


Q ss_pred             Ccc
Q 007742          296 SEA  298 (591)
Q Consensus       296 ~~~  298 (591)
                      +-.
T Consensus       149 ~Fv  151 (170)
T KOG0130|consen  149 CFV  151 (170)
T ss_pred             EEe
Confidence            743

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.35  E-value=2.3e-12  Score=119.79  Aligned_cols=79  Identities=25%  Similarity=0.472  Sum_probs=73.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|+|.|||+...+.||+.+|.+||.|.+|.||.+..  -|||||||+|.+.++|.+|- +|||..|.|+.|.|..+.
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNER--GSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNER--GSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccC--CCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            458999999999999999999999999999999999865  48999999999999999999 799999999999998876


Q ss_pred             cc
Q 007742          298 AE  299 (591)
Q Consensus       298 ~~  299 (591)
                      ..
T Consensus       173 ar  174 (376)
T KOG0125|consen  173 AR  174 (376)
T ss_pred             hh
Confidence            54

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.34  E-value=5e-12  Score=115.00  Aligned_cols=77  Identities=30%  Similarity=0.459  Sum_probs=71.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      .+.+|||+||++.+|+++|+++|+.||.|.+|.|+.+.   ...|||||+|.+.++|..|+.|+|..|.+++|.|.+...
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcc
Confidence            45899999999999999999999999999999999884   456899999999999999999999999999999987654

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.34  E-value=9.6e-12  Score=94.53  Aligned_cols=70  Identities=50%  Similarity=0.796  Sum_probs=63.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEE
Q 007742          324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLK  395 (591)
Q Consensus       324 l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~  395 (591)
                      |+|+|||+.+++++|.++|+.+|.|..+.+..++. +..+|+|||+|.+.++|..|++.+++. .|.|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~-~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGK-EIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTE-EETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCc-EECCEEcC
Confidence            79999999999999999999999999999999875 889999999999999999999998874 79999874

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 ....

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.33  E-value=7.9e-12  Score=96.05  Aligned_cols=79  Identities=23%  Similarity=0.473  Sum_probs=72.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      .-.+-|||.|||+.+|.+++.++|.+||+|..|++-..+.|   +|.|||.|.++.+|.+|+ .|+|..+.++.+.|.+.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            34588999999999999999999999999999999877765   999999999999999999 79999999999999766


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      .+.
T Consensus        93 q~~   95 (124)
T KOG0114|consen   93 QPE   95 (124)
T ss_pred             CHH
Confidence            543

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.32  E-value=1.1e-12  Score=120.51  Aligned_cols=78  Identities=32%  Similarity=0.628  Sum_probs=74.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      -+||||.-|++.++|..|+..|+.||+|+.|.|+.++.+|+++|||||+|...-++..|.+..+|. .|+|+.|.|.+-
T Consensus       101 y~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~-~Idgrri~VDvE  178 (335)
T KOG0113|consen  101 YKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGI-KIDGRRILVDVE  178 (335)
T ss_pred             cceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCc-eecCcEEEEEec
Confidence            489999999999999999999999999999999999999999999999999999999999999995 799999999864

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

Probab=99.32  E-value=5.9e-11  Score=116.74  Aligned_cols=172  Identities=20%  Similarity=0.261  Sum_probs=124.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ...|.+.+||+.+|+++|+++|+.++ |..+.+...  +|...|-|||||.+.+++.+|+ .++-. .+..+-|.|-.+.
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Al-kkdR~-~mg~RYIEVf~~~   84 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKAL-KKDRE-SMGHRYIEVFTAG   84 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHHH-HhhHH-HhCCceEEEEccC
Confidence            36889999999999999999999996 555555443  6888999999999999999999 55553 5777888886553


Q ss_pred             CCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCC
Q 007742          401 DHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPA  480 (591)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (591)
                      .........                                                            ..+        
T Consensus        85 ~~e~d~~~~------------------------------------------------------------~~g--------   96 (510)
T KOG4211|consen   85 GAEADWVMR------------------------------------------------------------PGG--------   96 (510)
T ss_pred             Ccccccccc------------------------------------------------------------CCC--------
Confidence            211100000                                                            000        


Q ss_pred             CCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEE-EEEe----cCCCeeEEEEeCCH
Q 007742          481 VTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKH-IYVD----KRSAGFVYLRFEST  555 (591)
Q Consensus       481 ~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~-v~l~----~~~~g~afV~F~~~  555 (591)
                                 +.......+|.|.+|  |+.++        ++||.++|+.--.|.. +.++    ..+.|-|||+|++.
T Consensus        97 -----------~~s~~~d~vVRLRGL--Pfsct--------e~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sq  155 (510)
T KOG4211|consen   97 -----------PNSSANDGVVRLRGL--PFSCT--------EEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQ  155 (510)
T ss_pred             -----------CCCCCCCceEEecCC--CccCc--------HHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCH
Confidence                       000123347999999  99999        8999999997766655 2232    23688999999999


Q ss_pred             HHHHHHHHHhcccccCCeEEEEEEeCchhhhh
Q 007742          556 EAAASAQRAMHMRWFARRLISAIFMKPEDYEA  587 (591)
Q Consensus       556 e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  587 (591)
                      +.|++|+.. |...|+-+=|.|--+...++..
T Consensus       156 e~ae~Al~r-hre~iGhRYIEvF~Ss~~e~~~  186 (510)
T KOG4211|consen  156 ESAEIALGR-HRENIGHRYIEVFRSSRAEVKR  186 (510)
T ss_pred             HHHHHHHHH-HHHhhccceEEeehhHHHHHHh
Confidence            999999985 6666777778776665555544

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=99.32  E-value=3.8e-11  Score=121.92  Aligned_cols=349  Identities=15%  Similarity=0.132  Sum_probs=190.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      -...|||.+||..+++.++.++|...-.|++...+....++...+.|||+|.+.+++..|+ ..+.+.++-+.|.|....
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~  512 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIA  512 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeechh
Confidence            4578999999999999999999999988888544545556888999999999998888888 567777888888884322


Q ss_pred             cccccc---------------------------------------ccc--------------CCC-C-------------
Q 007742          298 AEKNLV---------------------------------------QSN--------------TSA-G-------------  310 (591)
Q Consensus       298 ~~~~~~---------------------------------------~~~--------------~~~-~-------------  310 (591)
                      .+....                                       ...              ... .             
T Consensus       513 ~~~m~~ek~~~~~~~lq~~~~dqre~~l~~p~~~v~~~~~~~~~~~~~~F~~~~rr~~~e~~~~~~~~n~~p~~~dN~~~  592 (944)
T KOG4307|consen  513 DYAMMMEKNGEQGIKLQQSDKDQRETALDGPIPSVSMVPSKEQRSHEDDFDKKSRRSRWENTSPIRSPNRSPLRRDNRDR  592 (944)
T ss_pred             hHHHHHHHhHHHHHHHhhhhhHHHHHhhcCCccchhhhhhhhhhccCcccccchHHHHhhhcCCccCccccccccccCCc
Confidence            111000                                       000              000 0             


Q ss_pred             --CCCCCC------CCCC--CceEEEcCCCCCCCHHHHHHHhccC-----------------------------------
Q 007742          311 --GTATGP------YGAI--DRKLYVGNLHFNMTETQLRKLFEPF-----------------------------------  345 (591)
Q Consensus       311 --~~~~~~------~~~~--~~~l~v~nl~~~~~~~~l~~~f~~~-----------------------------------  345 (591)
                        +.....      ..+.  -.++-|.|.|+.+..+.+++.|..-                                   
T Consensus       593 ~~~~~~v~~~n~p~~r~~~~~~~~~vnn~pF~m~~~~~~~~~sekn~Pa~~~~~~~~gv~~~p~v~~~~~~~l~~~r~~~  672 (944)
T KOG4307|consen  593 SRSRSPVRRRNSPRRREEHTRWCVQVNNVPFRMKDEELLEWFSEKNRPAKLTRTFYDGVASDPWVAEFSSESLMKRRSFG  672 (944)
T ss_pred             ccccCccccCCCccccchhhhhhhcccCcceeecchhhhhhhcccCCcccccccccCCCCCCcccccccccccccccCCC
Confidence              000000      0000  1466788888888888888777630                                   


Q ss_pred             -CC--------eeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCC
Q 007742          346 -GP--------VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFD  416 (591)
Q Consensus       346 -g~--------i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~  416 (591)
                       |.        +..|.-++. ......|..|++|.+....+.|+...+.. ++.+..+.+..+.................
T Consensus       673 ~g~l~tg~~lr~~~i~~~~~-~~~~~~g~~~~e~~~~~~ee~a~~~~~~~-~an~~~~fn~p~~~~gs~~~~p~~p~p~~  750 (944)
T KOG4307|consen  673 IGTLCTGRTLRLRYIDNAKA-DEILKIGDVYGEGKRQMNEEAALQHEVAE-KANPPSFFNAPAATRGSGPMPPLNPAPLP  750 (944)
T ss_pred             ccccccCcccccchhhhhhh-ccccccccceeccCCccchhHHHHHHhhh-hccCCCcccccccccccCCCCCCCCCCCC
Confidence             00        001100011 12234678899999999999999888876 68888777766554433222211111000


Q ss_pred             CCCCCCc--cc------cHHHHHHHHHH-hhhc-CCcccc-CCcCCCCCc------ccCcc--------ccccccccCcC
Q 007742          417 DDDGGGL--AL------NAQSRALLMQK-LDRT-GIATSI-AGSLGVAPA------VNGSA--------VNQQAISLPVV  471 (591)
Q Consensus       417 ~~~~~~~--~~------~~~~~~~~~~~-~~~~-~~~~~~-~~~~~~~~~------~~~~~--------~~~~~~~~~~~  471 (591)
                      .....+.  ..      .........+. .... ...... ++.-++...      ++...        +........+.
T Consensus       751 ~gg~nG~~~p~pn~~NdGapg~g~~vp~~f~~gp~~~~gp~g~gggP~~~qngP~sl~~~p~~~f~sn~p~~~gf~pg~r  830 (944)
T KOG4307|consen  751 SGGQNGMNVPPPNGFNDGAPGRGGFVPRGFSQGPGMGRGPHGGGGGPNFYQNGPNSLNNGPQGQFRSNQPNDGGFRPGFR  830 (944)
T ss_pred             CCccCCCCCCCCCCCCCCCCCcCCcCCccccCCCCCCCCCCCCCCCccccccCCcccCCCCccccCCCCCCcCCcCCccC
Confidence            0000000  00      00000000000 0000 000000 000000000      00000        00000000011


Q ss_pred             CCCC------CCCCCC---CCCccccccccccCCCc-ceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceE-EEEE
Q 007742          472 GQPA------VPVPAV---TAPVIPNMAAEFIGSPS-ECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVK-HIYV  540 (591)
Q Consensus       472 ~~~~------~~~~~~---~~~~~~~~~~~~~~~~s-~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~-~v~l  540 (591)
                      +.++      -..++.   ..+.-++........+. ++|.+.|+  |+.++        .+||.++|..|-.+- +|.+
T Consensus       831 ggpp~~g~gpg~~~g~~p~~~~~P~~~~~~~~~~pGp~V~~~~n~--Pf~v~--------l~dI~~FF~dY~~~p~sI~~  900 (944)
T KOG4307|consen  831 GGPPGRGGGPGGFQGGSPGDDSQPSQELMELIKSPGPRVLSCNNF--PFDVT--------LEDIVEFFNDYEPDPNSIRI  900 (944)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCChHHHHHhcCCCCCeEEEecCC--Ccccc--------HHHHHHHhcccccCCCceeE
Confidence            1111      111111   11112222222334444 48999999  99988        899999999997664 3333


Q ss_pred             ----ecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEE
Q 007742          541 ----DKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIF  579 (591)
Q Consensus       541 ----~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~  579 (591)
                          ....+|.|.|-|++.++|..|...|+++.|..++|.|.+
T Consensus       901 r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  901 RRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence                234689999999999999999999999999999998865

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.32  E-value=1.7e-11  Score=114.14  Aligned_cols=81  Identities=33%  Similarity=0.596  Sum_probs=74.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .+.|+|.|||+..-+.||..+|.+||+|.+|.|+.+  ...++||+||+|.+.++|.+|-..|||. .+.|++|.|..++
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt-~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGT-VVEGRKIEVNNAT  172 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcc-eeeceEEEEeccc
Confidence            489999999999999999999999999999999987  3457999999999999999999999998 4999999999988


Q ss_pred             CCCC
Q 007742          401 DHVG  404 (591)
Q Consensus       401 ~~~~  404 (591)
                      ...-
T Consensus       173 arV~  176 (376)
T KOG0125|consen  173 ARVH  176 (376)
T ss_pred             hhhc
Confidence            7743

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.30  E-value=6.4e-12  Score=106.53  Aligned_cols=75  Identities=21%  Similarity=0.388  Sum_probs=69.6

Q ss_pred             cceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEE
Q 007742          498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISA  577 (591)
Q Consensus       498 s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v  577 (591)
                      .+.|+|.||  +..++        ..+|..+|..||.|.+|.|...+.|||||+|+++-+|..|+..|+|+.|.|..|.|
T Consensus        10 ~~kVYVGnL--~~~a~--------k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rV   79 (195)
T KOG0107|consen   10 NTKVYVGNL--GSRAT--------KRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRV   79 (195)
T ss_pred             CceEEeccC--CCCcc--------hHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEE
Confidence            457999999  66666        78999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeCc
Q 007742          578 IFMKP  582 (591)
Q Consensus       578 ~~~~~  582 (591)
                      ++.+-
T Consensus        80 E~S~G   84 (195)
T KOG0107|consen   80 ELSTG   84 (195)
T ss_pred             EeecC
Confidence            98764

>PF13893 RRM_5: RNA recognition motif

Probab=99.29  E-value=1.5e-11  Score=88.68  Aligned_cols=56  Identities=30%  Similarity=0.477  Sum_probs=51.6

Q ss_pred             HHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEe
Q 007742          525 VEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFM  580 (591)
Q Consensus       525 l~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~  580 (591)
                      |.++|++||.|..+.+.....++|||+|.+.++|..|+..|||..|+|++|.|.|+
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            67899999999999997666799999999999999999999999999999999985

(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 ....

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.28  E-value=6.4e-13  Score=112.94  Aligned_cols=80  Identities=31%  Similarity=0.613  Sum_probs=76.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      .-|||+|||+.+|+.+|..+|++||.|+.|.+++++.||.++||||+.|.+.-+...|+..||| +.|.|+.|+|..+-.
T Consensus        36 A~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NG-iki~gRtirVDHv~~  114 (219)
T KOG0126|consen   36 AYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNG-IKILGRTIRVDHVSN  114 (219)
T ss_pred             eEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCC-ceecceeEEeeeccc
Confidence            6899999999999999999999999999999999999999999999999999999999999999 689999999988754


Q ss_pred             C
Q 007742          402 H  402 (591)
Q Consensus       402 ~  402 (591)
                      +
T Consensus       115 Y  115 (219)
T KOG0126|consen  115 Y  115 (219)
T ss_pred             c
Confidence            4

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.28  E-value=9.3e-12  Score=114.40  Aligned_cols=79  Identities=23%  Similarity=0.417  Sum_probs=74.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      .+-+||||+-|+++++|..|+..|..||+|..|.|+.++.||+++|||||+|.+.-+..+|. ..+|.+|.|+.|.|.+-
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            35699999999999999999999999999999999999999999999999999999999999 69999999999999654

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.28  E-value=1.1e-11  Score=107.70  Aligned_cols=82  Identities=24%  Similarity=0.419  Sum_probs=77.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      -..|.|-||.+-+|.++|..+|++||.|.+|.|..|..|+.++|||||.|....+|+.|| .|+|.+|.|+.|.|+.+..
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            378999999999999999999999999999999999999999999999999999999999 6999999999999998876


Q ss_pred             ccc
Q 007742          299 EKN  301 (591)
Q Consensus       299 ~~~  301 (591)
                      ...
T Consensus        93 gr~   95 (256)
T KOG4207|consen   93 GRP   95 (256)
T ss_pred             CCC
Confidence            655

>PLN03213 repressor of silencing 3; Provisional

Probab=99.27  E-value=1.6e-11  Score=119.83  Aligned_cols=77  Identities=17%  Similarity=0.286  Sum_probs=69.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCc--chHHHHH-HHcCCccCCeeEEec
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV--MSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~--e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      ....+||||||++.+|+++|..+|..||.|..|.|+  +.+|  +|||||+|...  .++.+|| .|||..+.|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            345899999999999999999999999999999999  4566  99999999987  6789999 699999999999997


Q ss_pred             cCcc
Q 007742          295 PSEA  298 (591)
Q Consensus       295 ~~~~  298 (591)
                      .+.+
T Consensus        84 KAKP   87 (759)
T PLN03213         84 KAKE   87 (759)
T ss_pred             eccH
Confidence            5543

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.27  E-value=1.8e-11  Score=109.53  Aligned_cols=81  Identities=38%  Similarity=0.545  Sum_probs=76.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ..+|.|.||+.++++.+|.++|.+||.|..|.|.+++.||.++|||||.|.+-++|.+||..|||. -++.-.|.|.+++
T Consensus       189 ~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~-gyd~LILrvEwsk  267 (270)
T KOG0122|consen  189 EATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGY-GYDNLILRVEWSK  267 (270)
T ss_pred             cceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCc-ccceEEEEEEecC
Confidence            468999999999999999999999999999999999999999999999999999999999999995 6888999999987


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      +.
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            64

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.26  E-value=1.2e-11  Score=107.47  Aligned_cols=80  Identities=35%  Similarity=0.552  Sum_probs=75.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ..|.|-||.+.++.++|..+|++||.|-.|.|+.+..|..++|||||.|....+|+.||.+|+|. .++|+.|.|..+..
T Consensus        14 ~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~-~ldgRelrVq~ary   92 (256)
T KOG4207|consen   14 TSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGA-VLDGRELRVQMARY   92 (256)
T ss_pred             eeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcce-eeccceeeehhhhc
Confidence            78999999999999999999999999999999999999999999999999999999999999997 59999999987764


Q ss_pred             C
Q 007742          402 H  402 (591)
Q Consensus       402 ~  402 (591)
                      .
T Consensus        93 g   93 (256)
T KOG4207|consen   93 G   93 (256)
T ss_pred             C
Confidence            3

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.24  E-value=7.2e-11  Score=90.85  Aligned_cols=80  Identities=21%  Similarity=0.384  Sum_probs=71.8

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEE--ecCCCeeEEEEeCCHHHHHHHHHHhcccccCC
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYV--DKRSAGFVYLRFESTEAAASAQRAMHMRWFAR  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l--~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g  572 (591)
                      +.-+++|+|+||  |+..|        .+++.++|.+||.|..|.|  ....+|-|||.|+++.+|.+|+.+|+|..+.+
T Consensus        15 pevnriLyirNL--p~~IT--------seemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~   84 (124)
T KOG0114|consen   15 PEVNRILYIRNL--PFKIT--------SEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDN   84 (124)
T ss_pred             hhhheeEEEecC--Ccccc--------HHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCC
Confidence            445678999999  99888        8999999999999999988  45678999999999999999999999999999


Q ss_pred             eEEEEEEeCchh
Q 007742          573 RLISAIFMKPED  584 (591)
Q Consensus       573 ~~l~v~~~~~~~  584 (591)
                      +-|.|-|..+..
T Consensus        85 ryl~vlyyq~~~   96 (124)
T KOG0114|consen   85 RYLVVLYYQPED   96 (124)
T ss_pred             ceEEEEecCHHH
Confidence            999999876543

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.23  E-value=1e-10  Score=108.54  Aligned_cols=77  Identities=25%  Similarity=0.431  Sum_probs=70.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||+.+++++|+++|+.||.|..|.|+.+..   .+|||||+|.+.++|..|| .|+|. .|.|+.|.|..+.+
T Consensus         5 rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~Al-lLnG~-~l~gr~V~Vt~a~~   79 (260)
T PLN03120          5 RTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETAL-LLSGA-TIVDQSVTITPAED   79 (260)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHH-HhcCC-eeCCceEEEEeccC
Confidence            7999999999999999999999999999999987652   4789999999999999999 69997 69999999999875


Q ss_pred             CC
Q 007742          402 HV  403 (591)
Q Consensus       402 ~~  403 (591)
                      +.
T Consensus        80 ~~   81 (260)
T PLN03120         80 YQ   81 (260)
T ss_pred             CC
Confidence            54

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.21  E-value=1.1e-11  Score=108.58  Aligned_cols=83  Identities=24%  Similarity=0.468  Sum_probs=78.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +-++|||++|...+||.-|...|-+||.|.+|.+..|-.+++.+|||||+|.-.|+|.+|| .||+..+.|+.|+|.++.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            4589999999999999999999999999999999999999999999999999999999999 699999999999999887


Q ss_pred             cccc
Q 007742          298 AEKN  301 (591)
Q Consensus       298 ~~~~  301 (591)
                      +...
T Consensus        89 P~ki   92 (298)
T KOG0111|consen   89 PEKI   92 (298)
T ss_pred             Cccc
Confidence            6543

>smart00362 RRM_2 RNA recognition motif

Probab=99.20  E-value=8.5e-11  Score=89.54  Aligned_cols=71  Identities=38%  Similarity=0.595  Sum_probs=65.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       222 ~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      +|||+|||..++.++|.++|..||.|..+.+..+.  +.++|+|||+|.+.++|..|+ .+++..+.|+.|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999998776  678899999999999999999 588899999998763

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.20  E-value=2.8e-11  Score=97.69  Aligned_cols=79  Identities=32%  Similarity=0.566  Sum_probs=75.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .-.|||.++...+++++|.+.|..||+|+.|.+..+..+|-.+|||+|+|.+.++|+.|+..|||. .+.|++|.|.||-
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~-~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGA-ELLGQNVSVDWCF  150 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccch-hhhCCceeEEEEE
Confidence            368999999999999999999999999999999999999999999999999999999999999995 7999999999874

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=99.19  E-value=3.7e-10  Score=113.05  Aligned_cols=169  Identities=21%  Similarity=0.267  Sum_probs=110.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      .....+|+|-|||..+++++|..+|..||.|..|+...     ...|..||+|.++-+|+.|+ +|++..|.|+.|+...
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~  146 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPG  146 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCC
Confidence            34569999999999999999999999999999976643     45789999999999999999 7999999999998432


Q ss_pred             CccccccccccCCC------CCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEE
Q 007742          296 SEAEKNLVQSNTSA------GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ  369 (591)
Q Consensus       296 ~~~~~~~~~~~~~~------~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Ve  369 (591)
                      ........+.....      ......+.+..-..++ +.|++.....-+..++.-+|.+.. ..     ++.-.-..|++
T Consensus       147 ~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~-g~l~P~~s~~~~~~~~~~~~~~~~-~~-----~~~~~hq~~~~  219 (549)
T KOG4660|consen  147 GARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLF-GMLSPTRSSILLEHISSVDGSSPG-RE-----TPLLNHQRFVE  219 (549)
T ss_pred             cccccchhcccchhhhhccchhhcCCCCCCcCCcce-eeeccchhhhhhhcchhccCcccc-cc-----ccchhhhhhhh
Confidence            22222211111110      0011112222112333 338887777555566666776654 22     22222367889


Q ss_pred             eCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          370 FAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       370 f~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      |.+..++..++... | +.+.+....+.+.
T Consensus       220 ~~~~~s~a~~~~~~-G-~~~s~~~~v~t~S  247 (549)
T KOG4660|consen  220 FADNRSYAFSEPRG-G-FLISNSSGVITFS  247 (549)
T ss_pred             hccccchhhcccCC-c-eecCCCCceEEec
Confidence            99888885555322 4 3466666555554

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.19  E-value=4.6e-11  Score=123.12  Aligned_cols=74  Identities=20%  Similarity=0.358  Sum_probs=69.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      -++|||||+|+..+++.||..+|+.||.|.+|.++.      .+|||||.+.+-.+|.+|| .|++..+.++.|+|.|+.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            469999999999999999999999999999999974      5889999999999999999 799999999999999985


Q ss_pred             c
Q 007742          298 A  298 (591)
Q Consensus       298 ~  298 (591)
                      .
T Consensus       494 g  494 (894)
T KOG0132|consen  494 G  494 (894)
T ss_pred             c
Confidence            4

>smart00360 RRM RNA recognition motif

Probab=99.17  E-value=1.1e-10  Score=88.60  Aligned_cols=70  Identities=39%  Similarity=0.643  Sum_probs=65.1

Q ss_pred             EeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          225 AYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       225 V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      |+|||..+++++|..+|..||.|..+.+..+..++.++|||||+|.+.++|..|+ .+++..+.|+.|.|.
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            5799999999999999999999999999998888899999999999999999999 588899999988773

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.15  E-value=2.3e-10  Score=104.34  Aligned_cols=78  Identities=21%  Similarity=0.221  Sum_probs=70.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      .+|+|+||++.+|+++|+++|+.||.|..|.|+.+.   ...|+|||+|.+.++|..|+ .|+|. .|.++.|.|..+.+
T Consensus         6 ~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa-~l~d~~I~It~~~~   80 (243)
T PLN03121          6 YTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGA-TIVDQRVCITRWGQ   80 (243)
T ss_pred             eEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCC-eeCCceEEEEeCcc
Confidence            799999999999999999999999999999999874   34689999999999999999 89997 69999999998776


Q ss_pred             CCC
Q 007742          402 HVG  404 (591)
Q Consensus       402 ~~~  404 (591)
                      +..
T Consensus        81 y~~   83 (243)
T PLN03121         81 YED   83 (243)
T ss_pred             ccc
Confidence            543

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.13  E-value=7.1e-11  Score=105.44  Aligned_cols=77  Identities=34%  Similarity=0.518  Sum_probs=71.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      -+.|||++|++.+..+.|+..|+.||.|++..|+.|+.++.++||+||+|.+.+.|..|++.-+-  .|+|++..+..+
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~p--iIdGR~aNcnlA   88 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNP--IIDGRKANCNLA   88 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCC--cccccccccchh
Confidence            37999999999999999999999999999999999999999999999999999999999977666  499998877654

>smart00362 RRM_2 RNA recognition motif

Probab=99.12  E-value=5.1e-10  Score=85.15  Aligned_cols=71  Identities=49%  Similarity=0.861  Sum_probs=65.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       323 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      +|+|.|||..++.++|.++|..||.|..+.+..+.  +.+.|+|||+|.+.++|..|+..+++. .+.|+.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~-~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGT-KLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCc-EECCEEEee
Confidence            48999999999999999999999999999988765  667899999999999999999999985 699999876

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.12  E-value=1.2e-10  Score=117.41  Aligned_cols=81  Identities=32%  Similarity=0.541  Sum_probs=77.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      +.|||||||+.+++++|..+|...|.|.+++++.|+.||..+||||++|.+.++|..|+ .|||..+.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999999999999999999999999999999 69999999999999887654


Q ss_pred             cc
Q 007742          300 KN  301 (591)
Q Consensus       300 ~~  301 (591)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=99.10  E-value=3.2e-09  Score=108.18  Aligned_cols=200  Identities=15%  Similarity=0.119  Sum_probs=125.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ..+-+.++++...+.++.++|...- |.++.|..+...+...|.+||+|....++.+|+ .-|.. .+-.+.+.|..+.+
T Consensus       312 ~y~~~~gm~fn~~~nd~rkfF~g~~-~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~-~rn~~-~~~~R~~q~~P~g~  388 (944)
T KOG4307|consen  312 YYNNYKGMEFNNDFNDGRKFFPGRN-AQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAF-TRNPS-DDVNRPFQTGPPGN  388 (944)
T ss_pred             heeeecccccccccchhhhhcCccc-ccccchhhhhcCCCcCCceEEEecCcchHHHHH-hcCch-hhhhcceeecCCCc
Confidence            3445567788888899999987652 334444444445555889999999999999998 33443 47788888877654


Q ss_pred             CCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCC
Q 007742          402 HVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAV  481 (591)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (591)
                      ............                                    .+.....+.+            +.+.. .+..
T Consensus       389 ~~~~~a~~~~~~------------------------------------~~~~~~~~~h------------g~p~~-~pr~  419 (944)
T KOG4307|consen  389 LGRNGAPPFQAG------------------------------------VPPPVIQNNH------------GRPIA-PPRA  419 (944)
T ss_pred             cccccCcccccc------------------------------------CCCCcccccC------------CCCCC-Cccc
Confidence            322111110000                                    0000000000            00000 0000


Q ss_pred             CCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEE-EEEecC----CCeeEEEEeCCHH
Q 007742          482 TAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKH-IYVDKR----SAGFVYLRFESTE  556 (591)
Q Consensus       482 ~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~-v~l~~~----~~g~afV~F~~~e  556 (591)
                      ..  .+..-.........||+|..|  |.+++        +.++..+|...-.|+. |+|...    -.+.|||.|..++
T Consensus       420 ~~--~~gq~vp~P~~ag~~lyv~~l--P~~t~--------~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~  487 (944)
T KOG4307|consen  420 MV--RPGQNVPFPGGAGGALYVFQL--PVMTP--------IVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPT  487 (944)
T ss_pred             cc--CCCCCCCCCCCccceEEeccC--Ccccc--------ccchhhhhhhhhhhhheeEeccCCcccccchhhheecccc
Confidence            00  000011223456779999999  99988        7889999998877776 666432    3578899999999


Q ss_pred             HHHHHHHHhcccccCCeEEEEEEeCchhh
Q 007742          557 AAASAQRAMHMRWFARRLISAIFMKPEDY  585 (591)
Q Consensus       557 ~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  585 (591)
                      ++..|...-+-..++.+.|.|.-+.+...
T Consensus       488 a~~~a~~~~~k~y~G~r~irv~si~~~~m  516 (944)
T KOG4307|consen  488 APLTASSVKTKFYPGHRIIRVDSIADYAM  516 (944)
T ss_pred             ccchhhhcccccccCceEEEeechhhHHH
Confidence            99999988777778888899988776654

>PLN03213 repressor of silencing 3; Provisional

Probab=99.09  E-value=3.9e-10  Score=110.36  Aligned_cols=77  Identities=26%  Similarity=0.473  Sum_probs=70.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCH--HHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQL--EHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~--~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...|||+||++.+++++|..+|..||.|..|.|++.  +|  +|||||+|.+.  .++.+||..|||. .+.|+.|+|..
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGA-EWKGR~LKVNK   84 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGC-VWKGGRLRLEK   84 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCC-eecCceeEEee
Confidence            379999999999999999999999999999999944  55  99999999987  7899999999996 79999999998


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      +++.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            8754

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.08  E-value=2.5e-10  Score=115.16  Aligned_cols=79  Identities=41%  Similarity=0.665  Sum_probs=76.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ..|||+|+|+.+++++|..+|...|.|..+.++.|..+|..+||||++|.+.++|..|+..|||. ++.|++|+|.|+..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~-~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGA-EFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCc-ccCCceEEeecccc
Confidence            78999999999999999999999999999999999999999999999999999999999999995 89999999999754

>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=99.07  E-value=9.4e-10  Score=84.17  Aligned_cols=73  Identities=41%  Similarity=0.667  Sum_probs=66.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       222 ~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      +|+|+|||+.+++++|.++|..+|.|..+.+..+..+ ...|+|||+|.+.++|..|+ .+++..+.|..+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999987664 67899999999999999999 6889889999998753

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).

>smart00360 RRM RNA recognition motif

Probab=99.07  E-value=7.4e-10  Score=83.92  Aligned_cols=70  Identities=54%  Similarity=0.814  Sum_probs=64.6

Q ss_pred             EcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          326 VGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       326 v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      |.|||..+++++|+++|..||.|..+.+..+..++.++|+|||+|.+.++|..|+..|++. .+.|+.|.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~-~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGK-ELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCC-eeCCcEEEe
Confidence            5799999999999999999999999999888767888999999999999999999999985 689999876

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.04  E-value=1.5e-10  Score=101.53  Aligned_cols=81  Identities=42%  Similarity=0.713  Sum_probs=77.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||++|...+++..|...|-+||.|..|.++.+..+++.+||+||+|...++|..||..||+. ++.|+.|+|.++++
T Consensus        11 rtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnes-EL~GrtirVN~AkP   89 (298)
T KOG0111|consen   11 RTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNES-ELFGRTIRVNLAKP   89 (298)
T ss_pred             eeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchh-hhcceeEEEeecCC
Confidence            89999999999999999999999999999999999989999999999999999999999999996 89999999999876


Q ss_pred             CC
Q 007742          402 HV  403 (591)
Q Consensus       402 ~~  403 (591)
                      ..
T Consensus        90 ~k   91 (298)
T KOG0111|consen   90 EK   91 (298)
T ss_pred             cc
Confidence            43

>PF13893 RRM_5: RNA recognition motif

Probab=99.01  E-value=2.7e-09  Score=76.76  Aligned_cols=56  Identities=45%  Similarity=0.713  Sum_probs=49.9

Q ss_pred             HHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          338 LRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       338 l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      |+++|++||.|..|.+....     .++|||+|.+.++|..|+..|||. .|.|++|.|.++
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-----RGFAFVEFASVEDAQKAIEQLNGR-QFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTS-EETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEEEC
Confidence            68999999999999997653     589999999999999999999997 699999999875

(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 ....

>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=99.01  E-value=3e-09  Score=81.31  Aligned_cols=74  Identities=50%  Similarity=0.761  Sum_probs=66.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       323 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      +|+|.|||..+++++|.++|..+|.|..+.+..+..+ ...|+|||+|.+.++|..|+..+++. .+.|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~-~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGK-ELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEeC
Confidence            4899999999999999999999999999999877533 66899999999999999999999996 59999998863

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.01  E-value=8.5e-09  Score=102.08  Aligned_cols=80  Identities=48%  Similarity=0.811  Sum_probs=75.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ..+|||+|||..+++++|.++|..||.|..|.+..+..++.++|+|||+|.+.++|..|+..++|. .|.|+.|.|.+..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~-~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGK-ELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCC-eECCceeEeeccc
Confidence            489999999999999999999999999999999999879999999999999999999999999996 7999999999865


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      .
T Consensus       194 ~  194 (306)
T COG0724         194 P  194 (306)
T ss_pred             c
Confidence            3

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=99.00  E-value=4.5e-10  Score=106.96  Aligned_cols=214  Identities=18%  Similarity=0.216  Sum_probs=129.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCC---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE---TGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~---~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ..|.|.||.+.++.++++.+|...|.|..+.|+.+..   .......|||.|.+...+..|. .|.+.+ |-++.|.|..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntv-fvdraliv~p   85 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTV-FVDRALIVRP   85 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccce-eeeeeEEEEe
Confidence            4899999999999999999999999999998875432   2344568999999999999887 677754 7777777765


Q ss_pred             ecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCC
Q 007742          399 VTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPV  478 (591)
Q Consensus       399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  478 (591)
                      ..+....                       ...    .+........+++.+.+...+.+..+..      ..+..+.. 
T Consensus        86 ~~~~~~p-----------------------~r~----af~~l~~~navprll~pdg~Lp~~~~lt------~~nh~p~a-  131 (479)
T KOG4676|consen   86 YGDEVIP-----------------------DRF----AFVELADQNAVPRLLPPDGVLPGDRPLT------KINHSPNA-  131 (479)
T ss_pred             cCCCCCc-----------------------cHH----HHHhcCcccccccccCCCCccCCCCccc------cccCCccc-
Confidence            4321110                       000    1111111122222222222111111110      01111110 


Q ss_pred             CCCCCCccccccccc-cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEe-cCCCeeEEEEeCCHH
Q 007742          479 PAVTAPVIPNMAAEF-IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVD-KRSAGFVYLRFESTE  556 (591)
Q Consensus       479 ~~~~~~~~~~~~~~~-~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~-~~~~g~afV~F~~~e  556 (591)
                       ..-.|.+|..+... ...-.++|+|.+|.+.+.          ..++.++|..+|.|.+..+. +....+|.|+|....
T Consensus       132 -ilktP~Lp~~~~A~kleeirRt~~v~sl~~~~~----------l~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qt  200 (479)
T KOG4676|consen  132 -ILKTPELPPQAAAKKLEEIRRTREVQSLISAAI----------LPESGESFERKGEVSYAHTASKSRSSSCSHSFRKQT  200 (479)
T ss_pred             -eecCCCCChHhhhhhhHHHHhhhhhhcchhhhc----------chhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhh
Confidence             00113333333221 122237899999944333          67899999999999988763 334556779999988


Q ss_pred             HHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          557 AAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       557 ~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      +...|+. ++|+.|.-+...+....+.
T Consensus       201 s~~halr-~~gre~k~qhsr~ai~kP~  226 (479)
T KOG4676|consen  201 SSKHALR-SHGRERKRQHSRRAIIKPH  226 (479)
T ss_pred             hHHHHHH-hcchhhhhhhhhhhhcCcc
Confidence            8888887 6888887555555554443

>smart00361 RRM_1 RNA recognition motif

Probab=99.00  E-value=1.3e-09  Score=82.38  Aligned_cols=60  Identities=27%  Similarity=0.404  Sum_probs=53.9

Q ss_pred             HHHHHHHHh----cCCCeeEEE-EeecCCC--CCccceEEEEecCcchHHHHH-HHcCCccCCeeEEe
Q 007742          234 ERDVYEFFS----KAGKVRDVR-LIMDRNS--RRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV  293 (591)
Q Consensus       234 e~~l~~~f~----~~G~i~~v~-~~~d~~~--g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v  293 (591)
                      +++|.++|.    .||.|..|. ++.++.+  |.++|||||+|.+.++|.+|+ .|||..+.|+.|.+
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            568888998    999999995 7777766  899999999999999999999 69999999999976

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.97  E-value=4.3e-11  Score=124.97  Aligned_cols=238  Identities=18%  Similarity=0.167  Sum_probs=182.4

Q ss_pred             CcEEEEeCCCCCCCHH-HHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATER-DVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~-~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      ....++.++-+..... .....|..+|.|..|++......-...-++++++.....+..|....+..+.++.+.|..+.+
T Consensus       571 ~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~pa~~~~a~~~~av~~ad~  650 (881)
T KOG0128|consen  571 RREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVPAGGALANRSAAVGLADA  650 (881)
T ss_pred             hhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcccccccccCCccccCCCCCc
Confidence            3556677776665444 567889999999999887633322333389999999999999999999999999888877665


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA  378 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~  378 (591)
                      ..........+.      ..-...++|+.||++.+.+.+|...|.++|.+..+.+......+..+|+|||+|..++++.+
T Consensus       651 ~~~~~~~kvs~n------~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~a  724 (881)
T KOG0128|consen  651 EEKEENFKVSPN------EIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGA  724 (881)
T ss_pred             hhhhhccCcCch------HHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhh
Confidence            442211111100      00112578999999999999999999999998888877666688889999999999999999


Q ss_pred             HHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccC
Q 007742          379 AQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNG  458 (591)
Q Consensus       379 a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  458 (591)
                      |+....+.  +.|+                                                                  
T Consensus       725 aV~f~d~~--~~gK------------------------------------------------------------------  736 (881)
T KOG0128|consen  725 AVAFRDSC--FFGK------------------------------------------------------------------  736 (881)
T ss_pred             hhhhhhhh--hhhh------------------------------------------------------------------
Confidence            99555553  3331                                                                  


Q ss_pred             ccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEE
Q 007742          459 SAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHI  538 (591)
Q Consensus       459 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v  538 (591)
                                                              ..|+|.|.  |+..|        .+.|..+|.++|++.++
T Consensus       737 ----------------------------------------~~v~i~g~--pf~gt--------~e~~k~l~~~~gn~~~~  766 (881)
T KOG0128|consen  737 ----------------------------------------ISVAISGP--PFQGT--------KEELKSLASKTGNVTSL  766 (881)
T ss_pred             ----------------------------------------hhhheeCC--CCCCc--------hHHHHhhccccCCcccc
Confidence                                                    13789998  88887        78999999999999998


Q ss_pred             EEe----cCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeC
Q 007742          539 YVD----KRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMK  581 (591)
Q Consensus       539 ~l~----~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~  581 (591)
                      .++    +.++|.|||.|.+..+|..++..+.+..+.-+.+.|...+
T Consensus       767 ~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsn  813 (881)
T KOG0128|consen  767 RLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSN  813 (881)
T ss_pred             chhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccC
Confidence            763    4578999999999999999999888887777776666633

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.96  E-value=8.5e-09  Score=102.59  Aligned_cols=164  Identities=23%  Similarity=0.193  Sum_probs=109.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecC--CCCCccc---eEEEEecCcchHHHHHHHcCCccCCeeEEe
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKG---VGYIEFYDVMSVPMAIALSGQLLLGQPVMV  293 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~--~~g~~~G---~afV~F~~~e~A~~Al~l~g~~i~g~~i~v  293 (591)
                      -+++||||+||++++|+.|...|..||.+.-=.-.+..  ..-..+|   |+|+.|.+...+..-|...-..-.+--+.|
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~v  337 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYFKV  337 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceEEEE
Confidence            35889999999999999999999999987532221111  1113456   999999999888777632111111122222


Q ss_pred             ccCccccccccccCC-CCC----CCCCCCCCCCceEEEcCCCCCCCHHHHHHHhc-cCCCeeEEEEeccCCCCCcccEEE
Q 007742          294 KPSEAEKNLVQSNTS-AGG----TATGPYGAIDRKLYVGNLHFNMTETQLRKLFE-PFGPVELVQLPLDIETGQCKGFGF  367 (591)
Q Consensus       294 ~~~~~~~~~~~~~~~-~~~----~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~-~~g~i~~v~i~~~~~~~~~~g~a~  367 (591)
                      ..........+.... ...    ......--+.+||||++||-.++.++|..+|+ -||.|..+-|-.|+.-+=++|.|-
T Consensus       338 ss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGR  417 (520)
T KOG0129|consen  338 SSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGR  417 (520)
T ss_pred             ecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcce
Confidence            211111110110000 000    00111222358999999999999999999999 799999999988876777899999


Q ss_pred             EEeCCHHHHHHHHHH
Q 007742          368 VQFAQLEHAKAAQSA  382 (591)
Q Consensus       368 Vef~~~~~a~~a~~~  382 (591)
                      |.|.+..+-.+||.+
T Consensus       418 VtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  418 VTFSNQQAYIKAISA  432 (520)
T ss_pred             eeecccHHHHHHHhh
Confidence            999999998888854

>smart00361 RRM_1 RNA recognition motif

Probab=98.96  E-value=3.2e-09  Score=80.18  Aligned_cols=61  Identities=28%  Similarity=0.444  Sum_probs=53.0

Q ss_pred             HHHHHHHhc----cCCCeeEEE-EeccCCC--CCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          335 ETQLRKLFE----PFGPVELVQ-LPLDIET--GQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       335 ~~~l~~~f~----~~g~i~~v~-i~~~~~~--~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      +++|+++|.    +||.|..|. |+.+..+  +.++|+|||+|.+.++|..|+..|||. .|.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~-~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGR-YFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCC-EECCEEEEe
Confidence            467788887    999999985 6666555  889999999999999999999999997 699999976

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.92  E-value=2.6e-09  Score=103.11  Aligned_cols=177  Identities=26%  Similarity=0.329  Sum_probs=139.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCC-ccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQ-LLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~-~i~g~~i~v~~~~  297 (591)
                      ..+++|++++.+.+.+.++..++..+|.+....+.....+..++|+++|.|...+.+..|+.+.+. .+.+..+......
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            468999999999998888999999999998888888778889999999999999999999988875 4555554443222


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHH
Q 007742          298 AEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK  377 (591)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~  377 (591)
                      .-..  ...   .........+....++|.+|+..++.++|+..|..+|.|..+.++....++...|++||.|.+...+.
T Consensus       167 ~~~~--~~~---n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~  241 (285)
T KOG4210|consen  167 RRGL--RPK---NKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKK  241 (285)
T ss_pred             cccc--ccc---chhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHH
Confidence            2110  000   00101111222244559999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          378 AAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       378 ~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      .++.. +.. .+.+.++.+.+..+.
T Consensus       242 ~~~~~-~~~-~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  242 LALND-QTR-SIGGRPLRLEEDEPR  264 (285)
T ss_pred             HHhhc-ccC-cccCcccccccCCCC
Confidence            99865 554 689999999887654

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.88  E-value=3.8e-09  Score=92.68  Aligned_cols=80  Identities=20%  Similarity=0.352  Sum_probs=72.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcC-CCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKA-GKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~-G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ....+||..+|..+-+.+|..+|.+| |.+..+++-+++.||.++|||||+|.+.+.|..|. .||+..+.|+-|.+...
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            45678999999999999999999988 78888899899999999999999999999999999 69999999998888665


Q ss_pred             cc
Q 007742          297 EA  298 (591)
Q Consensus       297 ~~  298 (591)
                      .+
T Consensus       128 pp  129 (214)
T KOG4208|consen  128 PP  129 (214)
T ss_pred             Cc
Confidence            44

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.86  E-value=4.1e-09  Score=99.17  Aligned_cols=81  Identities=23%  Similarity=0.335  Sum_probs=76.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+-..|||-.|.+.+|.++|.-+|+.||+|.+|.+++|..||.+-.||||+|.+.+++.+|. .|++..|..+.|.|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            345589999999999999999999999999999999999999999999999999999999999 8999999999999976


Q ss_pred             Cc
Q 007742          296 SE  297 (591)
Q Consensus       296 ~~  297 (591)
                      +.
T Consensus       316 SQ  317 (479)
T KOG0415|consen  316 SQ  317 (479)
T ss_pred             hh
Confidence            64

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.86  E-value=2.9e-10  Score=118.93  Aligned_cols=146  Identities=21%  Similarity=0.313  Sum_probs=126.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCccc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~~  299 (591)
                      ..++||.||++.+.+.+|...|..+|.+..+++..-.+.+..+|+|||+|...+++.+|+.+.-..+.|+          
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK----------  736 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGK----------  736 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhh----------
Confidence            4678999999999999999999999999888888777788999999999999999999998776666652          


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHH
Q 007742          300 KNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA  379 (591)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a  379 (591)
                                            ..|+|.|+|+..|.+.+..+|.++|.+..+.++... .|.++|.|||.|.+..+|..+
T Consensus       737 ----------------------~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~  793 (881)
T KOG0128|consen  737 ----------------------ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRK  793 (881)
T ss_pred             ----------------------hhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhh
Confidence                                  578999999999999999999999999999887775 889999999999999999999


Q ss_pred             HHHhcCCeeeCCeEEEEEEe
Q 007742          380 QSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       380 ~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +....+. .+.-..+.|...
T Consensus       794 ~~s~d~~-~~rE~~~~v~vs  812 (881)
T KOG0128|consen  794 VASVDVA-GKRENNGEVQVS  812 (881)
T ss_pred             cccchhh-hhhhcCcccccc
Confidence            8777764 355555555443

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.84  E-value=2.2e-09  Score=94.43  Aligned_cols=148  Identities=26%  Similarity=0.371  Sum_probs=119.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~~~~  298 (591)
                      -++|||+||-..++|+-|.++|-+.|+|+.|.|..++. +..+ ||||.|.+.-.+..|+. +||..+.+..+.|++-..
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            38999999999999999999999999999999887765 4555 99999999999999995 899999999888765421


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA  378 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~  378 (591)
                      ..-                         .-|...++++.+...|+..|++..+.+..+. .|....++|+.+.-......
T Consensus        87 ~sh-------------------------apld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~  140 (267)
T KOG4454|consen   87 NSH-------------------------APLDERVTEEILYEVFSQAGPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVPF  140 (267)
T ss_pred             CCc-------------------------chhhhhcchhhheeeecccCCCCCccccccc-cCCccCccchhhhhhhcCcH
Confidence            100                         1255678889999999999999999998876 46677889999988888778


Q ss_pred             HHHHhcCCeeeCCeEEEE
Q 007742          379 AQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       379 a~~~l~g~~~~~g~~l~v  396 (591)
                      ++....+ +...-+++.+
T Consensus       141 ~~~~y~~-l~~~~~~~~~  157 (267)
T KOG4454|consen  141 ALDLYQG-LELFQKKVTI  157 (267)
T ss_pred             Hhhhhcc-cCcCCCCccc
Confidence            8866666 4455555544

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.81  E-value=9.7e-09  Score=96.70  Aligned_cols=85  Identities=21%  Similarity=0.313  Sum_probs=78.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          317 YGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       317 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      ..|+...|||..|.+-++.++|.-+|+.||+|.+|.|+.+..+|.+-.||||+|.+.+++.+|.-.|++. .|+++.|.|
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNv-LIDDrRIHV  313 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNV-LIDDRRIHV  313 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcce-eeccceEEe
Confidence            3456799999999999999999999999999999999999999999999999999999999999999995 699999999


Q ss_pred             EEecCC
Q 007742          397 SSVTDH  402 (591)
Q Consensus       397 ~~~~~~  402 (591)
                      .+++.-
T Consensus       314 DFSQSV  319 (479)
T KOG0415|consen  314 DFSQSV  319 (479)
T ss_pred             ehhhhh
Confidence            987543

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=98.79  E-value=6.3e-09  Score=95.47  Aligned_cols=89  Identities=31%  Similarity=0.592  Sum_probs=75.1

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEec------CCCeeEEEEeCCHHHHHHHHHHhcc
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK------RSAGFVYLRFESTEAAASAQRAMHM  567 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~------~~~g~afV~F~~~e~A~~A~~~l~g  567 (591)
                      ..-++++|++.|++.+-.     ..++|++++.++|.+||.|..|.|-.      +-.--.||+|..+++|.+|+-.|||
T Consensus       277 l~~ptkvlllrnmVg~ge-----vd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnG  351 (378)
T KOG1996|consen  277 LKCPTKVLLLRNMVGAGE-----VDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNG  351 (378)
T ss_pred             HhcchHHHHhhhhcCccc-----ccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCC
Confidence            456788899999976554     45677899999999999999887621      1233579999999999999999999


Q ss_pred             cccCCeEEEEEEeCchhhhh
Q 007742          568 RWFARRLISAIFMKPEDYEA  587 (591)
Q Consensus       568 ~~~~g~~l~v~~~~~~~~~~  587 (591)
                      ++|+|+.|...|++...|..
T Consensus       352 RyFGGr~v~A~Fyn~ekfs~  371 (378)
T KOG1996|consen  352 RYFGGRVVSACFYNLEKFSN  371 (378)
T ss_pred             ceecceeeeheeccHHhhhh
Confidence            99999999999999999875

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.76  E-value=2.8e-08  Score=87.34  Aligned_cols=82  Identities=29%  Similarity=0.503  Sum_probs=74.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccC-CCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPF-GPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~-g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ....++|..+|..+.+..|...|.++ |.|..+++-+++.||.++|||||+|.+.+.|.-|...||+.| |.|+.|.+.+
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYL-l~e~lL~c~v  126 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYL-LMEHLLECHV  126 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhh-hhhheeeeEE
Confidence            34689999999999999999999998 678888888999999999999999999999999999999974 9999999998


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      ..+.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            7654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.68  E-value=1.7e-08  Score=96.35  Aligned_cols=164  Identities=20%  Similarity=0.215  Sum_probs=119.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCC---CCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRN---SRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~---~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~  297 (591)
                      ..|.|.||.+.+|.++++.+|...|.|..+.|+....   .....-.|||.|.+...+..|..|.++++-+..|.|.+..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            4899999999999999999999999999999987322   2334568999999999999999999999999999986543


Q ss_pred             ccccccc-------------ccCCCCCCC-----C------------CCCCC----------CCceEEEcCCCCCCCHHH
Q 007742          298 AEKNLVQ-------------SNTSAGGTA-----T------------GPYGA----------IDRKLYVGNLHFNMTETQ  337 (591)
Q Consensus       298 ~~~~~~~-------------~~~~~~~~~-----~------------~~~~~----------~~~~l~v~nl~~~~~~~~  337 (591)
                      .......             ...++.+..     .            .+..+          ..++|+|.+|+..+...+
T Consensus        88 ~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~e  167 (479)
T KOG4676|consen   88 DEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILPE  167 (479)
T ss_pred             CCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcchh
Confidence            2221100             000000000     0            00000          136899999999999999


Q ss_pred             HHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC
Q 007742          338 LRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV  390 (591)
Q Consensus       338 l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~  390 (591)
                      +.++|..+|.|....+-    .+...-+|.|+|........|+ .++|. .+.
T Consensus       168 ~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~hal-r~~gr-e~k  214 (479)
T KOG4676|consen  168 SGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHAL-RSHGR-ERK  214 (479)
T ss_pred             hhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHH-Hhcch-hhh
Confidence            99999999999776664    3334557889999999999998 45553 344

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.68  E-value=4.1e-08  Score=92.73  Aligned_cols=74  Identities=18%  Similarity=0.343  Sum_probs=67.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH--HcCCccCCeeEEeccC
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA--LSGQLLLGQPVMVKPS  296 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~--l~g~~i~g~~i~v~~~  296 (591)
                      ...+|||++|-..+++.+|+++|.+||.|..|.++..      +|+|||+|.+-+.|+.|++  +|...|.|..|+|.|.
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            4589999999999999999999999999999999854      5699999999999999993  7888899999999998


Q ss_pred             cc
Q 007742          297 EA  298 (591)
Q Consensus       297 ~~  298 (591)
                      .+
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            76

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.60  E-value=4.3e-08  Score=103.48  Aligned_cols=160  Identities=21%  Similarity=0.343  Sum_probs=129.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      .+++||++||+..+++.+|+..|..+|.|..|.|-.-. .+...-||||.|.+...+..|. ++.+..|....+.+.+..
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            35889999999999999999999999999998886543 2455679999999999999998 788888776666554442


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHH
Q 007742          298 AEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK  377 (591)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~  377 (591)
                      .                  .+.+++.+++++|.+.+....|..+|..||+|..|.+-.      ..-||||+|.+...|+
T Consensus       450 ~------------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h------gq~yayi~yes~~~aq  505 (975)
T KOG0112|consen  450 P------------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH------GQPYAYIQYESPPAAQ  505 (975)
T ss_pred             c------------------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc------CCcceeeecccCccch
Confidence            2                  122348899999999999999999999999999887642      2459999999999999


Q ss_pred             HHHHHhcCCeeeCC--eEEEEEEecCCCC
Q 007742          378 AAQSALNGKLEIVG--RTLKVSSVTDHVG  404 (591)
Q Consensus       378 ~a~~~l~g~~~~~g--~~l~v~~~~~~~~  404 (591)
                      .|+..|-|. .|+|  +.+.|.++.+-..
T Consensus       506 ~a~~~~rga-p~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  506 AATHDMRGA-PLGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             hhHHHHhcC-cCCCCCcccccccccCCCC
Confidence            999999995 5666  6788888765433

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.54  E-value=5.1e-08  Score=102.87  Aligned_cols=158  Identities=22%  Similarity=0.341  Sum_probs=124.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      .+.+|+++||+..+++.+|...|..+|.|..|.|-... .+...-|+||.|.+...+..|...+.+.+ |..-.+.+.+.
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~-I~~g~~r~glG  448 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPL-IGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCc-cccCccccccc
Confidence            36899999999999999999999999999999986654 44445689999999999999988888864 32223322221


Q ss_pred             cCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCC
Q 007742          400 TDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVP  479 (591)
Q Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  479 (591)
                      ..                                                                              
T Consensus       449 ~~------------------------------------------------------------------------------  450 (975)
T KOG0112|consen  449 QP------------------------------------------------------------------------------  450 (975)
T ss_pred             cc------------------------------------------------------------------------------
Confidence            00                                                                              


Q ss_pred             CCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHH
Q 007742          480 AVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAA  559 (591)
Q Consensus       480 ~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~  559 (591)
                                    ...++.-+++.+|  +.+..        ...|..+|..||.|..|.+. ++.-+|||.|++...|+
T Consensus       451 --------------kst~ttr~~sggl--g~w~p--------~~~l~r~fd~fGpir~Idy~-hgq~yayi~yes~~~aq  505 (975)
T KOG0112|consen  451 --------------KSTPTTRLQSGGL--GPWSP--------VSRLNREFDRFGPIRIIDYR-HGQPYAYIQYESPPAAQ  505 (975)
T ss_pred             --------------ccccceeeccCCC--CCCCh--------HHHHHHHhhccCcceeeecc-cCCcceeeecccCccch
Confidence                          1234456889998  55544        78899999999999999886 46779999999999999


Q ss_pred             HHHHHhcccccCC--eEEEEEEeCc
Q 007742          560 SAQRAMHMRWFAR--RLISAIFMKP  582 (591)
Q Consensus       560 ~A~~~l~g~~~~g--~~l~v~~~~~  582 (591)
                      .|++.|.|..|+|  +.|.|.|+.+
T Consensus       506 ~a~~~~rgap~G~P~~r~rvdla~~  530 (975)
T KOG0112|consen  506 AATHDMRGAPLGGPPRRLRVDLASP  530 (975)
T ss_pred             hhHHHHhcCcCCCCCcccccccccC
Confidence            9999999999975  5588888764

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.53  E-value=2.4e-07  Score=92.63  Aligned_cols=82  Identities=23%  Similarity=0.411  Sum_probs=75.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .+.|||.+|...+-..+|+++|++||.|+...|+.+..+.-.+||+||++.+.++|.+||..||.+ +|.|+.|.|..++
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrT-ELHGrmISVEkaK  483 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRT-ELHGRMISVEKAK  483 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhh-hhcceeeeeeecc
Confidence            589999999999999999999999999999999988877788999999999999999999999996 8999999999876


Q ss_pred             CCC
Q 007742          401 DHV  403 (591)
Q Consensus       401 ~~~  403 (591)
                      ...
T Consensus       484 NEp  486 (940)
T KOG4661|consen  484 NEP  486 (940)
T ss_pred             cCc
Confidence            443

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.53  E-value=2e-07  Score=93.16  Aligned_cols=79  Identities=19%  Similarity=0.315  Sum_probs=73.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      -++.|||.+|...+...+|+.+|++||.|+..+++.+..+.-.++||||++.+..+|.+|| .|+.+.+.|+-|.|..+.
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            4588999999999999999999999999999999999888888999999999999999999 699999999999996544

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.52  E-value=2.2e-07  Score=96.59  Aligned_cols=85  Identities=16%  Similarity=0.290  Sum_probs=73.6

Q ss_pred             ccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhc
Q 007742          487 PNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMH  566 (591)
Q Consensus       487 ~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~  566 (591)
                      +.+.......-+++|+|+.|  +..++        +.||..+|..||.|.+|.+. .+.|||||.+...++|.+|+.+|+
T Consensus       410 P~I~pd~isV~SrTLwvG~i--~k~v~--------e~dL~~~feefGeiqSi~li-~~R~cAfI~M~~RqdA~kalqkl~  478 (894)
T KOG0132|consen  410 PTIPPDHISVCSRTLWVGGI--PKNVT--------EQDLANLFEEFGEIQSIILI-PPRGCAFIKMVRRQDAEKALQKLS  478 (894)
T ss_pred             CCCCCcceeEeeeeeeeccc--cchhh--------HHHHHHHHHhcccceeEeec-cCCceeEEEEeehhHHHHHHHHHh
Confidence            33344444566889999999  77766        89999999999999999887 469999999999999999999999


Q ss_pred             ccccCCeEEEEEEeCc
Q 007742          567 MRWFARRLISAIFMKP  582 (591)
Q Consensus       567 g~~~~g~~l~v~~~~~  582 (591)
                      +..|.++.|+|.|+--
T Consensus       479 n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  479 NVKVADKTIKIAWAVG  494 (894)
T ss_pred             cccccceeeEEeeecc
Confidence            9999999999999743

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.49  E-value=1.2e-08  Score=98.26  Aligned_cols=160  Identities=19%  Similarity=0.270  Sum_probs=126.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGP-VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ..+|++||.+.++..+|..+|...-. ...-+|+       ..||+||.+.+...|.+|++.|+|++++.|+.+.|.+..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            46899999999999999999986521 1111222       257999999999999999999999999999999887653


Q ss_pred             CCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCC
Q 007742          401 DHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPA  480 (591)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (591)
                      ++                                                                              
T Consensus        75 ~k------------------------------------------------------------------------------   76 (584)
T KOG2193|consen   75 PK------------------------------------------------------------------------------   76 (584)
T ss_pred             hH------------------------------------------------------------------------------
Confidence            21                                                                              


Q ss_pred             CCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEe--cCCCeeEEEEeCCHHHH
Q 007742          481 VTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVD--KRSAGFVYLRFESTEAA  558 (591)
Q Consensus       481 ~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~--~~~~g~afV~F~~~e~A  558 (591)
                                    .-.++.+.|.|+  |.-+.        ++.|..+...||.|..|+..  ..-....-|+|.+.+.+
T Consensus        77 --------------kqrsrk~Qirni--ppql~--------wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~  132 (584)
T KOG2193|consen   77 --------------KQRSRKIQIRNI--PPQLQ--------WEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQH  132 (584)
T ss_pred             --------------HHHhhhhhHhcC--CHHHH--------HHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHH
Confidence                          012234779999  66554        88899999999999998752  22344557889999999


Q ss_pred             HHHHHHhcccccCCeEEEEEEeCchhhhhccC
Q 007742          559 ASAQRAMHMRWFARRLISAIFMKPEDYEAKFK  590 (591)
Q Consensus       559 ~~A~~~l~g~~~~g~~l~v~~~~~~~~~~~~~  590 (591)
                      ..||++|+|..|....+.|.|.+.++..++-|
T Consensus       133 ~~ai~kl~g~Q~en~~~k~~YiPdeq~~q~~p  164 (584)
T KOG2193|consen  133 RQAIHKLNGPQLENQHLKVGYIPDEQNAQHQP  164 (584)
T ss_pred             HHHHHhhcchHhhhhhhhcccCchhhhhccCc
Confidence            99999999999999999999999888766544

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.44  E-value=4.9e-06  Score=83.32  Aligned_cols=162  Identities=23%  Similarity=0.280  Sum_probs=106.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccC---CCCCccc---EEEEEeCCHHHHHHHHHHhcCCeeeCCeEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDI---ETGQCKG---FGFVQFAQLEHAKAAQSALNGKLEIVGRTL  394 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~---~~~~~~g---~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l  394 (591)
                      ++.|||++||+.++|+.|...|..||.+. |..+...   ..-.++|   |+|+.|.+...+...|.++.-  .-.+--+
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~--~~~~~yf  335 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE--GEGNYYF  335 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh--cccceEE
Confidence            58999999999999999999999999874 4444211   1123456   999999999988877776653  1222233


Q ss_pred             EEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCC
Q 007742          395 KVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQP  474 (591)
Q Consensus       395 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  474 (591)
                      .|.....+...    .+..+|...+                                            ....       
T Consensus       336 ~vss~~~k~k~----VQIrPW~laD--------------------------------------------s~fv-------  360 (520)
T KOG0129|consen  336 KVSSPTIKDKE----VQIRPWVLAD--------------------------------------------SDFV-------  360 (520)
T ss_pred             EEecCcccccc----eeEEeeEecc--------------------------------------------chhh-------
Confidence            33322211110    0000000000                                            0000       


Q ss_pred             CCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhc-cccceEEEEEecC-----CCeeE
Q 007742          475 AVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECS-KYGRVKHIYVDKR-----SAGFV  548 (591)
Q Consensus       475 ~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~-~~G~V~~v~l~~~-----~~g~a  548 (591)
                                    ......-.+.++|||++|  |-.++        -++|..+|. -||.|..|-|+.+     ++|-|
T Consensus       361 --------------~d~sq~lDprrTVFVGgv--prpl~--------A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaG  416 (520)
T KOG0129|consen  361 --------------LDHNQPIDPRRTVFVGGL--PRPLT--------AEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAG  416 (520)
T ss_pred             --------------hccCcccCccceEEecCC--CCcch--------HHHHHHHHHHhcCceEEEEeccCcccCCCCCcc
Confidence                          000112356789999999  76666        688999998 8999999988654     68999


Q ss_pred             EEEeCCHHHHHHHHHH
Q 007742          549 YLRFESTEAAASAQRA  564 (591)
Q Consensus       549 fV~F~~~e~A~~A~~~  564 (591)
                      -|.|.+..+-.+||.+
T Consensus       417 RVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  417 RVTFSNQQAYIKAISA  432 (520)
T ss_pred             eeeecccHHHHHHHhh
Confidence            9999999999999874

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.41  E-value=3.1e-07  Score=85.78  Aligned_cols=85  Identities=22%  Similarity=0.308  Sum_probs=78.3

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEec
Q 007742          215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK  294 (591)
Q Consensus       215 ~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~  294 (591)
                      ....+...+||+|+.+.+|.+++..+|..||.|..|.+.+++.+|.++|||||+|.+.+.+..|+.|++..|.|.++.|.
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVT  175 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceee
Confidence            34556799999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCccc
Q 007742          295 PSEAE  299 (591)
Q Consensus       295 ~~~~~  299 (591)
                      +....
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            76543

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.39  E-value=9.8e-07  Score=82.02  Aligned_cols=80  Identities=24%  Similarity=0.375  Sum_probs=72.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      +....+|+|.|||+.++++||+++|..||.+..+.+.+++. |.+.|+|-|.|..-++|..|+ .+++..+.|..|++..
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~-G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRA-GRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCC-CCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            33458899999999999999999999999999999888865 899999999999999999999 6999999999988865


Q ss_pred             Cc
Q 007742          296 SE  297 (591)
Q Consensus       296 ~~  297 (591)
                      ..
T Consensus       159 i~  160 (243)
T KOG0533|consen  159 IS  160 (243)
T ss_pred             ec
Confidence            43

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.39  E-value=1.5e-06  Score=82.50  Aligned_cols=76  Identities=29%  Similarity=0.407  Sum_probs=68.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ...+|||++|-..+++.+|.+.|.+||+|..|.+...      ++.|||+|.+-+.|+.|...+-+.+.|+|..|.|.|.
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            3589999999999999999999999999999998754      4589999999999999988877778899999999987


Q ss_pred             cC
Q 007742          400 TD  401 (591)
Q Consensus       400 ~~  401 (591)
                      ..
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            65

>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=98.38  E-value=1.8e-06  Score=64.47  Aligned_cols=72  Identities=26%  Similarity=0.327  Sum_probs=51.2

Q ss_pred             eEEEeccCCCCCCCCchhhhhHHHHHHHHhcccc-ceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEE
Q 007742          500 CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYG-RVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAI  578 (591)
Q Consensus       500 ~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G-~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~  578 (591)
                      .|+|.||  |....    ...|..-|..++..+| .|..|     ..+.|+|.|.+.+.|..|.+.|+|..+.|+.|.|+
T Consensus         4 ~L~V~NL--P~~~d----~~~I~~RL~qLsdNCGGkVl~v-----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    4 LLYVSNL--PTNKD----PSSIKNRLRQLSDNCGGKVLSV-----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEES----TTS-----HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             EEEEecC--CCCCC----HHHHHHHHHHHhhccCCEEEEE-----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            5899999  76543    3445678999999996 66666     35789999999999999999999999999999999


Q ss_pred             EeCc
Q 007742          579 FMKP  582 (591)
Q Consensus       579 ~~~~  582 (591)
                      |.+.
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            9854

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.36  E-value=1.1e-06  Score=88.62  Aligned_cols=78  Identities=22%  Similarity=0.352  Sum_probs=67.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEecc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP  295 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~  295 (591)
                      .....|||+|||+++++.+|.++|..||.|....|......+...+||||+|.+..++..|+..+...|++++|.|.-
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Vee  363 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEE  363 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEe
Confidence            344669999999999999999999999999887776654334444999999999999999999888889999999964

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.36  E-value=3.8e-07  Score=82.59  Aligned_cols=165  Identities=19%  Similarity=0.267  Sum_probs=115.9

Q ss_pred             EEEEeCCCCCCCHHH-H--HHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          222 TVFAYQMPLKATERD-V--YEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       222 ~l~V~nLp~~~te~~-l--~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      .++++++-..+..+- |  ...|..+-.+....++.+.. +.-.++||+.|.....-..+- .-+++.+.-.+|++....
T Consensus        98 ~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p-~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gt  176 (290)
T KOG0226|consen   98 RPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRP-QPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGT  176 (290)
T ss_pred             cccccccccccCCCCCCcchhhhccchhhhhhhhhhcCC-CccCcccccCcchhhhhhhhccccccccccCcceeecccc
Confidence            345555544443322 2  55566655555555665544 567899999998766665555 456667776666664332


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHH
Q 007742          298 AEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK  377 (591)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~  377 (591)
                      ..........          ....-.||.+.|...++.+.|-..|.+|-.-....+++++.+++++||+||-|.++.++.
T Consensus       177 swedPsl~ew----------~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~  246 (290)
T KOG0226|consen  177 SWEDPSLAEW----------DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYV  246 (290)
T ss_pred             ccCCcccccC----------ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHH
Confidence            2111110000          111368999999999999999999999988888888999999999999999999999999


Q ss_pred             HHHHHhcCCeeeCCeEEEEEE
Q 007742          378 AAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       378 ~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      .||..|+|+ .++.++|++..
T Consensus       247 rAmrem~gk-yVgsrpiklRk  266 (290)
T KOG0226|consen  247 RAMREMNGK-YVGSRPIKLRK  266 (290)
T ss_pred             HHHHhhccc-ccccchhHhhh
Confidence            999999997 47888887753

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.30  E-value=7.9e-07  Score=80.58  Aligned_cols=81  Identities=21%  Similarity=0.389  Sum_probs=74.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ...-+||-+.|...++.+.|...|.+|-.....++++++.||+++|||||-|.++.++..|| +|+|..++.++|++.-+
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            34588999999999999999999999999999999999999999999999999999999999 89999999999988655


Q ss_pred             cc
Q 007742          297 EA  298 (591)
Q Consensus       297 ~~  298 (591)
                      ..
T Consensus       268 ~w  269 (290)
T KOG0226|consen  268 EW  269 (290)
T ss_pred             hH
Confidence            43

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.28  E-value=2.6e-06  Score=79.28  Aligned_cols=78  Identities=28%  Similarity=0.525  Sum_probs=72.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ..|+|.|||+.++..+|+++|..||.+..+.|..+. .|.+.|.|-|.|..-++|..|++.++| +.++|..+.+.....
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~g-v~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNG-VALDGRPMKIEIISS  161 (243)
T ss_pred             ceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcC-cccCCceeeeEEecC
Confidence            789999999999999999999999999999998886 889999999999999999999999999 689999998887643

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.27  E-value=5.3e-06  Score=65.68  Aligned_cols=77  Identities=17%  Similarity=0.219  Sum_probs=63.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcC--CCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC----eeEEe
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKA--GKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG----QPVMV  293 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~--G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g----~~i~v  293 (591)
                      +||+|+|||...|.++|.+++...  |...-+-+..|-.++...|||||-|.+++.|.... .++|..+..    +...|
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            689999999999999999998753  67777888889889999999999999999999988 689888752    34444


Q ss_pred             ccCc
Q 007742          294 KPSE  297 (591)
Q Consensus       294 ~~~~  297 (591)
                      .++.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            4443

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.25  E-value=1.2e-05  Score=83.19  Aligned_cols=89  Identities=25%  Similarity=0.337  Sum_probs=76.1

Q ss_pred             CCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCC---CCcccEEEEEeCCHHHHHHHHHHhcCCee
Q 007742          312 TATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIET---GQCKGFGFVQFAQLEHAKAAQSALNGKLE  388 (591)
Q Consensus       312 ~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~---~~~~g~a~Vef~~~~~a~~a~~~l~g~~~  388 (591)
                      +....+.|.++.|||+||++.++++.|...|..||+|..|.|.+....   .....++||-|.+-.+|..|+..|+|. .
T Consensus       165 gsfDdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~-i  243 (877)
T KOG0151|consen  165 GSFDDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGI-I  243 (877)
T ss_pred             CcCCCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcce-e
Confidence            444556777899999999999999999999999999999999876421   234568999999999999999999996 6


Q ss_pred             eCCeEEEEEEecC
Q 007742          389 IVGRTLKVSSVTD  401 (591)
Q Consensus       389 ~~g~~l~v~~~~~  401 (591)
                      +.+..+++.|.+.
T Consensus       244 v~~~e~K~gWgk~  256 (877)
T KOG0151|consen  244 VMEYEMKLGWGKA  256 (877)
T ss_pred             eeeeeeeeccccc
Confidence            9999999998754

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.24  E-value=7.2e-06  Score=64.94  Aligned_cols=78  Identities=22%  Similarity=0.376  Sum_probs=66.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccC--CCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC----CeEEE
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPF--GPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV----GRTLK  395 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~--g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~----g~~l~  395 (591)
                      ++|+|.|||...+.++|.+++...  |...-+.++.|..++...|||||-|.+++.|....+.++|. .+.    .+...
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~-~w~~~~s~Kvc~   80 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGK-KWPNFNSKKVCE   80 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCC-ccccCCCCcEEE
Confidence            689999999999999999888764  67788899999888999999999999999999999999996 343    45666


Q ss_pred             EEEec
Q 007742          396 VSSVT  400 (591)
Q Consensus       396 v~~~~  400 (591)
                      |.|+.
T Consensus        81 i~yAr   85 (97)
T PF04059_consen   81 ISYAR   85 (97)
T ss_pred             EehhH
Confidence            76653

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.24  E-value=2.9e-06  Score=87.55  Aligned_cols=83  Identities=16%  Similarity=0.346  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecC---CCCCccceEEEEecCcchHHHHH-HHcCCccCCeeE
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR---NSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV  291 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~---~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i  291 (591)
                      .....+.|||+||++.+++..|...|..||+|.+|+++.-.   ..-...-||||.|.+-.+|.+|+ .|+|+.+.+..+
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            34456889999999999999999999999999999998743   22345679999999999999999 699999999999


Q ss_pred             EeccCcc
Q 007742          292 MVKPSEA  298 (591)
Q Consensus       292 ~v~~~~~  298 (591)
                      ++.|...
T Consensus       250 K~gWgk~  256 (877)
T KOG0151|consen  250 KLGWGKA  256 (877)
T ss_pred             eeccccc
Confidence            9988854

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.21  E-value=6.6e-07  Score=79.14  Aligned_cols=79  Identities=27%  Similarity=0.335  Sum_probs=69.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      +..++|||.||...++++-|.++|-..|+|..|.|+..+ .+..+ ||||.|.+..+..-|++.+|| +.+.+..+.|.+
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng-~~l~~~e~q~~~   83 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENG-DDLEEDEEQRTL   83 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhccc-chhccchhhccc
Confidence            345899999999999999999999999999999998776 55556 999999999999999999999 578999888876


Q ss_pred             ec
Q 007742          399 VT  400 (591)
Q Consensus       399 ~~  400 (591)
                      -+
T Consensus        84 r~   85 (267)
T KOG4454|consen   84 RC   85 (267)
T ss_pred             cc
Confidence            43

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.15  E-value=2.2e-06  Score=86.53  Aligned_cols=73  Identities=21%  Similarity=0.316  Sum_probs=67.9

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCe
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARR  573 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~  573 (591)
                      ...++.+|+|.||  |.+++        .++|..+|+.||.|..|.......|.+||+|-++-+|+.|+++|+++.|.|+
T Consensus        71 ~~~~~~~L~v~nl--~~~Vs--------n~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~  140 (549)
T KOG4660|consen   71 KDMNQGTLVVFNL--PRSVS--------NDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGK  140 (549)
T ss_pred             ccCccceEEEEec--CCcCC--------HHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhh
Confidence            3567889999999  88888        8999999999999999988888899999999999999999999999999999


Q ss_pred             EEE
Q 007742          574 LIS  576 (591)
Q Consensus       574 ~l~  576 (591)
                      .|.
T Consensus       141 ~~k  143 (549)
T KOG4660|consen  141 RIK  143 (549)
T ss_pred             hhc
Confidence            987

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.12  E-value=2.5e-06  Score=82.57  Aligned_cols=172  Identities=18%  Similarity=0.172  Sum_probs=125.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ..+++++++...+.+.++..++..+|.+....+........++|++++.|...+.+..|+ ++.+...+.++.+.....+
T Consensus        88 ~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l-~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   88 SSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAAL-EESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             cccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHH-HhhhccccccccccCcccc
Confidence            378999999999998889999999998877777665567788999999999999999999 4555323444444333221


Q ss_pred             CCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCC
Q 007742          401 DHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPA  480 (591)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (591)
                      ...  ..                                                                       +.
T Consensus       167 ~~~--~~-----------------------------------------------------------------------~~  173 (285)
T KOG4210|consen  167 RRG--LR-----------------------------------------------------------------------PK  173 (285)
T ss_pred             ccc--cc-----------------------------------------------------------------------cc
Confidence            100  00                                                                       00


Q ss_pred             CCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----CCeeEEEEeCCH
Q 007742          481 VTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----SAGFVYLRFEST  555 (591)
Q Consensus       481 ~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~~g~afV~F~~~  555 (591)
                      .      .........+....+|.|+  ++.++        .++|..+|..+|.|..+.++..     ..|++||.|.+.
T Consensus       174 n------~~~~~~~~~s~~~~~~~~~--~f~~~--------~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~  237 (285)
T KOG4210|consen  174 N------KLSRLSSGPSDTIFFVGEL--DFSLT--------RDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAG  237 (285)
T ss_pred             c------hhcccccCccccceeeccc--ccccc--------hHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhc
Confidence            0      0000001223334559999  88777        7889999999999999998643     578999999999


Q ss_pred             HHHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          556 EAAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       556 e~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      ..+..|+.. ....++|.++.+.+-.+.
T Consensus       238 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  238 NSKKLALND-QTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             hhHHHHhhc-ccCcccCcccccccCCCC
Confidence            999999987 888899999999886654

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.12  E-value=4.7e-06  Score=77.94  Aligned_cols=78  Identities=33%  Similarity=0.555  Sum_probs=72.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ...+||+|+.+.++.++|...|+.||.|..|.|+.+...++++||+||+|.+.+.+.+|+. |++. .|.|+.+.|.+..
T Consensus       101 ~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs-~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  101 APSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGS-EIPGPAIEVTLKR  178 (231)
T ss_pred             CceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCc-ccccccceeeeee
Confidence            4799999999999999999999999999999999998888999999999999999999996 9997 6999999998764

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=98.09  E-value=1.6e-06  Score=79.24  Aligned_cols=70  Identities=31%  Similarity=0.504  Sum_probs=60.7

Q ss_pred             hhhHHHHHHHHhc-cccceEEEEEec----CCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchhhhh
Q 007742          518 DLEIQGDVEEECS-KYGRVKHIYVDK----RSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEA  587 (591)
Q Consensus       518 ~~~~~edl~~~f~-~~G~V~~v~l~~----~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  587 (591)
                      +.++.++|+.+|. +||.|..+.|-.    .-.|.+||.|...++|++|+..|||++|.|++|.+.|++...|..
T Consensus        78 ~defyEd~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~~re  152 (260)
T KOG2202|consen   78 EDEFYEDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTDFRE  152 (260)
T ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCchhh
Confidence            3355788888888 999999986633    357899999999999999999999999999999999999887764

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.05  E-value=7.2e-06  Score=82.78  Aligned_cols=78  Identities=31%  Similarity=0.482  Sum_probs=65.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      .+|||.|||.+++..+|.++|..||+|+...|..-...+...+||||+|.+..++..||++-  .+.+++++|.|.--..
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As--p~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS--PLEIGGRKLNVEEKRP  366 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC--ccccCCeeEEEEeccc
Confidence            56999999999999999999999999998877654323444499999999999999999654  4679999999986544

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.02  E-value=6.1e-07  Score=86.76  Aligned_cols=156  Identities=22%  Similarity=0.295  Sum_probs=122.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCc-cCCeeEEeccCcc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQL-LLGQPVMVKPSEA  298 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~-i~g~~i~v~~~~~  298 (591)
                      ..+|++||.+.++..+|..+|.....-.+..++.      -.|||||.+.+..-|..|++ ++|+. +.|..+.|..+.+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            4689999999999999999998763222222222      25899999999999999994 77665 7899998877765


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA  378 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~  378 (591)
                      +....                  +.+.|.|+|+....+.|..++..||.+..|....   +....-..-|+|.+.+.+..
T Consensus        76 kkqrs------------------rk~Qirnippql~wevld~Ll~qyg~ve~~eqvn---t~~etavvnvty~~~~~~~~  134 (584)
T KOG2193|consen   76 KKQRS------------------RKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVN---TDSETAVVNVTYSAQQQHRQ  134 (584)
T ss_pred             HHHHh------------------hhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhc---cchHHHHHHHHHHHHHHHHH
Confidence            44321                  5688999999999999999999999998886642   22233345678899999999


Q ss_pred             HHHHhcCCeeeCCeEEEEEEecCCCC
Q 007742          379 AQSALNGKLEIVGRTLKVSSVTDHVG  404 (591)
Q Consensus       379 a~~~l~g~~~~~g~~l~v~~~~~~~~  404 (591)
                      ||..|+|. .+....+.|.|..+...
T Consensus       135 ai~kl~g~-Q~en~~~k~~YiPdeq~  159 (584)
T KOG2193|consen  135 AIHKLNGP-QLENQHLKVGYIPDEQN  159 (584)
T ss_pred             HHHhhcch-HhhhhhhhcccCchhhh
Confidence            99999995 79999999999876544

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.81  E-value=7.4e-05  Score=56.07  Aligned_cols=69  Identities=19%  Similarity=0.302  Sum_probs=46.4

Q ss_pred             cEEEEeCCCCCCCHHHH----HHHHhcCC-CeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          221 RTVFAYQMPLKATERDV----YEFFSKAG-KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l----~~~f~~~G-~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      ..|+|.|||...+...|    ++++..|| .|..|          +.|.|+|.|.+.+.|..|. -|+|..+.|..|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            46999999999987665    55566675 67665          2478999999999999999 599999999999998


Q ss_pred             cCccc
Q 007742          295 PSEAE  299 (591)
Q Consensus       295 ~~~~~  299 (591)
                      +....
T Consensus        73 ~~~~~   77 (90)
T PF11608_consen   73 FSPKN   77 (90)
T ss_dssp             SS--S
T ss_pred             EcCCc
Confidence            87543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.79  E-value=1.7e-05  Score=80.39  Aligned_cols=84  Identities=24%  Similarity=0.434  Sum_probs=72.0

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhc-cccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccccc--
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECS-KYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWF--  570 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~-~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~--  570 (591)
                      -..++++|+|.||+-||+          ..+|+.++. .+|.|..+.|.. -+..|||.|.+.++|...+.+|||..|  
T Consensus       440 R~~~SnvlhI~nLvRPFT----------lgQLkelL~rtgg~Vee~WmDk-IKShCyV~yss~eEA~atr~AlhnV~WP~  508 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFT----------LGQLKELLGRTGGNVEEFWMDK-IKSHCYVSYSSVEEAAATREALHNVQWPP  508 (718)
T ss_pred             CCCccceEeeecccccch----------HHHHHHHHhhccCchHHHHHHH-hhcceeEecccHHHHHHHHHHHhccccCC
Confidence            467889999999999988          679999998 566777776653 466789999999999999999999997  


Q ss_pred             -CCeEEEEEEeCchhhhhc
Q 007742          571 -ARRLISAIFMKPEDYEAK  588 (591)
Q Consensus       571 -~g~~l~v~~~~~~~~~~~  588 (591)
                       +++.|.+.|+..+.+..|
T Consensus       509 sNPK~L~adf~~~deld~h  527 (718)
T KOG2416|consen  509 SNPKHLIADFVRADELDKH  527 (718)
T ss_pred             CCCceeEeeecchhHHHHH
Confidence             788999999999887754

>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=97.78  E-value=8.9e-05  Score=60.34  Aligned_cols=73  Identities=18%  Similarity=0.267  Sum_probs=46.3

Q ss_pred             ceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccc-----ccCCe
Q 007742          499 ECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMR-----WFARR  573 (591)
Q Consensus       499 ~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~-----~~~g~  573 (591)
                      .+|.|.++  ...++        .++|+++|+.||.|.+|.+.. +...|||.|.+++.|+.|+..+.-.     .+.+.
T Consensus         2 ~il~~~g~--~~~~~--------re~iK~~f~~~g~V~yVD~~~-G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~   70 (105)
T PF08777_consen    2 CILKFSGL--GEPTS--------REDIKEAFSQFGEVAYVDFSR-GDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGK   70 (105)
T ss_dssp             -EEEEEE----SS----------HHHHHHHT-SS--EEEEE--T-T-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSS
T ss_pred             eEEEEecC--CCCcC--------HHHHHHHHHhcCCcceEEecC-CCCEEEEEECCcchHHHHHHHHHhccCCceEEcCc
Confidence            47889998  44444        899999999999999998874 4557899999999999999988644     57888


Q ss_pred             EEEEEEeCc
Q 007742          574 LISAIFMKP  582 (591)
Q Consensus       574 ~l~v~~~~~  582 (591)
                      .+.+.....
T Consensus        71 ~~~~~vLeG   79 (105)
T PF08777_consen   71 EVTLEVLEG   79 (105)
T ss_dssp             SEEEE---H
T ss_pred             eEEEEECCC
Confidence            888877653

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.72  E-value=0.00026  Score=59.98  Aligned_cols=86  Identities=16%  Similarity=0.288  Sum_probs=59.1

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCe
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARR  573 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~  573 (591)
                      .++|..+|.|.=+. |....+..+...+...|.+.|..||.|.-|.+..   +..+|.|.+-+.|.+|+. |+|.+++|+
T Consensus        23 ~GPpDaTVvVsv~~-~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~---~~mwVTF~dg~sALaals-~dg~~v~g~   97 (146)
T PF08952_consen   23 QGPPDATVVVSVDS-PSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG---DTMWVTFRDGQSALAALS-LDGIQVNGR   97 (146)
T ss_dssp             ---TT-EEEEEECS--SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET---TCEEEEESSCHHHHHHHH-GCCSEETTE
T ss_pred             cCCCCceEEEEecC-CCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC---CeEEEEECccHHHHHHHc-cCCcEECCE
Confidence            35666677776652 2333334556667889999999999988887663   467999999999999998 899999999


Q ss_pred             EEEEEEeCchh
Q 007742          574 LISAIFMKPED  584 (591)
Q Consensus       574 ~l~v~~~~~~~  584 (591)
                      .|.|.+-+++-
T Consensus        98 ~l~i~LKtpdW  108 (146)
T PF08952_consen   98 TLKIRLKTPDW  108 (146)
T ss_dssp             EEEEEE-----
T ss_pred             EEEEEeCCccH
Confidence            99999877653

; PDB: 1UFW_A 2DNR_A.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.71  E-value=4.5e-05  Score=73.31  Aligned_cols=84  Identities=23%  Similarity=0.455  Sum_probs=74.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCee--------EEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVR--------DVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLL  287 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~--------~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~  287 (591)
                      ....-+|||.+||..+++.+|.++|.++|.|.        .|.|.+++.|+..+|-|.|.|.+...|++|+. +++..+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            44568999999999999999999999998774        48888999999999999999999999999995 8999999


Q ss_pred             CeeEEeccCcccc
Q 007742          288 GQPVMVKPSEAEK  300 (591)
Q Consensus       288 g~~i~v~~~~~~~  300 (591)
                      |.+|+|..+....
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999997665433

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.61  E-value=0.00018  Score=72.70  Aligned_cols=84  Identities=12%  Similarity=0.248  Sum_probs=68.7

Q ss_pred             CcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEec----CCCeeEEEEeCCHHHHHHHHHHhccccc-C
Q 007742          497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK----RSAGFVYLRFESTEAAASAQRAMHMRWF-A  571 (591)
Q Consensus       497 ~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~----~~~g~afV~F~~~e~A~~A~~~l~g~~~-~  571 (591)
                      -..||+|.|+  |....  +-..-|...|..+|+++|.|..+++|.    ..+|++|++|.+..+|..|++.|||+.| .
T Consensus        57 ~D~vVvv~g~--PvV~~--~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldk  132 (698)
T KOG2314|consen   57 FDSVVVVDGA--PVVGP--ARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDK  132 (698)
T ss_pred             cceEEEECCC--cccCh--hHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecc
Confidence            3458999999  77643  334456778999999999999999973    3689999999999999999999999998 5


Q ss_pred             CeEEEEEEeCchh
Q 007742          572 RRLISAIFMKPED  584 (591)
Q Consensus       572 g~~l~v~~~~~~~  584 (591)
                      .++..|..++.=+
T Consensus       133 nHtf~v~~f~d~e  145 (698)
T KOG2314|consen  133 NHTFFVRLFKDFE  145 (698)
T ss_pred             cceEEeehhhhHH
Confidence            7888888766543

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.51  E-value=0.00024  Score=67.44  Aligned_cols=78  Identities=26%  Similarity=0.328  Sum_probs=67.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFG--PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g--~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      .++||+||-+.+|.++|.+.+...|  .+..+.++.+..+|+++|||+|...+....++.|..|-.+ .|.|+.-.|..+
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k-~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTK-TIHGQSPTVLSY  159 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccc-eecCCCCeeecc
Confidence            6899999999999999999999887  5667778888778999999999999999999999888886 689976666544


Q ss_pred             c
Q 007742          400 T  400 (591)
Q Consensus       400 ~  400 (591)
                      +
T Consensus       160 N  160 (498)
T KOG4849|consen  160 N  160 (498)
T ss_pred             c
Confidence            3

>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=97.48  E-value=0.00038  Score=55.61  Aligned_cols=71  Identities=11%  Similarity=0.192  Sum_probs=51.6

Q ss_pred             ceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEE------------EecCCCeeEEEEeCCHHHHHHHHHHhc
Q 007742          499 ECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIY------------VDKRSAGFVYLRFESTEAAASAQRAMH  566 (591)
Q Consensus       499 ~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~------------l~~~~~g~afV~F~~~e~A~~A~~~l~  566 (591)
                      ..|.|.++  |...         ...|..+|++||.|....            -......+..|+|.++.+|.+||. -|
T Consensus         7 ~wVtVFGf--p~~~---------~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~N   74 (100)
T PF05172_consen    7 TWVTVFGF--PPSA---------SNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KN   74 (100)
T ss_dssp             CEEEEE-----GGG---------HHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TT
T ss_pred             eEEEEEcc--CHHH---------HHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hC
Confidence            45888888  6543         578999999999998875            122346688999999999999999 49


Q ss_pred             ccccCCeEEE-EEEeC
Q 007742          567 MRWFARRLIS-AIFMK  581 (591)
Q Consensus       567 g~~~~g~~l~-v~~~~  581 (591)
                      |..|+|..|. |.+++
T Consensus        75 G~i~~g~~mvGV~~~~   90 (100)
T PF05172_consen   75 GTIFSGSLMVGVKPCD   90 (100)
T ss_dssp             TEEETTCEEEEEEE-H
T ss_pred             CeEEcCcEEEEEEEcH
Confidence            9999987654 66663

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.39  E-value=0.0001  Score=68.30  Aligned_cols=79  Identities=23%  Similarity=0.198  Sum_probs=59.9

Q ss_pred             CCceEEEcCCC--CCCC---HHHHHHHhccCCCeeEEEEeccCCCC-CcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeE
Q 007742          320 IDRKLYVGNLH--FNMT---ETQLRKLFEPFGPVELVQLPLDIETG-QCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRT  393 (591)
Q Consensus       320 ~~~~l~v~nl~--~~~~---~~~l~~~f~~~g~i~~v~i~~~~~~~-~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~  393 (591)
                      +++.|++.|+-  -.+.   ++++.+.|++||.|..|.|....... ...--.||+|..+++|.+|+-.|||+ .|+|+.
T Consensus       280 ptkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGR-yFGGr~  358 (378)
T KOG1996|consen  280 PTKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGR-YFGGRV  358 (378)
T ss_pred             chHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCc-eeccee
Confidence            34567777763  2233   46789999999999988877654221 12335899999999999999999998 599999


Q ss_pred             EEEEEe
Q 007742          394 LKVSSV  399 (591)
Q Consensus       394 l~v~~~  399 (591)
                      |...|.
T Consensus       359 v~A~Fy  364 (378)
T KOG1996|consen  359 VSACFY  364 (378)
T ss_pred             eeheec
Confidence            998875

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.35  E-value=0.00021  Score=68.80  Aligned_cols=83  Identities=27%  Similarity=0.323  Sum_probs=73.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVEL--------VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG  391 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~--------v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g  391 (591)
                      ...+|||.+||..+++.+|.++|.++|.|..        |.|.+++.|+.++|-|.|.|.+...|+.|+.-++++ .|.|
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agk-df~g  143 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGK-DFCG  143 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccc-cccC
Confidence            3579999999999999999999999987643        677788889999999999999999999999999997 7999


Q ss_pred             eEEEEEEecCCC
Q 007742          392 RTLKVSSVTDHV  403 (591)
Q Consensus       392 ~~l~v~~~~~~~  403 (591)
                      .+|+|..+....
T Consensus       144 n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 NTIKVSLAERRT  155 (351)
T ss_pred             CCchhhhhhhcc
Confidence            999998776544

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.32  E-value=0.00068  Score=47.46  Aligned_cols=52  Identities=25%  Similarity=0.491  Sum_probs=42.3

Q ss_pred             ceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHH
Q 007742          499 ECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQ  562 (591)
Q Consensus       499 ~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~  562 (591)
                      +.|.|.+.  +...         .+.|..+|..||.|..+.++ ....++||+|.+..+|++|+
T Consensus         2 ~wI~V~Gf--~~~~---------~~~vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGF--PPDL---------AEEVLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeE--CchH---------HHHHHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            35778887  4332         57888899999999999988 34567899999999999985

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.25  E-value=0.00023  Score=69.72  Aligned_cols=65  Identities=20%  Similarity=0.309  Sum_probs=54.4

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC------------------CCeeEEEEeCCHH
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR------------------SAGFVYLRFESTE  556 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~------------------~~g~afV~F~~~e  556 (591)
                      ..++++|++.||  |..-.        .+.|.++|+.+|.|..|.|..+                  .+-||+|+|.+.+
T Consensus       228 el~srtivaenL--P~Dh~--------~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~  297 (484)
T KOG1855|consen  228 ELPSRTIVAENL--PLDHS--------YENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVE  297 (484)
T ss_pred             ccccceEEEecC--CcchH--------HHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhH
Confidence            358899999999  76544        6899999999999999988543                  1458999999999


Q ss_pred             HHHHHHHHhcccc
Q 007742          557 AAASAQRAMHMRW  569 (591)
Q Consensus       557 ~A~~A~~~l~g~~  569 (591)
                      .|.+|.+.|+...
T Consensus       298 ~A~KA~e~~~~e~  310 (484)
T KOG1855|consen  298 AARKARELLNPEQ  310 (484)
T ss_pred             HHHHHHHhhchhh
Confidence            9999999886444

>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=97.22  E-value=0.00063  Score=55.38  Aligned_cols=70  Identities=24%  Similarity=0.359  Sum_probs=44.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCC----eeeCCeEEEEE
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK----LEIVGRTLKVS  397 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~----~~~~g~~l~v~  397 (591)
                      ..|.|.+++..++-++|+++|..||.|..|.+....      ..|||.|.+.+.|+.|+..+...    +.+.+..+.+.
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            468899999999999999999999999999886432      36999999999999998877532    44566555554

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.16  E-value=0.00089  Score=63.44  Aligned_cols=80  Identities=16%  Similarity=0.351  Sum_probs=62.8

Q ss_pred             ceEEEcCCCCCCCHHHH------HHHhccCCCeeEEEEeccCCC-CCcccE--EEEEeCCHHHHHHHHHHhcCCeeeCCe
Q 007742          322 RKLYVGNLHFNMTETQL------RKLFEPFGPVELVQLPLDIET-GQCKGF--GFVQFAQLEHAKAAQSALNGKLEIVGR  392 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l------~~~f~~~g~i~~v~i~~~~~~-~~~~g~--a~Vef~~~~~a~~a~~~l~g~~~~~g~  392 (591)
                      .-+||.+||+.+..+++      .+.|.+||.|..|.|.+.... +...+.  +||.|.+.++|..||...+|.+ ++|+
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~-~DGr  193 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSL-LDGR  193 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccc-ccCc
Confidence            67899999988766652      378999999999888755422 122222  4999999999999999999984 9999


Q ss_pred             EEEEEEecCC
Q 007742          393 TLKVSSVTDH  402 (591)
Q Consensus       393 ~l~v~~~~~~  402 (591)
                      .|+..|.+.+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999987654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.05  E-value=0.0018  Score=61.40  Aligned_cols=82  Identities=21%  Similarity=0.375  Sum_probs=61.3

Q ss_pred             cceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCC------Ce--eEEEEeCCHHHHHHHHHHhcccc
Q 007742          498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRS------AG--FVYLRFESTEAAASAQRAMHMRW  569 (591)
Q Consensus       498 s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~------~g--~afV~F~~~e~A~~A~~~l~g~~  569 (591)
                      .+.++|-+|  +..+.+++....|  .-.++|..||.|..|.|.+..      .+  -+||.|.+.++|..||....|..
T Consensus       114 KNLvYVigi--~pkva~Ee~~~vL--k~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~  189 (480)
T COG5175         114 KNLVYVIGI--PPKVADEEVAPVL--KRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSL  189 (480)
T ss_pred             cceeEEecC--CCCCCcccccccc--cchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccc
Confidence            345788888  4444443332222  236899999999999885432      12  24999999999999999999999


Q ss_pred             cCCeEEEEEEeCch
Q 007742          570 FARRLISAIFMKPE  583 (591)
Q Consensus       570 ~~g~~l~v~~~~~~  583 (591)
                      ++|+.|.+.|-+.+
T Consensus       190 ~DGr~lkatYGTTK  203 (480)
T COG5175         190 LDGRVLKATYGTTK  203 (480)
T ss_pred             ccCceEeeecCchH
Confidence            99999999996654

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.92  E-value=0.00039  Score=63.88  Aligned_cols=65  Identities=22%  Similarity=0.293  Sum_probs=52.8

Q ss_pred             HHHHHHhc-cCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          336 TQLRKLFE-PFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       336 ~~l~~~f~-~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      ++|...|+ +||+|+.+.|-.+. .....|-+||+|...++|++|++.||+.| |.|++|...++.-.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw-~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRW-YNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCcc-ccCCcceeeecCcC
Confidence            45555555 89999988665443 55678999999999999999999999995 99999999876533

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.91  E-value=0.0018  Score=65.73  Aligned_cols=81  Identities=31%  Similarity=0.383  Sum_probs=64.0

Q ss_pred             CceEEEcCCCCCC------CHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEE
Q 007742          321 DRKLYVGNLHFNM------TETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTL  394 (591)
Q Consensus       321 ~~~l~v~nl~~~~------~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l  394 (591)
                      ..+|+|.|+|.--      -...|..+|+++|+|..+.++.+.. |..+||+|++|.+..+|..|++.|||.-......+
T Consensus        58 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   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            3789999998532      1235678999999999999988874 44899999999999999999999999633456777


Q ss_pred             EEEEecCC
Q 007742          395 KVSSVTDH  402 (591)
Q Consensus       395 ~v~~~~~~  402 (591)
                      .|...++-
T Consensus       137 ~v~~f~d~  144 (698)
T KOG2314|consen  137 FVRLFKDF  144 (698)
T ss_pred             EeehhhhH
Confidence            77765543

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.91  E-value=0.00083  Score=63.94  Aligned_cols=78  Identities=17%  Similarity=0.282  Sum_probs=65.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEecc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAG--KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKP  295 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G--~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~  295 (591)
                      ....+||+||-|.+|++||.+.+...|  .|.+++++-+..+|.++|||+|...+...+...|+ |....|.|+.-.|..
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            346789999999999999999998776  57888899999999999999999999888888885 667778887666644


Q ss_pred             C
Q 007742          296 S  296 (591)
Q Consensus       296 ~  296 (591)
                      .
T Consensus       159 ~  159 (498)
T KOG4849|consen  159 Y  159 (498)
T ss_pred             c
Confidence            3

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.77  E-value=0.0046  Score=52.49  Aligned_cols=73  Identities=19%  Similarity=0.259  Sum_probs=52.1

Q ss_pred             CcEEEEeCCCC------CCCH---HHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCee
Q 007742          220 QRTVFAYQMPL------KATE---RDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQP  290 (591)
Q Consensus       220 ~~~l~V~nLp~------~~te---~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~  290 (591)
                      -.+|.|.=+.+      ...+   .+|.+.|..||.++-|+++-        +.-+|+|.+-+.|.+|+.++|..+.|+.
T Consensus        27 DaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~--------~~mwVTF~dg~sALaals~dg~~v~g~~   98 (146)
T PF08952_consen   27 DATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG--------DTMWVTFRDGQSALAALSLDGIQVNGRT   98 (146)
T ss_dssp             T-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET--------TCEEEEESSCHHHHHHHHGCCSEETTEE
T ss_pred             CceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC--------CeEEEEECccHHHHHHHccCCcEECCEE
Confidence            35666665541      2222   36778899999999998884        3589999999999999999999999999


Q ss_pred             EEeccCcccc
Q 007742          291 VMVKPSEAEK  300 (591)
Q Consensus       291 i~v~~~~~~~  300 (591)
                      |.|....+.+
T Consensus        99 l~i~LKtpdW  108 (146)
T PF08952_consen   99 LKIRLKTPDW  108 (146)
T ss_dssp             EEEEE-----
T ss_pred             EEEEeCCccH
Confidence            9997665544

; PDB: 1UFW_A 2DNR_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.71  E-value=0.0039  Score=43.63  Aligned_cols=52  Identities=19%  Similarity=0.285  Sum_probs=41.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI  279 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al  279 (591)
                      +.|-|.|.|+...+ .+..+|..||.|..+.+..      ..-+.||.|.+..+|..||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            56888898877654 4556899999999988762      2448999999999999985

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.62  E-value=0.0038  Score=57.37  Aligned_cols=100  Identities=27%  Similarity=0.361  Sum_probs=80.0

Q ss_pred             HHHHH-HHcCCccCCeeEEeccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEE
Q 007742          275 VPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQL  353 (591)
Q Consensus       275 A~~Al-~l~g~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i  353 (591)
                      |..|- +|++....|+.+.|.++..                       ..|+|.||...+..+.+.+.|+.||+|....+
T Consensus         7 ae~ak~eLd~~~~~~~~lr~rfa~~-----------------------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~   63 (275)
T KOG0115|consen    7 AEIAKRELDGRFPKGRSLRVRFAMH-----------------------AELYVVNLMQGASNDLLEQAFRRFGPIERAVA   63 (275)
T ss_pred             HHHHHHhcCCCCCCCCceEEEeecc-----------------------ceEEEEecchhhhhHHHHHhhhhcCccchhee
Confidence            44555 6999999999999988753                       57999999999999999999999999988777


Q ss_pred             eccCCCCCcccEEEEEeCCHHHHHHHHHHhcCC---eeeCCeEEEEEE
Q 007742          354 PLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK---LEIVGRTLKVSS  398 (591)
Q Consensus       354 ~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~---~~~~g~~l~v~~  398 (591)
                      ..+. .+...+-++|+|...-.|.+|+..+.-.   +...+.++.|..
T Consensus        64 ~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   64 KVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             eecc-cccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            6664 6778889999999999999999887432   223345555543

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.42  E-value=0.0018  Score=59.47  Aligned_cols=72  Identities=26%  Similarity=0.382  Sum_probs=59.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCC--------CCc----ccEEEEEeCCHHHHHHHHHHhcCCeee
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIET--------GQC----KGFGFVQFAQLEHAKAAQSALNGKLEI  389 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~--------~~~----~g~a~Vef~~~~~a~~a~~~l~g~~~~  389 (591)
                      -.|||.+||+.+...-|+++|+.||.|-.|.+-....+        +..    -.-|+|||.+...|..+...|||. .|
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~-~I  153 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNT-PI  153 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCC-cc
Confidence            48999999999999999999999999999988755433        111    235799999999999999999997 58


Q ss_pred             CCeEE
Q 007742          390 VGRTL  394 (591)
Q Consensus       390 ~g~~l  394 (591)
                      +|+.-
T Consensus       154 ggkk~  158 (278)
T KOG3152|consen  154 GGKKK  158 (278)
T ss_pred             CCCCC
Confidence            88753

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.32  E-value=0.0044  Score=61.06  Aligned_cols=67  Identities=21%  Similarity=0.357  Sum_probs=56.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeec---CCC--CC--------ccceEEEEecCcchHHHHHHHc
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMD---RNS--RR--------SKGVGYIEFYDVMSVPMAIALS  282 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d---~~~--g~--------~~G~afV~F~~~e~A~~Al~l~  282 (591)
                      ++-++++|.+.|||.+-..+.|.++|..+|.|..|+|+.-   ...  +.        .+-+|||+|...+.|.+|.+++
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            3457899999999999989999999999999999999875   221  11        1568999999999999999754

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.27  E-value=0.0039  Score=57.30  Aligned_cols=72  Identities=19%  Similarity=0.240  Sum_probs=59.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC--------CCccc----eEEEEecCcchHHHHH-HHcCCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS--------RRSKG----VGYIEFYDVMSVPMAI-ALSGQL  285 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~--------g~~~G----~afV~F~~~e~A~~Al-~l~g~~  285 (591)
                      ....||+++||+.+...-|+++|..||.|--|.|.....+        |...+    -|.|+|.+...|.... .||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4478999999999999999999999999999998876554        33333    3569999999998777 699999


Q ss_pred             cCCee
Q 007742          286 LLGQP  290 (591)
Q Consensus       286 i~g~~  290 (591)
                      |+|..
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99874

>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=96.18  E-value=0.015  Score=46.57  Aligned_cols=76  Identities=18%  Similarity=0.275  Sum_probs=51.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecC-------CCCCccceEEEEecCcchHHHHHHHcCCccCCeeEE
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR-------NSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM  292 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~-------~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~  292 (591)
                      .+.|.|-+.|+. ....|...|++||.|+...-+...       ........-.|.|.+..+|.+||..||..|.|.-|.
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~mv   84 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLMV   84 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEEE
Confidence            467889999887 456788999999999876411000       001234588999999999999999999999886554


Q ss_pred             -eccC
Q 007742          293 -VKPS  296 (591)
Q Consensus       293 -v~~~  296 (591)
                       |.+.
T Consensus        85 GV~~~   89 (100)
T PF05172_consen   85 GVKPC   89 (100)
T ss_dssp             EEEE-
T ss_pred             EEEEc
Confidence             5555

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.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.74  E-value=0.059  Score=40.82  Aligned_cols=56  Identities=21%  Similarity=0.354  Sum_probs=41.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG  385 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g  385 (591)
                      ..||--.+|..+...||.++|++||.|. |..+.+.       -|||.+.+.+.|..|+..+.-
T Consensus         9 dHVFhltFPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLTFPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE--TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEeCchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            3455445999999999999999999985 5554442       599999999999999977763

; 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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.68  E-value=0.046  Score=45.75  Aligned_cols=55  Identities=13%  Similarity=0.169  Sum_probs=46.2

Q ss_pred             HHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEE
Q 007742          522 QGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIF  579 (591)
Q Consensus       522 ~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~  579 (591)
                      ...|...++.||.|.+|.+-  ++-.|.|.|.+..+|.+|+.+++. ..-|..+.++|
T Consensus       104 l~sV~~~Ls~fGpI~SVT~c--GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen  104 LKSVIQRLSVFGPIQSVTLC--GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             HHHHHHHHHhcCCcceeeec--CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            35667777899999999876  456789999999999999999876 66788888887

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.11  E-value=0.06  Score=50.84  Aligned_cols=67  Identities=13%  Similarity=0.121  Sum_probs=52.3

Q ss_pred             eEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEE-EEE
Q 007742          500 CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI-SAI  578 (591)
Q Consensus       500 ~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l-~v~  578 (591)
                      -|.|.++  |...         ..-|..+|.+||.|+..... ..-.+.+|.|.+.-+|++||.+ ||+.|+|..+ -|.
T Consensus       199 WVTVfGF--ppg~---------~s~vL~~F~~cG~Vvkhv~~-~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVk  265 (350)
T KOG4285|consen  199 WVTVFGF--PPGQ---------VSIVLNLFSRCGEVVKHVTP-SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVK  265 (350)
T ss_pred             eEEEecc--Cccc---------hhHHHHHHHhhCeeeeeecC-CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeee
Confidence            3677777  4433         35789999999999988766 3344679999999999999995 9999998874 344


Q ss_pred             E
Q 007742          579 F  579 (591)
Q Consensus       579 ~  579 (591)
                      -
T Consensus       266 p  266 (350)
T KOG4285|consen  266 P  266 (350)
T ss_pred             e
Confidence            4

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=94.95  E-value=0.029  Score=57.81  Aligned_cols=77  Identities=26%  Similarity=0.227  Sum_probs=59.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhcc-CCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeee--CCeEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEP-FGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI--VGRTL  394 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~-~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~--~g~~l  394 (591)
                      ..++..|+|.||--.+|.-+|++++.. .|.|...+|  ++    -+..|||.|.+.++|.....+|||-.+-  +++.|
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HH----hhcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            445789999999999999999999994 556655533  22    3557999999999999999999994222  35778


Q ss_pred             EEEEec
Q 007742          395 KVSSVT  400 (591)
Q Consensus       395 ~v~~~~  400 (591)
                      .|.|..
T Consensus       515 ~adf~~  520 (718)
T KOG2416|consen  515 IADFVR  520 (718)
T ss_pred             Eeeecc
Confidence            887764

>PF15519 RBM39linker: linker between RRM2 and RRM3 domains in RBM39 protein; PDB: 3S6E_A 2LQ5_A

Probab=94.66  E-value=0.02  Score=42.92  Aligned_cols=69  Identities=46%  Similarity=0.617  Sum_probs=15.7

Q ss_pred             CCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCCCCCccccccccccCC
Q 007742          417 DDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGS  496 (591)
Q Consensus       417 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  496 (591)
                      ..+.+|..++..++.+++.++..............+.               +        .         ....+....
T Consensus         5 d~d~~G~~l~a~sR~~LM~KLA~~~~~~~~~~~~~~~---------------~--------~---------~~~~~~~~~   52 (73)
T PF15519_consen    5 DDDRGGVNLNATSRAALMAKLARGDGPQIPPAAQQAL---------------Q--------P---------NGSIPIPPI   52 (73)
T ss_dssp             ------------------------------------------------------------------------------S-
T ss_pred             ccccccccccccccccccccccccccccccccccccc---------------C--------c---------CCCCCCCCC
Confidence            4456778889999999999998854211111000000               0        0         000011137


Q ss_pred             CcceEEEeccCCCCCCCCchh
Q 007742          497 PSECLLLKNMFDPAMETDPDF  517 (591)
Q Consensus       497 ~s~~l~v~Nl~~p~~~~~~~~  517 (591)
                      ++.||+|+|+|+|...++++|
T Consensus        53 aS~C~lLkNMFDP~~Ete~~W   73 (73)
T PF15519_consen   53 ASRCFLLKNMFDPAEETEPDW   73 (73)
T ss_dssp             --SEEEEESSS-TTCGGSTTH
T ss_pred             CCceeeeecCCCcccccCCCC
Confidence            889999999999998876554

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.65  E-value=0.045  Score=55.92  Aligned_cols=72  Identities=18%  Similarity=0.180  Sum_probs=55.0

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhcc--ccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccc--ccC
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSK--YGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMR--WFA  571 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~--~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~--~~~  571 (591)
                      ...++|+|.-|  |.++-        +++|+.+|..  +-.+++|.+.-+  ..+||.|++..+|+.|++.|.-.  .|.
T Consensus       173 ~kRcIvilREI--pettp--------~e~Vk~lf~~encPk~iscefa~N--~nWyITfesd~DAQqAykylreevk~fq  240 (684)
T KOG2591|consen  173 HKRCIVILREI--PETTP--------IEVVKALFKGENCPKVISCEFAHN--DNWYITFESDTDAQQAYKYLREEVKTFQ  240 (684)
T ss_pred             cceeEEEEeec--CCCCh--------HHHHHHHhccCCCCCceeeeeeec--CceEEEeecchhHHHHHHHHHHHHHhhc
Confidence            44567889999  88776        8999999975  667777776532  24799999999999999998644  377


Q ss_pred             CeEEEEEE
Q 007742          572 RRLISAIF  579 (591)
Q Consensus       572 g~~l~v~~  579 (591)
                      |+.|....
T Consensus       241 gKpImARI  248 (684)
T KOG2591|consen  241 GKPIMARI  248 (684)
T ss_pred             Ccchhhhh
Confidence            77775543

>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=94.37  E-value=0.42  Score=39.10  Aligned_cols=75  Identities=19%  Similarity=0.154  Sum_probs=54.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC---CeEEEEE
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFG-PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV---GRTLKVS  397 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~---g~~l~v~  397 (591)
                      ..+++...|..++.++|..+.+.+- .|..++|+++.  ...+..++++|.+.+.|......+||+ .|.   ....+|.
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk-~FnslEpE~Chvv   90 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGK-PFNSLEPETCHVV   90 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCC-ccCCCCCceeEEE
Confidence            5566666666677777877777765 67788888864  235778899999999999999999996 344   3344444


Q ss_pred             Ee
Q 007742          398 SV  399 (591)
Q Consensus       398 ~~  399 (591)
                      +.
T Consensus        91 fV   92 (110)
T PF07576_consen   91 FV   92 (110)
T ss_pred             EE
Confidence            43

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=94.35  E-value=0.1  Score=47.14  Aligned_cols=60  Identities=27%  Similarity=0.300  Sum_probs=45.7

Q ss_pred             HHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhc--ccccCCeEEEEEEeCc
Q 007742          522 QGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMH--MRWFARRLISAIFMKP  582 (591)
Q Consensus       522 ~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~--g~~~~g~~l~v~~~~~  582 (591)
                      ...|..+|..|+.+..+.+.+ +-+-+.|.|.+.+.|..|...|+  +..|.|..|.|.|+..
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~-sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLK-SFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEET-TTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             HHHHHHHHHhcCCceEEEEcC-CCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            678999999999888776553 45567999999999999999999  9999999999999843

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=94.35  E-value=0.18  Score=36.86  Aligned_cols=52  Identities=21%  Similarity=0.336  Sum_probs=43.6

Q ss_pred             HHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEE
Q 007742          522 QGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISA  577 (591)
Q Consensus       522 ~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v  577 (591)
                      .++|+..+.+|+...   |..+.+|+ ||.|.+..+|.++....+|+.+.+..|.+
T Consensus        14 v~d~K~~Lr~y~~~~---I~~d~tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   14 VEDFKKRLRKYRWDR---IRDDRTGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             HHHHHHHHhcCCcce---EEecCCEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            689999999997433   23456886 99999999999999999999999888765

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=94.19  E-value=0.024  Score=56.85  Aligned_cols=77  Identities=14%  Similarity=0.144  Sum_probs=65.1

Q ss_pred             CCCCcEEEEeCCCCCC-CHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKA-TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~-te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~  295 (591)
                      ..+.+.|-+.-.|+.+ |-.+|..+|.+||.|..|.+-..      .-.|.|+|.+.-+|-.|...++..|.++.|+|.|
T Consensus       369 ~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~w  442 (526)
T KOG2135|consen  369 VVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFW  442 (526)
T ss_pred             hcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhccccceecCceeEEEE
Confidence            3455777777788877 67899999999999999988654      3369999999999999999999999999999999


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      .++.
T Consensus       443 hnps  446 (526)
T KOG2135|consen  443 HNPS  446 (526)
T ss_pred             ecCC
Confidence            8653

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=93.98  E-value=0.15  Score=47.16  Aligned_cols=60  Identities=13%  Similarity=0.144  Sum_probs=47.0

Q ss_pred             eEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEE----ecCCCeeEEEEeCCHHHHHHHHHHhcccc
Q 007742          500 CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYV----DKRSAGFVYLRFESTEAAASAQRAMHMRW  569 (591)
Q Consensus       500 ~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l----~~~~~g~afV~F~~~e~A~~A~~~l~g~~  569 (591)
                      .|+|.||  ...+.        .+.|...|+.||.|....+    ...+.+-++|+|...-.|.+|+...+-.-
T Consensus        33 ~l~V~nl--~~~~s--------ndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g   96 (275)
T KOG0115|consen   33 ELYVVNL--MQGAS--------NDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGG   96 (275)
T ss_pred             eEEEEec--chhhh--------hHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCc
Confidence            5999999  55555        6889999999999876544    23467788999999999999998774333

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=93.60  E-value=0.31  Score=35.02  Aligned_cols=54  Identities=17%  Similarity=0.175  Sum_probs=44.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccC---CCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHh
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPF---GPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL  383 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~---g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l  383 (591)
                      ..|+|.++. .++.++|+..|..|   .....|..+-+.       -|-|.|.+.+.|..||.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            679999996 58889999999998   234567777664       4899999999999999764

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.43  E-value=0.18  Score=42.25  Aligned_cols=69  Identities=22%  Similarity=0.239  Sum_probs=52.5

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          322 RKLYVGNL----HFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       322 ~~l~v~nl----~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      .+|.|.=|    .+.-+...|...++.||+|.+|.+.       ++-.|.|.|.+..+|-+|+.+++..  .-|..+...
T Consensus        87 sTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-------GrqsavVvF~d~~SAC~Av~Af~s~--~pgtm~qCs  157 (166)
T PF15023_consen   87 STIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-------GRQSAVVVFKDITSACKAVSAFQSR--APGTMFQCS  157 (166)
T ss_pred             eeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-------CCceEEEEehhhHHHHHHHHhhcCC--CCCceEEee
Confidence            46666544    4444445677788999999999773       2335999999999999999999984  678888877


Q ss_pred             Ee
Q 007742          398 SV  399 (591)
Q Consensus       398 ~~  399 (591)
                      +-
T Consensus       158 Wq  159 (166)
T PF15023_consen  158 WQ  159 (166)
T ss_pred             cc
Confidence            64

>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=93.32  E-value=0.14  Score=46.04  Aligned_cols=69  Identities=14%  Similarity=0.166  Sum_probs=45.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhcc-CCCe---eEEE--EeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEP-FGPV---ELVQ--LPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV  390 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~-~g~i---~~v~--i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~  390 (591)
                      ..|.|++||+.+|++++.+.+.+ ++..   ..+.  ..........-.-|||.|.+.+++...+..++|...++
T Consensus         8 ~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D   82 (176)
T PF03467_consen    8 TKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVD   82 (176)
T ss_dssp             -EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-
T ss_pred             ceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEEC
Confidence            68999999999999999998887 6654   2332  11111112234569999999999999999999964333

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.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=92.98  E-value=0.027  Score=59.01  Aligned_cols=122  Identities=16%  Similarity=0.138  Sum_probs=78.8

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEe
Q 007742          215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV  293 (591)
Q Consensus       215 ~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v  293 (591)
                      .+-.+..++||+|+-..+..+-++.++..+|.|.++..+.         |||..|..+..+..|+ .++...+.|..+.+
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            3445678999999999999999999999999988765442         9999999999999999 57777788888877


Q ss_pred             ccCccccccccccCCCC---CCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCC
Q 007742          294 KPSEAEKNLVQSNTSAG---GTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG  346 (591)
Q Consensus       294 ~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g  346 (591)
                      ..-...-..........   .....+.. .-+.++|.|+|..+.+......|.-.+
T Consensus       106 ~~d~q~~~n~~k~~~~~~~~~~~f~p~~-srr~e~i~~k~~~l~~~~~~~~~~is~  160 (668)
T KOG2253|consen  106 NVDEQTIENADKEKSIANKESHKFVPSS-SRRQESIQNKPLSLDEQIHKKSLQISS  160 (668)
T ss_pred             cchhhhhcCccccccchhhhhcccCCch-hHHHHHhhccccchhHHHHHHHHhccc
Confidence            54311000000000000   00001110 035667777777666665555555433

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=92.67  E-value=0.59  Score=35.57  Aligned_cols=53  Identities=11%  Similarity=0.278  Sum_probs=39.8

Q ss_pred             eEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhc
Q 007742          500 CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMH  566 (591)
Q Consensus       500 ~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~  566 (591)
                      +.+|. +  |.+..        ..||.++|+.||.|.--.|.   ...|||...+.+.|..|+..+.
T Consensus        11 VFhlt-F--PkeWK--------~~DI~qlFspfG~I~VsWi~---dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   11 VFHLT-F--PKEWK--------TSDIYQLFSPFGQIYVSWIN---DTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             EEEEE-----TT----------HHHHHHHCCCCCCEEEEEEC---TTEEEEEECCCHHHHHHHHHHT
T ss_pred             EEEEe-C--chHhh--------hhhHHHHhccCCcEEEEEEc---CCcEEEEeecHHHHHHHHHHhc
Confidence            34444 6  77665        78999999999988766665   4578999999999999988775

; 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.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=92.66  E-value=0.19  Score=54.30  Aligned_cols=64  Identities=20%  Similarity=0.247  Sum_probs=54.7

Q ss_pred             HHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccccc--CCeEEEEEEeCchhhh
Q 007742          522 QGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWF--ARRLISAIFMKPEDYE  586 (591)
Q Consensus       522 ~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~--~g~~l~v~~~~~~~~~  586 (591)
                      -.-|..+|++||.|.++...++ -..|.|+|.+.+.|..|+.+|+|+.+  -|-+.+|.|++...+.
T Consensus       312 SssL~~l~s~yg~v~s~wtlr~-~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~~~  377 (1007)
T KOG4574|consen  312 SSSLATLCSDYGSVASAWTLRD-LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLPMY  377 (1007)
T ss_pred             HHHHHHHHHhhcchhhheeccc-ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccccc
Confidence            4578999999999999987543 45789999999999999999999984  7889999998876654

>KOG0670 consensus U4/U6-associated splicing factor PRP4 [RNA processing and modification]

Probab=92.52  E-value=0.066  Score=54.98  Aligned_cols=11  Identities=9%  Similarity=0.160  Sum_probs=4.4

Q ss_pred             EeccCCCCCCC
Q 007742          503 LKNMFDPAMET  513 (591)
Q Consensus       503 v~Nl~~p~~~~  513 (591)
                      -+-|..|-.++
T Consensus       630 tGkIlFpG~TN  640 (752)
T KOG0670|consen  630 TGKILFPGRTN  640 (752)
T ss_pred             ccceecCCCCc
Confidence            33343344443

>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=92.04  E-value=0.17  Score=45.66  Aligned_cols=69  Identities=16%  Similarity=0.203  Sum_probs=43.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhc-CCCe---eEEEEeecCCC--CCccceEEEEecCcchHHHHH-HHcCCccC
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSK-AGKV---RDVRLIMDRNS--RRSKGVGYIEFYDVMSVPMAI-ALSGQLLL  287 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~-~G~i---~~v~~~~d~~~--g~~~G~afV~F~~~e~A~~Al-~l~g~~i~  287 (591)
                      ...+|.|++||+.+|++++.+.+.. ++..   ..+.-.....+  ...-.-|||.|.+.+++...+ .++|..+.
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~   81 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFV   81 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEE
Confidence            4579999999999999999887776 5544   33332222111  112356899999999988888 58887653

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=91.66  E-value=0.1  Score=52.42  Aligned_cols=59  Identities=20%  Similarity=0.366  Sum_probs=52.5

Q ss_pred             HHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCc
Q 007742          522 QGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKP  582 (591)
Q Consensus       522 ~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~  582 (591)
                      ..+|..+|..||.|..|.+.-. .-.|.|+|.+.-+|-.|.+ .++-.|+|+-|+|.|.++
T Consensus       387 ~a~ln~hfA~fG~i~n~qv~~~-~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  387 IADLNPHFAQFGEIENIQVDYS-SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             HhhhhhhhhhcCccccccccCc-hhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            6899999999999999988644 4568999999999988887 699999999999999887

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=91.41  E-value=0.28  Score=51.75  Aligned_cols=70  Identities=17%  Similarity=0.126  Sum_probs=56.9

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      -++..++||+|+  .....        .+-++.+...+|.|.+.....    |+|+.|..+..+..|+..|+-..++|..
T Consensus        37 ~~~~~~vfv~~~--~~~~s--------~~~~~~il~~~g~v~s~kr~~----fgf~~f~~~~~~~ra~r~~t~~~~~~~k  102 (668)
T KOG2253|consen   37 LPPRDTVFVGNI--SYLVS--------QEFWKSILAKSGFVPSWKRDK----FGFCEFLKHIGDLRASRLLTELNIDDQK  102 (668)
T ss_pred             CCCCceeEecch--hhhhh--------HHHHHHHHhhCCcchhhhhhh----hcccchhhHHHHHHHHHHhcccCCCcch
Confidence            456678999999  44433        567888889999998886553    8999999999999999999988898888


Q ss_pred             EEEE
Q 007742          575 ISAI  578 (591)
Q Consensus       575 l~v~  578 (591)
                      +.+.
T Consensus       103 l~~~  106 (668)
T KOG2253|consen  103 LIEN  106 (668)
T ss_pred             hhcc
Confidence            7654

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=90.77  E-value=0.49  Score=51.29  Aligned_cols=74  Identities=27%  Similarity=0.350  Sum_probs=59.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCC-eeeCCeEEEEEEecCC
Q 007742          324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK-LEIVGRTLKVSSVTDH  402 (591)
Q Consensus       324 l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~-~~~~g~~l~v~~~~~~  402 (591)
                      .++.|.+...+-..|..+|..||.|.+++..++.      ..|.|+|.+++.|..|+.+|+|+ +..-|.+.+|.+++..
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            3344445566778899999999999999887664      36999999999999999999996 4466888999988654


Q ss_pred             C
Q 007742          403 V  403 (591)
Q Consensus       403 ~  403 (591)
                      .
T Consensus       375 ~  375 (1007)
T KOG4574|consen  375 P  375 (1007)
T ss_pred             c
Confidence            3

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=90.55  E-value=0.75  Score=46.30  Aligned_cols=68  Identities=16%  Similarity=0.184  Sum_probs=57.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFG-PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG  391 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g  391 (591)
                      +..|+|-.+|..++..||..++..+- .|..|.|+++.  ...+-.++|+|.+.++|..+.+.+||. .|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~--~pnrymvLIkFr~q~da~~Fy~efNGk-~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG--MPNRYMVLIKFRDQADADTFYEEFNGK-QFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC--CCceEEEEEEeccchhHHHHHHHcCCC-cCCC
Confidence            47899999999999999999999876 68899999853  234567899999999999999999996 4543

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=90.22  E-value=1.7  Score=43.83  Aligned_cols=67  Identities=16%  Similarity=0.282  Sum_probs=57.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcC-CCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKA-GKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG  288 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~-G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g  288 (591)
                      +..|.|-.+|..+|.-||..|+..| -.|.+|++++|.-  ..+-..+|.|.+..+|.... ++||..|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            7899999999999999999998876 4688999999653  35567899999999999999 799998864

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=89.84  E-value=1  Score=43.88  Aligned_cols=82  Identities=18%  Similarity=0.258  Sum_probs=62.1

Q ss_pred             ceEEEcCCCCCCCHHHHH---HHhccCCCeeEEEEeccCC--C-CCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEE
Q 007742          322 RKLYVGNLHFNMTETQLR---KLFEPFGPVELVQLPLDIE--T-GQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLK  395 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~---~~f~~~g~i~~v~i~~~~~--~-~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~  395 (591)
                      .-+||.+|+..+..+.+.   +.|..||.|..|.+..+..  . .....-+||.|...++|..||...+|. .++|+.|+
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~-~~dg~~lk  156 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGF-VDDGRALK  156 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhH-HhhhhhhH
Confidence            567788888776655555   4788889999998887652  1 112334899999999999999999995 69999988


Q ss_pred             EEEecCCCC
Q 007742          396 VSSVTDHVG  404 (591)
Q Consensus       396 v~~~~~~~~  404 (591)
                      +.+.+....
T Consensus       157 a~~gttkyc  165 (327)
T KOG2068|consen  157 ASLGTTKYC  165 (327)
T ss_pred             HhhCCCcch
Confidence            887765543

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=89.53  E-value=1.3  Score=42.13  Aligned_cols=73  Identities=23%  Similarity=0.262  Sum_probs=55.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC-eEEEEEEe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG-RTLKVSSV  399 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g-~~l~v~~~  399 (591)
                      ..-|.|.++|+.. ..-|..+|+.||.|.......      ...+.+|.|.+..+|.+|| ..+|++ |+| ..|-|..|
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~~------ngNwMhirYssr~~A~KAL-skng~i-i~g~vmiGVkpC  267 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTPS------NGNWMHIRYSSRTHAQKAL-SKNGTI-IDGDVMIGVKPC  267 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecCC------CCceEEEEecchhHHHHhh-hhcCee-eccceEEeeeec
Confidence            4677788888653 456889999999997776542      2458999999999999999 788874 766 45566777


Q ss_pred             cCC
Q 007742          400 TDH  402 (591)
Q Consensus       400 ~~~  402 (591)
                      +++
T Consensus       268 tDk  270 (350)
T KOG4285|consen  268 TDK  270 (350)
T ss_pred             CCH
Confidence            664

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=88.95  E-value=0.86  Score=47.04  Aligned_cols=69  Identities=12%  Similarity=0.110  Sum_probs=54.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhcc--CCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCC-eeeCCeEEEEE
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEP--FGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK-LEIVGRTLKVS  397 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~--~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~-~~~~g~~l~v~  397 (591)
                      +.|+|+-||..+..++|+.+|..  +-++.+|.+-.+.       -=||+|.+..+|+.|.+.|... -.|.|++|...
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            57778999999999999999987  4567677665432       2699999999999999888752 25888888654

>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=88.91  E-value=4  Score=33.46  Aligned_cols=67  Identities=16%  Similarity=0.205  Sum_probs=47.4

Q ss_pred             CcEEEEeCC-CCCCCHHHHHHHHhcC-CCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC
Q 007742          220 QRTVFAYQM-PLKATERDVYEFFSKA-GKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG  288 (591)
Q Consensus       220 ~~~l~V~nL-p~~~te~~l~~~f~~~-G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g  288 (591)
                      ...+.+-.. |+.++-++|..+...+ ..|..++|+++..  ..+-.+.+.|.+.+.|..+. ..||+.+..
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            344444444 4445556666555555 4577888888754  46778999999999999999 699988753

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>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=88.47  E-value=1.4  Score=39.84  Aligned_cols=60  Identities=23%  Similarity=0.234  Sum_probs=44.8

Q ss_pred             CHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhc--CCeeeCCeEEEEEEec
Q 007742          334 TETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN--GKLEIVGRTLKVSSVT  400 (591)
Q Consensus       334 ~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~--g~~~~~g~~l~v~~~~  400 (591)
                      ....|.++|..++.+..+..+..      -+-+.|.|.+.+.|..|...|+  +. .|.|..+.+.++.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~-~~~g~~l~~yf~~   69 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGT-SFNGKRLRVYFGQ   69 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TS-EETTEE-EEE---
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhccccc-ccCCCceEEEEcc
Confidence            45789999999998887776643      3459999999999999999999  86 6999999999874

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.

>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=88.37  E-value=0.34  Score=37.67  Aligned_cols=72  Identities=21%  Similarity=0.107  Sum_probs=45.4

Q ss_pred             EEEEecCcchHHHHHHHcC--CccCCeeEEeccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHh
Q 007742          265 GYIEFYDVMSVPMAIALSG--QLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLF  342 (591)
Q Consensus       265 afV~F~~~e~A~~Al~l~g--~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f  342 (591)
                      |+|+|...+-|+.-+.+..  ..+.+..+.|............-.       .......++|.|.|||..+.++.|++.+
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~q-------v~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQ-------VFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEE-------EEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            6899999999998886543  346666666654332221111100       0112224899999999999999888755


Q ss_pred             c
Q 007742          343 E  343 (591)
Q Consensus       343 ~  343 (591)
                      +
T Consensus        74 e   74 (88)
T PF07292_consen   74 E   74 (88)
T ss_pred             E
Confidence            4

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=86.92  E-value=4.2  Score=29.32  Aligned_cols=53  Identities=23%  Similarity=0.226  Sum_probs=37.5

Q ss_pred             ceEEEeccCCCCCCCCchhhhhHHHHHHHHhccc----cceEEEEEecCCCeeEEEEeCCHHHHHHHHHHh
Q 007742          499 ECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKY----GRVKHIYVDKRSAGFVYLRFESTEAAASAQRAM  565 (591)
Q Consensus       499 ~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~----G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l  565 (591)
                      ..|.|.++.  . ++        .++|+.+|..|    + ...|.-..  ...|-|.|.+.+.|..|+.+|
T Consensus         6 eavhirGvd--~-ls--------T~dI~~y~~~y~~~~~-~~~IEWId--DtScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD--E-LS--------TDDIKAYFSEYFDEEG-PFRIEWID--DTSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC--C-CC--------HHHHHHHHHHhcccCC-CceEEEec--CCcEEEEECCHHHHHHHHHcC
Confidence            358999982  2 22        57999999988    3 33443322  235689999999999999865

>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]

Probab=86.67  E-value=0.88  Score=47.17  Aligned_cols=9  Identities=44%  Similarity=0.379  Sum_probs=4.4

Q ss_pred             hhhHHhHHH
Q 007742            7 EYLEKTVEE   15 (591)
Q Consensus         7 ~~~~~~~~~   15 (591)
                      |-|.++.+.
T Consensus       554 Erl~~aveA  562 (757)
T KOG4368|consen  554 ERLLAAVEA  562 (757)
T ss_pred             HHHHHHHHH
Confidence            344455554

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=85.65  E-value=3.6  Score=42.96  Aligned_cols=86  Identities=23%  Similarity=0.366  Sum_probs=63.9

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHhccC----CCeeEEEEeccC----------CCCC---------------------
Q 007742          318 GAIDRKLYVGNLHFN-MTETQLRKLFEPF----GPVELVQLPLDI----------ETGQ---------------------  361 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~----g~i~~v~i~~~~----------~~~~---------------------  361 (591)
                      +..++.|-|.||.+. +...+|+-+|+.|    |.|.+|.|....          ..|.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            445689999999975 7788999888765    578888776321          0111                     


Q ss_pred             ----------------cccEEEEEeCCHHHHHHHHHHhcCCeeeC--CeEEEEEEecCCCC
Q 007742          362 ----------------CKGFGFVQFAQLEHAKAAQSALNGKLEIV--GRTLKVSSVTDHVG  404 (591)
Q Consensus       362 ----------------~~g~a~Vef~~~~~a~~a~~~l~g~~~~~--g~~l~v~~~~~~~~  404 (591)
                                      ...||.|+|.+++.|......|+| ++|.  |..|-+.|..+...
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG-~EfEsS~~~~DLRFIPDdm~  310 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDG-IEFESSANKLDLRFIPDDMT  310 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCc-ceeccccceeeeeecCCCCc
Confidence                            124899999999999999999999 4676  56777778776654

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=83.38  E-value=0.48  Score=46.01  Aligned_cols=58  Identities=21%  Similarity=0.264  Sum_probs=47.2

Q ss_pred             HHHhccccceEEEEEecCC--------CeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          526 EEECSKYGRVKHIYVDKRS--------AGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       526 ~~~f~~~G~V~~v~l~~~~--------~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      .+.|..||.|..|.+....        ...+||.|...++|..||...+|..++|+.|.+.|.+.+
T Consensus        98 ~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~~gttk  163 (327)
T KOG2068|consen   98 TEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKASLGTTK  163 (327)
T ss_pred             cccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHHhhCCCc
Confidence            4678899999999774321        234799999999999999999999999999888775543

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.89  E-value=6.7  Score=41.09  Aligned_cols=81  Identities=15%  Similarity=0.165  Sum_probs=61.9

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccc----cceEEEEEec---------------C-----------
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKY----GRVKHIYVDK---------------R-----------  543 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~----G~V~~v~l~~---------------~-----------  543 (591)
                      .+.+++.|.|.||  -|..-.       .+||+-+|..|    |.|.+|.|-+               +           
T Consensus       170 ~~~~T~RLAVvNM--DWd~v~-------AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~  240 (650)
T KOG2318|consen  170 LGEETKRLAVVNM--DWDRVK-------AKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEY  240 (650)
T ss_pred             cccccceeeEecc--cccccc-------HHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccC
Confidence            4667888999999  553322       67888888765    6899987721               1           


Q ss_pred             --C------------------------CeeEEEEeCCHHHHHHHHHHhcccccC--CeEEEEEEeCch
Q 007742          544 --S------------------------AGFVYLRFESTEAAASAQRAMHMRWFA--RRLISAIFMKPE  583 (591)
Q Consensus       544 --~------------------------~g~afV~F~~~e~A~~A~~~l~g~~~~--g~~l~v~~~~~~  583 (591)
                        +                        --||+|+|.+++.|.+.+..-.|..|.  |..|-+.|++..
T Consensus       241 ~~s~sD~ee~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIPDd  308 (650)
T KOG2318|consen  241 KESESDDEEEEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIPDD  308 (650)
T ss_pred             cccccchhhhhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeecCCC
Confidence              0                        127899999999999999999999984  777888887754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	591
2cq4_A	114	Solution Structure Of Rna Binding Domain In Rna Bin		2e-25
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-18
2lq5_A	113	Nmr Structure Of The Rna Binding Motif 39 (Rbm39) F		3e-16
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		5e-15
3s6e_A	114	Crystal Structure Of A Rna Binding Motif Protein 39		4e-14
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		2e-11
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		1e-10
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-10
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		1e-09
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		4e-06
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		1e-09
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-06
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-09
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-06
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-09
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		4e-06
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-09
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		5e-06
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-09
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-09
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		2e-09
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		3e-09
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-09
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		4e-09
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		4e-09
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		4e-09
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		6e-09
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		7e-09
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		8e-09
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-08
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-08
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-08
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-06
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-08
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		5e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-08
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		3e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		6e-08
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		7e-08
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		4e-06
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		8e-08
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-07
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		2e-07
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-07
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-06
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-07
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-06
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-07
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		4e-07
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		6e-07
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		1e-06
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		1e-06
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		1e-06
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		2e-06
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-06
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		3e-06
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		3e-06
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		3e-06
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		3e-06
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		3e-06
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		3e-06
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		4e-06
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		4e-06
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		4e-06
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		4e-06
1opi_A	104	Solution Structure Of The Third Rna Recognition Mot		5e-06
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		5e-06
2dit_A	112	Solution Structure Of The Rrm_1 Domain Of Hiv Tat S		6e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		6e-06
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		7e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		1e-05
2dny_A	119	Solution Structure Of The Third Rna Binding Domain		1e-05
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		1e-05
3dxb_A	222	Structure Of The Uhm Domain Of Puf60 Fused To Thior		1e-05
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		2e-05
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		1e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		2e-05
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		1e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		2e-05
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		1e-04
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		2e-05
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		2e-05
1o0p_A	104	Solution Structure Of The Third Rna Recognition Mot		2e-05
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		2e-05
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		2e-05
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-05
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		3e-05
2dnh_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		3e-05
2pe8_A	105	Crystal Structure Of The Uhm Domain Of Human Spf45		3e-05
3v4m_A	105	Crystal Structure Of A Rna Binding Domain Of A U2 S		3e-05
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		3e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		4e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		4e-05
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		4e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		5e-05
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		5e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		5e-05
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		6e-05
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		6e-05
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		8e-05
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		8e-05
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		8e-05
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		8e-05
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		9e-05
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		9e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		1e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		1e-04
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		2e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		2e-04
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-04
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		2e-04
3ue2_A	118	Crystal Structure Of A Rna Binding Domain Of Poly-U		3e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		3e-04
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		3e-04
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		3e-04
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		4e-04
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		5e-04
2khc_A	118	Bruno Rrm3+ Length = 118		5e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		5e-04
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		7e-04
1x4h_A	111	Solution Structure Of Rrm Domain In Rna-Binding Pro		8e-04
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		9e-04

>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 23 Length = 114

Iteration: 1
 Score =  113 bits (283), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 54/103 (52%), Positives = 74/103 (71%)
Query: 207 KEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGY 266
           +E V+  +  ERD RTVF  Q+  +   RD+ +FFS  GKVRDVR+I DRNSRRSKG+ Y
Sbjct: 12  REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 71
Query: 267 IEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSA 309
           +EF ++ SVP+AI L+GQ LLG P++V+ S+AEKN +   +S 
Sbjct: 72  VEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGPSSG 114

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 90.5 bits (223), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 43/79 (54%), Positives = 57/79 (72%), Gaps = 1/79 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ KG+GF+ F+  E AK A   
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 383 LNGKLEIVGRTLKVSSVTD 401
           LNG  E+ GR +KV  VT+
Sbjct: 88  LNG-FELAGRPMKVGHVTE 105

>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From Mus Musculus Length = 113

Iteration: 1
 Score = 83.2 bits (204), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 43/93 (46%), Positives = 60/93 (64%), Gaps = 1/93 (1%)
Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTE 556
           ++C  L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S  
Sbjct: 6   TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIA 65
Query: 557 AAASAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
           AA +A  A+H RWFA ++I+A ++    Y   F
Sbjct: 66  AAIAAVNALHGRWFAGKMITAAYVPLPTYHNLF 98

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 79.3 bits (194), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 38/80 (47%), Positives = 55/80 (68%), Gaps = 1/80 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVG+LHFN+TE  LR +FEPFG ++ + L  D +TG+ KG+GF+ F+  E A+ A   L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 384 NGKLEIVGRTLKVSSVTDHV 403
           NG  E+ GR ++V  VT+ +
Sbjct: 68  NG-FELAGRPMRVGHVTERL 86

>pdb|3S6E|A Chain A, Crystal Structure Of A Rna Binding Motif Protein 39 (Rbm39) From Mus Musculus At 0.95 A Resolution Length = 114

Iteration: 1
 Score = 76.6 bits (187), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 42/93 (45%), Positives = 58/93 (62%), Gaps = 1/93 (1%)
Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTE 556
           ++C  L N F+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S  
Sbjct: 7   TQCFQLSNXFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIA 66
Query: 557 AAASAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
           AA +A  A+H RWFA + I+A ++    Y   F
Sbjct: 67  AAIAAVNALHGRWFAGKXITAAYVPLPTYHNLF 99

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 50/175 (28%), Positives = 83/175 (47%), Gaps = 22/175 (12%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGVGYIEFYDVM 273
           P+ D   +F  Q+P   +E+D+ E F + G V ++ ++ DR  N  +SKG  ++ FY   
Sbjct: 11  PDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRK 70
Query: 274 SVPMA-IALSGQLLL---GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNL 329
           +   A  AL    +L     P+ +KP+++EKN                   DRKL++G +
Sbjct: 71  AALEAQNALHNMKVLPGMHHPIQMKPADSEKN---------------NAVEDRKLFIGMI 115
Query: 330 HFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
               TE  +R +F  FG +E  ++ L    G  +G  FV F     A+ A  A++
Sbjct: 116 SKKCTENDIRVMFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 49/172 (28%), Positives = 81/172 (47%), Gaps = 22/172 (12%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGVGYIEFYDVMSVP 276
           D   +F  Q+P   +E+D+ E F + G V ++ ++ DR  N  +SKG  ++ FY   +  
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 277 MA-IALSGQLLL---GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFN 332
            A  AL    +L     P+ +KP+++EKN                   DRKL++G +   
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKN---------------NAVEDRKLFIGMISKK 106
Query: 333 MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
            TE  +R +F  FG +E  ++ L    G  +G  FV F     A+ A  A++
Sbjct: 107 CTENDIRVMFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/83 (42%), Positives = 50/83 (60%), Gaps = 4/83 (4%)
Query: 319 AIDRKL---YVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH 375
           A+DR L   +VGN+ +  TE QL+ +F   GPV   +L  D ETG+ KG+GF ++   E 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 376 AKAAQSALNGKLEIVGRTLKVSS 398
           A +A   LNG+ E  GR L+V +
Sbjct: 63  ALSAMRNLNGR-EFSGRALRVDN 84

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 41/160 (25%), Positives = 77/160 (48%), Gaps = 11/160 (6%)
Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
           E   +PE+  R +F   +  + T+  +   F + G + D  ++ D N++RS+G G++ + 
Sbjct: 6   ESPKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 64
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
            V  V  A+      + G+  +V+P  A          A  T         +K++VG + 
Sbjct: 65  TVEEVDAAMNARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIK 114
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
            +  E  LR  FE +G +E++++  D  +G+ +GF FV F
Sbjct: 115 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL++G L F  T+  LR  FE +G +    +  D  T + +GFGFV +A +E   AA +
Sbjct: 15  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 382 ALNGKLE 388
           A   K++
Sbjct: 75  ARPHKVD 81

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 41/160 (25%), Positives = 77/160 (48%), Gaps = 11/160 (6%)
Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
           E   +PE+  R +F   +  + T+  +   F + G + D  ++ D N++RS+G G++ + 
Sbjct: 4   ESPKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 62
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
            V  V  A+      + G+  +V+P  A          A  T         +K++VG + 
Sbjct: 63  TVEEVDAAMNARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIK 112
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
            +  E  LR  FE +G +E++++  D  +G+ +GF FV F
Sbjct: 113 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL++G L F  T+  LR  FE +G +    +  D  T + +GFGFV +A +E   AA +
Sbjct: 13  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 382 ALNGKLE 388
           A   K++
Sbjct: 73  ARPHKVD 79

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 41/160 (25%), Positives = 77/160 (48%), Gaps = 11/160 (6%)
Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
           E   +PE+  R +F   +  + T+  +   F + G + D  ++ D N++RS+G G++ + 
Sbjct: 5   ESPKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
            V  V  A+      + G+  +V+P  A          A  T         +K++VG + 
Sbjct: 64  TVEEVDAAMNARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIK 113
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
            +  E  LR  FE +G +E++++  D  +G+ +GF FV F
Sbjct: 114 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL++G L F  T+  LR  FE +G +    +  D  T + +GFGFV +A +E   AA +
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 382 ALNGKLE 388
           A   K++
Sbjct: 74  ARPHKVD 80

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 38/150 (25%), Positives = 72/150 (48%), Gaps = 10/150 (6%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           R +F   +  + T+  +   F + G + D  ++ D N++RS+G G++ +  V  V  A+ 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 281 LSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRK 340
                + G+  +V+P  A          A  T         +K++VG +  +  E  LR 
Sbjct: 67  ARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIKEDTEEHHLRD 116
Query: 341 LFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
            FE +G +E++++  D  +G+ +GF FV F
Sbjct: 117 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL++G L F  T+  LR  FE +G +    +  D  T + +GFGFV +A +E   AA +
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 382 ALNGKLEIVGRTLK 395
           A   K++  GR ++
Sbjct: 67  ARPHKVD--GRVVE 78

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 41/160 (25%), Positives = 77/160 (48%), Gaps = 11/160 (6%)
Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
           E   +PE+  R +F   +  + T+  +   F + G + D  ++ D N++RS+G G++ + 
Sbjct: 5   ESPKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
            V  V  A+      + G+  +V+P  A          A  T         +K++VG + 
Sbjct: 64  TVEEVDAAMNARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIK 113
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
            +  E  LR  FE +G +E++++  D  +G+ +GF FV F
Sbjct: 114 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL++G L F  T+  LR  FE +G +    +  D  T + +GFGFV +A +E   AA +
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 382 ALNGKLE 388
           A   K++
Sbjct: 74  ARPHKVD 80

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 41/160 (25%), Positives = 77/160 (48%), Gaps = 11/160 (6%)
Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
           E   +PE+  R +F   +  + T+  +   F + G + D  ++ D N++RS+G G++ + 
Sbjct: 3   ESPKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 61
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
            V  V  A+      + G+  +V+P  A          A  T         +K++VG + 
Sbjct: 62  TVEEVDAAMNARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIK 111
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
            +  E  LR  FE +G +E++++  D  +G+ +GF FV F
Sbjct: 112 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL++G L F  T+  LR  FE +G +    +  D  T + +GFGFV +A +E   AA +
Sbjct: 12  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 382 ALNGKLE 388
           A   K++
Sbjct: 72  ARPHKVD 78

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL+VG L F+  E  L ++F  +G +  V +  D ET + +GFGFV F  ++ AK A  A
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 383 LNGKLEIVGRTLKV 396
           +NGK  + GR ++V
Sbjct: 74  MNGK-SVDGRQIRV 86

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
           G      R LYVG L   + +  L   F PFG +  +Q+PLD ET + +GF FV+F   E
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 375 HAKAAQSALNGKLEIVGRTLKVS 397
            A AA   +N + E+ GRT++V+
Sbjct: 61  DAAAAIDNMN-ESELFGRTIRVN 82

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 310 GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
           G + +       R LYVG L   + +  L   F PFG +  +Q+PLD ET + +GF FV+
Sbjct: 1   GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           F   E A AA   +N + E+ GRT++V+
Sbjct: 61  FELAEDAAAAIDNMN-ESELFGRTIRVN 87

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 34/86 (39%), Positives = 50/86 (58%), Gaps = 1/86 (1%)
Query: 312 TATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFA 371
           T   P   + R L V  +   + E QLR+LFE +GP+E V++  D ET Q +G+GFV+F 
Sbjct: 33  TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ 92
Query: 372 QLEHAKAAQSALNGKLEIVGRTLKVS 397
               A+ A + LNG   I+ + LKV+
Sbjct: 93  SGSSAQQAIAGLNG-FNILNKRLKVA 117

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 60.1 bits (144), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R LYVG L   + +  L   F PFG +  +Q+PLD ET + +GF FV+F   E A AA  
Sbjct: 3   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 382 ALNGKLEIVGRTLKVS 397
            +N + E+ GRT++V+
Sbjct: 63  NMN-ESELFGRTIRVN 77

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R LYVG L   + +  L   F PFG +  +Q+PLD ET + +GF FV+F   E A AA  
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 382 ALNGKLEIVGRTLKVS 397
            +N + E+ GRT++V+
Sbjct: 66  NMN-ESELFGRTIRVN 80

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R LYVG L   + +  L   F PFG +  +Q+PLD ET + +GF FV+F   E A AA  
Sbjct: 64  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 382 ALNGKLEIVGRTLKVS 397
            +N + E+ GRT++V+
Sbjct: 124 NMN-ESELFGRTIRVN 138

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 59.3 bits (142), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 49/170 (28%), Positives = 76/170 (44%), Gaps = 22/170 (12%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGVGYIEFYDVMSVP 276
           D    F  Q+P   +E+D+ E F + G V ++ ++ DR  N  +SKG  ++ FY   +  
Sbjct: 2   DAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 277 MAI-ALSGQLLL---GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFN 332
            A  AL    +L     P+  KP+++EKN                   DRKL++G +   
Sbjct: 62  EAQNALHNXKVLPGXHHPIQXKPADSEKN---------------NAVEDRKLFIGXISKK 106
Query: 333 MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            TE  +R  F  FG +E  ++ L    G  +G  FV F     A+ A  A
Sbjct: 107 CTENDIRVXFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAXAQTAIKA 155

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 58.9 bits (141), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 46/157 (29%), Positives = 72/157 (45%), Gaps = 15/157 (9%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLL 287
           +P   T+R++Y  F   G +   R++ D  +  S G  +++F   M    AI    ++L 
Sbjct: 11  LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI----KVLN 66
Query: 288 GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGP 347
           G  V        K L  S    GG +       D  LYV NL   +T+ QL  +F  +G 
Sbjct: 67  GITVR------NKRLKVSYARPGGESIK-----DTNLYVTNLPRTITDDQLDTIFGKYGS 115
Query: 348 VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
           +    +  D  TG+ +G  FV++ + E A+ A SALN
Sbjct: 116 IVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 58.9 bits (141), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 90/177 (50%), Gaps = 15/177 (8%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           R ++   +    TE  + ++F   G + ++++++D+N++ +    ++E++      +A+ 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK-NVNYAFVEYHQSHDANIAL- 58
Query: 281 LSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRK 340
              Q L G+ +       E N+V+ N +     +      +  L+VG+L+ N+ +  LR 
Sbjct: 59  ---QTLNGKQI-------ENNIVKINWAFQSQQSSSDDTFN--LFVGDLNVNVDDETLRN 106
Query: 341 LFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
            F+ F       +  D++TG  +G+GFV F   + A+ A  ++ G+ ++ GR L+++
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ-DLNGRPLRIN 162

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 40/145 (27%), Positives = 68/145 (46%), Gaps = 31/145 (21%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           TE ++ E+F K G V D++++ D  + RS+G G++ F                       
Sbjct: 16  TEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFE---------------------- 53
Query: 293 VKPSEAEKNLVQSNTSAGGTATGPYGAIDR-------KLYVGNLHFNMTETQLRKLFEPF 345
            KPS  ++ +V++     G    P  AI R       K++VG +  ++   +  + F  +
Sbjct: 54  -KPSSVDE-VVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQW 111
Query: 346 GPVELVQLPLDIETGQCKGFGFVQF 370
           G +   QL LD +TGQ +GFGFV +
Sbjct: 112 GTIIDAQLMLDKDTGQSRGFGFVTY 136

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 3/68 (4%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF---AQLEHAKAA 379
           K+++G L+++ TE  LR+ F  +G V  +++  D  TG+ +GFGF+ F   + ++     
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 380 QSALNGKL 387
           Q  L+GK+
Sbjct: 65  QHILDGKV 72

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 47/170 (27%), Positives = 73/170 (42%), Gaps = 15/170 (8%)
Query: 215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMS 274
           DP      +    +P   T+R++Y  F   G +   R+  D  +  S G  +++F     
Sbjct: 9   DPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXD 68
Query: 275 VPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMT 334
              AI    ++L G  V        K L  S    GG +       D  LYV NL   +T
Sbjct: 69  SQRAI----KVLNGITVR------NKRLKVSYARPGGESIK-----DTNLYVTNLPRTIT 113
Query: 335 ETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
           + QL  +F  +G +    +  D  TG+ +G  FV++ + E A+ A SALN
Sbjct: 114 DDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 42/163 (25%), Positives = 73/163 (44%), Gaps = 23/163 (14%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +P   T+ +    F   G++   +L+ D+ + +S G G++ + D      AI  L+G  L
Sbjct: 10  LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL 69
Query: 287 LGQPVMV---KPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFE 343
             + + V   +PS A                      D  LYV  L   MT+ +L +LF 
Sbjct: 70  QTKTIKVSYARPSSASIR-------------------DANLYVSGLPKTMTQKELEQLFS 110
Query: 344 PFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK 386
            +G +   ++ +D  TG  +G GF++F +   A+ A   LNG+
Sbjct: 111 QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L  NMT+ + R LF   G +E  +L  D  TGQ  G+GFV +   + A+ A + L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 384 NGKLEIVGRTLKVS 397
           NG L +  +T+KVS
Sbjct: 65  NG-LRLQTKTIKVS 77

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 44/156 (28%), Positives = 72/156 (46%), Gaps = 17/156 (10%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
           TE  +YE FS AG +  +R+  D  +RRS G  Y+ F        A+  ++  ++ G+PV
Sbjct: 23  TEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 82
Query: 292 MVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELV 351
            +  S+ + +L +S                  +++ NL  ++    L   F  FG +   
Sbjct: 83  RIMWSQRDPSLRKSGVG--------------NIFIKNLDKSIDNKALYDTFSAFGNILSC 128
Query: 352 QLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKL 387
           ++  D E G  KG+GFV F   E A+ A   +NG L
Sbjct: 129 KVVCD-ENGS-KGYGFVHFETQEAAERAIEKMNGML 162

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVG+LH ++TE  L + F P GP+  +++  D+ T +  G+ +V F Q   A+ A   +
Sbjct: 13  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 384 NGKLEIVGRTLKV 396
           N  + I G+ +++
Sbjct: 73  NFDV-IKGKPVRI 84

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 44/156 (28%), Positives = 72/156 (46%), Gaps = 17/156 (10%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
           TE  +YE FS AG +  +R+  D  +RRS G  Y+ F        A+  ++  ++ G+PV
Sbjct: 28  TEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 87
Query: 292 MVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELV 351
            +  S+ + +L +S                  +++ NL  ++    L   F  FG +   
Sbjct: 88  RIMWSQRDPSLRKSGVG--------------NIFIKNLDKSIDNKALYDTFSAFGNILSC 133
Query: 352 QLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKL 387
           ++  D E G  KG+GFV F   E A+ A   +NG L
Sbjct: 134 KVVCD-ENGS-KGYGFVHFETQEAAERAIEKMNGML 167

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 9/90 (10%)
Query: 315 GPYGAID--------RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFG 366
           GP G+++          LYVG+LH ++TE  L + F P GP+  +++  D+ T +  G+ 
Sbjct: 1   GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA 60
Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           +V F Q   A+ A   +N  + I G+ +++
Sbjct: 61  YVNFQQPADAERALDTMNFDV-IKGKPVRI 89

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 48/78 (61%), Gaps = 1/78 (1%)
Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
           AI  ++YVG++++ + E  +R+ F PFGP++ + +  D  T + KGF FV++   E A+ 
Sbjct: 26  AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL 85
Query: 379 AQSALNGKLEIVGRTLKV 396
           A   +N  + + GR +KV
Sbjct: 86  ALEQMNSVM-LGGRNIKV 102

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 55.8 bits (133), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 41/163 (25%), Positives = 72/163 (44%), Gaps = 23/163 (14%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +P   T+ +    F   G +   +L+ D+ + +S G G++ + D      AI  L+G  L
Sbjct: 12  LPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKL 71
Query: 287 LGQPVMV---KPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFE 343
             + + V   +PS A                      D  LYV  L   M++ ++ +LF 
Sbjct: 72  QTKTIKVSYARPSSASIR-------------------DANLYVSGLPKTMSQKEMEQLFS 112
Query: 344 PFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK 386
            +G +   ++ LD  TG  +G GF++F +   A+ A   LNG+
Sbjct: 113 QYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 155

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L  NMT+ + + LF   G +E  +L  D  TGQ  G+GFV ++    A  A + L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 384 NGKLEIVGRTLKVS 397
           NG L++  +T+KVS
Sbjct: 67  NG-LKLQTKTIKVS 79

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 55.5 bits (132), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 48/76 (63%), Gaps = 2/76 (2%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R +YVGNL ++ T  Q+++LF  FG V  V+L  D ET + KGFGFV+  Q E    A +
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIA 60
Query: 382 ALNGKLEIVGRTLKVS 397
            L+   + +GRT++V+
Sbjct: 61  KLDN-TDFMGRTIRVT 75

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 48/78 (61%), Gaps = 1/78 (1%)
Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
           AI  ++YVG++++ + E  +R+ F PFGP++ + +  D  T + KGF FV++   E A+ 
Sbjct: 11  AIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL 70
Query: 379 AQSALNGKLEIVGRTLKV 396
           A   +N  + + GR +KV
Sbjct: 71  ALEQMNSVM-LGGRNIKV 87

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +L+V NL +  +E  L KLF  +GP+  +  P+D  T + KGF FV F   EHA  A + 
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 383 LNGKLEIVGRTLKV 396
           ++G++   GR L V
Sbjct: 70  VDGQV-FQGRMLHV 82

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/159 (23%), Positives = 70/159 (44%), Gaps = 17/159 (10%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +P   T+ ++   FS  G+V   +LI D+ +  S G G++ +        AI  L+G  L
Sbjct: 10  LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Query: 287 LGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG 346
             + + V  +     +++                D  LY+  L   MT+  +  +F  FG
Sbjct: 70  QSKTIKVSYARPSSEVIK----------------DANLYISGLPRTMTQKDVEDMFSRFG 113
Query: 347 PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
            +   ++ +D  TG  +G  F++F +   A+ A ++ NG
Sbjct: 114 RIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L V  L  NMT+ +LR LF   G VE  +L  D   G   G+GFV +   + A+ A + 
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 383 LNGKLEIVGRTLKVS 397
           LNG L +  +T+KVS
Sbjct: 64  LNG-LRLQSKTIKVS 77

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/159 (23%), Positives = 70/159 (44%), Gaps = 17/159 (10%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +P   T+ ++   FS  G+V   +LI D+ +  S G G++ +        AI  L+G  L
Sbjct: 10  LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Query: 287 LGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG 346
             + + V  +     +++                D  LY+  L   MT+  +  +F  FG
Sbjct: 70  QSKTIKVSYARPSSEVIK----------------DANLYISGLPRTMTQKDVEDMFSRFG 113
Query: 347 PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
            +   ++ +D  TG  +G  F++F +   A+ A ++ NG
Sbjct: 114 RIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L V  L  NMT+ +LR LF   G VE  +L  D   G   G+GFV +   + A+ A + 
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 383 LNGKLEIVGRTLKVS 397
           LNG L +  +T+KVS
Sbjct: 64  LNG-LRLQSKTIKVS 77

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
           AI  ++YVG++++ + E  +R+ F PFGP++ +    D  T + KGF FV++   E A+ 
Sbjct: 10  AIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQL 69
Query: 379 AQSALNGKLEIVGRTLKV 396
           A    N  + + GR +KV
Sbjct: 70  ALEQXN-SVXLGGRNIKV 86

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 33/100 (33%), Positives = 50/100 (50%), Gaps = 1/100 (1%)
Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE-TGQCKGFG 366
           S+G +   P      K+ V N+ F   + ++R+LF  FG ++ V+LP  +  TG  +GFG
Sbjct: 2   SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61
Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQ 406
           FV F   + AK A +AL     + GR L +      V  Q
Sbjct: 62  FVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 26/64 (40%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYV NL   + + +LRK F PFG +   ++ +  E G+ KGFGFV F+  E A  A + +
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 384 NGKL 387
           NG++
Sbjct: 76  NGRI 79

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+V ++H    E ++++ F  +G ++ + L LD  TG  KG+  V++   + A AA+ AL
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 384 NGKLEIVGRTLKVS 397
           NG  EI+G+T++V 
Sbjct: 135 NG-AEIMGQTIQVD 147

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V NL +  +   LR++FE +G V  V +P +  T   +GF FV+F     A+ A++A+
Sbjct: 16  LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 384 NGKLEIVGRTLKV 396
           +G  E+ GR L+V
Sbjct: 76  DG-AELDGRELRV 87

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V NL +  +   LR++FE +G V  V +P D  T + +GF FV+F     A+ A  A+
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 384 NGKLEIVGRTLKV 396
           +G + + GR L+V
Sbjct: 133 DGAV-LDGRELRV 144

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           + TV+   +P   T  D+Y  FSK GKV  V ++ D+++R+SKGV +I F D
Sbjct: 16  KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD 67

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L    TE  LR++F  +GP+  V +  D ++ + +GF FV F  ++ AK A+   
Sbjct: 18  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 384 NGKLEIVGRTLKVS 397
           NG +E+ GR ++VS
Sbjct: 78  NG-MELDGRRIRVS 90

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L V  L  NMT+ +LR LF   G VE  +L  D   G   G+GFV +   + A+ A + 
Sbjct: 6   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 383 LNGKLEIVGRTLKVS 397
           LNG L +  +T+KVS
Sbjct: 66  LNG-LRLQSKTIKVS 79

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R +Y+G++ ++ TE Q+  L    GPV  +++  D +TG+ KG+ F++F  LE + +A  
Sbjct: 4   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 382 ALNG 385
            LNG
Sbjct: 64  NLNG 67

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+V ++H    E ++++ F  +G ++ + L LD  TG  KG+  V++   + A AA+ AL
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 384 NGKLEIVGRTLKVS 397
           NG  EI+G+T++V 
Sbjct: 89  NGA-EIMGQTIQVD 101

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V NL +  +   LR++FE +G V  V +P D  T + +GF FV+F     A+ A  A+
Sbjct: 50  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 384 NGKLEIVGRTLKV 396
           +G + + GR L+V
Sbjct: 110 DGAV-LDGRELRV 121

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R +Y+G++ ++ TE Q+  L    GPV  +++  D +TG+ KG+ F++F  LE + +A  
Sbjct: 5   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 382 ALNG 385
            LNG
Sbjct: 65  NLNG 68

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R +Y+G++ ++ TE Q+  L    GPV  +++  D +TG+ KG+ F++F  LE + +A  
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 382 ALNG 385
            LNG
Sbjct: 63  NLNG 66

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 37/174 (21%), Positives = 74/174 (42%), Gaps = 9/174 (5%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDV-----RLIMDRNSRRSKGVGYIEFYDVMSV 275
           R ++   +P   TE  + +FF+   ++  +       ++     + K   ++EF  V   
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 276 PMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI----DRKLYVGNLHF 331
             A+A  G +  GQ + ++     + L   + +      G    +      KL++G L  
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 332 NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
            + + Q+++L   FGP++   L  D  TG  KG+ F ++  +     A + LNG
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 27/78 (34%), Positives = 41/78 (52%)
Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +        +  + V NL  +  ET L++LF PFG +  + L  D  TGQ KGF F
Sbjct: 2   SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
Query: 368 VQFAQLEHAKAAQSALNG 385
           + F + E A  A + ++G
Sbjct: 62  ISFHRREDAARAIAGVSG 79

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 37/175 (21%), Positives = 73/175 (41%), Gaps = 21/175 (12%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDV-----RLIMDRNSRRSKGVGYIEFY 270
           P    R ++   +P   TE  + +FF+   ++  +       ++     + K   ++EF 
Sbjct: 2   PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 61
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
            V     A+A  G +  GQ + ++     + L  ++                KL++G L 
Sbjct: 62  SVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAH----------------KLFIGGLP 105
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
             + + Q+++L   FGP++   L  D  TG  KG+ F ++  +     A + LNG
Sbjct: 106 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 160

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  +YVG L   ++E  L +LF   GPV    +P D  TGQ +G+GFV+F   E A  A 
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 381 SALNGKLEIVGRTLKVSSVTDH 402
             ++  +++ G+ ++V+  + H
Sbjct: 75  KIMD-MIKLYGKPIRVNKASAH 95

>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif (Rrm) Of U2af65 In Complex With An N-Terminal Sf1 Peptide Length = 104

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 32/101 (31%), Positives = 47/101 (46%), Gaps = 7/101 (6%)
Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGF 547
           G P+E L L NM  P    D +   EI  DV +ECSKYG VK I + +          G 
Sbjct: 1   GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 60
Query: 548 VYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 588
           +++ F S      A + +  R FA R++   +  P+ Y  +
Sbjct: 61  IFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRR 101

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 36/170 (21%), Positives = 72/170 (42%), Gaps = 21/170 (12%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDV-----RLIMDRNSRRSKGVGYIEFYDVMSV 275
           R ++   +P   TE  + +FF+   ++  +       ++     + K   ++EF  V   
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 276 PMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTE 335
             A+A  G +  GQ + ++     + L  ++                KL++G L   + +
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAH----------------KLFIGGLPNYLND 108
Query: 336 TQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
            Q+++L   FGP++   L  D  TG  KG+ F ++  +     A + LNG
Sbjct: 109 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 158

>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific Factor 1 Variant Length = 112

Iteration: 1
 Score = 49.3 bits (116), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 501 LLLKNMFDPA-METDPDFDLEIQGDVEEECSKYGRVKHIYV-DKRSAGFVYLRFESTEAA 558
           +++KNMF P   E DP    EI+ D+  ECSK+G+++ + + D+   G   + F   E A
Sbjct: 18  VIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEA 77
Query: 559 ASAQRAMHMRWFARRLISA 577
               + +  RWF  R I+A
Sbjct: 78  DYCIQTLDGRWFGGRQITA 96

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 49.3 bits (116), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L    TE  LR++F  +GP+  V +  D ++ + +GF FV F  ++ AK A+   
Sbjct: 15  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 384 NGKLEIVGRTLKV 396
           NG +E+ GR ++V
Sbjct: 75  NG-MELDGRRIRV 86

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K++VG L ++ T+  LRK FE FG +E   +  D +TG+ +G+GFV  A  + A A ++ 
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA--DRAAAERAC 76
Query: 383 LNGKLEIVGRTLKVS 397
            +    I GR   V+
Sbjct: 77  KDPNPIIDGRKANVN 91

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L    TE  LR++F  +GP+  V +  D ++ + +GF FV F  ++ AK A+   
Sbjct: 49  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 384 NGKLEIVGRTLKV 396
           NG +E+ GR ++V
Sbjct: 109 NG-MELDGRRIRV 120

>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp- Interacting Repressor, Siahbp1 Length = 119

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/92 (27%), Positives = 48/92 (52%), Gaps = 15/92 (16%)
Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAG---------FV 548
           S  ++L+NM DP      D D +++G+V EEC K+G V  + + +   G          +
Sbjct: 15  STVMVLRNMVDP-----KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 69
Query: 549 YLRFESTEAAASAQRAMHMRWFA-RRLISAIF 579
           ++ F        A +A++ RWFA R++++ ++
Sbjct: 70  FVEFSIASETHKAIQALNGRWFAGRKVVAEVY 101

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 9/92 (9%)
Query: 204 KEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
           +EKKE+         D+R+V+   +   +T +D+   FS  G +  + ++ D+ S   KG
Sbjct: 29  EEKKEI---------DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKG 79
Query: 264 VGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP 295
             YIEF +  SV  A+A+   +  G+ + V P
Sbjct: 80  YAYIEFAERNSVDAAVAMDETVFRGRTIKVLP 111

>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin Length = 222

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 14/89 (15%)
Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAG---------FV 548
           S  ++L+NM DP      D D +++G+V EEC K+G V  + + +   G          +
Sbjct: 124 STVMVLRNMVDP-----KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 178
Query: 549 YLRFESTEAAASAQRAMHMRWFARRLISA 577
           ++ F        A +A++ RWFA R + A
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGRKVVA 207

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F   +P    E ++ E+F K G V +V +I D   +R +G G+I F D  SV  A+ + 
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 283 GQLLLGQPVMVKPSE 297
              ++G+ V VK +E
Sbjct: 73  FHDIMGKKVEVKRAE 87

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 4/75 (5%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K++VG +  N  ET+LR+ F+ FG V  V +  D E  + +GFGF+ F   E  ++   A
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF---EDEQSVDQA 68
Query: 383 LNGKL-EIVGRTLKV 396
           +N    +I+G+ ++V
Sbjct: 69  VNMHFHDIMGKKVEV 83

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/96 (30%), Positives = 53/96 (55%), Gaps = 6/96 (6%)
Query: 204 KEKKEVVEPEADPERDQRTV-----FAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS 258
           +E  + VE + D    QR+V     F   +  +ATE D+++ F++ G+++++ L +DR +
Sbjct: 2   REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 61
Query: 259 RRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
              KG   +E+        A+  L+GQ L+GQP+ V
Sbjct: 62  GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 97

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/87 (29%), Positives = 47/87 (54%), Gaps = 2/87 (2%)
Query: 311 GTATGPYGAIDR-KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
           G   GP  +++   L+V  +H   TE  +   F  +G ++ + L LD  TG  KG+  V+
Sbjct: 12  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71
Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKV 396
           +   + A+AA   LNG+ +++G+ + V
Sbjct: 72  YETYKEAQAAMEGLNGQ-DLMGQPISV 97

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/96 (30%), Positives = 53/96 (55%), Gaps = 6/96 (6%)
Query: 204 KEKKEVVEPEADPERDQRTV-----FAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS 258
           +E  + VE + D    QR+V     F   +  +ATE D+++ F++ G+++++ L +DR +
Sbjct: 1   REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 60
Query: 259 RRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
              KG   +E+        A+  L+GQ L+GQP+ V
Sbjct: 61  GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 96

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/87 (29%), Positives = 47/87 (54%), Gaps = 2/87 (2%)
Query: 311 GTATGPYGAIDR-KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
           G   GP  +++   L+V  +H   TE  +   F  +G ++ + L LD  TG  KG+  V+
Sbjct: 11  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70
Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKV 396
           +   + A+AA   LNG+ +++G+ + V
Sbjct: 71  YETYKEAQAAMEGLNGQ-DLMGQPISV 96

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L  NMT+ + + LF   G +E  +L  D  TGQ  G+GFV ++    A  A + L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 384 NGKLEIVGRTLKVS 397
           NG L++  +T+KVS
Sbjct: 67  NG-LKLQTKTIKVS 79

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L    TE  LR++F  +GP+  V +  D ++ + +GF FV F  ++ AK A+   
Sbjct: 18  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 384 NGKLEIVGRTLKV 396
           NG +E+ GR ++V
Sbjct: 78  NG-MELDGRRIRV 89

>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif (Rrm) Of U2af65 In Complex With An N-Terminal Sf1 Peptide Length = 104

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/99 (31%), Positives = 46/99 (46%), Gaps = 7/99 (7%)
Query: 497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGFVY 549
           P+E L L NM  P    D +   EI  DV +ECSKYG VK I + +          G ++
Sbjct: 3   PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62
Query: 550 LRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 588
           + F S      A + +  R FA R++   +  P+ Y  +
Sbjct: 63  VEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRR 101

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+VG+L+ N+ +  LR  F+ F       +  D++TG  +G+GFV F   + A+ A  ++
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 384 NGKLEIVGRTLKVS 397
            G+ ++ GR L+++
Sbjct: 64  QGQ-DLNGRPLRIN 76

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
           L V  L +  TE  L++ F  FG V +VQ+  D++TG  KGFGFV+F + E
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL+VG L+   +E  +R+LFE FG +E   + L    G  KG  FV+++    A+AA +
Sbjct: 16  RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTI-LRGPDGNSKGCAFVKYSSHAEAQAAIN 74
Query: 382 ALNGKLEIVG 391
           AL+G   + G
Sbjct: 75  ALHGSQTMPG 84

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 34/61 (55%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL++G L F  TE  LR  +E +G +    +  D  + + +GFGFV F+ +    AA +
Sbjct: 28  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 382 A 382
           A
Sbjct: 88  A 88

>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5 Rna Binding Protein Length = 105

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           DRKL+VG L+   +E  + +LF+PFG ++   + L    G  KG  FV+F+    A+AA 
Sbjct: 15  DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTV-LRGPDGSSKGCAFVKFSSHTEAQAAI 73
Query: 381 SALNGKLEIVG 391
            AL+G   + G
Sbjct: 74  HALHGSQTMPG 84

>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free Form) Length = 105

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 11/90 (12%)
Query: 496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYV------DKRSAGFVY 549
            P++ +LL+NM   A E D D ++E +    EEC KYG+V    +          A  ++
Sbjct: 6   CPTKVVLLRNMVG-AGEVDEDLEVETK----EECEKYGKVGKCVIFEIPGAPDDEAVRIF 60
Query: 550 LRFESTEAAASAQRAMHMRWFARRLISAIF 579
           L FE  E+A  A   ++ R+F  R++ A F
Sbjct: 61  LEFERVESAIKAVVDLNGRYFGGRVVKACF 90

>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From Mus Musculus At 1.80 A Resolution Length = 105

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/101 (30%), Positives = 46/101 (45%), Gaps = 7/101 (6%)
Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGF 547
           G P+E L L N   P    D +   EI  DV +ECSKYG VK I + +          G 
Sbjct: 2   GHPTEVLCLXNXVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 61
Query: 548 VYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 588
           +++ F S      A + +  R FA R++   +  P+ Y  +
Sbjct: 62  IFVEFTSVFDCQKAXQGLTGRKFANRVVVTKYCDPDSYHRR 102

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           DRKL+VG L    T+  +RK+FEPFG ++   + L    G  KG  FV+F     A+AA 
Sbjct: 12  DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTV-LRGPDGTSKGCAFVKFQTHAEAQAAI 70
Query: 381 SALNGKLEIVG 391
           + L+    + G
Sbjct: 71  NTLHSSRTLPG 81

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  L V NL  ++T+ Q  +L  PFG +E   L     TGQ KG+GF ++ + + A  A+
Sbjct: 95  DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 381 SALNGKLEIVGRTLKV 396
           S L GK  +  RTL V
Sbjct: 155 SDLLGK-PLGPRTLYV 169

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  L V NL  ++T+ Q  +L  PFG +E   L     TGQ KG+GF ++ + + A  A+
Sbjct: 93  DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 152
Query: 381 SALNGKLEIVGRTLKV 396
           S L GK  +  RTL V
Sbjct: 153 SDLLGK-PLGPRTLYV 167

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  L V NL  ++T+ Q  +L  PFG +E   L     TGQ KG+GF ++ + + A  A+
Sbjct: 95  DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 381 SALNGKLEIVGRTLKV 396
           S L GK  +  RTL V
Sbjct: 155 SDLLGK-PLGPRTLYV 169

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 20/76 (26%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + L+V  ++++ TE++LR+ FE +GP++ + +     +G+ +G+ F+++       +A  
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 382 ALNGKLEIVGRTLKVS 397
             +GK +I GR + V 
Sbjct: 163 HADGK-KIDGRRVLVD 177

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 2/84 (2%)
Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +    + AI  KL++G +  N+ E  L+ LFE FG +  + +  D  TG  KG  F
Sbjct: 2   SSGSSGMKDHDAI--KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAF 59
Query: 368 VQFAQLEHAKAAQSALNGKLEIVG 391
           + + + E A  AQSAL+ +  + G
Sbjct: 60  LTYCERESALKAQSALHEQKTLPG 83

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L V  L  N T+ +LR LF   G VE  +L  D   G   G+GFV +   + A+ A + L
Sbjct: 22  LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 384 NGKLEIVGRTLKVS 397
           NG L +  +T+KVS
Sbjct: 82  NG-LRLQSKTIKVS 94

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 46/76 (60%), Gaps = 5/76 (6%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
            + L + NL ++ TE  L+++FE       +++P + + G+ KG+ F++FA  E AK A 
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQN-QNGKSKGYAFIEFASFEDAKEAL 70
Query: 381 SALNGKLEIVGRTLKV 396
           ++ N K EI GR +++
Sbjct: 71  NSCN-KREIEGRAIRL 85

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 21/56 (37%), Positives = 36/56 (64%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
           +K++VG L  +  E ++R+ F  FG VE ++LP+D +T + +GF F+ F + E  K
Sbjct: 2   KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 57

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+V  +H   TE  +   F  +G ++ + L LD  TG  KG+  V++   + A+AA   L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 384 NGKLEIVGRTLKV 396
           NG+ +++G+ + V
Sbjct: 70  NGQ-DLMGQPISV 81

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/76 (26%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + L+V  ++++ TE++LR+ FE +GP++ + +     +G+ +G+ F+++       +A  
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 382 ALNGKLEIVGRTLKVS 397
             +GK +I GR + V 
Sbjct: 163 HADGK-KIDGRRVLVD 177

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+V  +H   TE  +   F  +G ++ + L LD  TG  KG+  V++   + A+AA   L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 384 NGKLEIVGRTLKV 396
           NG+ +++G+ + V
Sbjct: 70  NGQ-DLMGQPISV 81

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+V  +H   TE  +   F  +G ++ + L LD  TG  KG+  V++   + A+AA   L
Sbjct: 12  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 384 NGKLEIVGRTLKV 396
           NG+ +++G+ + V
Sbjct: 72  NGQ-DLMGQPISV 83

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L+V  +H   TE  +   F  +G ++ + L LD  TG  KG+  V++   + A+AA   L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 384 NGKLEIVGRTLKV 396
           NG+ +++G+ + V
Sbjct: 70  NGQ-DLMGQPISV 81

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 31/77 (40%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           DR ++VGNL   + E  L +LF   GP+  V +  D E G+ K FGFV F   E    A 
Sbjct: 16  DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAI 74
Query: 381 SALNGKLEIVGRTLKVS 397
           + LNG + + GR + VS
Sbjct: 75  ALLNG-IRLYGRPINVS 90

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/98 (27%), Positives = 49/98 (50%), Gaps = 5/98 (5%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
           VF   +  + T  D+   F+  G++ D R++ D  + +SKG G++ F++      AI  +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 282 SGQLLLGQPV----MVKPSEAEKNLVQSNTSAGGTATG 315
            GQ L G+ +      +   A K+  +SNT   G ++G
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/84 (34%), Positives = 48/84 (57%), Gaps = 3/84 (3%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           ++L+V N+ F   +  LR++F  FG +  V++  + E G  KGFGFV F     A  A+ 
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGS-KGFGFVTFENSADADRARE 73
Query: 382 ALNGKLEIVGRTLKVSSVTDHVGT 405
            L+G + + GR ++V++ T  V T
Sbjct: 74  KLHGTV-VEGRKIEVNNATARVMT 96

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + L+V  L  + TE  L++ F+  G V   ++  D ETG  KGFGFV F   E AKAA+ 
Sbjct: 16  KTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 382 AL 383
           A+
Sbjct: 73  AM 74

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 36/64 (56%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  LYV NL   +T+ QL  +F  +G +    +  D  TG+ +G  FV++ + E A+ A 
Sbjct: 13  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 381 SALN 384
           SALN
Sbjct: 73  SALN 76

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL++G L+    E  L+ +F   GP+  V L  D  T + +GF F+ F     AK A   
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKD 67
Query: 383 LNGKLEIVGRTLKV 396
           +NGK  + G+ +KV
Sbjct: 68  MNGK-SLHGKAIKV 80

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/82 (34%), Positives = 47/82 (57%), Gaps = 3/82 (3%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           ++L+V N+ F   +  LR++F  FG +  V++  + E G  KGFGFV F     A  A+ 
Sbjct: 30  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGS-KGFGFVTFENSADADRARE 87
Query: 382 ALNGKLEIVGRTLKVSSVTDHV 403
            L+G + + GR ++V++ T  V
Sbjct: 88  KLHGTV-VEGRKIEVNNATARV 108

>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 1.23 A Resolution Length = 118

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/92 (26%), Positives = 46/92 (50%), Gaps = 15/92 (16%)
Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAG---------FV 548
           S   +L+N  DP      D D +++G+V EEC K+G V  + + +   G          +
Sbjct: 20  STVXVLRNXVDP-----KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 74
Query: 549 YLRFESTEAAASAQRAMHMRWFA-RRLISAIF 579
           ++ F        A +A++ RWFA R++++ ++
Sbjct: 75  FVEFSIASETHKAIQALNGRWFAGRKVVAEVY 106

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 37/66 (56%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  LYV  L   M++ ++ +LF  +G +   ++ LD  TG  +G GF++F +   A+ A 
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 381 SALNGK 386
             LNG+
Sbjct: 61  KGLNGQ 66

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/54 (37%), Positives = 34/54 (62%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
           ++VG L  +  E ++R+ F  FG VE ++LP+D +T + +GF F+ F + E  K
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 55

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA---- 379
           +++G L ++ T+  L+  F  FG V    L LD  TG+ +GFGFV F + E         
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 380 QSALNGKL 387
           +  LNGK+
Sbjct: 62  EHKLNGKV 69

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/60 (38%), Positives = 33/60 (55%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LY+  L    T+  L KL +P+G +   +  LD  T +CKG+GFV F     A+ A +AL
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 20/63 (31%), Positives = 34/63 (53%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL++G L   + + Q+++L   FGP++   L  D  TG  KG+ F ++  +     A + 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 383 LNG 385
           LNG
Sbjct: 63  LNG 65

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 30/87 (34%), Positives = 44/87 (50%), Gaps = 4/87 (4%)
Query: 310 GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
           G    GP G     L++ +L    T+T L   F PFG V   ++ +D +T   K FGFV 
Sbjct: 32  GKQIEGPEGC---NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVS 88
Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKV 396
           F   + A+ A  A+NG  ++  + LKV
Sbjct: 89  FDNPDSAQVAIKAMNG-FQVGTKRLKV 114

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L 281
           VF   +  + T  D+   F+  GK+ D R++ D  + +SKG G++ FY+ +    AI  +
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 282 SGQLLLGQPV 291
            GQ L G+ +
Sbjct: 78  GGQWLGGRQI 87

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 49/93 (52%), Gaps = 4/93 (4%)
Query: 304 QSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 363
           QS  +AG    GP GA    L++ +L     +  L ++F PFG V   ++ +D +T   K
Sbjct: 11  QSIGAAGSQKEGPEGA---NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67
Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
            FGFV +     A+AA  ++NG  +I  + LKV
Sbjct: 68  CFGFVSYDNPVSAQAAIQSMNG-FQIGMKRLKV 99

>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28 Length = 111

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 32/94 (34%), Positives = 49/94 (52%), Gaps = 9/94 (9%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF-----AQLEHA 376
           + +++ NL F+  E  L ++ + FG ++ V++ L  +T   KG  F QF     AQ   A
Sbjct: 16  KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 377 KAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAA 410
            A+  A  G L++ GR LKV    D   T+D AA
Sbjct: 76  AASLEAEGGGLKLDGRQLKV----DLAVTRDEAA 105

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LYVGNL F  TE Q+ +LF   G ++ + + LD     C GF FV++     A+ A   +
Sbjct: 21  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC-GFCFVEYYSRADAENAMRYI 79
Query: 384 NG 385
           NG
Sbjct: 80  NG 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	591
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-50
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-17
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-47
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-44
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-42
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-17
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-05
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-41
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	8e-36
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-35
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-34
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-24
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-34
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-10
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-32
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-31
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-28
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-31
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-29
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-15
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-31
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-29
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	3e-29
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	1e-28
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-28
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	9e-10
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-27
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-10
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-27
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-08
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-27
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-10
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-26
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-13
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	6e-26
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-25
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-10
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-25
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-09
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-25
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-10
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-25
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-09
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-25
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-24
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-04
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-24
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-08
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-24
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-11
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-24
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-04
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	6e-24
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	9e-10
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	8e-24
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-08
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-23
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-12
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-23
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-11
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-23
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-04
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-23
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-23
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-23
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-12
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	7e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-23
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	5e-13
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-23
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-10
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-23
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-23
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-23
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-22
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	6e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-04
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-22
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	8e-08
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-04
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-22
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-07
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-22
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-17
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-22
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	8e-06
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-22
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-22
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-09
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-21
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-10
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-21
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	8e-08
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-21
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-21
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-21
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-10
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	4e-21
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-21
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-06
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-21
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	7e-12
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-21
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-21
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-21
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-08
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-21
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-10
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-20
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	7e-06
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-20
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-20
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-07
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-20
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-10
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-20
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	9e-08
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	8e-20
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	9e-15
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-19
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-10
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-19
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-08
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-19
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-08
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-19
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-19
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-19
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-19
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-05
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	5e-19
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-10
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-19
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	8e-04
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-19
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-08
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	9e-19
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-06
2div_A	99	TRNA selenocysteine associated protein; structural	1e-18
2div_A	99	TRNA selenocysteine associated protein; structural	6e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-18
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-05
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-18
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-04
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-18
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-08
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-18
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	6e-07
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-18
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-18
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-05
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-18
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-18
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	9e-11
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	6e-18
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	7e-12
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	7e-18
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-17
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-11
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-17
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-17
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-07
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-17
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-05
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-17
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-05
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-17
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-17
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-05
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-17
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-07
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-17
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-06
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-17
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-16
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-16
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-16
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	9e-09
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-16
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-12
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-16
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-12
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-16
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	5e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	6e-04
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-16
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	6e-16
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-11
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-16
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-15
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	7e-09
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-15
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-04
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-15
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-15
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-06
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-15
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-15
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-05
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-04
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-15
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	8e-15
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-14
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-13
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-06
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-13
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-13
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-08
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-13
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	7e-08
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-13
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	6e-13
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	6e-13
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-13
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-10
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-12
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	7e-09
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-12
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-12
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-06
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-12
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-12
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-12
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-04
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-08
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-12
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	6e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-12
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-12
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	8e-06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	6e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	7e-12
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-12
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-06
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	9e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	6e-04
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	6e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	9e-12
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	9e-12
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	7e-04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-11
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	6e-09
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	4e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-05
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	8e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	9e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	9e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-10
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	6e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-10
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-10
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-10
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-10
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-10
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-09
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-10
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	8e-10
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	9e-10
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	5e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	6e-08
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	3e-09
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-09
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-08
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	9e-09
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-05
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	9e-09
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	1e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	8e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	8e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	4e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	8e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-07
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	8e-04
2ycu_A	995	Non muscle myosin 2C, alpha-actinin; motor protein	1e-06
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-06
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-05
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-04
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	2e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-05
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	2e-05
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	5e-05
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	7e-05
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	2e-04
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	7e-04
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	3e-05
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	3e-05
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	5e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	9e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04

>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 =  171 bits (436), Expect = 2e-50
 Identities = 39/186 (20%), Positives = 79/186 (42%), Gaps = 10/186 (5%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRL-----IMDRNSRRSKGVGYIEFYDVMSV 275
           R ++   +P   TE  + +FF+   ++  +       ++     + K   ++EF  V   
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 276 PMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAID----RKLYVGNLHF 331
             A+A  G +  GQ + ++     + L   + +      G    +      KL++G L  
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124

Query: 332 NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG 391
            + + Q+++L   FGP++   L  D  TG  KG+ F ++  +     A + LNG  ++  
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM-QLGD 183

Query: 392 RTLKVS 397
           + L V 
Sbjct: 184 KKLLVQ 189

>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 = 79.7 bits (197), Expect = 2e-17
 Identities = 25/110 (22%), Positives = 46/110 (41%), Gaps = 7/110 (6%)

Query: 318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLP-----LDIETGQCKGFGFVQFAQ 372
           GA+ R+LYVGN+ F +TE  +   F     +  +        L ++  Q K F F++F  
Sbjct: 1   GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 373 LEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGG 422
           ++    A  A +G     G++LK+    D+      +   + +       
Sbjct: 61  VDETTQAM-AFDGI-IFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVST 108

>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 =  162 bits (412), Expect = 3e-47
 Identities = 35/185 (18%), Positives = 73/185 (39%), Gaps = 21/185 (11%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
           E         +F   +    +  ++    S+     D+  ++D  +  ++  GY++F   
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESA 64

Query: 273 MSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFN 332
             +  A+ L+G  + G  + ++  +   +                    R L   NL FN
Sbjct: 65  EDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAA--------------RTLLAKNLSFN 110

Query: 333 MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGR 392
           +TE +L+++FE    + LV      + G+ KG  +++F     A+       G  EI GR
Sbjct: 111 ITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGA-EIDGR 164

Query: 393 TLKVS 397
           ++ + 
Sbjct: 165 SVSLY 169

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  156 bits (397), Expect = 1e-44
 Identities = 34/188 (18%), Positives = 85/188 (45%), Gaps = 7/188 (3%)

Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
                       V+   +  +  E  + + F+  G ++ + +  D  + + KG  ++E+ 
Sbjct: 19  AQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYE 78

Query: 271 DVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNL 329
              +  +A+  ++  +L G+ + V                   A         ++YV ++
Sbjct: 79  VPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFN-----RIYVASV 133

Query: 330 HFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI 389
           H ++++  ++ +FE FG ++   L  D  TG+ KG+GF+++ + + ++ A S++N   ++
Sbjct: 134 HQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF-DL 192

Query: 390 VGRTLKVS 397
            G+ L+V 
Sbjct: 193 GGQYLRVG 200

>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 =  150 bits (380), Expect = 1e-42
 Identities = 50/187 (26%), Positives = 84/187 (44%), Gaps = 24/187 (12%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGVGYIEFYDVMSVP 276
           D   +F  Q+P   +E+D+ E F + G V ++ ++ DR  N  +SKG  ++ FY   +  
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 277 MAI-ALSGQLLLGQ---PVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFN 332
            A  AL    +L     P+ +KP+++EKN                   DRKL++G +   
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNN---------------AVEDRKLFIGMISKK 106

Query: 333 MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK--LEIV 390
            TE  +R +F  FG +E  ++      G  +G  FV F     A+ A  A++    +E  
Sbjct: 107 CTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGC 165

Query: 391 GRTLKVS 397
              + V 
Sbjct: 166 SSPMVVK 172

>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 = 80.0 bits (198), Expect = 1e-17
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 3/80 (3%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAA 379
            K++VG +    +E  LR+LFE +G V  + +  D      Q KG  FV F   + A  A
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

Query: 380 QSALNGKLEIVGRTLKVSSV 399
           Q+AL+   +++        +
Sbjct: 64  QNALHNM-KVLPGMHHPIQM 82

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 42.6 bits (101), Expect = 8e-05
 Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 7/72 (9%)

Query: 524 DVEEECSKYGRVKHIYV--DK-----RSAGFVYLRFESTEAAASAQRAMHMRWFARRLIS 576
           D+ E   +YG V  I V  D+     +S G  ++ F + +AA  AQ A+H       +  
Sbjct: 19  DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH 78

Query: 577 AIFMKPEDYEAK 588
            I MKP D E  
Sbjct: 79  PIQMKPADSEKN 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 =  146 bits (372), Expect = 1e-41
 Identities = 38/182 (20%), Positives = 77/182 (42%), Gaps = 22/182 (12%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRL-----IMDRNSRRSKGVGYIEFYDVMSV 275
           R ++   +P   TE  + +FF+   ++  +       ++     + K   ++EF  V   
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 276 PMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTE 335
             A+A  G +  GQ + ++     + L  ++                KL++G L   + +
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAH----------------KLFIGGLPNYLND 108

Query: 336 TQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLK 395
            Q+++L   FGP++   L  D  TG  KG+ F ++  +     A + LNG  ++  + L 
Sbjct: 109 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM-QLGDKKLL 167

Query: 396 VS 397
           V 
Sbjct: 168 VQ 169

>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 Length = 114

 Score =  129 bits (326), Expect = 8e-36
 Identities = 43/96 (44%), Positives = 60/96 (62%), Gaps = 1/96 (1%)

Query: 496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFES 554
             ++C  L NMF+P  E +  +D EI+ DV EEC+K+G V HIYVDK SA G VY++  S
Sbjct: 5   LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPS 64

Query: 555 TEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKFK 590
             AA +A  A+H RWFA ++I+A ++    Y   F 
Sbjct: 65  IAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFP 100

>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 =  128 bits (325), Expect = 6e-35
 Identities = 41/180 (22%), Positives = 76/180 (42%), Gaps = 18/180 (10%)

Query: 220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
           +  +    +P   T+ +    F   G++   +L+ D+ + +S G G++ + D      AI
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 280 -ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQL 338
             L+G  L  + +  K S A  +      +               LYV  L   MT+ +L
Sbjct: 62  NTLNGLRLQTKTI--KVSYARPSSASIRDA--------------NLYVSGLPKTMTQKEL 105

Query: 339 RKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK-LEIVGRTLKVS 397
            +LF  +G +   ++ +D  TG  +G GF++F +   A+ A   LNG+        + V 
Sbjct: 106 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165

>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 =  127 bits (321), Expect = 2e-34
 Identities = 45/179 (25%), Positives = 75/179 (41%), Gaps = 18/179 (10%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
             +    +P   T+R++Y  F   G +   R++ D  +  S G  +++F   M    AI 
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 280 ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLR 339
            L+G  +  + + V  +           S   T           LYV NL   +T+ QL 
Sbjct: 64  VLNGITVRNKRLKVSYAR------PGGESIKDT----------NLYVTNLPRTITDDQLD 107

Query: 340 KLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK-LEIVGRTLKVS 397
            +F  +G +    +  D  TG+ +G  FV++ + E A+ A SALN    E   + L V 
Sbjct: 108 TIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166

>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 =   99 bits (250), Expect = 1e-24
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           +  L V  L  +MT+ +L  LF   GP+   ++  D +TG   G+ FV F     ++ A 
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 381 SALNGKLEIVGRTLKVS 397
             LNG   +  + LKVS
Sbjct: 63  KVLNGI-TVRNKRLKVS 78

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  124 bits (314), Expect = 6e-34
 Identities = 38/115 (33%), Positives = 58/115 (50%), Gaps = 2/115 (1%)

Query: 284 QLLLGQPVMVKPSEAEKNLVQSNTSAGGTA-TGPYGAIDRKLYVGNLHFNMTETQLRKLF 342
           ++L   P  V  +         +  +GG+  +G      R LYVG L   + +  L   F
Sbjct: 25  EILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAF 84

Query: 343 EPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
            PFG +  +Q+PLD ET + +GF FV+F   E A AA   +N   E+ GRT++V+
Sbjct: 85  IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVN 138

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 56.7 bits (137), Expect = 6e-10
 Identities = 13/83 (15%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
                   +R ++   +  +  ++ ++  F   G + D+++ +D  + + +G  ++EF  
Sbjct: 55  GSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 114

Query: 272 VMSVPMAI-ALSGQLLLGQPVMV 293
                 AI  ++   L G+ + V
Sbjct: 115 AEDAAAAIDNMNESELFGRTIRV 137

>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 =  120 bits (302), Expect = 1e-32
 Identities = 55/112 (49%), Positives = 75/112 (66%)

Query: 198 RESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRN 257
             S      +E V+  +  ERD RTVF  Q+  +   RD+ +FFS  GKVRDVR+I DRN
Sbjct: 3   SGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN 62

Query: 258 SRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSA 309
           SRRSKG+ Y+EF ++ SVP+AI L+GQ LLG P++V+ S+AEKN +   +S 
Sbjct: 63  SRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGPSSG 114

>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 = 73.5 bits (181), Expect = 4e-16
 Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R ++   L   +    L   F   G V  V++  D  + + KG  +V+F +++    A  
Sbjct: 26  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI- 84

Query: 382 ALNGKLEIVGRTLKVS 397
            L G+  ++G  + V 
Sbjct: 85  GLTGQ-RLLGVPIIVQ 99

>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 =  122 bits (309), Expect = 1e-31
 Identities = 37/171 (21%), Positives = 60/171 (35%), Gaps = 17/171 (9%)

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL 287
           P   T++   E     G +    L+    + +SKG G+ E+    S   A   L G+ L 
Sbjct: 104 PPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLG 163

Query: 288 GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQ-LRKLFEPFG 346
            + + V     +   +                  R L V  L     +   L +      
Sbjct: 164 PRTLYVHW--TDAGQLTPALLHS-----------RCLCVDRLPPGFNDVDALCRALSAVH 210

Query: 347 PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
                QL    + GQ KGF  +++   E A+ AQ   +G   + G  L+VS
Sbjct: 211 SPTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQQQADGL-SLGGSHLRVS 259

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  113 bits (285), Expect = 3e-28
 Identities = 44/195 (22%), Positives = 77/195 (39%), Gaps = 31/195 (15%)

Query: 204 KEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
           +E ++ +E      R++R +    +P   T ++V++  S          +      + KG
Sbjct: 6   EEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKG 58

Query: 264 VGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDR 322
             ++   +      AI A     L  + + V+    +  L                    
Sbjct: 59  TAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALL-------------------- 98

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
              V NL  ++T+ Q  +L  PFG +E   L     TGQ KG+GF ++ + + A  A+S 
Sbjct: 99  --CVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156

Query: 383 LNGKLEIVGRTLKVS 397
           L GK  +  RTL V 
Sbjct: 157 LLGK-PLGPRTLYVH 170

>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 =  122 bits (309), Expect = 2e-31
 Identities = 36/206 (17%), Positives = 68/206 (33%), Gaps = 28/206 (13%)

Query: 192 ERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVR 251
           +R L+           +         R+  TV    +P    +  VY++F   G +  V 
Sbjct: 13  KRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVD 72

Query: 252 LIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGG 311
           +       ++     IEF        AI  + +++    ++V                  
Sbjct: 73  VADSLK--KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSH---------------- 114

Query: 312 TATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVEL-VQLPLDIETGQCKGFGFVQF 370
                    +  L++ N   + T+  +R L +    V L ++LP        + F ++  
Sbjct: 115 -------LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSL-RFNTSRRFAYIDV 166

Query: 371 AQLEHAKAAQSALNGKLEIVGRTLKV 396
              E A+     LNG  +I G TL  
Sbjct: 167 TSKEDARYCVEKLNGL-KIEGYTLVT 191

>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 =  115 bits (291), Expect = 5e-29
 Identities = 37/182 (20%), Positives = 69/182 (37%), Gaps = 14/182 (7%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
            + T++    P   T+R++ +       V     +       S+   YI+          
Sbjct: 116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 175

Query: 279 I-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMT-ET 336
           +  L+G  + G  ++ K S   +   +S  +   T  G      R++ + NL   +  E 
Sbjct: 176 VEKLNGLKIEGYTLVTKVSNPLE---KSKRTDSATLEG------REIMIRNLSTELLDEN 226

Query: 337 QLRKLFEPFGPVELVQLPLDI-ETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLK 395
            LR+ FE FG +E + +P    E        F+ F   + A+ A   +N    +  R + 
Sbjct: 227 LLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRS-LLGNREIS 284

Query: 396 VS 397
           VS
Sbjct: 285 VS 286

>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 = 75.4 bits (186), Expect = 3e-15
 Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 4/79 (5%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           + V NL  +  + ++ K F+  GP+  V +       +   F  ++FA+ + A AA +  
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKT 101

Query: 384 NGKLEIVGRTLKVSSVTDH 402
           +  +      + VS +T+ 
Sbjct: 102 HKVVG--QNEIIVSHLTEC 118

>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 =  117 bits (296), Expect = 5e-31
 Identities = 37/178 (20%), Positives = 88/178 (49%), Gaps = 17/178 (9%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
           R ++   +    TE  + ++F   G + ++++++D+N  ++    ++E++      +A+ 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQ 59

Query: 280 ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLR 339
            L+G+ +    V +  +   +   QS++                L+VG+L+ N+ +  LR
Sbjct: 60  TLNGKQIENNIVKINWAFQSQ---QSSSDDTFN-----------LFVGDLNVNVDDETLR 105

Query: 340 KLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
             F+ F       +  D++TG  +G+GFV F   + A+ A  ++ G+ ++ GR L+++
Sbjct: 106 NAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ-DLNGRPLRIN 162

>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 =  115 bits (290), Expect = 1e-29
 Identities = 45/185 (24%), Positives = 80/185 (43%), Gaps = 18/185 (9%)

Query: 214 ADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVM 273
           + P     +++   +    TE  +YE FS AG +  +R+  D  +RRS G  Y+ F    
Sbjct: 9   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68

Query: 274 SVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFN 332
               A+  ++  ++ G+PV +  S+ + +L +S                  +++ NL  +
Sbjct: 69  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG--------------NIFIKNLDKS 114

Query: 333 MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGR 392
           +    L   F  FG +   ++  D      KG+GFV F   E A+ A   +NG L +  R
Sbjct: 115 IDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGML-LNDR 171

Query: 393 TLKVS 397
            + V 
Sbjct: 172 KVFVG 176

>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 Length = 112

 Score =  110 bits (278), Expect = 3e-29
 Identities = 27/96 (28%), Positives = 42/96 (43%), Gaps = 2/96 (2%)

Query: 496 SPSECLLLKNMFDPA-METDPDFDLEIQGDVEEECSKYGRVKHIYVDKRS-AGFVYLRFE 553
                +++KNMF P   E DP    EI+ D+  ECSK+G+++ + +  R   G   + F 
Sbjct: 13  RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFR 72

Query: 554 STEAAASAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
             E A    + +  RWF  R I+A            
Sbjct: 73  DPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQSG 108

>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 Length = 105

 Score =  109 bits (273), Expect = 1e-28
 Identities = 32/101 (31%), Positives = 47/101 (46%), Gaps = 7/101 (6%)

Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRS-------AGF 547
           G P+E L L NM  P    D +   EI  DV +ECSKYG VK I + +          G 
Sbjct: 2   GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 61

Query: 548 VYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 588
           +++ F S      A + +  R FA R++   +  P+ Y  +
Sbjct: 62  IFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRR 102

>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 =  111 bits (279), Expect = 2e-28
 Identities = 41/188 (21%), Positives = 81/188 (43%), Gaps = 13/188 (6%)

Query: 210 VEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
            E   +PE+  R +F   +  + T+  +   F + G + D  ++ D N++RS+G G++ +
Sbjct: 4   SESPKEPEQL-RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62

Query: 270 YDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNL 329
             V  V  A+      + G+ V  K +           S   +         +K++VG +
Sbjct: 63  ATVEEVDAAMNARPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGI 112

Query: 330 HFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI 389
             +  E  LR  FE +G +E++++  D  +G+ +GF FV F   +        +     +
Sbjct: 113 KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI--VIQKYHTV 170

Query: 390 VGRTLKVS 397
            G   +V 
Sbjct: 171 NGHNCEVR 178

>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 = 57.7 bits (140), Expect = 9e-10
 Identities = 21/113 (18%), Positives = 51/113 (45%), Gaps = 2/113 (1%)

Query: 199 ESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS 258
           E +R   +++   P A      + +F   +     E  + ++F + GK+  + ++ DR S
Sbjct: 85  EPKRAVSREDSQRPGAHLT--VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS 142

Query: 259 RRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGG 311
            + +G  ++ F D  SV   +      + G    V+ + +++ +  +++S  G
Sbjct: 143 GKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRG 195

>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 =  108 bits (271), Expect = 1e-27
 Identities = 39/180 (21%), Positives = 80/180 (44%), Gaps = 19/180 (10%)

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPM 277
           ++   +F   +    TE ++ E+F K G V D++++ D  + RS+G G++ F    SV  
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60

Query: 278 AIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQ 337
            +  +  +L G+ +  K +       ++                 K++VG +  ++   +
Sbjct: 61  VVK-TQHILDGKVIDPKRAIPRDEQDKT----------------GKIFVGGIGPDVRPKE 103

Query: 338 LRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
             + F  +G +   QL LD +TGQ +GFGFV +   +         N  ++   R +++ 
Sbjct: 104 FEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV--CQNKFIDFKDRKIEIK 161

>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 = 59.5 bits (145), Expect = 1e-10
 Identities = 16/83 (19%), Positives = 39/83 (46%)

Query: 215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMS 274
           D +     +F   +      ++  EFFS+ G + D +L++D+++ +S+G G++ +    +
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 275 VPMAIALSGQLLLGQPVMVKPSE 297
           V             + + +K +E
Sbjct: 142 VDRVCQNKFIDFKDRKIEIKRAE 164

>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 =  104 bits (262), Expect = 4e-27
 Identities = 45/98 (45%), Positives = 60/98 (61%), Gaps = 1/98 (1%)

Query: 304 QSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 363
               +A         A   +LYVG+LHFN+TE  LR +FEPFG +E +QL +D ETG+ K
Sbjct: 9   SHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68

Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD 401
           G+GF+ F+  E AK A   LNG  E+ GR +KV  VT+
Sbjct: 69  GYGFITFSDSECAKKALEQLNGF-ELAGRPMKVGHVTE 105

>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 = 51.2 bits (123), Expect = 3e-08
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +    TE  +   F   G++  ++L+MD  + RSKG G+I F D      A+  L+G  L
Sbjct: 34  LHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFEL 93

Query: 287 LGQPVMV 293
            G+P+ V
Sbjct: 94  AGRPMKV 100

>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 =  103 bits (260), Expect = 5e-27
 Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
           G  G     LY+  L    T+  L KL +P+G +   +  LD  T +CKG+GFV F    
Sbjct: 1   GSSG--SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPS 58

Query: 375 HAKAAQSALNGKLEIVGRTLKVS 397
            A+ A +AL     +  +  K S
Sbjct: 59  AAQKAVTALKAS-GVQAQMAKQS 80

>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 = 56.4 bits (137), Expect = 2e-10
 Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 2/82 (2%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
               ++   +    T++D+ +     GK+   + I+D+ + + KG G+++F    +   A
Sbjct: 4   GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 279 I-ALSGQLLLGQPVMV-KPSEA 298
           + AL    +  Q      PS  
Sbjct: 64  VTALKASGVQAQMAKQSGPSSG 85

>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 =  101 bits (255), Expect = 2e-26
 Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S     +G        +YV NL F++T   L ++F  +G V  V +  D +T + KG  F
Sbjct: 3   SGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAF 62

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           + F   + A+    A+N K ++ GR +K S
Sbjct: 63  ILFLDKDSAQNCTRAINNK-QLFGRVIKAS 91

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 64.2 bits (157), Expect = 5e-13
 Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 1/81 (1%)

Query: 214 ADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVM 273
                 + TV+   +P   T  D+Y  FSK GKV  V ++ D+++R+SKGV +I F D  
Sbjct: 10  GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69

Query: 274 SVPMAI-ALSGQLLLGQPVMV 293
           S      A++ + L G+ +  
Sbjct: 70  SAQNCTRAINNKQLFGRVIKA 90

>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} PDB: 3us5_A 2dny_A Length = 118

 Score =  101 bits (254), Expect = 6e-26
 Identities = 26/103 (25%), Positives = 46/103 (44%), Gaps = 14/103 (13%)

Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRS---------A 545
              S  ++L+NM DP      D D +++G+V EEC K+G V  + + +            
Sbjct: 17  KQESTVMVLRNMVDPK-----DIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEII 71

Query: 546 GFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 588
             +++ F        A +A++ RWFA R + A     E ++  
Sbjct: 72  VKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNS 114

>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 =  100 bits (251), Expect = 1e-25
 Identities = 38/79 (48%), Positives = 54/79 (68%), Gaps = 1/79 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            LYVG+LHFN+TE  LR +FEPFG ++ + L  D +TG+ KG+GF+ F+  E A+ A   
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 383 LNGKLEIVGRTLKVSSVTD 401
           LNG  E+ GR ++V  VT+
Sbjct: 67  LNGF-ELAGRPMRVGHVTE 84

>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 = 57.2 bits (139), Expect = 1e-10
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 232 ATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQP 290
            TE  +   F   GK+ ++ L+ D ++ RSKG G+I F D      A+  L+G  L G+P
Sbjct: 17  ITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRP 76

Query: 291 VMVKPSEAEKNLVQSNTSAGG 311
           + V      + L   +  + G
Sbjct: 77  MRV--GHVTERLDGGSGPSSG 95

>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 =  101 bits (254), Expect = 1e-25
 Identities = 35/94 (37%), Positives = 51/94 (54%), Gaps = 1/94 (1%)

Query: 304 QSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 363
           Q       T   P   + R L V  +   + E QLR+LFE +GP+E V++  D ET Q +
Sbjct: 25  QQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSR 84

Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           G+GFV+F     A+ A + LNG   I+ + LKV+
Sbjct: 85  GYGFVKFQSGSSAQQAIAGLNGF-NILNKRLKVA 117

>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 = 54.4 bits (131), Expect = 4e-09
 Identities = 20/103 (19%), Positives = 49/103 (47%), Gaps = 1/103 (0%)

Query: 192 ERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVR 251
            +  ++++ ++ +++              R +    +P    E  + + F + G +  V+
Sbjct: 14  GQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK 73

Query: 252 LIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
           ++ DR +R+S+G G+++F    S   AI  L+G  +L + + V
Sbjct: 74  IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV 116

>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 = 98.0 bits (245), Expect = 4e-25
 Identities = 33/83 (39%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
           G      R LYVG L   + +  L   F PFG +  +Q+PLD ET + +GF FV+F   E
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60

Query: 375 HAKAAQSALNGKLEIVGRTLKVS 397
            A AA   +N   E+ GRT++V+
Sbjct: 61  DAAAAIDNMNES-ELFGRTIRVN 82

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 56.0 bits (136), Expect = 3e-10
 Identities = 13/78 (16%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
              +R ++   +  +  ++ ++  F   G + D+++ +D  + + +G  ++EF       
Sbjct: 4   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 277 MAI-ALSGQLLLGQPVMV 293
            AI  ++   L G+ + V
Sbjct: 64  AAIDNMNESELFGRTIRV 81

>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 = 98.5 bits (246), Expect = 5e-25
 Identities = 31/90 (34%), Positives = 48/90 (53%), Gaps = 1/90 (1%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE-TGQCKGFG 366
           S+G +   P      K+ V N+ F   + ++R+LF  FG ++ V+LP  +  TG  +GFG
Sbjct: 2   SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61

Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           FV F   + AK A +AL     + GR L +
Sbjct: 62  FVDFITKQDAKKAFNALCHSTHLYGRRLVL 91

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 53.5 bits (129), Expect = 4e-09
 Identities = 24/101 (23%), Positives = 50/101 (49%), Gaps = 4/101 (3%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR-NSRRSKGVGYIEFYD 271
           +   ++    +    +P +A +R++ E FS  G+++ VRL      +   +G G+++F  
Sbjct: 8   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67

Query: 272 VMSVPMAI-ALS-GQLLLGQPVMVKPSEAEKNLVQSNTSAG 310
                 A  AL     L G+ ++++ +++E   VQS  S+G
Sbjct: 68  KQDAKKAFNALCHSTHLYGRRLVLEWADSEVT-VQSGPSSG 107

>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 = 97.7 bits (244), Expect = 8e-25
 Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +L+V NL +  +E  L KLF  +GP+  +  P+D  T + KGF FV F   EHA  A + 
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 383 LNGKLEIVGRTLKV 396
           ++G+    GR L V
Sbjct: 70  VDGQ-VFQGRMLHV 82

>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 = 61.8 bits (151), Expect = 3e-12
 Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 1/84 (1%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +   ++E D+ + FS  G + ++   +D  +++ KG  ++ F        A   + GQ+ 
Sbjct: 16  LSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVF 75

Query: 287 LGQPVMVKPSEAEKNLVQSNTSAG 310
            G+ + V PS  +K   QS  S+G
Sbjct: 76  QGRMLHVLPSTIKKEASQSGPSSG 99

>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 = 39.1 bits (92), Expect = 3e-04
 Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 5/64 (7%)

Query: 524 DVEEECSKYGRVK--HIYVDK---RSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAI 578
           D+E+  S YG +   H  +D    +  GF ++ F   E A  A   +  + F  R++  +
Sbjct: 24  DLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL 83

Query: 579 FMKP 582
               
Sbjct: 84  PSTI 87

>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 =  101 bits (252), Expect = 1e-24
 Identities = 34/209 (16%), Positives = 70/209 (33%), Gaps = 30/209 (14%)

Query: 210 VEPEADPERDQRTVFAYQM-PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIE 268
           +            +    + P + T + ++  F   G V+ V+++        K    ++
Sbjct: 24  IAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQ 78

Query: 269 FYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRK---- 323
             D     +A+  L+G  L G+P+ +  S+ +   +          T  YG         
Sbjct: 79  MADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 138

Query: 324 ---------------LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFV 368
                          L++ N+  +++E  L+ LF   G V    +       + +    +
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALI 194

Query: 369 QFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           Q   +E A  A   L+         L+VS
Sbjct: 195 QMGSVEEAVQALIDLHNHDLGENHHLRVS 223

>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 = 42.3 bits (99), Expect = 2e-04
 Identities = 14/104 (13%), Positives = 30/104 (28%), Gaps = 10/104 (9%)

Query: 472 GQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSK 531
              +  VP  +      +     G+ +  LL+ N+    +     F L            
Sbjct: 9   HHSSGLVPRGSHMGRIAIPGL-AGAGNSVLLVSNLNPERVTPQSLFIL---------FGV 58

Query: 532 YGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI 575
           YG V+ + +         ++      A  A   ++      + I
Sbjct: 59  YGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPI 102

>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 = 41.1 bits (96), Expect = 4e-04
 Identities = 17/96 (17%), Positives = 32/96 (33%), Gaps = 6/96 (6%)

Query: 200 SRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSR 259
           S  ++ KK   +   +      T+    +P   +E D+   FS  G V        ++  
Sbjct: 131 SPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-- 188

Query: 260 RSKGVGYIEFYDVMSVPMAI-ALSG-QLLLGQPVMV 293
             + +  I+   V     A+  L    L     + V
Sbjct: 189 --RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV 222

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 97.8 bits (244), Expect = 2e-24
 Identities = 32/103 (31%), Positives = 49/103 (47%), Gaps = 4/103 (3%)

Query: 295 PSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLP 354
           P  +      +  +AG    GP G     L++ +L    T+T L   F PFG V   ++ 
Sbjct: 17  PLASVALSAAAAAAAGKQIEGPEGC---NLFIYHLPQEFTDTDLASTFLPFGNVISAKVF 73

Query: 355 LDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           +D +T   K FGFV F   + A+ A  A+NG  ++  + LKV 
Sbjct: 74  IDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGF-QVGTKRLKVQ 115

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 52.4 bits (126), Expect = 1e-08
 Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
           +F Y +P + T+ D+   F   G V   ++ +D+ +  SK  G++ F +  S  +AI A+
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 282 SGQLLLGQPVMVK 294
           +G  +  + + V+
Sbjct: 103 NGFQVGTKRLKVQ 115

>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 = 96.9 bits (242), Expect = 2e-24
 Identities = 26/80 (32%), Positives = 47/80 (58%), Gaps = 1/80 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R +Y+G++ ++ TE Q+  L    GPV  +++  D +TG+ KG+ F++F  LE + +A  
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 382 ALNGKLEIVGRTLKVSSVTD 401
            LNG  ++  R LK    ++
Sbjct: 63  NLNGY-QLGSRFLKCGYSSN 81

>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 = 58.4 bits (142), Expect = 5e-11
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
           R V+   +P   TE  + +  S  G V +++++ D  + RSKG  +IEF D+ S   A+ 
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 280 ALSGQLLLGQPVMV 293
            L+G  L  + +  
Sbjct: 63  NLNGYQLGSRFLKC 76

>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 = 98.8 bits (246), Expect = 5e-24
 Identities = 34/199 (17%), Positives = 69/199 (34%), Gaps = 30/199 (15%)

Query: 220 QRTVFAYQM-PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
              +    + P + T + ++  F   G V+ V+++        K    ++  D     +A
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLA 57

Query: 279 I-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAID---------------- 321
           +  L+G  L G+P+ +  S+ +   +          T  YG                   
Sbjct: 58  MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117

Query: 322 ---RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
                L++ N+  +++E  L+ LF   G V    +       + +    +Q   +E A  
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQ 173

Query: 379 AQSALNGKLEIVGRTLKVS 397
           A   L+         L+VS
Sbjct: 174 ALIDLHNHDLGENHHLRVS 192

>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 = 41.8 bits (98), Expect = 2e-04
 Identities = 19/116 (16%), Positives = 36/116 (31%), Gaps = 8/116 (6%)

Query: 180 RERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYE 239
           +     +E +   +D       R+K+          P     T+    +P   +E D+  
Sbjct: 82  QLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP--PSATLHLSNIPPSVSEEDLKV 139

Query: 240 FFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSG-QLLLGQPVMV 293
            FS  G V        ++    + +  I+   V     A+  L    L     + V
Sbjct: 140 LFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV 191

>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 = 94.9 bits (237), Expect = 6e-24
 Identities = 18/78 (23%), Positives = 47/78 (60%), Gaps = 2/78 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLD-IETGQCKGFGFVQFAQLEHAKAAQS 381
           K+++G L  N+T+  + ++F  +G ++++ +P++ +     KG+ +V+F   + A+ A  
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 382 ALNGKLEIVGRTLKVSSV 399
            ++G  +I G+ +  ++V
Sbjct: 66  HMDGG-QIDGQEITATAV 82

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 54.5 bits (132), Expect = 9e-10
 Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 232 ATERDVYEFFSKAGKVRDVRLIMDRN-SRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQ 289
            T+  + E FS  GK++ + + ++R     SKG  Y+EF +      A+  + G  + GQ
Sbjct: 16  VTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQ 75

Query: 290 PVMVKPSEAEKN 301
            +      A   
Sbjct: 76  EITATAVLAPWP 87

>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 = 95.5 bits (238), Expect = 8e-24
 Identities = 32/94 (34%), Positives = 49/94 (52%), Gaps = 4/94 (4%)

Query: 304 QSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 363
           QS  +AG    GP GA    L++ +L     +  L ++F PFG V   ++ +D +T   K
Sbjct: 11  QSIGAAGSQKEGPEGA---NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67

Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
            FGFV +     A+AA  ++NG  +I  + LKV 
Sbjct: 68  CFGFVSYDNPVSAQAAIQSMNGF-QIGMKRLKVQ 100

>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 = 52.3 bits (126), Expect = 1e-08
 Identities = 17/83 (20%), Positives = 42/83 (50%), Gaps = 4/83 (4%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
           +F Y +P +  ++D+ + F   G V   ++ +D+ +  SK  G++ + + +S   AI ++
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 282 SGQLLLGQPVMV---KPSEAEKN 301
           +G  +  + + V   +     K+
Sbjct: 88  NGFQIGMKRLKVQLKRSKNDSKS 110

>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 = 94.2 bits (235), Expect = 1e-23
 Identities = 33/91 (36%), Positives = 45/91 (49%), Gaps = 3/91 (3%)

Query: 308 SAGGTATGP-YGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFG 366
           S+G +   P     DR ++VGNL   + E  L +LF   GP+  V +  D   G+ K FG
Sbjct: 2   SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFG 60

Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           FV F   E    A + LNG   + GR + VS
Sbjct: 61  FVCFKHPESVSYAIALLNGI-RLYGRPINVS 90

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 60.7 bits (148), Expect = 8e-12
 Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
                E   RTVF   +  +  E  +YE F +AG +  V +  DR   + K  G++ F  
Sbjct: 8   MFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKH 66

Query: 272 VMSVPMAI-ALSGQLLLGQPVMVKPSEA 298
             SV  AI  L+G  L G+P+ V    +
Sbjct: 67  PESVSYAIALLNGIRLYGRPINVSGPSS 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 = 93.8 bits (234), Expect = 2e-23
 Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 1/90 (1%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +        +  L V  L    TE  LR++F  +GP+  V +  D ++ + +GF F
Sbjct: 2   SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           V F  ++ AK A+   NG  E+ GR ++VS
Sbjct: 62  VYFENVDDAKEAKERANGM-ELDGRRIRVS 90

>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 = 58.4 bits (142), Expect = 6e-11
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
             +  + + L  TERD+ E FSK G + DV ++ D+ SRRS+G  ++ F +V     A  
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75

Query: 280 ALSGQLLLGQPVMV 293
             +G  L G+ + V
Sbjct: 76  RANGMELDGRRIRV 89

>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 = 93.9 bits (234), Expect = 2e-23
 Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            KLY+GNL   +T   LR+LF          LPL  +     G+ FV +     A  A  
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIE 62

Query: 382 ALNGKLEIVGRTLKVS 397
            L+GK+E+ G+ ++V 
Sbjct: 63  TLSGKVELHGKIMEVD 78

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
             ++   +    T  D+ + F         +++         G  ++++ D      AI 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAIRAIE 62

Query: 280 ALSGQL-LLGQPVMVKPSEAEK 300
            LSG++ L G+ + V  S ++K
Sbjct: 63  TLSGKVELHGKIMEVDYSVSKK 84

>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 = 93.9 bits (234), Expect = 2e-23
 Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 2/87 (2%)

Query: 313 ATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ 372
           ++G       KL++G +  N+ E  L+ LFE FG +  + +  D  TG  KG  F+ + +
Sbjct: 5   SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64

Query: 373 LEHAKAAQSALNGK--LEIVGRTLKVS 397
            E A  AQSAL+ +  L  + R ++V 
Sbjct: 65  RESALKAQSALHEQKTLPGMNRPIQVK 91

>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 = 64.3 bits (157), Expect = 6e-13
 Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 4/92 (4%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
               + D   +F  Q+P    E+D+   F + GK+ ++ ++ DR +   KG  ++ + + 
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65

Query: 273 MSVPMAI-ALSGQLLL---GQPVMVKPSEAEK 300
            S   A  AL  Q  L    +P+ VKP+++E 
Sbjct: 66  ESALKAQSALHEQKTLPGMNRPIQVKPADSES 97

>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 = 93.4 bits (233), Expect = 3e-23
 Identities = 33/88 (37%), Positives = 48/88 (54%), Gaps = 1/88 (1%)

Query: 310 GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
           G + +       R LYVG L   + +  L   F PFG +  +Q+PLD ET + +GF FV+
Sbjct: 1   GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60

Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           F   E A AA   +N   E+ GRT++V+
Sbjct: 61  FELAEDAAAAIDNMNES-ELFGRTIRVN 87

>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 = 55.7 bits (135), Expect = 5e-10
 Identities = 13/81 (16%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 214 ADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVM 273
           +     +R ++   +  +  ++ ++  F   G + D+++ +D  + + +G  ++EF    
Sbjct: 6   SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65

Query: 274 SVPMAI-ALSGQLLLGQPVMV 293
               AI  ++   L G+ + V
Sbjct: 66  DAAAAIDNMNESELFGRTIRV 86

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 93.6 bits (233), Expect = 3e-23
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           +++    L+ N+ ET L+ +   +G VE V++ L   T +  G   V F     AK    
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 382 ALNGKLEIVGRTLKVS 397
            L+    ++G  +   
Sbjct: 67  NLHLT-SVMGNIIHAQ 81

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 64.0 bits (156), Expect = 1e-12
 Identities = 11/76 (14%), Positives = 30/76 (39%), Gaps = 1/76 (1%)

Query: 220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
            + V   ++     E  + +   K G+V +V +++   +R+  G+  + F         +
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 280 -ALSGQLLLGQPVMVK 294
             L    ++G  +  +
Sbjct: 66  KNLHLTSVMGNIIHAQ 81

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 44.3 bits (105), Expect = 7e-06
 Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 5/57 (8%)

Query: 524 DVEEECSKYGRVK--HIYVD---KRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI 575
            +++ C KYG V+   I +    ++  G   + F ST  A    + +H+      +I
Sbjct: 22  FLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNII 78

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 93.5 bits (233), Expect = 3e-23
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L+V  +H   TE  +   F  +G ++ + L LD  TG  KG+  V++   + A+AA   
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 383 LNGKLEIVGRTLKV 396
           LNG+ +++G+ + V
Sbjct: 85  LNGQ-DLMGQPISV 97

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 64.6 bits (158), Expect = 5e-13
 Identities = 28/96 (29%), Positives = 52/96 (54%), Gaps = 6/96 (6%)

Query: 204 KEKKEVVEPEADPERDQR-----TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS 258
           +E  + VE + D    QR      +F   +  +ATE D+++ F++ G+++++ L +DR +
Sbjct: 2   REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 61

Query: 259 RRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
              KG   +E+        A+  L+GQ L+GQP+ V
Sbjct: 62  GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 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 = 93.4 bits (233), Expect = 4e-23
 Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            + V NL  +  ET L++LF PFG +  + L  D  TGQ KGF F+ F + E A  A + 
Sbjct: 17  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76

Query: 383 LNGKLEIVGRTLKVS 397
           ++G        L V 
Sbjct: 77  VSGF-GYDHLILNVE 90

>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 = 56.5 bits (137), Expect = 3e-10
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
           D  T+    +     E D+ E F   G +  + L  D+ + +SKG  +I F+       A
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 279 I-ALSGQLLLGQPVMV 293
           I  +SG       + V
Sbjct: 74  IAGVSGFGYDHLILNV 89

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 92.8 bits (231), Expect = 5e-23
 Identities = 26/115 (22%), Positives = 40/115 (34%), Gaps = 19/115 (16%)

Query: 283 GQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLF 342
           G   +G P  V P   +   +  +     T            Y+GN+    TE  L  LF
Sbjct: 1   GSQTIGLPPQVNPQAVDH--IIRSAPPRVT----------TAYIGNIPHFATEADLIPLF 48

Query: 343 EPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           + FG +   +   +      KG  F+++   E A     AL       GR L+  
Sbjct: 49  QNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVALANF-PFQGRNLRTG 96

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 9/85 (10%)

Query: 208 EVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYI 267
           + +   A P     T +   +P  ATE D+   F   G + D +          KG  +I
Sbjct: 17  DHIIRSAPP--RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFI 68

Query: 268 EFYDVMSVPMAI-ALSGQLLLGQPV 291
           ++       + I AL+     G+ +
Sbjct: 69  KYDTHEQAAVCIVALANFPFQGRNL 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 = 97.1 bits (242), Expect = 9e-23
 Identities = 42/196 (21%), Positives = 73/196 (37%), Gaps = 30/196 (15%)

Query: 205 EKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGV 264
           + K  ++P       +  +F   +P   TE D    F + G+  +V +       R +G 
Sbjct: 7   DIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RDRGF 60

Query: 265 GYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRK 323
           G+I         +A   L G +L  +P+ ++ +     L                     
Sbjct: 61  GFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAAL--------------------- 99

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
             V NL   ++   L + F  FGPVE   + +D + G+  G GFV+FA    A+ A    
Sbjct: 100 -TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERC 157

Query: 384 NGKLEIVGRTLKVSSV 399
                ++  T +   V
Sbjct: 158 GDGAFLLTTTPRPVIV 173

>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 = 92.3 bits (230), Expect = 9e-23
 Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 1/89 (1%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +        D  +YVG L   ++E  L +LF   GPV    +P D  TGQ +G+GF
Sbjct: 2   SSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF 61

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           V+F   E A  A   ++   ++ G+ ++V
Sbjct: 62  VEFLSEEDADYAIKIMDMI-KLYGKPIRV 89

>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 = 62.3 bits (152), Expect = 3e-12
 Identities = 24/91 (26%), Positives = 44/91 (48%), Gaps = 2/91 (2%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           P ++  +D  TV+   +  K +E  ++E F +AG V +  +  DR + + +G G++EF  
Sbjct: 8   PISERNQD-ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66

Query: 272 VMSVPMAI-ALSGQLLLGQPVMVKPSEAEKN 301
                 AI  +    L G+P+ V  + A   
Sbjct: 67  EEDADYAIKIMDMIKLYGKPIRVNKASAHNK 97

>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 = 95.2 bits (236), Expect = 1e-22
 Identities = 27/202 (13%), Positives = 57/202 (28%), Gaps = 29/202 (14%)

Query: 219 DQRTVFAYQM-PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPM 277
           D   +  Y +   K     V+  F   G V  V+ +     +   G   +E  D  +V  
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFM-----KSKPGAAMVEMADGYAVDR 57

Query: 278 AI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKL------------ 324
           AI  L+   + GQ + V  S+    +   +      +       + +             
Sbjct: 58  AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117

Query: 325 ---------YVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH 375
                    +  N    +TE    ++ +  G      + +     +    G +++     
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSD 177

Query: 376 AKAAQSALNGKLEIVGRTLKVS 397
           A      LN   ++        
Sbjct: 178 ALETLGFLNHY-QMKNPNGPYP 198

>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 = 52.4 bits (125), Expect = 6e-08
 Identities = 12/101 (11%), Positives = 28/101 (27%)

Query: 180 RERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYE 239
              +            +  ESR  +        +   +     +  +  PL+ TE + +E
Sbjct: 83  MPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFE 142

Query: 240 FFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
              + G  R   + +          G +E+         + 
Sbjct: 143 ICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLG 183

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 42.4 bits (99), Expect = 2e-04
 Identities = 13/81 (16%), Positives = 27/81 (33%), Gaps = 9/81 (11%)

Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFES 554
           G+ S  L++  +    M  D  F++            YG V+ +   K   G   +    
Sbjct: 1   GADSPVLMVYGLDQSKMNCDRVFNV---------FCLYGNVEKVKFMKSKPGAAMVEMAD 51

Query: 555 TEAAASAQRAMHMRWFARRLI 575
             A   A   ++  +   + +
Sbjct: 52  GYAVDRAITHLNNNFMFGQKM 72

>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 = 91.6 bits (228), Expect = 2e-22
 Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 3/91 (3%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G + +   G  DRKL+VG L+   +E  + +LF+PFG ++   +      G  KG  F
Sbjct: 2   SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAF 60

Query: 368 VQFAQLEHAKAAQSALNGK--LEIVGRTLKV 396
           V+F+    A+AA  AL+G   +     +L V
Sbjct: 61  VKFSSHTEAQAAIHALHGSQTMPGASSSLVV 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 = 49.6 bits (119), Expect = 8e-08
 Identities = 22/103 (21%), Positives = 42/103 (40%), Gaps = 8/103 (7%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
                    R +F   +  + +E DV   F   G + +  ++   +   SKG  +++F  
Sbjct: 7   GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDG-SSKGCAFVKFSS 65

Query: 272 VMSVPMAI-ALSGQLLL---GQPVMVKPSEAEKNLVQSNTSAG 310
                 AI AL G   +      ++VK ++ +K   +S  S+G
Sbjct: 66  HTEAQAAIHALHGSQTMPGASSSLVVKFADTDK---ESGPSSG 105

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 4/47 (8%)

Query: 524 DVEEECSKYGRVKHIYV----DKRSAGFVYLRFESTEAAASAQRAMH 566
           DV      +G +    V    D  S G  +++F S   A +A  A+H
Sbjct: 31  DVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77

>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 = 90.8 bits (226), Expect = 2e-22
 Identities = 25/89 (28%), Positives = 49/89 (55%), Gaps = 5/89 (5%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +    +    + L + NL ++ TE  L+++FE    +++       + G+ KG+ F
Sbjct: 2   SSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYAF 57

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           ++FA  E AK A ++ N + EI GR +++
Sbjct: 58  IEFASFEDAKEALNSCNKR-EIEGRAIRL 85

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
            +    + +T+    +   ATE  + E F KA  ++    +    + +SKG  +IEF   
Sbjct: 8   NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASF 63

Query: 273 MSVPMAI-ALSGQLLLGQPVMV 293
                A+ + + + + G+ + +
Sbjct: 64  EDAKEALNSCNKREIEGRAIRL 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 = 90.3 bits (225), Expect = 3e-22
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R +YVGN+ +  T  +L   F   G V  V +  D  +G  KGF +++F+  E  + +  
Sbjct: 7   RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 65

Query: 382 ALNGKLEIVGRTLKVS 397
           AL+      GR +KV 
Sbjct: 66  ALDES-LFRGRQIKVI 80

>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 = 76.4 bits (189), Expect = 2e-17
 Identities = 26/85 (30%), Positives = 40/85 (47%)

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
            E D R+++   +   AT  ++   F   G V  V ++ D+ S   KG  YIEF D  SV
Sbjct: 2   MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61

Query: 276 PMAIALSGQLLLGQPVMVKPSEAEK 300
             ++AL   L  G+ + V P    +
Sbjct: 62  RTSLALDESLFRGRQIKVIPKRTNR 86

>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 = 91.3 bits (227), Expect = 4e-22
 Identities = 27/114 (23%), Positives = 46/114 (40%), Gaps = 7/114 (6%)

Query: 288 GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGP 347
           GQ +   P + + +L  S    G            KL V NL F +++  +++LF  FG 
Sbjct: 7   GQQMGRDPDKWQHDLFDSGCGGGEGVETG-----AKLLVSNLDFGVSDADIQELFAEFGT 61

Query: 348 VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD 401
           ++   +  D  +G+  G   V F +   A  A     G   + GR + +  V  
Sbjct: 62  LKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKGV-PLDGRPMDIQLVAS 113

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 44.7 bits (106), Expect = 8e-06
 Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
           ++ D+ E F++ G ++   +  DR S RS G   + F        A+    G  L G+P+
Sbjct: 48  SDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM 106

Query: 292 MV 293
            +
Sbjct: 107 DI 108

>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 = 90.4 bits (225), Expect = 5e-22
 Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L+V ++H    E ++++ F  +G ++ + L LD  TG  KG+  V++   + A AA+ A
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 383 LNGKLEIVGRTLKV 396
           LNG  EI+G+T++V
Sbjct: 88  LNGA-EIMGQTIQV 100

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 60.8 bits (148), Expect = 1e-11
 Identities = 25/100 (25%), Positives = 48/100 (48%), Gaps = 4/100 (4%)

Query: 197 MRESRRYKEKKEVVEPEADPER--DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIM 254
           +    R    ++  E E  P+R  +   +F   +  +A E ++ E F   G+++++ L +
Sbjct: 2   IHSYER-VRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 60

Query: 255 DRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
           DR +  SKG   +E+        A  AL+G  ++GQ + V
Sbjct: 61  DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100

>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 = 90.0 bits (224), Expect = 5e-22
 Identities = 28/90 (31%), Positives = 50/90 (55%), Gaps = 3/90 (3%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +         R LYVGNL  ++TE  + +LF   GP +  ++  +  +     + F
Sbjct: 2   SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCF 59

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           V+F +   A AA +A+NG+ +I+G+ +KV+
Sbjct: 60  VEFYEHRDAAAALAAMNGR-KILGKEVKVN 88

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 22/100 (22%), Positives = 47/100 (47%), Gaps = 4/100 (4%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
              + +   RT++   +    TE  + + FS+ G  +  ++I +  S       ++EFY+
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYE 64

Query: 272 VMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAG 310
                 A+ A++G+ +LG+ V V  +    +  +S  S+G
Sbjct: 65  HRDAAAALAAMNGRKILGKEVKVNWATTPSS-QKSGPSSG 103

>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 = 88.4 bits (220), Expect = 2e-21
 Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 1/82 (1%)

Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
           GP       L V NL +  +   LR++FE +G V  V +P +  T   +GF FV+F    
Sbjct: 7   GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRR 66

Query: 375 HAKAAQSALNGKLEIVGRTLKV 396
            A+ A++A++G  E+ GR L+V
Sbjct: 67  DAQDAEAAMDGA-ELDGRELRV 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 = 56.5 bits (137), Expect = 3e-10
 Identities = 15/67 (22%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
           +  + +   +   F K G+V DV +  + +++  +G  ++ F+D      A  A+ G  L
Sbjct: 21  LTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAEL 80

Query: 287 LGQPVMV 293
            G+ + V
Sbjct: 81  DGRELRV 87

>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 = 88.5 bits (220), Expect = 2e-21
 Identities = 25/100 (25%), Positives = 47/100 (47%), Gaps = 14/100 (14%)

Query: 305 SNTSAGGTATGPYGAIDRK-------LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDI 357
           S+ S+G T    +  +  +       +Y G +   +T+  +R+ F PFG +  +++  + 
Sbjct: 2   SSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE- 60

Query: 358 ETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
                KG+ FV+F+  E A  A  ++NG   I G  +K  
Sbjct: 61  -----KGYSFVRFSTHESAAHAIVSVNGT-TIEGHVVKCY 94

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 49.6 bits (119), Expect = 8e-08
 Identities = 19/94 (20%), Positives = 41/94 (43%), Gaps = 9/94 (9%)

Query: 199 ESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS 258
                + + E V  ++ P     TV+   +    T++ + + FS  G++ ++R+  +   
Sbjct: 6   SGNTKQLRFEDVVNQSSP--KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE--- 60

Query: 259 RRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
              KG  ++ F    S   AI +++G  + G  V
Sbjct: 61  ---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91

>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 = 88.1 bits (219), Expect = 2e-21
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 4/78 (5%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQC---KGFGFVQFAQLEHAKAA 379
            L++ NL+F+ TE  L+ +F   G ++   +             GFGFV++ + E A+ A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 380 QSALNGKLEIVGRTLKVS 397
              L G   + G  L+V 
Sbjct: 67  LKQLQGH-TVDGHKLEVR 83

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNS---RRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG 288
           TE  +   FSK G ++   +   +N      S G G++E+        A+  L G  + G
Sbjct: 18  TEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG 77

Query: 289 QPVMVKPSE 297
             + V+ SE
Sbjct: 78  HKLEVRISE 86

>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 = 88.1 bits (219), Expect = 2e-21
 Identities = 31/87 (35%), Positives = 50/87 (57%), Gaps = 1/87 (1%)

Query: 310 GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
           G + +    + + KL+VG L F+  E  L ++F  +G +  V +  D ET + +GFGFV 
Sbjct: 1   GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60

Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKV 396
           F  ++ AK A  A+NGK  + GR ++V
Sbjct: 61  FENIDDAKDAMMAMNGK-SVDGRQIRV 86

>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 = 56.9 bits (138), Expect = 2e-10
 Identities = 23/94 (24%), Positives = 52/94 (55%), Gaps = 3/94 (3%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
           D+  +F   +     E+ + + FSK G++ +V ++ DR ++RS+G G++ F ++     A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70

Query: 279 I-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGG 311
           + A++G+ + G+ + V   +A K+    +  + G
Sbjct: 71  MMAMNGKSVDGRQIRVD--QAGKSSDNRSGPSSG 102

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 87.7 bits (218), Expect = 3e-21
 Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            KL++  L F+ T+ +L ++ +  G V+ ++L  +   G+ KG  +V++     A  A  
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVM 76

Query: 382 ALNGKLEIVGRTLKVS 397
            ++G   I    +KV+
Sbjct: 77  KMDGM-TIKENIIKVA 91

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 18/88 (20%), Positives = 41/88 (46%), Gaps = 2/88 (2%)

Query: 215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMS 274
               ++  +F   +P   T+ ++ E     G V+D+RL+ +R + + KG+ Y+E+ +   
Sbjct: 12  STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQ 70

Query: 275 VPMAI-ALSGQLLLGQPVMVKPSEAEKN 301
              A+  + G  +    + V  S +  +
Sbjct: 71  ASQAVMKMDGMTIKENIIKVAISNSGPS 98

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 87.6 bits (217), Expect = 4e-21
 Identities = 25/100 (25%), Positives = 47/100 (47%), Gaps = 11/100 (11%)

Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYV------DKRSAGFV 548
             P++ +LL+NM         + D +++ + +EEC KYG+V    +          A  +
Sbjct: 5   KCPTKVVLLRNMVGAG-----EVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRI 59

Query: 549 YLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 588
           +L FE  E+A  A   ++ R+F  R++ A F   + +   
Sbjct: 60  FLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLDKFRVL 99

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 87.7 bits (218), Expect = 4e-21
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL V NL F +++  +++LF  FG ++   +  D  +G+  G   V F +   A  A   
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 89

Query: 383 LNGKLEIVGRTLKVSSVT 400
            NG   + GR + +  VT
Sbjct: 90  YNGV-PLDGRPMNIQLVT 106

>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 = 44.2 bits (105), Expect = 6e-06
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
           ++ D+ E F++ G ++   +  DR S RS G   + F        A+   +G  L G+P+
Sbjct: 42  SDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 100

Query: 292 MV 293
            +
Sbjct: 101 NI 102

>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 = 87.3 bits (217), Expect = 4e-21
 Identities = 32/80 (40%), Positives = 47/80 (58%), Gaps = 1/80 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R ++VGN+ +  TE QL+ +F   GPV   +L  D ETG+ KG+GF ++   E A +A  
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 382 ALNGKLEIVGRTLKVSSVTD 401
            LNG+ E  GR L+V +   
Sbjct: 69  NLNGR-EFSGRALRVDNAAS 87

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 61.1 bits (149), Expect = 7e-12
 Identities = 30/100 (30%), Positives = 53/100 (53%), Gaps = 1/100 (1%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
           +   +R  R+VF   +P +ATE  + + FS+ G V   RL+ DR + + KG G+ E+ D 
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 273 MSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGG 311
            +   A+  L+G+   G+ + V  + +EKN  +  +   G
Sbjct: 61  ETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 87.6 bits (217), Expect = 4e-21
 Identities = 23/99 (23%), Positives = 36/99 (36%), Gaps = 5/99 (5%)

Query: 485 VIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRS 544
            + N+      S      L++      E    +D   +    E   KYG V+ + V    
Sbjct: 5   ALLNIYRNPQNSSQSADGLRSAVSDV-EMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL 63

Query: 545 A----GFVYLRFESTEAAASAQRAMHMRWFARRLISAIF 579
                G VY++F   E A  A   ++ RWF  + I A  
Sbjct: 64  GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>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 = 87.4 bits (217), Expect = 5e-21
 Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 5/81 (6%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + +++ NL F+  E  L ++ + FG ++ V++ L  +T   KG  F QF   E A+   +
Sbjct: 16  KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75

Query: 382 ALN-----GKLEIVGRTLKVS 397
           A +     G L++ GR LKV 
Sbjct: 76  AASLEAEGGGLKLDGRQLKVD 96

>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 = 60.8 bits (148), Expect = 1e-11
 Identities = 20/100 (20%), Positives = 43/100 (43%), Gaps = 8/100 (8%)

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPM 277
            + +TVF   +   + E  + E   + G ++ VR+++  ++  SKG  + +F    +   
Sbjct: 13  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72

Query: 278 AIA-------LSGQLLLGQPVMVKPSEAEKNLVQSNTSAG 310
            +A         G  L G+ + V  +   ++   S  S+G
Sbjct: 73  CLAAASLEAEGGGLKLDGRQLKVDLAV-TRDEAASGPSSG 111

>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 = 86.9 bits (216), Expect = 5e-21
 Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 6/85 (7%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R L   NL FN+TE +L+++FE    + LV      + G+ KG  +++F     A+    
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLE 71

Query: 382 ALNGKLEIVGRTLKVSSVTDHVGTQ 406
              G  EI GR++ +    +  GT+
Sbjct: 72  EKQGA-EIDGRSVSLYYTGEKGGTR 95

>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 = 50.7 bits (122), Expect = 2e-08
 Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 6/84 (7%)

Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
              +   R  RT+ A  +    TE ++ E F  A ++R     +     +SKG+ YIEF 
Sbjct: 7   PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFK 61

Query: 271 DVMSVPMAI-ALSGQLLLGQPVMV 293
                   +    G  + G+ V +
Sbjct: 62  SEADAEKNLEEKQGAEIDGRSVSL 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 = 86.1 bits (214), Expect = 7e-21
 Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 2/86 (2%)

Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
           GP G+    ++VG+L   +T   +   F PFG +   ++  D+ TG+ KG+GFV F    
Sbjct: 1   GPLGS-HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 59

Query: 375 HAKAAQSALNGKLEIVGRTLKVSSVT 400
            A+ A   + G+  + GR ++ +  T
Sbjct: 60  DAENAIQQMGGQ-WLGGRQIRTNWAT 84

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 54.9 bits (133), Expect = 7e-10
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
           T   +   F+  G++ D R++ D  + +SKG G++ F++      AI  + GQ L G+ +
Sbjct: 19  TTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78

Query: 292 MV 293
             
Sbjct: 79  RT 80

>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 = 86.2 bits (214), Expect = 1e-20
 Identities = 31/93 (33%), Positives = 49/93 (52%), Gaps = 10/93 (10%)

Query: 305 SNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKG 364
           S+ S+GG  T        +L+VGNL  ++TE ++RKLFE +G    V +  D      KG
Sbjct: 2   SSGSSGGEKTFTQR---SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KG 52

Query: 365 FGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           FGF++      A+ A+  L+    + G+ L+V 
Sbjct: 53  FGFIRLETRTLAEIAKVELDNM-PLRGKQLRVR 84

>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 = 43.8 bits (104), Expect = 7e-06
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 9/94 (9%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
            +  +F   +P   TE ++ + F K GK  +V +       + KG G+I         +A
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAEIA 67

Query: 279 I-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGG 311
              L    L G+ + V    A  +   ++  + G
Sbjct: 68  KVELDNMPLRGKQLRV--RFACHSASLTSGPSSG 99

>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 = 86.2 bits (214), Expect = 2e-20
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + LY+ NL   +TE  L  LF  F   +   +   + TG+ +G  F+ F   E A  A  
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 382 ALNGKLEIVGRTLKV 396
            +NG  ++ G+ L +
Sbjct: 86  LVNGY-KLYGKILVI 99

>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 = 49.6 bits (119), Expect = 1e-07
 Identities = 13/66 (19%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL 287
             + TERD+   F++  + +   +     + R +G  +I F +      A+  ++G  L 
Sbjct: 34  SPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLY 93

Query: 288 GQPVMV 293
           G+ +++
Sbjct: 94  GKILVI 99

>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 = 85.8 bits (213), Expect = 2e-20
 Identities = 29/101 (28%), Positives = 50/101 (49%), Gaps = 3/101 (2%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +      +  ++L+V N+ F   +  LR++F  FG +  V++  +      KGFGF
Sbjct: 2   SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGF 59

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDT 408
           V F     A  A+  L+G   + GR ++V++ T  V T   
Sbjct: 60  VTFENSADADRAREKLHGT-VVEGRKIEVNNATARVMTNSG 99

>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 = 48.8 bits (117), Expect = 2e-07
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 5/84 (5%)

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL 287
           P +  + D+ + F + GK+ DV +I +   R SKG G++ F +      A   L G ++ 
Sbjct: 24  PFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVE 81

Query: 288 GQPVMVKPSEAEKNLVQSNTSAGG 311
           G+ + V  + A   ++ ++  + G
Sbjct: 82  GRKIEV--NNATARVMTNSGPSSG 103

>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 = 84.5 bits (210), Expect = 2e-20
 Identities = 23/75 (30%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L+VG+L+ N+ +  LR  F+ F       +  D++TG  +G+GFV F   + A+ A  +
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 383 LNGKLEIVGRTLKVS 397
           + G+ ++ GR L+++
Sbjct: 63  MQGQ-DLNGRPLRIN 76

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 54.8 bits (133), Expect = 7e-10
 Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 3/69 (4%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
            +  +   F          ++ D  +  S+G G++ F        A+ ++ GQ L G+P+
Sbjct: 14  DDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL 73

Query: 292 MVKPSEAEK 300
            +  + A K
Sbjct: 74  RI--NWAAK 80

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 84.3 bits (209), Expect = 4e-20
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFG--PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
             + + N+  +     +     P+    V  ++L  D +T Q +GF FVQ +    A   
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 380 QSALNGK---LEIVGRTLKVS 397
              L      L+I G+T+ V 
Sbjct: 70  LQILQSLHPPLKIDGKTIGVD 90

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 49.2 bits (118), Expect = 9e-08
 Identities = 12/85 (14%), Positives = 30/85 (35%), Gaps = 7/85 (8%)

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGK--VRDVRLIMDRNSRRSKGVGYIEFYDVM 273
                 T+    +        +    S      V ++RLI D+ +++++G  +++    M
Sbjct: 5   HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64

Query: 274 SVPMAI-ALSGQ----LLLGQPVMV 293
                +  L        + G+ + V
Sbjct: 65  DASQLLQILQSLHPPLKIDGKTIGV 89

>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 = 84.4 bits (209), Expect = 8e-20
 Identities = 25/102 (24%), Positives = 42/102 (41%), Gaps = 2/102 (1%)

Query: 296 SEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPL 355
           S+              +A        R +YVGN+ +  T   L   F   G +  + +  
Sbjct: 11  SKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILC 70

Query: 356 DIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           D  +G  KG+ +++FA+     AA  A++      GRT+KV 
Sbjct: 71  DKFSGHPKGYAYIEFAERNSVDAA-VAMDET-VFRGRTIKVL 110

>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 = 70.1 bits (172), Expect = 9e-15
 Identities = 26/107 (24%), Positives = 49/107 (45%)

Query: 191 RERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDV 250
           +    +M      +   + +  E   E D+R+V+   +   +T +D+   FS  G +  +
Sbjct: 7   QTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRI 66

Query: 251 RLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSE 297
            ++ D+ S   KG  YIEF +  SV  A+A+   +  G+ + V P  
Sbjct: 67  TILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKR 113

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 83.6 bits (207), Expect = 1e-19
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            ++VG+L   +T   ++  F PFG +   ++  D+ TG+ KG+GFV F     A+ A   
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 383 LNGKLEIVGRTLKVSSVT 400
           + G+  + GR ++ +  T
Sbjct: 77  MGGQ-WLGGRQIRTNWAT 93

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 56.6 bits (137), Expect = 3e-10
 Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
           T  D+   F+  G++ D R++ D  + +SKG G++ F++      AI  + GQ L G+ +
Sbjct: 28  TTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87

Query: 292 MVKPSEAEKNLVQSNTSAGGTATGPYG 318
               +  +    +S   +    +GP  
Sbjct: 88  RTNWATRKPPAPKSTYESNTKQSGPSS 114

>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 = 82.6 bits (205), Expect = 1e-19
 Identities = 31/76 (40%), Positives = 48/76 (63%), Gaps = 2/76 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R +YVGNL ++ T  Q+++LF  FG V  V+L  D ET + KGFGFV+  + E    A +
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60

Query: 382 ALNGKLEIVGRTLKVS 397
            L+   + +GRT++V+
Sbjct: 61  KLDNT-DFMGRTIRVT 75

>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 = 50.2 bits (121), Expect = 3e-08
 Identities = 23/81 (28%), Positives = 41/81 (50%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           R ++   +   AT   V E FS+ GKV +V+LI DR +++ KG G++E  +         
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61

Query: 281 LSGQLLLGQPVMVKPSEAEKN 301
           L     +G+ + V  +  +K+
Sbjct: 62  LDNTDFMGRTIRVTEANPKKS 82

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 84.0 bits (208), Expect = 2e-19
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L V NL +  +   LR++FE +G V  V +P D  T + +GF FV+F     A+ A  A
Sbjct: 49  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108

Query: 383 LNGKLEIVGRTLKV 396
           ++G   + GR L+V
Sbjct: 109 MDGA-VLDGRELRV 121

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 52.8 bits (127), Expect = 1e-08
 Identities = 22/114 (19%), Positives = 43/114 (37%), Gaps = 2/114 (1%)

Query: 181 ERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEF 240
                   R           +  +       P  D E    ++    +  + +   +   
Sbjct: 9   HHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVE-GMTSLKVDNLTYRTSPDTLRRV 67

Query: 241 FSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
           F K G+V DV +  DR ++ S+G  ++ F+D      A+ A+ G +L G+ + V
Sbjct: 68  FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 82.9 bits (205), Expect = 2e-19
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 7/93 (7%)

Query: 315 GPYGA-----IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
           GP G+     ++    + +    + +  L  LF   G V  ++ P+D  TG+ KGF FV+
Sbjct: 1   GPLGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVE 60

Query: 370 FAQLEHAKAAQSALNGKLEIVGR-TLKVSSVTD 401
              +  AK    + +GK  +  +  L + ++ D
Sbjct: 61  CGSMNDAKKIIKSFHGK-RLDLKHRLFLYTMKD 92

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 47.8 bits (114), Expect = 3e-07
 Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL 287
            +   ++ +   FSKAGKV ++   +D  + ++KG  ++E   +      I +  G+ L 
Sbjct: 21  KVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80

Query: 288 GQPVM 292
            +  +
Sbjct: 81  LKHRL 85

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 82.2 bits (204), Expect = 2e-19
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            +++V NL F+ T   L+  F   G V      + +E G+ KG G V+F   E A+ A  
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYAD--IKMENGKSKGCGVVKFESPEVAERACR 66

Query: 382 ALNGKLEIVGRTLKV 396
            +NG  ++ GR + V
Sbjct: 67  MMNGM-KLSGREIDV 80

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
             +F   +P   T + + + F++ G V    + M+    +SKG G ++F        A  
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENG--KSKGCGVVKFESPEVAERACR 66

Query: 280 ALSGQLLLGQPVMVK 294
            ++G  L G+ + V+
Sbjct: 67  MMNGMKLSGREIDVR 81

>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 = 83.2 bits (206), Expect = 2e-19
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             L V  L    TE  LR++F  +GP+  V +  D ++ + +GF FV F  ++ AK A+ 
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106

Query: 382 ALNGKLEIVGRTLKV 396
             NG  E+ GR ++V
Sbjct: 107 RANGM-ELDGRRIRV 120

>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 = 60.5 bits (147), Expect = 2e-11
 Identities = 31/132 (23%), Positives = 53/132 (40%), Gaps = 8/132 (6%)

Query: 170 SERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMP 229
           S             R   +       +M    R+   +   +P          +  + + 
Sbjct: 3   SSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPN-------CCLGVFGLS 55

Query: 230 LKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG 288
           L  TERD+ E FSK G + DV ++ D+ SRRS+G  ++ F +V     A    +G  L G
Sbjct: 56  LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG 115

Query: 289 QPVMVKPSEAEK 300
           + + V  S  ++
Sbjct: 116 RRIRVDFSITKR 127

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 81.3 bits (201), Expect = 5e-19
 Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 4/99 (4%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G + + P     RKL + N+  ++    L  L   +G VE  +    + T        
Sbjct: 2   SSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ---VNTDSETAVVN 58

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQ 406
           V ++  + A+ A   LNG  ++   TLKV+ + D +  Q
Sbjct: 59  VTYSSKDQARQALDKLNGF-QLENFTLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 6/55 (10%), Positives = 13/55 (23%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGY 266
                 +  R +    +P       +     + G V     +   +      V Y
Sbjct: 7   GSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTY 61

>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 = 82.4 bits (204), Expect = 5e-19
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L+V  +H   TE  +   F  +G ++ + L LD  TG  KG+  V++   + A+AA   
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 383 LNGKLEIVGRTLKV 396
           LNG+ +++G+ + V
Sbjct: 84  LNGQ-DLMGQPISV 96

>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 = 58.5 bits (142), Expect = 1e-10
 Identities = 28/96 (29%), Positives = 52/96 (54%), Gaps = 6/96 (6%)

Query: 204 KEKKEVVEPEADPERDQR-----TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS 258
           +E  + VE + D    QR      +F   +  +ATE D+++ F++ G+++++ L +DR +
Sbjct: 1   REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 60

Query: 259 RRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
              KG   +E+        A+  L+GQ L+GQP+ V
Sbjct: 61  GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 96

>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 = 81.2 bits (201), Expect = 6e-19
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 9/76 (11%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + L+V NL   +TE  L K F  FG +E V+          K + F+ F + + A  A  
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAME 63

Query: 382 ALNGKLEIVGRTLKVS 397
            +NGK ++ G  +++ 
Sbjct: 64  EMNGK-DLEGENIEIV 78

>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 = 38.0 bits (89), Expect = 8e-04
 Identities = 19/92 (20%), Positives = 38/92 (41%), Gaps = 13/92 (14%)

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL 287
               TE  + + FS+ GK+  V+ +        K   +I F +      A+  ++G+ L 
Sbjct: 20  ANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLE 71

Query: 288 GQPVMV----KPSEAEKNLVQSNTSAGGTATG 315
           G+ + +     P +  K       +A G ++G
Sbjct: 72  GENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103

>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 = 85.2 bits (210), Expect = 6e-19
 Identities = 31/158 (19%), Positives = 50/158 (31%), Gaps = 7/158 (4%)

Query: 267 IEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYV 326
           I+ YD   V    A +G     +  M        +       A       Y      LY+
Sbjct: 18  IDLYD--DVISPSANNGDAPEDRDYMDTLPPTVGD--DVGKGAAPNVVYTYTGKRIALYI 73

Query: 327 GNLHFNMTETQLRKLFEPFGPVEL--VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
           GNL +  T+  L +     G  ++  ++   +   GQ KGF  V       +K     L 
Sbjct: 74  GNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLP 133

Query: 385 GKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGG 422
            + E+ G+   V+ V     +Q               G
Sbjct: 134 KR-ELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSG 170

>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 = 54.3 bits (130), Expect = 2e-08
 Identities = 20/133 (15%), Positives = 43/133 (32%), Gaps = 4/133 (3%)

Query: 233 TERDVYEFFSKAG--KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQ 289
           T+ D+ E     G   + +++   +R + +SKG   +      S    +  L  + L GQ
Sbjct: 81  TDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQ 140

Query: 290 PVMVKP-SEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPV 348
             +V P ++   +  +  +     +    G        G+      +    +   P    
Sbjct: 141 NPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVP 200

Query: 349 ELVQLPLDIETGQ 361
              + P     G 
Sbjct: 201 GGDRFPGPAGPGG 213

>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 = 81.2 bits (201), Expect = 9e-19
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL++G L+    E  L+ +F   GP+  V L  D  T + +GF F+ F     AK A   
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKD 67

Query: 383 LNGKLEIVGRTLKV 396
           +NGK  + G+ +KV
Sbjct: 68  MNGK-SLHGKAIKV 80

>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 = 45.8 bits (109), Expect = 3e-06
 Identities = 23/96 (23%), Positives = 42/96 (43%), Gaps = 7/96 (7%)

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL 287
             +  E+ +   F K G + +V LI DR + +S+G  +I F +      A   ++G+ L 
Sbjct: 16  NRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLH 74

Query: 288 GQPVMV----KPSEAEKNLVQSNTSAGG-TATGPYG 318
           G+ + V    KPS       +   S+   + +G   
Sbjct: 75  GKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLE 110

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 80.4 bits (199), Expect = 1e-18
 Identities = 23/92 (25%), Positives = 40/92 (43%), Gaps = 7/92 (7%)

Query: 310 GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG-PVELVQLPLDIETGQCKGFGFV 368
           G + +         L++G+L   M E  + + F   G  V  V++  +  TG   G+ FV
Sbjct: 1   GSSGSSGMA---ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFV 57

Query: 369 QFAQLEHAKAAQSALNGKL---EIVGRTLKVS 397
           +FA L  A+     +NGK        +  K++
Sbjct: 58  EFADLATAEKCLHKINGKPLPGATPAKRFKLN 89

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 52.7 bits (127), Expect = 6e-09
 Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 2/63 (3%)

Query: 233 TERDVYEFFSKAG-KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQP 290
            E  +   F+  G  V  V++I +R +    G  ++EF D+ +    +  ++G+ L G  
Sbjct: 22  DENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGAT 81

Query: 291 VMV 293
              
Sbjct: 82  PAK 84

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 80.0 bits (198), Expect = 1e-18
 Identities = 26/88 (29%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 310 GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
           G + +         LYVG L   +TET LR  F  FG +  + +         +   F+Q
Sbjct: 1   GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQ 54

Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           FA  + A+ A      KL + GR L V 
Sbjct: 55  FATRQAAEVAAEKSFNKLIVNGRRLNVK 82

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 14/85 (16%), Positives = 35/85 (41%), Gaps = 10/85 (11%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
              D      T++   +    TE D+   F + G++R + ++        +   +I+F  
Sbjct: 6   SGEDKT--ITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFAT 57

Query: 272 VMSVPMAI--ALSGQLLLGQPVMVK 294
             +  +A   + +  ++ G+ + VK
Sbjct: 58  RQAAEVAAEKSFNKLIVNGRRLNVK 82

>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 = 80.4 bits (199), Expect = 1e-18
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + LYV NL  + +E  + K F    P  + ++         + + FV F+  E A  A  
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI------RDYAFVHFSNREDAVEAMK 69

Query: 382 ALNGKLEIVGRTLKVS 397
           ALNGK  + G  ++V+
Sbjct: 70  ALNGK-VLDGSPIEVT 84

>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 = 38.8 bits (91), Expect = 4e-04
 Identities = 14/84 (16%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
             + D     + ++   + L  +E  + + F+        R+      ++ +   ++ F 
Sbjct: 6   SGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFS 59

Query: 271 DVMSVPMAI-ALSGQLLLGQPVMV 293
           +      A+ AL+G++L G P+ V
Sbjct: 60  NREDAVEAMKALNGKVLDGSPIEV 83

>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 = 79.5 bits (197), Expect = 1e-18
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVEL--VQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
            LY+GNL +  T+  L +     G  ++  ++   +   GQ KGF  V       +K   
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 381 SALNGKLEIVGRTLKVS 397
             L  + E+ G+   V+
Sbjct: 63  DLLPKR-ELHGQNPVVT 78

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 51.4 bits (124), Expect = 1e-08
 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 3/69 (4%)

Query: 232 ATERDVYEFFSKAG--KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG 288
            T+ D+ E     G   + +++   +R + +SKG   +      S    +  L  + L G
Sbjct: 13  TTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG 72

Query: 289 QPVMVKPSE 297
           Q  +V PS 
Sbjct: 73  QNPVVTPSN 81

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 80.1 bits (198), Expect = 2e-18
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           ++L+V N+ F   +  LR++F  FG +  V++  +      KGFGFV F     A  A+ 
Sbjct: 30  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRARE 87

Query: 382 ALNGKLEIVGRTLKVS 397
            L+G   + GR ++V+
Sbjct: 88  KLHGT-VVEGRKIEVN 102

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 47.3 bits (113), Expect = 6e-07
 Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 3/97 (3%)

Query: 198 RESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRN 257
                            + +   + +    +P +  + D+ + F + GK+ DV +I +  
Sbjct: 7   HHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE- 65

Query: 258 SRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
            R SKG G++ F +      A   L G ++ G+ + V
Sbjct: 66  -RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 101

>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 = 80.0 bits (198), Expect = 2e-18
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            LY+ NL  +M E +L  + +PFG V   ++  D  +G  +G GF +    E  +A    
Sbjct: 27  NLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGH 85

Query: 383 LNGKLEIVGRTLKVS 397
            NGK  I       +
Sbjct: 86  FNGK-FIKTPPGVSA 99

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 48.0 bits (115), Expect = 4e-07
 Identities = 20/109 (18%), Positives = 39/109 (35%), Gaps = 10/109 (9%)

Query: 190 ERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRD 249
                L        K      +     E+D   ++   +PL   E+++       G+V  
Sbjct: 3   SGSSGL--------KASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVIS 54

Query: 250 VRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE 297
            R++ D +   S+GVG+            I   +G+ +   P +  P+E
Sbjct: 55  TRILRDSSG-TSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 102

>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 = 84.5 bits (208), Expect = 3e-18
 Identities = 29/260 (11%), Positives = 74/260 (28%), Gaps = 19/260 (7%)

Query: 322 RKLYVGNLHFNMTETQLRK----LFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
             +Y+ NL+  + + +L+K    +F  FG +  + +     + + +G  FV F ++  A 
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAFVIFKEVSSAT 66

Query: 378 AAQSALNGKLEIVGRTLKV------SSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRA 431
            A  ++ G      + +++      S +   +                        +   
Sbjct: 67  NALRSMQGF-PFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAV 125

Query: 432 LLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAA 491
                    G        +           +       +     +P P +    IP  A 
Sbjct: 126 QGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAM 185

Query: 492 EFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEEC-----SKYGRVKHIYVDKRSAG 546
                    +               F   +  +  E       +++   K + +      
Sbjct: 186 PPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD 245

Query: 547 FVYLRFESTEAAASAQRAMH 566
             ++ F++   A +A+ A+ 
Sbjct: 246 IAFVEFDNEVQAGAARDALQ 265

>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 = 56.8 bits (136), Expect = 5e-09
 Identities = 24/110 (21%), Positives = 33/110 (30%), Gaps = 5/110 (4%)

Query: 288 GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGP 347
           G      P  A                      +  L++ NL     E  L  LF  F  
Sbjct: 174 GLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPG 233

Query: 348 VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
            + V+L             FV+F     A AA+ AL G        +K+S
Sbjct: 234 FKEVRLVPG-----RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS 278

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 44.9 bits (105), Expect = 4e-05
 Identities = 18/99 (18%), Positives = 47/99 (47%), Gaps = 11/99 (11%)

Query: 211 EPEADPERDQRTVFAYQMPLKATERDV----YEFFSKAGKVRDVRLIMDRNSRRSKGVGY 266
            PE  P     T++   +  K  + ++    Y  FS+ G++ D+ +     S + +G  +
Sbjct: 3   VPETRPNH---TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAF 56

Query: 267 IEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQ 304
           + F +V S   A+ ++ G     +P+ ++ ++ + +++ 
Sbjct: 57  VIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIA 95

>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 = 81.0 bits (200), Expect = 4e-18
 Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L+V ++H    E ++++ F  +G ++ + L LD  TG  KG+  V++   + A AA+ A
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 383 LNGKLEIVGRTLKV 396
           LNG  EI+G+T++V
Sbjct: 134 LNGA-EIMGQTIQV 146

>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 = 66.0 bits (161), Expect = 6e-13
 Identities = 31/143 (21%), Positives = 63/143 (44%), Gaps = 6/143 (4%)

Query: 165 ERERESERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQR--- 221
           E E + + ++ +   +E+ + R+ R    D   RE+    E+    + +      QR   
Sbjct: 12  EFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVE 71

Query: 222 --TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
              +F   +  +A E ++ E F   G+++++ L +DR +  SKG   +E+        A 
Sbjct: 72  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131

Query: 280 -ALSGQLLLGQPVMVKPSEAEKN 301
            AL+G  ++GQ + V     +  
Sbjct: 132 EALNGAEIMGQTIQVDWCFVKGP 154

>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 = 80.7 bits (199), Expect = 4e-18
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            L V NL +  +   LR++FE +G V  V +P D  T + +GF FV+F     A+ A  A
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131

Query: 383 LNGKLEIVGRTLKV 396
           ++G   + GR L+V
Sbjct: 132 MDGA-VLDGRELRV 144

>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 = 59.5 bits (144), Expect = 9e-11
 Identities = 22/130 (16%), Positives = 50/130 (38%), Gaps = 3/130 (2%)

Query: 167 ERESERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPE--RDQRTVF 224
           E  +E       E+  ++       + +    ++ +     E               ++ 
Sbjct: 15  ETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLK 74

Query: 225 AYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSG 283
              +  + +   +   F K G+V DV +  DR ++ S+G  ++ F+D      A+ A+ G
Sbjct: 75  VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134

Query: 284 QLLLGQPVMV 293
            +L G+ + V
Sbjct: 135 AVLDGRELRV 144

>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 = 78.8 bits (195), Expect = 6e-18
 Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
           GP G+    +++ NL  ++    L   F  FG +   ++  D      KG+GFV F   E
Sbjct: 1   GPLGS--GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQE 56

Query: 375 HAKAAQSALNGKLEIVGRTLKVS 397
            A+ A   +NG   +  R + V 
Sbjct: 57  AAERAIEKMNGM-LLNDRKVFVG 78

>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 = 61.5 bits (150), Expect = 7e-12
 Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 11/106 (10%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
             + +Y+ FS  G +   +++ D N   SKG G++ F    +   AI  ++G LL  + V
Sbjct: 18  DNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 75

Query: 292 MVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQ 337
            V   ++ K   +     G  A          +Y+ N     T   
Sbjct: 76  FVGRFKSRK---EREAELGARA-----KEFTNVYIKNFGPGSTRAA 113

>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 = 78.0 bits (193), Expect = 7e-18
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPV-ELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            +++GNL   + E  L   F  FG + +  ++  D +TG  KG+ F+ FA  + + AA  
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 382 ALNGKLEIVGRTLKVS 397
           A+NG+  +  R + VS
Sbjct: 67  AMNGQ-YLCNRPITVS 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 = 50.3 bits (121), Expect = 4e-08
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 233 TERDVYEFFSKAGKV-RDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQP 290
            E+ +Y+ FS  G + +  +++ D ++  SKG  +I F    +   AI A++GQ L  +P
Sbjct: 18  DEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRP 77

Query: 291 VMV 293
           + V
Sbjct: 78  ITV 80

>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 = 77.3 bits (191), Expect = 1e-17
 Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
              L++GNL+ N +  +L+           + + +D+ TG  + FG+V F   E  + A 
Sbjct: 17  PFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLEKAL 75

Query: 381 SALNGKLEIVGRTLKVS 397
             L G  ++ G  +K+ 
Sbjct: 76  -ELTGL-KVFGNEIKLE 90

>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 = 59.2 bits (144), Expect = 3e-11
 Identities = 12/90 (13%), Positives = 34/90 (37%), Gaps = 1/90 (1%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
            E         +F   +    +  ++    S+     D+  ++D  +  ++  GY++F  
Sbjct: 9   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFES 67

Query: 272 VMSVPMAIALSGQLLLGQPVMVKPSEAEKN 301
              +  A+ L+G  + G  + ++  +    
Sbjct: 68  AEDLEKALELTGLKVFGNEIKLEKPKGRDG 97

>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 = 77.7 bits (192), Expect = 1e-17
 Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 5/93 (5%)

Query: 305 SNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKG 364
           S+ S+G    G  G     ++V NL + +   +L+++F   G V    +  D + G+ +G
Sbjct: 2   SSGSSGALQAGRLG---STVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRG 57

Query: 365 FGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
            G V F Q   A  A S  NG+  +  R + V 
Sbjct: 58  IGTVTFEQSIEAVQAISMFNGQ-LLFDRPMHVK 89

>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 = 43.8 bits (104), Expect = 9e-06
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 2/67 (2%)

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL 287
             K   + + E FS AG V    ++ D++  +S+G+G + F   +    AI   +GQLL 
Sbjct: 24  DYKVGWKKLKEVFSMAGVVVRADILEDKDG-KSRGIGTVTFEQSIEAVQAISMFNGQLLF 82

Query: 288 GQPVMVK 294
            +P+ VK
Sbjct: 83  DRPMHVK 89

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 79.2 bits (195), Expect = 1e-17
 Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 7/111 (6%)

Query: 289 QPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPV 348
            PV  +PS    N     T A              +YVG+  +  T+ QL ++    G  
Sbjct: 27  PPVRQEPSPKPNN----KTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVY 82

Query: 349 EL--VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           ++  ++   +   GQ KG+  V  A           L GK  + G  + V 
Sbjct: 83  DVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGK-VLNGEKVDVR 132

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 50.3 bits (120), Expect = 2e-07
 Identities = 19/133 (14%), Positives = 48/133 (36%), Gaps = 3/133 (2%)

Query: 167 ERESERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAY 226
                    ++L  E    + +       +    +   +   ++   +     +  V+  
Sbjct: 2   HHHHHHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVG 61

Query: 227 QMPLKATERDVYEFFSKAG--KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSG 283
                 T++ + +     G   V +++   +R + +SKG   +      SV   +  L G
Sbjct: 62  SFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPG 121

Query: 284 QLLLGQPVMVKPS 296
           ++L G+ V V+P+
Sbjct: 122 KVLNGEKVDVRPA 134

>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 = 76.9 bits (190), Expect = 2e-17
 Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 12/93 (12%)

Query: 305 SNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKG 364
           S+ S+G       G     LYV     +MT T LR  F PFG +  + +         + 
Sbjct: 2   SSGSSGERRAPRKG---NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RN 50

Query: 365 FGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
             FV + ++E A  A + LNG  ++    LKV+
Sbjct: 51  CAFVTYEKMESADQAVAELNGT-QVESVQLKVN 82

>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 = 43.0 bits (102), Expect = 1e-05
 Identities = 18/101 (17%), Positives = 39/101 (38%), Gaps = 12/101 (11%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
            E    R   T++ Y      T   +   FS  G + D+ +         +   ++ +  
Sbjct: 7   GERRAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEK 58

Query: 272 VMSVPMAI-ALSGQLLLGQPVMVKPSEA-EKNLVQSNTSAG 310
           + S   A+  L+G  +    + V  + A ++ ++ S  S+G
Sbjct: 59  MESADQAVAELNGTQVESVQLKV--NIARKQPMLDSGPSSG 97

>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 = 77.3 bits (191), Expect = 2e-17
 Identities = 31/93 (33%), Positives = 49/93 (52%), Gaps = 6/93 (6%)

Query: 305 SNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKG 364
           S+ S+G   T         LYV NL   + + +LRK F PFG +   ++ ++   G+ KG
Sbjct: 2   SSGSSGDRITRYQVV---NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKG 56

Query: 365 FGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           FGFV F+  E A  A + +NG+  +  + L V+
Sbjct: 57  FGFVCFSSPEEATKAVTEMNGR-IVATKPLYVA 88

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 16/80 (20%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
            +  + + FS  G +   +++M+    RSKG G++ F        A+  ++G+++  +P+
Sbjct: 28  DDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPL 85

Query: 292 MVKPSEAEKNLVQSNTSAGG 311
            V  + A++   + +  + G
Sbjct: 86  YV--ALAQRKEERQSGPSSG 103

>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 = 76.6 bits (189), Expect = 2e-17
 Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 9/87 (10%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVEL--------VQLPLDIETGQCKGFGFVQFAQL 373
             ++V  L  N+T   +   F+  G ++         + L  D ETG+ KG   V F   
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 374 EHAKAAQSALNGKLEIVGRTLKVSSVT 400
             AKAA    +GK E  G  +KVS  T
Sbjct: 74  PSAKAAIDWFDGK-EFSGNPIKVSFAT 99

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 9/91 (9%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRD--------VRLIMDRNSRRSKG 263
                  D  T+F   +    T   V ++F + G ++         + L  DR + + KG
Sbjct: 5   HHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKG 64

Query: 264 VGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
              + F D  S   AI    G+   G P+ V
Sbjct: 65  EATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95

>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 = 76.5 bits (189), Expect = 3e-17
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            ++VG +   M ET++R  F  +G V+ V++  D  TG  KG+GFV F    +    Q  
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSF---YNDVDVQKI 66

Query: 383 LNGKLEIVGRTLKV 396
           +  ++   G+ LK+
Sbjct: 67  VESQINFHGKKLKL 80

>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 = 47.6 bits (114), Expect = 4e-07
 Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLG 288
            ++  E ++  FF++ G V++V++I DR +  SKG G++ FY+ + V   +  S     G
Sbjct: 18  DVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHG 75

Query: 289 QPVMVKP 295
           + + + P
Sbjct: 76  KKLKLGP 82

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 75.8 bits (187), Expect = 5e-17
 Identities = 30/89 (33%), Positives = 42/89 (47%), Gaps = 4/89 (4%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +         + L+V  L  + TE  L+   E F      ++  D ETG  KGFGF
Sbjct: 2   SSGSSGPNARSQPSKTLFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGF 58

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           V F   E AKAA+ A+    EI G  + +
Sbjct: 59  VDFNSEEDAKAAKEAMEDG-EIDGNKVTL 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 = 46.5 bits (111), Expect = 1e-06
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 4/74 (5%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
           +T+F   +    TE  + E F         R++ DR +  SKG G+++F        A  
Sbjct: 16  KTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72

Query: 280 ALSGQLLLGQPVMV 293
           A+    + G  V +
Sbjct: 73  AMEDGEIDGNKVTL 86

>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 = 77.2 bits (190), Expect = 6e-17
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             LYVGNL F  TE Q+ +LF   G ++ + + LD       GF FV++     A+ A  
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 382 ALNGKLEIVGRTLKV 396
            +NG   +  R ++ 
Sbjct: 100 YINGT-RLDDRIIRT 113

>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 = 56.0 bits (135), Expect = 2e-09
 Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
           E +    +   T++   +    TE  +YE FSK+G ++ + + +D+  + + G  ++E+Y
Sbjct: 30  EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYY 89

Query: 271 DVMSVPMAI-ALSGQLLLGQPVMV 293
                  A+  ++G  L  + +  
Sbjct: 90  SRADAENAMRYINGTRLDDRIIRT 113

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 75.1 bits (185), Expect = 1e-16
 Identities = 26/84 (30%), Positives = 37/84 (44%), Gaps = 9/84 (10%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVEL--------VQLPLDIETGQCKGFGFVQFAQL 373
             ++V  L  N+T   +   F+  G ++         + L  D ETG+ KG   V F   
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 374 EHAKAAQSALNGKLEIVGRTLKVS 397
             AKAA    +GK E  G  +KVS
Sbjct: 68  PSAKAAIDWFDGK-EFSGNPIKVS 90

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 57.8 bits (140), Expect = 1e-10
 Identities = 22/104 (21%), Positives = 39/104 (37%), Gaps = 9/104 (8%)

Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVR--------DVRLIMDRNSRRSKGVGYIE 268
             D  T+F   +    T   V ++F + G ++         + L  DR + + KG   + 
Sbjct: 4   NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 269 FYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGG 311
           F D  S   AI    G+   G P+ V  +    +  +   +  G
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRG 107

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 76.8 bits (189), Expect = 2e-16
 Identities = 24/103 (23%), Positives = 42/103 (40%), Gaps = 2/103 (1%)

Query: 304 QSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 363
           Q +    G   G       KL V NL F +++  +++LF  FG ++   +  D  +G+  
Sbjct: 71  QHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSL 129

Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQ 406
           G   V F +   A  A     G   + GR + +  V   +  +
Sbjct: 130 GTADVHFERRADALKAMKQYKGV-PLDGRPMDIQLVASQIDLE 171

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 50.2 bits (120), Expect = 2e-07
 Identities = 25/156 (16%), Positives = 49/156 (31%), Gaps = 22/156 (14%)

Query: 140 GERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEMRE 199
              R+  R  R     R   + +R  R R +   R      +   ++   +         
Sbjct: 28  KLNRNQRRVNRGGGPRRNRPAIARGGRNRPAPYSR-----PKPLPDKWQHDLFDSGCGGG 82

Query: 200 SRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSR 259
                  K               +    +    ++ D+ E F++ G ++   +  DR S 
Sbjct: 83  EGVETGAK---------------LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SG 126

Query: 260 RSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVK 294
           RS G   + F        A+    G  L G+P+ ++
Sbjct: 127 RSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ 162

>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 = 73.9 bits (182), Expect = 2e-16
 Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 1/90 (1%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G + +         + V N+ F ++  ++   F  +  +         E G   G   
Sbjct: 2   SSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           V F   + A AA   LN +  I  R +K+S
Sbjct: 62  VAFESRDEATAAVIDLNDR-PIGSRKVKLS 90

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 51.9 bits (125), Expect = 9e-09
 Identities = 9/76 (11%), Positives = 23/76 (30%), Gaps = 1/76 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA- 280
            +    MP   +  ++ +FF     +     +         G   + F        A+  
Sbjct: 17  VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 281 LSGQLLLGQPVMVKPS 296
           L+ + +  + V +   
Sbjct: 77  LNDRPIGSRKVKLSGP 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 = 73.8 bits (182), Expect = 2e-16
 Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDI-ETGQCKGFGFVQFAQLEHAKAAQ 380
              ++GNL +++TE  +++ F        V+LP +     + KGFG+ +F  L+   +A 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74

Query: 381 SALNGKLEIVGRTLKVS 397
            +LN +  +  + ++V 
Sbjct: 75  -SLNEE-SLGNKRIRVD 89

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 26/92 (28%), Positives = 43/92 (46%), Gaps = 2/92 (2%)

Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMD-RNSRRSKGVGYIEF 269
                P+    T F   +P   TE  + EFF     +  VRL  +  N  R KG GY EF
Sbjct: 6   SGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 64

Query: 270 YDVMSVPMAIALSGQLLLGQPVMVKPSEAEKN 301
            D+ S+  A++L+ + L  + + V  ++  ++
Sbjct: 65  EDLDSLLSALSLNEESLGNKRIRVDVADQAQD 96

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 73.5 bits (181), Expect = 3e-16
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
              YVGNL FN  +  +  +F+    +  V+L  D +T + KGF +V+F +++  K A  
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL- 73

Query: 382 ALNGKLEIVGRTLKVS 397
             +G   +  R+L+V 
Sbjct: 74  TYDGA-LLGDRSLRVD 88

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 1/91 (1%)

Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
             +  P     T +   +P    + D+   F     +R VRL+ D+++ + KG  Y+EF 
Sbjct: 6   SGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFD 64

Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKN 301
           +V S+  A+   G LL  + + V  +E  K 
Sbjct: 65  EVDSLKEALTYDGALLGDRSLRVDIAEGRKQ 95

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 73.6 bits (181), Expect = 4e-16
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R LY+ NL + +T  ++  +F  +GP+  +++     T + +G  +V +  +  AK A  
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNAVD 65

Query: 382 ALNGKLEIVGRTLKV 396
            L+G   +  R L V
Sbjct: 66  HLSGF-NVSNRYLVV 79

>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 = 53.5 bits (129), Expect = 5e-09
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 4/87 (4%)

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
           P    R ++   +P K T  ++Y+ F K G +R +R+        ++G  Y+ + D+   
Sbjct: 4   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDA 60

Query: 276 PMAI-ALSGQLLLGQPVMVKPSEAEKN 301
             A+  LSG  +  + ++V    A + 
Sbjct: 61  KNAVDHLSGFNVSNRYLVVLYYNANRA 87

>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 = 38.9 bits (91), Expect = 6e-04
 Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 2/67 (2%)

Query: 524 DVEEECSKYGRVKHIYV--DKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMK 581
           ++ +   KYG ++ I V     + G  Y+ +E    A +A   +     + R +  ++  
Sbjct: 24  EMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN 83

Query: 582 PEDYEAK 588
                 K
Sbjct: 84  ANRAFQK 90

>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 = 73.0 bits (180), Expect = 5e-16
 Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIET-GQCKGFGFVQFAQLEHAKAAQ 380
              ++GNL +++TE  +++ F        V+LP +     + KGFG+ +F  L+   +A 
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78

Query: 381 SALNGKLEIVGRTLKVS 397
            +LN +  +  R ++V 
Sbjct: 79  -SLNEE-SLGNRRIRVD 93

>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 = 64.6 bits (158), Expect = 5e-13
 Identities = 29/106 (27%), Positives = 49/106 (46%), Gaps = 7/106 (6%)

Query: 197 MRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR 256
           MR S  +   +  +     P+    T F   +P   TE  + EFF     +  VRL  + 
Sbjct: 1   MRGSHHHHHHRSRL-----PKSPPYTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREP 54

Query: 257 -NSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKN 301
            N  R KG GY EF D+ S+  A++L+ + L  + + V  ++  ++
Sbjct: 55  SNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQD 100

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 73.1 bits (180), Expect = 5e-16
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 9/76 (11%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            +L+V     ++ E++L ++F PFGP++ V++          GF FV+F + E A  A  
Sbjct: 32  TRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIE 83

Query: 382 ALNGKLEIVGRTLKVS 397
            ++GK     + L+V 
Sbjct: 84  EVHGK-SFANQPLEVV 98

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 42.7 bits (101), Expect = 3e-05
 Identities = 21/105 (20%), Positives = 40/105 (38%), Gaps = 9/105 (8%)

Query: 198 RESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRN 257
             S     +   +    + E     +F    PL   E ++ E F   G +++V+++    
Sbjct: 9   HHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---- 64

Query: 258 SRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKN 301
                G  ++EF +  S   AI  + G+    QP+ V  S+    
Sbjct: 65  ----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 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 = 72.8 bits (179), Expect = 6e-16
 Identities = 29/98 (29%), Positives = 45/98 (45%), Gaps = 9/98 (9%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPV--------ELVQLPLDIET 359
           S+G +      + +  +YV  L+ ++T   L   F+  G V         ++ + LD ET
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61

Query: 360 GQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           G+ KG   V +     AKAA    +GK +  G  LKVS
Sbjct: 62  GKPKGDATVSYEDPPTAKAAVEWFDGK-DFQGSKLKVS 98

>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 = 60.1 bits (146), Expect = 2e-11
 Identities = 20/110 (18%), Positives = 44/110 (40%), Gaps = 11/110 (10%)

Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVR--------DVRLIMDRNSRRSK 262
             + D + D   ++   +    T  D+ +FF + G V+         + + +D+ + + K
Sbjct: 6   SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65

Query: 263 GVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGG 311
           G   + + D  +   A+    G+   G  + V  S A K    ++  + G
Sbjct: 66  GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKV--SLARKKPPMNSGPSSG 113

>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 = 72.3 bits (178), Expect = 6e-16
 Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 5/93 (5%)

Query: 306 NTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVEL-VQLPLDIETGQCKG 364
           ++ + G ++G  G     + V N+ F ++  ++   F  +  +   V L  + E G   G
Sbjct: 2   SSGSSGASSGKPG--PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTG 58

Query: 365 FGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
              V F   + A AA   LN +  I  R +K+ 
Sbjct: 59  EAMVAFESRDEATAAVIDLNDR-PIGSRKVKLV 90

>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 = 50.8 bits (122), Expect = 3e-08
 Identities = 9/76 (11%), Positives = 23/76 (30%), Gaps = 1/76 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA- 280
            +    MP   +  ++ +FF     +     +         G   + F        A+  
Sbjct: 17  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 281 LSGQLLLGQPVMVKPS 296
           L+ + +  + V +   
Sbjct: 77  LNDRPIGSRKVKLVLG 92

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 72.3 bits (178), Expect = 1e-15
 Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 2/91 (2%)

Query: 306 NTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGF 365
           ++ + G           K++VG L ++ T+  LRK FE FG +E   +  D +TG+ +G+
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGY 61

Query: 366 GFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           GFV  A    A+ A    N  ++  GR   V
Sbjct: 62  GFVTMADRAAAERACKDPNPIID--GRKANV 90

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 53.1 bits (128), Expect = 7e-09
 Identities = 13/62 (20%), Positives = 29/62 (46%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           T+  + ++F   G + +  +I DR + +S+G G++   D  +   A      ++ G+   
Sbjct: 30  TDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKAN 89

Query: 293 VK 294
           V 
Sbjct: 90  VN 91

>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 = 70.7 bits (174), Expect = 3e-15
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 7/77 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            +L+VG L  N +   L + F+ FG +  +    D   G    F ++Q+  L+ A+AA +
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTI----DHVKG--DSFAYIQYESLDAAQAACA 71

Query: 382 ALNGK-LEIVGRTLKVS 397
            + G  L    R L+V 
Sbjct: 72  KMRGFPLGGPDRRLRVD 88

>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 = 39.5 bits (93), Expect = 2e-04
 Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 3/44 (6%)

Query: 524 DVEEECSKYGRVKHIYVDK-RSAGFVYLRFESTEAAASAQRAMH 566
            +  E  ++G ++ I   K  S  ++   +ES +AA +A   M 
Sbjct: 33  ALAREFDRFGSIRTIDHVKGDSFAYIQ--YESLDAAQAACAKMR 74

>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 = 70.2 bits (172), Expect = 3e-15
 Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 8/87 (9%)

Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLP-----LDIETGQCKGFGFVQ 369
           GP G+  R+LYVGN+ F +TE  +   F     +  +        L ++  Q K F F++
Sbjct: 1   GPLGS-ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 59

Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKV 396
           F  ++    A  A +G     G++LK+
Sbjct: 60  FRSVDETTQAM-AFDGI-IFQGQSLKI 84

>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 = 50.5 bits (121), Expect = 3e-08
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 5/84 (5%)

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRL-----IMDRNSRRSKGVGYIEFY 270
           P    R ++   +P   TE  + +FF+   ++  +       ++     + K   ++EF 
Sbjct: 2   PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 61

Query: 271 DVMSVPMAIALSGQLLLGQPVMVK 294
            V     A+A  G +  GQ + ++
Sbjct: 62  SVDETTQAMAFDGIIFQGQSLKIR 85

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 70.8 bits (174), Expect = 3e-15
 Identities = 25/89 (28%), Positives = 39/89 (43%), Gaps = 4/89 (4%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S GG   GP G  D ++YVGNL  ++    +  +F  +G +  + L           F F
Sbjct: 9   SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAF 65

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           V+F     A+ A    +G  +  G  L+V
Sbjct: 66  VEFEDPRDAEDAVYGRDGY-DYDGYRLRV 93

>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 = 46.2 bits (110), Expect = 1e-06
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 4/79 (5%)

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
              +   ++   +P     +D+ + F K G +RD+ L      R      ++EF D    
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDA 74

Query: 276 PMAI-ALSGQLLLGQPVMV 293
             A+    G    G  + V
Sbjct: 75  EDAVYGRDGYDYDGYRLRV 93

>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 = 70.3 bits (173), Expect = 3e-15
 Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 9/84 (10%)

Query: 313 ATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ 372
           ++G  G    KL+VGN+    T  +LR  FE +GPV    +         K + FV   +
Sbjct: 2   SSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMER 53

Query: 373 LEHAKAAQSALNGKLEIVGRTLKV 396
            E A  A   L+   E  G+ + V
Sbjct: 54  AEDAVEAIRGLDNT-EFQGKRMHV 76

>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 = 71.0 bits (174), Expect = 3e-15
 Identities = 14/79 (17%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGP-VELVQLPLDI-ETGQCKGFGFVQFAQLEHAKAA 379
            +L++G +       ++ +        V  V +     +  + +GF FV++     A  A
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 380 QSAL-NGKLEIVGRTLKVS 397
           +  L  G++++ G  + V 
Sbjct: 69  RRKLMPGRIQLWGHQIAVD 87

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 16/91 (17%), Positives = 34/91 (37%), Gaps = 5/91 (5%)

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGK-VRDVRLIMD-RNSRRSKGVGYIEFYDVM 273
                  +F   +P      ++ E  +K  + V DV +     +  +++G  ++E+    
Sbjct: 4   GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63

Query: 274 SVPMAIAL---SGQLLLGQPVMVKPSEAEKN 301
           +  MA          L G  + V  +E E +
Sbjct: 64  AAAMARRKLMPGRIQLWGHQIAVDWAEPEID 94

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 69.9 bits (172), Expect = 4e-15
 Identities = 15/80 (18%), Positives = 37/80 (46%), Gaps = 8/80 (10%)

Query: 322 RKLYVGNLHFNMTETQLRK----LFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
             +Y+ NL+  + + +L+K    +F  FG +  + +     + + +G  FV F ++  A 
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFKEVSSAT 65

Query: 378 AAQSALNGKLEIVGRTLKVS 397
            A  ++ G      + +++ 
Sbjct: 66  NALRSMQGF-PFYDKPMRIQ 84

>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 = 41.4 bits (98), Expect = 4e-05
 Identities = 12/60 (20%), Positives = 31/60 (51%), Gaps = 4/60 (6%)

Query: 235 RDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
           + ++  FS+ G++ D+ +     S + +G  ++ F +V S   A+ ++ G     +P+ +
Sbjct: 27  KSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 83

>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 = 40.3 bits (95), Expect = 1e-04
 Identities = 20/99 (20%), Positives = 44/99 (44%), Gaps = 9/99 (9%)

Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK--RSAGFVYLRF 552
             P+  + + N+ +   +   D   E++  +    S++G++  I V +  +  G  ++ F
Sbjct: 5   TRPNHTIYINNLNE---KIKKD---ELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIF 58

Query: 553 ESTEAAASAQRAMHMRWFARRLISAIFMK-PEDYEAKFK 590
           +   +A +A R+M    F  + +   + K   D  AK K
Sbjct: 59  KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 69.1 bits (170), Expect = 7e-15
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 9/75 (12%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            KL++GNL    TE ++R LFE +G V    +         K +GFV       A+ A  
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIR 60

Query: 382 ALNGKLEIVGRTLKV 396
            L+   ++ G  + V
Sbjct: 61  NLHHY-KLHGVNINV 74

>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 = 39.5 bits (93), Expect = 2e-04
 Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 9/82 (10%)

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
                  +F   +P +ATE+++   F + GKV +  +I        K  G++   D  + 
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAA 55

Query: 276 PMAI-ALSGQLLLGQPVMVKPS 296
             AI  L    L G  + V+ S
Sbjct: 56  EDAIRNLHHYKLHGVNINVEAS 77

>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 = 69.2 bits (170), Expect = 8e-15
 Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 9/75 (12%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            K++VGN+    T  +LR LFE  G V    +         K + FV   +   AKAA +
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIA 61

Query: 382 ALNGKLEIVGRTLKV 396
            LNGK E+ G+ + V
Sbjct: 62  QLNGK-EVKGKRINV 75

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 68.0 bits (167), Expect = 3e-14
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
             K++VG +  N  ET+LR+ F+ FG V  V +  D E  + +GFGF+ F   +    A 
Sbjct: 10  SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69

Query: 381 SALNGKLEIVGRTLKV 396
           +      +I+G+ ++V
Sbjct: 70  N--MHFHDIMGKKVEV 83

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 56.0 bits (136), Expect = 4e-10
 Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 232 ATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPV 291
             E ++ E+F K G V +V +I D   +R +G G+I F D  SV  A+ +    ++G+ V
Sbjct: 22  CGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKV 81

Query: 292 MVKPSEAEKNLVQSNTSAG 310
            VK +E  ++   S  S+G
Sbjct: 82  EVKRAEP-RDSKSSGPSSG 99

>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 = 1e-13
 Identities = 17/91 (18%), Positives = 36/91 (39%), Gaps = 7/91 (7%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G + +    ++   ++V  L  ++ E  L +  E FG +  V +         K    
Sbjct: 2   SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQAL 55

Query: 368 VQFAQLEHAKAAQSALNGK-LEIVGRTLKVS 397
           V+F  ++ AK   +      + I G+    +
Sbjct: 56  VEFENIDSAKECVTFAADVPVYIAGQQAFFN 86

>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 = 44.8 bits (106), Expect = 4e-06
 Identities = 15/91 (16%), Positives = 28/91 (30%), Gaps = 9/91 (9%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
             V    +     E D+ E   K G +  V +         K    +EF ++ S    + 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSAKECVT 69

Query: 281 ---LSGQLLLGQPVMVKPSEAEKNLVQSNTS 308
                   + GQ      S +++     N+ 
Sbjct: 70  FAADVPVYIAGQQAFFNYSTSKRITRPGNSG 100

>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 = 67.2 bits (164), Expect = 1e-13
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPV--ELVQLPLDI---ETGQCKGFGFVQFAQLEHA 376
            ++YV NL  ++ E  L+ +F  +     E  ++  DI   + G+ KG  F+     + A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 377 KAAQSALNGKLEIVGRTLKVS 397
             A    NG   + G+ + V 
Sbjct: 106 AKALKEANGY-VLFGKPMVVQ 125

>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 = 65.6 bits (160), Expect = 2e-13
 Identities = 14/77 (18%), Positives = 26/77 (33%), Gaps = 7/77 (9%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
              +   NL       ++++ F  FG +  V LP      +      V+F +   A+ A 
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAF 63

Query: 381 SALNGKLEIVGRTLKVS 397
             L    +     L + 
Sbjct: 64  RHLAYS-KFHHVPLYLE 79

>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 = 41.7 bits (98), Expect = 6e-05
 Identities = 14/82 (17%), Positives = 27/82 (32%), Gaps = 7/82 (8%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
                R +  + A  +P      ++ E FS+ G +  V L              +EF + 
Sbjct: 3   SGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEP 56

Query: 273 MSVPMAI-ALSGQLLLGQPVMV 293
           +    A   L+       P+ +
Sbjct: 57  LEARKAFRHLAYSKFHHVPLYL 78

>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 = 65.1 bits (159), Expect = 4e-13
 Identities = 24/94 (25%), Positives = 44/94 (46%), Gaps = 4/94 (4%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVE-LVQLPLDIETGQCKGFG 366
           S+G +  G   +     ++ N+ F++T+  + +  E     E  V + +D   GQ  G  
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD-NNGQGLGQA 60

Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT 400
            VQF   + A+ ++  L+ K ++ GR   V  VT
Sbjct: 61  LVQFKNEDDARKSER-LHRK-KLNGREAFVHVVT 92

>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 = 58.2 bits (141), Expect = 1e-10
 Identities = 15/88 (17%), Positives = 30/88 (34%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
           E D    +       +P   T+ DV +F        +   ++  N+ +  G   ++F + 
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67

Query: 273 MSVPMAIALSGQLLLGQPVMVKPSEAEK 300
                +  L  + L G+   V     E 
Sbjct: 68  DDARKSERLHRKKLNGREAFVHVVTLED 95

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 70.6 bits (172), Expect = 4e-13
 Identities = 39/193 (20%), Positives = 69/193 (35%)

Query: 16  QRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRD 75
               + D+         R+   +R   +RE S E ++E + R  +   R     +  + +
Sbjct: 214 DDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEE 273

Query: 76  RDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERE 135
           R R R+R K++ R  + R         RE ER  E      +  +  E  +    +    
Sbjct: 274 RRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPG 333

Query: 136 RERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDL 195
                         R   + RR S RS RER R+ +R+R+ + E +R      R R+   
Sbjct: 334 ELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEAR 393

Query: 196 EMRESRRYKEKKE 208
                +    +  
Sbjct: 394 GGGGGQDNGLEGL 406

>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 = 69.1 bits (168), Expect = 1e-12
 Identities = 36/193 (18%), Positives = 65/193 (33%), Gaps = 1/193 (0%)

Query: 14  EEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSR 73
              R + +D +   +++++  +K     R R          + +  +R  R+  ++    
Sbjct: 228 LPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRD 287

Query: 74  RDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKE 133
           R R   R R++ R  R+R  +   G     E     +   +     +          EK 
Sbjct: 288 RKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKG 347

Query: 134 RERERDGER-RSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERE 192
           R+R+R+  R   S R RR      R   R  +  ER SER R+        ++  L    
Sbjct: 348 RDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLG 407

Query: 193 RDLEMRESRRYKE 205
            D           
Sbjct: 408 NDSRDMYMESEGG 420

>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 = 67.6 bits (164), Expect = 4e-12
 Identities = 45/221 (20%), Positives = 78/221 (35%), Gaps = 1/221 (0%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGK 60
                  +  +    +  ++        +   R+ + ER  R RE  +E E        +
Sbjct: 203 GADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDR 262

Query: 61  RSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEK 120
           R R    ++   RR R+R +D+D++R RR         RERER+ E            E 
Sbjct: 263 RRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEA 322

Query: 121 ERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELER 180
                +     +      DG         R   +S RS    RR+R+R+ +R+RE +   
Sbjct: 323 GDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHK-RG 381

Query: 181 ERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQR 221
           ER  ER   E       +++       +  +   + E    
Sbjct: 382 ERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDG 422

>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 = 67.6 bits (164), Expect = 4e-12
 Identities = 32/202 (15%), Positives = 65/202 (32%)

Query: 14  EEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSR 73
           + +R++++      K++ +R  +S    R+    ++EE        K   RD    +   
Sbjct: 236 DRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRS 295

Query: 74  RDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKE 133
           R+R R     KE  R       +     +   +            +   E+   RDRE+ 
Sbjct: 296 RERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERR 355

Query: 134 RERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERER 193
           R    + ERR      R   +  +   R       E+      +         + R+   
Sbjct: 356 RSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYM 415

Query: 194 DLEMRESRRYKEKKEVVEPEAD 215
           + E  +     E   ++E   +
Sbjct: 416 ESEGGDGYLAPENGYLMEAAPE 437

>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 = 67.2 bits (163), Expect = 5e-12
 Identities = 51/198 (25%), Positives = 75/198 (37%), Gaps = 3/198 (1%)

Query: 14  EEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSR 73
                               E         R+   + E E + RS +R +  E   + SR
Sbjct: 201 RGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSR 260

Query: 74  RDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKE 133
             R R R RDKE  RR R+R +D+ R+R+R + R RER+R  RE+++E         E  
Sbjct: 261 DRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPS 320

Query: 134 RERERDGERRSSSRSRRSSSQSRRSSSRSR---RERERESERERELELERERERERELRE 190
              +   +                   R R   R R   SERER  + +R+R+R+RE + 
Sbjct: 321 EAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKR 380

Query: 191 RERDLEMRESRRYKEKKE 208
            ER  E            
Sbjct: 381 GERGSERGRDEARGGGGG 398

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 65.6 bits (159), Expect = 2e-11
 Identities = 37/200 (18%), Positives = 67/200 (33%), Gaps = 1/200 (0%)

Query: 2   EFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKR 61
           + D     E+    + + K+ +   S+ + +R     R   +R  S E  +++     +R
Sbjct: 232 DRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRR 291

Query: 62  SRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKE 121
           S R  +     R  ++  R    +        D         E   D     E + ++++
Sbjct: 292 SSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRD 351

Query: 122 RERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERE 181
           RERR     E+ER R+RD +R      +R    S R      R      +   E      
Sbjct: 352 RERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDE-ARGGGGGQDNGLEGLGNDS 410

Query: 182 RERERELRERERDLEMRESR 201
           R+   E    +  L      
Sbjct: 411 RDMYMESEGGDGYLAPENGY 430

>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 = 64.5 bits (156), Expect = 3e-11
 Identities = 34/193 (17%), Positives = 69/193 (35%)

Query: 4   DEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSR 63
                 E+  E +R++ +  D   + +++ +E+  RS  + +D + + +   SRS +R+R
Sbjct: 241 RRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERAR 300

Query: 64  RDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERE 123
           R+ + +   R       +  +       D           +   ++ R R+R  +   R 
Sbjct: 301 RERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRS 360

Query: 124 RRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERE 183
            RERR             +R    S R   ++R          E      R++ +E E  
Sbjct: 361 ERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGG 420

Query: 184 RERELRERERDLE 196
                 E    +E
Sbjct: 421 DGYLAPENGYLME 433

>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 = 62.2 bits (150), Expect = 2e-10
 Identities = 39/221 (17%), Positives = 71/221 (32%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGK 60
            + D    L      +  +                       +    ++    ++     
Sbjct: 167 KKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPS 226

Query: 61  RSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEK 120
                + + +  R  R+R R+RDKER RR       R R R R+ E  R      ++K++
Sbjct: 227 PLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDR 286

Query: 121 ERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELER 180
           +R+RR  R RE+ R      E         +       +               +   E+
Sbjct: 287 DRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEK 346

Query: 181 ERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQR 221
            R+R+RE R   R    R   R +++    E +      +R
Sbjct: 347 GRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSER 387

>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 = 61.4 bits (148), Expect = 4e-10
 Identities = 39/209 (18%), Positives = 70/209 (33%), Gaps = 2/209 (0%)

Query: 14  EEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSR 73
                  +   +    +    + + R   +   S     +      +  R    E +  R
Sbjct: 193 GGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKER 252

Query: 74  RDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRER-REKEKERERRERRDREK 132
             R       + R R     +R R RER ++ +RDR+R   R RE+ +    R+   R  
Sbjct: 253 ERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGG 312

Query: 133 ERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERE 192
             +     E   +        +          E+ R+ +RER      ERER R+ R+R+
Sbjct: 313 GGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRD-RDRD 371

Query: 193 RDLEMRESRRYKEKKEVVEPEADPERDQR 221
           RD +    R  +  +   +        Q 
Sbjct: 372 RDRDREHKRGERGSERGRDEARGGGGGQD 400

>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 = 55.2 bits (132), Expect = 3e-08
 Identities = 32/220 (14%), Positives = 62/220 (28%)

Query: 2   EFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKR 61
           E++    +    +    +K D         +         R+            +    R
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIR 209

Query: 62  SRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKE 121
               +D      R              R+R+R        +    R       RR     
Sbjct: 210 HSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSR 269

Query: 122 RERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERE 181
            +   RR RE+ ++++RD +RRSS    R+  +  R         +     E       +
Sbjct: 270 DKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDD 329

Query: 182 RERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQR 221
                   +     E +   R +E++     E +  RD+ 
Sbjct: 330 GPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRD 369

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 63.7 bits (156), Expect = 4e-13
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K++VG L  +  E ++R+ F  FG VE ++LP+D +T + +GF F+ F + E  K     
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME- 59

Query: 383 LNGKLEIVGRTLKV 396
                 +     ++
Sbjct: 60  -KKYHNVGLSKCEI 72

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 49.0 bits (118), Expect = 7e-08
 Identities = 13/62 (20%), Positives = 25/62 (40%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
            E  + E+F   G+V  + L MD  + + +G  +I F +   V   +      +      
Sbjct: 12  PEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCE 71

Query: 293 VK 294
           +K
Sbjct: 72  IK 73

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 64.8 bits (158), Expect = 5e-13
 Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 10/89 (11%)

Query: 320 IDRKLYVGNL------HFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQL 373
           ID  + V N+           +  + K+F  FG +         E G+ KG+ F+++A  
Sbjct: 14  IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI--TNDFYPEEDGKTKGYIFLEYASP 71

Query: 374 EHAKAAQSALNGKLEIVGR-TLKVSSVTD 401
            HA  A    +G  ++  + T +V+  TD
Sbjct: 72  AHAVDAVKNADGY-KLDKQHTFRVNLFTD 99

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 14/79 (17%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           P+  P+R ++            +  +++ FSK GK+            ++KG  ++E+  
Sbjct: 24  PQVGPDRLEKL-----------KNVIHKIFSKFGKI--TNDFYPEEDGKTKGYIFLEYAS 70

Query: 272 VMSVPMAI-ALSGQLLLGQ 289
                 A+    G  L  Q
Sbjct: 71  PAHAVDAVKNADGYKLDKQ 89

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 8/55 (14%), Positives = 26/55 (47%), Gaps = 3/55 (5%)

Query: 522 QGDVEEECSKYGRVKHIYVDK---RSAGFVYLRFESTEAAASAQRAMHMRWFARR 573
           +  + +  SK+G++ + +  +   ++ G+++L + S   A  A +        ++
Sbjct: 35  KNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 64.2 bits (157), Expect = 6e-13
 Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 321 DRKLYVGNLHFNMTETQLRKLF-EPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
           +  L+VG+L  ++ +  L + F + +      ++ LD +TG  KG+GFV+F      K A
Sbjct: 9   EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRA 67

Query: 380 QSALNGKLEIVGRTLKVS 397
            +   G + +  + +++S
Sbjct: 68  LTECQGAVGLGSKPVRLS 85

>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 = 64.6 bits (157), Expect = 6e-13
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 8/77 (10%)

Query: 322 RKLYVGN--LHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
           + L V N  L   ++  QL  + E  G V+ + +P +      K + F ++   E +K A
Sbjct: 26  QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRA 79

Query: 380 QSALNGKLEIVGRTLKV 396
              LNGK  +     K+
Sbjct: 80  YVTLNGKEVVDDLGQKI 96

>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 = 64.0 bits (156), Expect = 7e-13
 Identities = 25/97 (25%), Positives = 42/97 (43%), Gaps = 2/97 (2%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
           D   V  + MP  A E DV +FF    +V  V L+ D   R + G G ++F        A
Sbjct: 15  DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGR-NNGNGLVKFLSPQDTFEA 72

Query: 279 IALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATG 315
           +  +  L++ + V V P+   + +        G ++G
Sbjct: 73  LKRNRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109

>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 = 57.1 bits (138), Expect = 2e-10
 Identities = 22/95 (23%), Positives = 35/95 (36%), Gaps = 4/95 (4%)

Query: 307 TSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFG 366
           +S       P    D  + V  + F+  E  +R  F        V L  D   G+  G G
Sbjct: 2   SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDA-VHLLKD-HVGRNNGNG 59

Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD 401
            V+F   +    A    N    ++ R ++VS  T+
Sbjct: 60  LVKFLSPQDTFEALK-RNRM-LMIQRYVEVSPATE 92

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 62.5 bits (153), Expect = 1e-12
 Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 4/68 (5%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K++VG L  N T   ++  FE FG V+   L  D  T + +GFGFV F   +  +     
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 383 ----LNGK 386
               +N K
Sbjct: 61  HFHEINNK 68

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 51.7 bits (125), Expect = 7e-09
 Identities = 17/62 (27%), Positives = 28/62 (45%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           T  DV  +F + GKV D  L+ D+ + R +G G++ F     V     +    +  + V 
Sbjct: 12  TVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVE 71

Query: 293 VK 294
            K
Sbjct: 72  CK 73

>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 = 62.6 bits (153), Expect = 1e-12
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 8/76 (10%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             ++VG    +MTE +LR+ F  +G V  V +P        + F FV F      + AQS
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTF---ADDQIAQS 57

Query: 382 ALNGKLEIVGRTLKVS 397
                L I G ++ +S
Sbjct: 58  LCGEDLIIKGISVHIS 73

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 63.0 bits (154), Expect = 2e-12
 Identities = 27/89 (30%), Positives = 41/89 (46%), Gaps = 3/89 (3%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +           L V  L +  TE  L++ F  FG V +VQ+  D++TG  KGFGF
Sbjct: 2   SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           V+F      +     ++ +  I GR    
Sbjct: 62  VRFT---EYETQVKVMSQRHMIDGRWCDC 87

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           TE+D+ E+FS  G+V  V++  D  +  SKG G++ F +  +    ++    ++ G+   
Sbjct: 28  TEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCD 86

Query: 293 VKPSEAEKNLVQSNTSAG 310
            K   + K    S  S+G
Sbjct: 87  CKLPNS-KQSQDSGPSSG 103

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 63.2 bits (154), Expect = 2e-12
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 10/79 (12%)

Query: 320 IDRKLYVGNLHFN-MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
           I+ ++++GNL+   + ++ +  +F  +G V    +         KG+ FVQ++   HA+A
Sbjct: 26  INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARA 77

Query: 379 AQSALNGKLEIVGRTLKVS 397
           A    NG+  + G+TL ++
Sbjct: 78  AVLGENGR-VLAGQTLDIN 95

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 21/105 (20%), Positives = 40/105 (38%), Gaps = 10/105 (9%)

Query: 199 ESRRYKEKKEVVEPEADPERDQRTVFAYQMPL-KATERDVYEFFSKAGKVRDVRLIMDRN 257
                K +   V  + DP+     VF   +      + DV   FSK G+V    +     
Sbjct: 6   SGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV----- 60

Query: 258 SRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKN 301
               KG  ++++ +      A+   +G++L GQ + +  +   K 
Sbjct: 61  ---HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKP 102

>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 = 62.0 bits (151), Expect = 2e-12
 Identities = 13/76 (17%), Positives = 23/76 (30%), Gaps = 8/76 (10%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             + V NL  +    ++  L + +               + K   FV     E A+ A  
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 382 ALNGKLEIVGRTLKVS 397
             +      G+ L V 
Sbjct: 59  MFHQY-SFRGKDLIVQ 73

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 61.6 bits (150), Expect = 2e-12
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 321 DRKLYVGNL------HFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
           D  + V N+           +  + K+F  FG +     P +   G+ KG+ F+++A   
Sbjct: 1   DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 58

Query: 375 HAKAAQSALNGKLEIVGRTLKV 396
           HA  A    +G       T +V
Sbjct: 59  HAVDAVKNADGYKLDKQHTFRV 80

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 8/48 (16%), Positives = 24/48 (50%), Gaps = 3/48 (6%)

Query: 522 QGDVEEECSKYGRVKHIYVDK---RSAGFVYLRFESTEAAASAQRAMH 566
           +  + +  SK+G++ + +  +   ++ G+++L + S   A  A +   
Sbjct: 21  KNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNAD 68

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 12/68 (17%), Positives = 28/68 (41%), Gaps = 13/68 (19%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           P+  P+R ++            +  +++ FSK GK+ +          ++KG  ++E+  
Sbjct: 10  PQVGPDRLEKL-----------KNVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYAS 56

Query: 272 VMSVPMAI 279
                 A+
Sbjct: 57  PAHAVDAV 64

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.1 bits (151), Expect = 3e-12
 Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 3/83 (3%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           +R +Y+     + T   +++  E  G V  +Q+         KG  FV F  +E AK   
Sbjct: 11  NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFV 69

Query: 381 SALNGKLEIVGRTLKVSSVTDHV 403
                K +     L +    D+ 
Sbjct: 70  ETPGQKYK--ETDLLILFKDDYF 90

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 15/82 (18%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
           +   R+V+    P  AT  D+ E+    G+V ++++    + +  KG  ++ F  + S  
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAK 66

Query: 277 MAIALSGQLLLGQPVMVKPSEA 298
             +   GQ      +++   + 
Sbjct: 67  KFVETPGQKYKETDLLILFKDD 88

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 61.0 bits (149), Expect = 4e-12
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 4/68 (5%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K+++G L +  T+  LR+ F  FG V+   +  D  T + +GFGFV F          + 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 383 ----LNGK 386
               L+ K
Sbjct: 62  SRHELDSK 69

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 49.0 bits (118), Expect = 6e-08
 Identities = 17/62 (27%), Positives = 34/62 (54%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           T+  + E+F + G+V++  ++ D  ++RS+G G++ F D   V   +A S   L  + + 
Sbjct: 13  TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTID 72

Query: 293 VK 294
            K
Sbjct: 73  PK 74

>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 = 61.8 bits (150), Expect = 4e-12
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 7/77 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R L++  L   +TET++  L  PFG V       +I   + K   F++ A  E A    +
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPFGKVT------NILMLKGKNQAFLELATEEAAITMVN 69

Query: 382 ALNGK-LEIVGRTLKVS 397
             +     +  + + + 
Sbjct: 70  YYSAVTPHLRNQPIYIQ 86

>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 = 49.0 bits (117), Expect = 1e-07
 Identities = 19/93 (20%), Positives = 38/93 (40%), Gaps = 10/93 (10%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
           R +   ++P + TE +V       GKV ++ ++      + K   ++E     +    + 
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEEAAITMVN 69

Query: 280 --ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAG 310
             +     L  QP+ ++ S   K L  S  S+G
Sbjct: 70  YYSAVTPHLRNQPIYIQYSN-HKELKTSGPSSG 101

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 61.3 bits (149), Expect = 5e-12
 Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             +++  L   + E  L +  + FGP+  V +         K    V+F  +  A  A +
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVN 75

Query: 382 ALNGK-LEIVGRTLKVS 397
                 + I G    V+
Sbjct: 76  YAADNQIYIAGHPAFVN 92

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 43.6 bits (103), Expect = 8e-06
 Identities = 17/100 (17%), Positives = 31/100 (31%), Gaps = 12/100 (12%)

Query: 197 MRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR 256
           M     +  +      +         V    +     E D+ E   + G +  V ++   
Sbjct: 1   MGHHHHHHMENYDDPHKTPASP---VVHIRGLIDGVVEADLVEALQEFGPISYVVVM--- 54

Query: 257 NSRRSKGVGYIEFYDVMSVPMAI---ALSGQLLLGQPVMV 293
                K    +EF DV+    A+   A +   + G P  V
Sbjct: 55  ---PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV 91

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 61.1 bits (149), Expect = 6e-12
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 8/77 (10%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
             K++VG    +MT  +L++ F  +G V  V +P        + F FV F      K AQ
Sbjct: 11  GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTF---ADDKVAQ 62

Query: 381 SALNGKLEIVGRTLKVS 397
           S     L I G ++ +S
Sbjct: 63  SLCGEDLIIKGISVHIS 79

>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 = 61.8 bits (150), Expect = 6e-12
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 7/80 (8%)

Query: 324 LYVGNLHFNMTETQL---RKLFEPFGPVELVQLPLDIETGQCK---GFGFVQFAQLEHAK 377
           ++V  L   + + ++    + F  FG +  V +         +      +V + + E A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 378 AAQSALNGKLEIVGRTLKVS 397
            A   +N    + GRTLK S
Sbjct: 78  RAIQCVNNV-VVDGRTLKAS 96

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 222 TVFAYQMPLKATERDV---YEFFSKAGKVRDVRLIMDR---NSRRSKGVGYIEFYDVMSV 275
            VF   +  +  + +V    E+F K GK+  V +        S+      Y+ +      
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 276 PMAI-ALSGQLLLGQPVMV 293
             AI  ++  ++ G+ +  
Sbjct: 77  LRAIQCVNNVVVDGRTLKA 95

>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 = 40.6 bits (95), Expect = 1e-04
 Identities = 9/62 (14%), Positives = 23/62 (37%), Gaps = 8/62 (12%)

Query: 526 EEECSKYGRVKHIYVDKR--------SAGFVYLRFESTEAAASAQRAMHMRWFARRLISA 577
            E   K+G++  + ++           +   Y+ +  +E A  A + ++      R + A
Sbjct: 36  PEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA 95

Query: 578 IF 579
             
Sbjct: 96  SL 97

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 61.1 bits (149), Expect = 7e-12
 Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 5/84 (5%)

Query: 308 SAGGTATGPYGAID-RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFG 366
           S+G +     GA +  KL+VG L ++ T+  LR  F  +G V    +  D  T Q +GFG
Sbjct: 2   SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61

Query: 367 FVQFAQLEHAKAAQSA----LNGK 386
           FV+F          ++    L+G+
Sbjct: 62  FVKFKDPNCVGTVLASRPHTLDGR 85

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           T+  +  +FS+ G+V D  ++ D+ + +S+G G+++F D   V   +A     L G+ + 
Sbjct: 29  TQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNID 88

Query: 293 VKPSEAEKNLVQSNTSAG 310
            KP    + +  S  S+G
Sbjct: 89  PKPCTP-RGMQPSGPSSG 105

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 61.5 bits (149), Expect = 7e-12
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 7/77 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R +++  L  ++TE ++  L  PFG V  + +       + K   F++    E A    +
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVN 85

Query: 382 ALNGK-LEIVGRTLKVS 397
                   + G+ + + 
Sbjct: 86  YYTSVTPVLRGQPIYIQ 102

>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 = 46.8 bits (111), Expect = 1e-06
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 9/79 (11%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
           R +   ++P+  TE +V       GKV ++ ++      + K   +IE     +    + 
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVN 85

Query: 280 --ALSGQLLLGQPVMVKPS 296
                  +L GQP+ ++ S
Sbjct: 86  YYTSVTPVLRGQPIYIQFS 104

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 60.8 bits (148), Expect = 9e-12
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K+YVGNL     + +L + F  +GP+  V +  +       GF FV+F     A+ A   
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 383 LNGKLEIVGRTLKV 396
           L+GK  I G  ++V
Sbjct: 57  LDGK-VICGSRVRV 69

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 11/53 (20%), Positives = 24/53 (45%)

Query: 524 DVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLIS 576
           ++E   S YG ++ +++ +   GF ++ FE    A  A R +  +      + 
Sbjct: 16  ELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVR 68

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 6/66 (9%)

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL 287
              A + ++   FS  G +R V +      R   G  ++EF D      A+  L G+++ 
Sbjct: 9   GTGAGKGELERAFSYYGPLRTVWIA-----RNPPGFAFVEFEDPRDAEDAVRGLDGKVIC 63

Query: 288 GQPVMV 293
           G  V V
Sbjct: 64  GSRVRV 69

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 60.3 bits (147), Expect = 9e-12
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
             K++VG L ++ ++  L+  F  FG V    + +D  TG+ +GFGF+ F      +   
Sbjct: 11  AGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVL 70

Query: 381 SALNGKLEIVGRTLKV 396
                +L+  GR +  
Sbjct: 71  DQKEHRLD--GRVIDP 84

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 48.7 bits (117), Expect = 1e-07
 Identities = 21/62 (33%), Positives = 36/62 (58%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           +++D+ ++F+K G+V D  + MD N+ RS+G G+I F D  SV   +      L G+ + 
Sbjct: 24  SKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVID 83

Query: 293 VK 294
            K
Sbjct: 84  PK 85

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 61.5 bits (149), Expect = 9e-12
 Identities = 21/109 (19%), Positives = 43/109 (39%), Gaps = 8/109 (7%)

Query: 293 VKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRK----LFEPFGPV 348
           +K + A K   Q   S    +T P+    + + + N++  + + +L+     L    G +
Sbjct: 1   MKETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI 60

Query: 349 ELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
             + +     +    G  ++ FA  E A+A   A  G     G  L ++
Sbjct: 61  LDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGY-PFQGNPLVIT 105

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 39.1 bits (91), Expect = 7e-04
 Identities = 22/117 (18%), Positives = 45/117 (38%), Gaps = 13/117 (11%)

Query: 197 MRESRRYKEKKEVVEPE-----ADPERDQRTVF----AYQMPLKATERDVYEFFSKAGKV 247
           M+E+   K +++ ++              + V       ++P +  +  +Y   S  G +
Sbjct: 1   MKETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI 60

Query: 248 RDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLV 303
            D+ +     S  + G  YI F    S    + A  G    G P+++  SE  ++ V
Sbjct: 61  LDIVV---DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQV 114

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 60.6 bits (147), Expect = 1e-11
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 7/77 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA-Q 380
           R +++  L  ++TE ++  L  PFG V  + +       + K   F++    E A     
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVN 70

Query: 381 SALNGKLEIVGRTLKVS 397
              +    + G+ + + 
Sbjct: 71  YYTSVTPVLRGQPIYIQ 87

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 45.2 bits (107), Expect = 3e-06
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 9/79 (11%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           R +   ++P+  TE +V       GKV ++ ++      + K   +IE     +    + 
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVN 70

Query: 281 ---LSGQLLLGQPVMVKPS 296
                  +L GQP+ ++ S
Sbjct: 71  YYTSVTPVLRGQPIYIQFS 89

>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 = 61.0 bits (148), Expect = 1e-11
 Identities = 23/119 (19%), Positives = 43/119 (36%)

Query: 198 RESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRN 257
             S       +       P      V+   +P +A  + V +FF K   V D   I    
Sbjct: 3   SGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP 62

Query: 258 SRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGP 316
           + ++ G G++EF +      A+    Q +  + + V P   +  L + +       +GP
Sbjct: 63  NGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGP 121

>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 = 53.3 bits (128), Expect = 6e-09
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
              +Y+  L F      +   F+    VE          G+  G GFV+F      KAA 
Sbjct: 25  GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL 84

Query: 381 SALNGKLEIVGRTLKVSSVT 400
              + +  +  R ++V  +T
Sbjct: 85  C-RHKQ-YMGNRFIQVHPIT 102

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 60.4 bits (147), Expect = 1e-11
 Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 4/70 (5%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
             K+++G L +  T+  LR+ F  FG V+   +  D  T + +GFGFV F          
Sbjct: 25  GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84

Query: 381 SA----LNGK 386
           +     L+ K
Sbjct: 85  AQSRHELDSK 94

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 48.0 bits (115), Expect = 4e-07
 Identities = 17/62 (27%), Positives = 34/62 (54%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           T+  + E+F + G+V++  ++ D  ++RS+G G++ F D   V   +A S   L  + + 
Sbjct: 38  TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTID 97

Query: 293 VK 294
            K
Sbjct: 98  PK 99

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 58.8 bits (143), Expect = 4e-11
 Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 10/75 (13%)

Query: 323 KLYVGNLHF-NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           +L++GNL   N+++  L ++F P+G +  + +           FGF+QF   +  + A  
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 63

Query: 382 ALNGKLEIVGRTLKV 396
             + +    G+ L +
Sbjct: 64  CESQE-MNFGKKLIL 77

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 14/73 (19%), Positives = 32/73 (43%), Gaps = 9/73 (12%)

Query: 229 PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL 287
               ++ D++  FS  G +  + +            G+I+F +  SV  AI   S ++  
Sbjct: 20  LKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIECESQEMNF 71

Query: 288 GQPVMVKPSEAEK 300
           G+ ++++ S +  
Sbjct: 72  GKKLILEVSSSNA 84

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 58.5 bits (142), Expect = 5e-11
 Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 12/95 (12%)

Query: 303 VQSNTSAGGTATGPYGAIDRKLYVGNL-HFNMTETQLRKLFEPFGPVELVQLPLDIETGQ 361
              + S+G    G    +  +L++GNL   N+++  L ++F P+G +  + +        
Sbjct: 6   HHHHHSSGLVPRG--SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------- 56

Query: 362 CKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
              FGF+QF   +  + A    + +    G+ L +
Sbjct: 57  -NAFGFIQFDNPQSVRDAIEXESQE-MNFGKKLIL 89

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 40.8 bits (96), Expect = 8e-05
 Identities = 14/71 (19%), Positives = 32/71 (45%), Gaps = 9/71 (12%)

Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQ 289
             ++ D++  FS  G +  + +            G+I+F +  SV  AI   S ++  G+
Sbjct: 34  NVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEXESQEMNFGK 85

Query: 290 PVMVKPSEAEK 300
            ++++ S +  
Sbjct: 86  KLILEVSSSNA 96

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 58.8 bits (143), Expect = 7e-11
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
            RKL++G L F  TE  LR  +E +G +    +  D  + + +GFGFV F+ +    AA 
Sbjct: 27  FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86

Query: 381 SA----LNGK 386
           +A    ++G+
Sbjct: 87  AARPHSIDGR 96

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 46.9 bits (112), Expect = 9e-07
 Identities = 18/63 (28%), Positives = 33/63 (52%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
           TE  +  ++ + GK+ D  ++ D  S+RS+G G++ F  +  V  A+A     + G+ V 
Sbjct: 40  TEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVE 99

Query: 293 VKP 295
            K 
Sbjct: 100 PKR 102

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 57.9 bits (140), Expect = 9e-11
 Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 6/93 (6%)

Query: 305 SNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKG 364
           S +S  G+  G    +   +YVGNL  +   + L++     G V     PL +     + 
Sbjct: 3   SGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRR 57

Query: 365 FGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
             F+ +     A+ A S L G L +   TL+V+
Sbjct: 58  RAFLHYPDSAAAQQAVSCLQG-LRLGTDTLRVA 89

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 20/75 (26%), Positives = 30/75 (40%), Gaps = 7/75 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R ++V      +   QL + F  FGPV  V   +D + G    F  V+   +   +A  S
Sbjct: 9   RSVFVSGFPRGVDSAQLSEYFLAFGPVASVV--MDKDKG---VFAIVEMGDVGAREAVLS 63

Query: 382 ALNGKLEIVGRTLKV 396
                L   G  L+V
Sbjct: 64  QSQHSLG--GHRLRV 76

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 49.6 bits (119), Expect = 6e-08
 Identities = 22/94 (23%), Positives = 38/94 (40%), Gaps = 5/94 (5%)

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPM 277
              R+VF    P       + E+F   G V  V  +MD++         +E  DV +   
Sbjct: 6   SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREA 60

Query: 278 AIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGG 311
            ++ S   L G  + V+P E ++    ++ S  G
Sbjct: 61  VLSQSQHSLGGHRLRVRPREQKEFQSPASKSPKG 94

>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 = 58.7 bits (142), Expect = 1e-10
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D K+YVGNL  N  +T+L + F  +GP+  V +  +       GF FV+F     A  A 
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAV 127

Query: 381 SALNGKLEIVGRTLKV 396
             L+G+  + G  ++V
Sbjct: 128 RELDGR-TLCGCRVRV 142

>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 = 42.9 bits (101), Expect = 4e-05
 Identities = 22/137 (16%), Positives = 42/137 (30%), Gaps = 6/137 (4%)

Query: 165 ERERESERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVF 224
               ++    ++  +   +   +      D     +              D       V+
Sbjct: 18  TEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVY 77

Query: 225 AYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSG 283
              +     + ++   F   G +R V +      R   G  ++EF D      A+  L G
Sbjct: 78  VGNLGNNGNKTELERAFGYYGPLRSVWVA-----RNPPGFAFVEFEDPRDAADAVRELDG 132

Query: 284 QLLLGQPVMVKPSEAEK 300
           + L G  V V+ S  EK
Sbjct: 133 RTLCGCRVRVELSNGEK 149

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 4/88 (4%)

Query: 313 ATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ 372
           ++G  G     + +    FN+TE  + +   P  PV  +++  +   G   G+ FV F+ 
Sbjct: 2   SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVA-IRIVRN-AHGNKTGYIFVDFSN 59

Query: 373 LEHAKAAQSALNGKLEIVGRTLKVSSVT 400
            E  K A    N +  + GR ++V    
Sbjct: 60  EEEVKQALK-CNRE-YMGGRYIEVFREK 85

>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 = 55.8 bits (135), Expect = 4e-10
 Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
              TV     P   TE++V EF +   K   +R++ + +     G  +++F +   V  A
Sbjct: 9   TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHG-NKTGYIFVDFSNEEEVKQA 66

Query: 279 IALSGQLLLGQPVMVKPSEAEKN 301
           +  + + + G+ + V   ++  +
Sbjct: 67  LKCNREYMGGRYIEVFREKSGPS 89

>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 = 56.3 bits (136), Expect = 4e-10
 Identities = 22/105 (20%), Positives = 38/105 (36%), Gaps = 8/105 (7%)

Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
              +        V    +P +ATE D+Y FFS       V + +  +  R  G   +EF 
Sbjct: 6   SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDG-RVTGEADVEFA 63

Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATG 315
                  A+A     +  + V +  +        + TS  G ++G
Sbjct: 64  THEDAVAAMAKDKANMQHRYVELFLNS------TAGTSGSGPSSG 102

>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 = 56.3 bits (136), Expect = 4e-10
 Identities = 19/89 (21%), Positives = 38/89 (42%), Gaps = 4/89 (4%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G + +         +++  L +  TE  +   F P  P+  V + +    G+  G   
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIG-PDGRVTGEAD 59

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           V+FA  E A AA +  +    +  R +++
Sbjct: 60  VEFATHEDAVAAMA-KDKA-NMQHRYVEL 86

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 57.0 bits (137), Expect = 4e-10
 Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 6/94 (6%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           + V NL + +T   L ++F  FG V  +         Q      +Q+A    A+ A+ +L
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLSL 86

Query: 384 NGK-LEIVGRTLKVS-SVTDHVGTQDTAAKSADF 415
           +G+ +     TL++  S    +  +    KS D+
Sbjct: 87  DGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDY 120

>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 = 56.4 bits (136), Expect = 6e-10
 Identities = 22/106 (20%), Positives = 38/106 (35%), Gaps = 2/106 (1%)

Query: 295 PSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLP 354
           P  +    +      G  +     A D  + +  L F  T+ ++ + F     V      
Sbjct: 16  PRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITL 75

Query: 355 LDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT 400
                G+  G  FVQFA  E A+ A    + +  I  R ++V   +
Sbjct: 76  PVDPEGKITGEAFVQFASQELAEKALG-KHKE-RIGHRYIEVFKSS 119

>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 = 55.7 bits (134), Expect = 1e-09
 Identities = 12/85 (14%), Positives = 30/85 (35%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
             +    +   V    +P   T+ ++ +FFS    V +   +      +  G  +++F  
Sbjct: 34  SNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFAS 93

Query: 272 VMSVPMAIALSGQLLLGQPVMVKPS 296
                 A+    + +  + + V  S
Sbjct: 94  QELAEKALGKHKERIGHRYIEVFKS 118

>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 = 56.5 bits (136), Expect = 8e-10
 Identities = 19/125 (15%), Positives = 31/125 (24%), Gaps = 5/125 (4%)

Query: 178 LERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDV 237
                          R   M      ++             +   V    +P   +  DV
Sbjct: 3   SSHHHHHHSS-GLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDV 61

Query: 238 YEFFSK---AGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK 294
             F S          V  I  R   R  G  ++E      V MA+    + +  + + V 
Sbjct: 62  QNFLSDCTIHDGAAGVHFIYTREG-RQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVF 120

Query: 295 PSEAE 299
            S   
Sbjct: 121 KSHRT 125

>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 = 41.1 bits (96), Expect = 2e-04
 Identities = 14/95 (14%), Positives = 29/95 (30%), Gaps = 6/95 (6%)

Query: 305 SNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPF---GPVELVQLPLDIETGQ 361
                G    GP G     + +  L ++ +   ++              V        G+
Sbjct: 28  QQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYT-REGR 86

Query: 362 CKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
             G  FV+    +  K A    + +  +  R ++V
Sbjct: 87  QSGEAFVELGSEDDVKMALK-KDRE-SMGHRYIEV 119

>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 = 55.1 bits (133), Expect = 8e-10
 Identities = 19/72 (26%), Positives = 30/72 (41%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +   P  A D  + +  L F  ++ ++ + F     V           G+  G  F
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 368 VQFAQLEHAKAA 379
           VQFA  E A+ A
Sbjct: 62  VQFASQEIAEKA 73

>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 = 54.4 bits (131), Expect = 2e-09
 Identities = 12/88 (13%), Positives = 31/88 (35%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
             +    +   V    +P   ++ ++ +FFS    V +   +      RS G  +++F  
Sbjct: 7   GNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFAS 66

Query: 272 VMSVPMAIALSGQLLLGQPVMVKPSEAE 299
                 A+    + +  + + +  S   
Sbjct: 67  QEIAEKALKKHKERIGHRYIEIFKSSRA 94

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 55.7 bits (134), Expect = 9e-10
 Identities = 18/110 (16%), Positives = 43/110 (39%), Gaps = 8/110 (7%)

Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRD----VRLIMDRNSRRSKGVGY 266
             +   + +Q  V    +P  AT  +V  FF +   +      +  +   + R   G  +
Sbjct: 14  VAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR-PTGDAF 72

Query: 267 IEFYDVMSVPMAIALSGQLLLGQPVMVKPS---EAEKNLVQSNTSAGGTA 313
           + F        A+     LL  + + +  S   E ++ L + ++++G ++
Sbjct: 73  VLFACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGPSS 122

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 48.0 bits (114), Expect = 5e-07
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 9/83 (10%)

Query: 305 SNTSAGGTATGPYGAIDRK----LYVGNLHFNMTETQLRKLFEPFGPVEL----VQLPLD 356
           S +S GGT+      + ++    + +  L F  T  ++   F    P+      +     
Sbjct: 3   SGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY 62

Query: 357 IETGQCKGFGFVQFAQLEHAKAA 379
              G+  G  FV FA  E+A+ A
Sbjct: 63  -PDGRPTGDAFVLFACEEYAQNA 84

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 56.3 bits (135), Expect = 1e-09
 Identities = 25/115 (21%), Positives = 46/115 (40%), Gaps = 7/115 (6%)

Query: 303 VQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQC 362
             +     G A      + R + V NL + +T   L ++F  FG V  +         Q 
Sbjct: 29  ASAAAVDAGMAMAGQSPVLR-IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ- 86

Query: 363 KGFGFVQFAQLEHAKAAQSALNGK-LEIVGRTLKVS-SVTDHVGTQDTAAKSADF 415
                +Q+A    A+ A+ +L+G+ +     TL++  S    +  +    KS D+
Sbjct: 87  ---ALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDY 138

>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 = 54.9 bits (132), Expect = 2e-09
 Identities = 21/108 (19%), Positives = 35/108 (32%), Gaps = 4/108 (3%)

Query: 214 ADPERDQRTVFAYQMPLKATERDVYEFFS---KAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
                +   V    +P   +  DV  F S       V  V  I  R  R   G  ++E  
Sbjct: 11  GPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR-QSGEAFVELE 69

Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYG 318
               V +A+    + +  + + V  S   +       S   +A+GP  
Sbjct: 70  SEDDVKLALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSS 117

>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 = 50.3 bits (120), Expect = 6e-08
 Identities = 15/94 (15%), Positives = 33/94 (35%), Gaps = 6/94 (6%)

Query: 306 NTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPF---GPVELVQLPLDIETGQC 362
           ++ + G   GP G     + +  L ++ +   ++           V  V        G+ 
Sbjct: 2   SSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYT-REGRQ 60

Query: 363 KGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
            G  FV+    +  K A    + +  +  R ++V
Sbjct: 61  SGEAFVELESEDDVKLALK-KDRE-SMGHRYIEV 92

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score = 58.7 bits (142), Expect = 3e-09
 Identities = 26/165 (15%), Positives = 50/165 (30%), Gaps = 4/165 (2%)

Query: 1   MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKS--ERSYRKREDSEEEEEEEKSRS 58
           +   E     + ++ +  +   ++            S      ++   SE     E + +
Sbjct: 414 IAKQEKYEPSEEIKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIAST 473

Query: 59  GKRSRRDEDEEN--GSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERR 116
                 D   +     R        R          RD        +  + D +     R
Sbjct: 474 YGVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFR 533

Query: 117 EKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSR 161
             +    R + RD + E  R  +  RRS SRS   ++ S R+S+ 
Sbjct: 534 GNKNYNNRSQNRDYDDEPFRRSNNNRRSFSRSNDKNNYSSRNSNI 578

>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 = 54.1 bits (130), Expect = 5e-09
 Identities = 21/120 (17%), Positives = 37/120 (30%), Gaps = 3/120 (2%)

Query: 178 LERERERERE-LRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERD 236
                      L  R   +      +   +                V    +P KATE D
Sbjct: 3   SSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATEND 62

Query: 237 VYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS 296
           +Y FFS    VR V + +  +  R  G   +EF        A++     +  + + +  +
Sbjct: 63  IYNFFSPLNPVR-VHIEIGPDG-RVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLN 120

>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 = 52.2 bits (125), Expect = 2e-08
 Identities = 21/93 (22%), Positives = 37/93 (39%), Gaps = 4/93 (4%)

Query: 304 QSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 363
           Q    +G +           +++  L +  TE  +   F P  PV  V + +    G+  
Sbjct: 29  QMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VHIEIG-PDGRVT 86

Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           G   V+FA  E A AA S  +    +  R +++
Sbjct: 87  GEADVEFATHEEAVAAMS-KDRA-NMQHRYIEL 117

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 52.5 bits (126), Expect = 9e-09
 Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 4/88 (4%)

Query: 215 DPERDQRTVFAYQMPLKATERDVYEFFSK---AGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           +   D   + A  +P   T  DV  FFS          +  +++R+  + +G   IE   
Sbjct: 6   EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDG-KRRGDALIEMES 64

Query: 272 VMSVPMAIALSGQLLLGQPVMVKPSEAE 299
              V  A+      +  + V V     E
Sbjct: 65  EQDVQKALEKHRMYMGQRYVEVYEINNE 92

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 9/80 (11%), Positives = 26/80 (32%), Gaps = 6/80 (7%)

Query: 324 LYVGNLHFNMTETQLRKLFEPF---GPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           +    L ++ T   +   F           +   L+   G+ +G   ++    +  + A 
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLN-RDGKRRGDALIEMESEQDVQKAL 72

Query: 381 SALNGKLEIVGRTLKVSSVT 400
              +    +  R ++V  + 
Sbjct: 73  -EKHRM-YMGQRYVEVYEIN 90

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 57.5 bits (138), Expect = 9e-09
 Identities = 27/220 (12%), Positives = 66/220 (30%), Gaps = 2/220 (0%)

Query: 3   FDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRS 62
           F      +   +     K  D +   +        +    +  D    +  ++S      
Sbjct: 604 FGFEMSEDTGPDGTLLPKARDQAVFPQNGLVVSSVDVQSVEPVDQRTRDALQRSVQLAIE 663

Query: 63  RRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKER 122
                +E  ++ +  R     + R  R +  D+    +  +E       S         +
Sbjct: 664 ITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEAMSMAVESTGNAK 723

Query: 123 ERRERRDREKERERERDGER-RSSSRSRRSSSQSRRSSSRSRRERERESERER-ELELER 180
              E R      E E    + +  +++    +++     +  RE E    R + ELE+ +
Sbjct: 724 AEAESRAEAARIEGEGSVLQAKLKAQALAIETEAELERVKKVREMELIYARAQLELEVSK 783

Query: 181 ERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQ 220
            ++      ++ +++             V  PE   +  Q
Sbjct: 784 AQQLANVEAKKFKEMTEALGPGTIRDLAVAGPEMQVKLLQ 823

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative splicing, FBP interacting repressor, RRM, electron transport; 2.20A {Escherichia coli O157} Length = 222

 Score = 54.4 bits (131), Expect = 1e-08
 Identities = 29/109 (26%), Positives = 49/109 (44%), Gaps = 14/109 (12%)

Query: 488 NMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKH--IYVDKRSA 545
           +         S  ++L+NM DP      D D +++G+V EEC K+G V    IY +K+  
Sbjct: 114 DANLAGSAMESTVMVLRNMVDPK-----DIDDDLEGEVTEECGKFGAVNRVIIYQEKQGE 168

Query: 546 GF-------VYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEA 587
                    +++ F        A +A++ RWFA R + A     E ++ 
Sbjct: 169 EEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDN 217

>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 = 53.3 bits (127), Expect = 2e-08
 Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 3/82 (3%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R +Y+     + T   +++  E  G V  +Q+         KG  FV F  +E AK    
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE 168

Query: 382 ALNGKLEIVGRTLKVSSVTDHV 403
               K +     L +    D+ 
Sbjct: 169 TPGQKYK--ETDLLILFKDDYF 188

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 47.9 bits (113), Expect = 2e-06
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 4/89 (4%)

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
            +   R+V+    P  AT  D+ E+    G+V ++++      +  KG  ++ F  + S 
Sbjct: 105 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESA 163

Query: 276 PMAIALSGQLLLGQPVMVKPSE---AEKN 301
              +   GQ      +++   +   A+KN
Sbjct: 164 KKFVETPGQKYKETDLLILFKDDYFAKKN 192

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 56.3 bits (136), Expect = 2e-08
 Identities = 33/195 (16%), Positives = 64/195 (32%), Gaps = 1/195 (0%)

Query: 7    EYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDE 66
              L+  V  Q   ++       KK K E +S   Y+K     E +  +  R      ++ 
Sbjct: 885  RTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEY 944

Query: 67   DEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRE 126
                    + +     + E+ R D +R R    E +  T R      E  +  KE  + +
Sbjct: 945  KSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQ 1004

Query: 127  RRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERER 186
               +  E   ++         S      +   + +    R    +  +E+    E++   
Sbjct: 1005 TEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQ-AKEITETMEKKLVE 1063

Query: 187  ELRERERDLEMRESR 201
            E ++ E DL     R
Sbjct: 1064 ETKQLELDLNDERLR 1078

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 54.3 bits (131), Expect = 8e-08
 Identities = 28/215 (13%), Positives = 78/215 (36%), Gaps = 9/215 (4%)

Query: 7    EYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDE 66
            +++   +      +        +   R   ++R  +K     + E     R  K     E
Sbjct: 872  KHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKK----LKIEARSVERYKKLHIGLE 927

Query: 67   DEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRE 126
            ++         R  D   + ++   ++  +       ETE+ R      R  E+E +   
Sbjct: 928  NK----IMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNAT 983

Query: 127  RRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERER-E 185
             R    + E  +  +    +++ + + +      +   E+     +E+   L+ E+E   
Sbjct: 984  NRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELN 1043

Query: 186  RELRERERDLEMRESRRYKEKKEVVEPEADPERDQ 220
            R + ++ +++     ++  E+ + +E + + ER +
Sbjct: 1044 RRIHDQAKEITETMEKKLVEETKQLELDLNDERLR 1078

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 52.4 bits (126), Expect = 3e-07
 Identities = 22/185 (11%), Positives = 64/185 (34%), Gaps = 5/185 (2%)

Query: 5    EYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKS--RSGKRS 62
            +  Y     + + ++ + +  S ++  K     E    + +   +E+ +E         +
Sbjct: 894  QCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNN 953

Query: 63   RRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERR---EKE 119
                      +   D +R R  E   ++        +E   +  ++  +++  +   E+ 
Sbjct: 954  LEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEW 1013

Query: 120  KERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELE 179
             ++ + E      E + +    +       R      +  + +  ++  E  ++ EL+L 
Sbjct: 1014 ADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITETMEKKLVEETKQLELDLN 1073

Query: 180  RERER 184
             ER R
Sbjct: 1074 DERLR 1078

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 48.2 bits (115), Expect = 7e-06
 Identities = 35/247 (14%), Positives = 78/247 (31%), Gaps = 19/247 (7%)

Query: 28   KKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRRDRDRDRDRDKERH 87
            +      +   R Y  R   +    E KS   ++  R         R             
Sbjct: 839  RDATIALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYR 898

Query: 88   RRDRDRDRDRGRERERETERDRERSR---------ERREKEKERERRERRDREKERERER 138
            R    R+  + +   R  ER ++            +R+  E+ +E +   ++    E   
Sbjct: 899  RMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITY 958

Query: 139  DGER---RSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDL 195
              E    RS     R S +  ++++      + E  + R+   + + E++      ++  
Sbjct: 959  STETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYK 1018

Query: 196  EMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMD 255
               E    + K++    + + E   R        +    +++ E   K       +L +D
Sbjct: 1019 HETEQLVSELKEQNTLLKTEKEELNRR-------IHDQAKEITETMEKKLVEETKQLELD 1071

Query: 256  RNSRRSK 262
             N  R +
Sbjct: 1072 LNDERLR 1078

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 43.6 bits (103), Expect = 2e-04
 Identities = 22/139 (15%), Positives = 56/139 (40%), Gaps = 4/139 (2%)

Query: 4    DEYEYLEKTVEEQRQQKQDDDSSSKKKAKREE----KSERSYRKREDSEEEEEEEKSRSG 59
            DE     K++ E+    +   S+  +K + +      SE   +   +     +EE ++  
Sbjct: 938  DEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLR 997

Query: 60   KRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKE 119
            K   + + E+       D+ +   ++     ++++     E+E    R  ++++E  E  
Sbjct: 998  KELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITETM 1057

Query: 120  KERERRERRDREKERERER 138
            +++   E +  E +   ER
Sbjct: 1058 EKKLVEETKQLELDLNDER 1076

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 54.8 bits (132), Expect = 6e-08
 Identities = 31/230 (13%), Positives = 97/230 (42%), Gaps = 23/230 (10%)

Query: 9    LEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDE 68
            +++ + +  +Q ++++++ +K    +  ++   +K ED     E++ ++  K  +  E+ 
Sbjct: 953  MQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEER 1012

Query: 69   ENGSRRDRDRDRDR----DKERHRRDRDRDRDRGR-ERERETERDRERSRERREKE---- 119
             +    +   + ++     K +++ +        R ++E ++ ++ E+ + + E E    
Sbjct: 1013 VSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDL 1072

Query: 120  --------KERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRR---ERER 168
                     +    + +  +KE E +    R     S+++++  +     S     + + 
Sbjct: 1073 HEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDL 1132

Query: 169  ESERERELELERE-RERERELRERERDLE--MRESRRYKEKKEVVEPEAD 215
            ESE+    + E++ R+   EL   + +LE  +  +   +E +     + D
Sbjct: 1133 ESEKAARNKAEKQKRDLSEELEALKTELEDTLDTTATQQELRGSDYKDDD 1182

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 54.1 bits (130), Expect = 1e-07
 Identities = 32/223 (14%), Positives = 78/223 (34%), Gaps = 18/223 (8%)

Query: 1    MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGK 60
            ++ ++     K  + +      +D ++K   +R+   ER      +  EEEE+ K     
Sbjct: 974  LQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAK----- 1028

Query: 61   RSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEK 120
                +  +          + +   ++  + R       R+ E E+    +   +  E + 
Sbjct: 1029 ----NLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGES---SDLHEQIAELQA 1081

Query: 121  ERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRR---ERERESERERELE 177
            +    + +  +KE E +    R     S+++++  +     S     + + ESE+    +
Sbjct: 1082 QIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNK 1141

Query: 178  LERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQ 220
             E+++   R+L E    L+              E      +D 
Sbjct: 1142 AEKQK---RDLSEELEALKTELEDTLDTTATQQELRGSDYKDD 1181

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 53.3 bits (128), Expect = 2e-07
 Identities = 22/187 (11%), Positives = 69/187 (36%), Gaps = 7/187 (3%)

Query: 5    EYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRR 64
            E + LE+ V +      +++  +K   K + K E    + E   ++EE+ +    ++ +R
Sbjct: 1005 ERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQEL-EKIKR 1063

Query: 65   DEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERER 124
              + E+    ++  +        +    +     +E E +    R      ++    ++ 
Sbjct: 1064 KLEGESSDLHEQIAELQAQIAELKAQLAK-----KEEELQAALARLEDETSQKNNALKKI 1118

Query: 125  RERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERER 184
            RE      + + + + E+ + +++ +            + E E ++      + E     
Sbjct: 1119 RELESHISDLQEDLESEKAARNKAEKQKRDLSEELEALKTELE-DTLDTTATQQELRGSD 1177

Query: 185  ERELRER 191
             ++  ++
Sbjct: 1178 YKDDDDK 1184

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 51.8 bits (124), Expect = 5e-07
 Identities = 36/224 (16%), Positives = 80/224 (35%), Gaps = 13/224 (5%)

Query: 1    MEFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYR------KREDSEEEEEEE 54
             E + Y   E+       +KQ+ +    +   R E+ E   +      K+   +  + EE
Sbjct: 903  AETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEE 962

Query: 55   KSRSGKRSRRDEDEENGSRRDRDR---DRDRDKERHRRDRDRDRDRGRERERETERDRER 111
            +    + +R+    E  +   + +   D     E       ++R    ER  +   +   
Sbjct: 963  QLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAE 1022

Query: 112  SRERREK-EKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERES 170
              E+ +   K + + E    E E   +++ + R      +   +   S    +    +  
Sbjct: 1023 EEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQ 1082

Query: 171  ERERELELERERERERELRERERDLEMRESRRYKEKKEVVEPEA 214
              E + +L +   +E EL+     LE   S++    K++ E E+
Sbjct: 1083 IAELKAQLAK---KEEELQAALARLEDETSQKNNALKKIRELES 1123

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 49.4 bits (118), Expect = 3e-06
 Identities = 32/193 (16%), Positives = 80/193 (41%), Gaps = 3/193 (1%)

Query: 9    LEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDE 68
            +E  +EE+ ++ Q   +  KK  ++    E    + E + ++ + EK  +  + ++ ED+
Sbjct: 932  MEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDD 991

Query: 69   ENGSRRDRDRDRDRDK--ERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRE 126
                    ++     K  E    D   +     E+ +   + + +      + + R ++E
Sbjct: 992  ILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKE 1051

Query: 127  RRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESEREREL-ELERERERE 185
             + R++  + +R  E  SS    + +    + +    +  ++E E +  L  LE E  ++
Sbjct: 1052 EKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQK 1111

Query: 186  RELRERERDLEMR 198
                ++ R+LE  
Sbjct: 1112 NNALKKIRELESH 1124

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 49.1 bits (117), Expect = 4e-06
 Identities = 23/136 (16%), Positives = 60/136 (44%), Gaps = 4/136 (2%)

Query: 80  RDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERERD 139
           +   +E   + +D +  R +ER+++ E + +   ++  +  E +   +   + E E   +
Sbjct: 851 KVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAE 910

Query: 140 -GERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEMR 198
             E R    +++   +       +R E E E  ++ +     +++ ++++ + E  LE  
Sbjct: 911 AEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQ---AEKKKMQQQMLDLEEQLEEE 967

Query: 199 ESRRYKEKKEVVEPEA 214
           E+ R K + E V  + 
Sbjct: 968 EAARQKLQLEKVTADG 983

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 49.1 bits (117), Expect = 4e-06
 Identities = 28/189 (14%), Positives = 75/189 (39%), Gaps = 10/189 (5%)

Query: 36   KSERSYRKREDSEEEEEEEKSR-SGKRSRRDEDEENGSRRDRDRDRDRDKERHRRDRDRD 94
            K  R   + +  +EE +  K R     +   E E+  ++   +++  ++K +   +   +
Sbjct: 851  KVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAE 910

Query: 95   RDRGRERERETERDRERSR---ERREKEKERERRE-----RRDREKERERERDGERRSSS 146
             +  R R    +++ E      E R +E+E   ++     ++ +++  + E   E   ++
Sbjct: 911  AEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAA 970

Query: 147  RSRRSSSQSRRSSSRSRRERERESERERELELERERER-ERELRERERDLEMRESRRYKE 205
            R +    +        + E +     ++  +L +ER+  E  + +   +L   E +    
Sbjct: 971  RQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNL 1030

Query: 206  KKEVVEPEA 214
             K   + E+
Sbjct: 1031 TKLKNKHES 1039

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 47.5 bits (113), Expect = 1e-05
 Identities = 36/223 (16%), Positives = 86/223 (38%), Gaps = 11/223 (4%)

Query: 6    YEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRD 65
             E  +K   E ++ +Q      ++K   +EK +       ++EE      ++  +     
Sbjct: 870  KERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEIL 929

Query: 66   EDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRE------RSRERREKE 119
             + E   R + + +R +  +  ++   +      E+  E E  R+       + + + K+
Sbjct: 930  HEMEA--RIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKK 987

Query: 120  KERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELE-- 177
             E +     D+  +  +ER       S    + ++    +    + + +      ELE  
Sbjct: 988  MEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVR 1047

Query: 178  LERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQ 220
            L++E +  +EL + +R LE  ES    E+   ++ +    + Q
Sbjct: 1048 LKKEEKSRQELEKIKRKLE-GESSDLHEQIAELQAQIAELKAQ 1089

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 47.5 bits (113), Expect = 1e-05
 Identities = 33/213 (15%), Positives = 83/213 (38%), Gaps = 7/213 (3%)

Query: 9    LEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDE 68
            L++ ++ + +   + +    + A ++++ E    + E   EEEEE   +     ++ + +
Sbjct: 897  LQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQ 956

Query: 69   ENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREK-EKERERRER 127
                    +     ++E  R+    ++     + ++ E D     ++  K  KER+  E 
Sbjct: 957  MLDLEEQLE-----EEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEE 1011

Query: 128  RDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERE 187
            R  +       + E+  +    ++  +S  S    R ++E +S +E E    +      +
Sbjct: 1012 RVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSD 1071

Query: 188  LRERERDLEMRESRRYKEKKEVVEPEADPERDQ 220
            L E+  +L+  +    K +    E E      +
Sbjct: 1072 LHEQIAELQ-AQIAELKAQLAKKEEELQAALAR 1103

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 46.8 bits (111), Expect = 2e-05
 Identities = 19/121 (15%), Positives = 39/121 (32%)

Query: 88  RRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKERERERDGERRSSSR 147
           R   +                 + +R+  E + + E  +R    +++      E      
Sbjct: 829 RSFMNVXHWPWMXLFFXIXPLLKVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHT 888

Query: 148 SRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERERDLEMRESRRYKEKK 207
                    +   ++  E   E+E  R     +++E E  L E E  +E  E R  + + 
Sbjct: 889 QLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQA 948

Query: 208 E 208
           E
Sbjct: 949 E 949

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 50.0 bits (119), Expect = 8e-08
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE--TGQCKGFGFVQFAQLEHAKAA 379
           RK++VG L  ++ E ++   F  FGP+ +              KG+ F+ F +    +A 
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

Query: 380 QSA---LNGKL--EIVGRTLKVSSV 399
             A    +GKL   +   T+K   V
Sbjct: 69  IDACLEEDGKLYLCVSSPTIKDKPV 93

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 42.3 bits (99), Expect = 4e-05
 Identities = 16/91 (17%), Positives = 29/91 (31%), Gaps = 2/91 (2%)

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMD--RNSRRSKGVGYIEFYDVM 273
                R VF   +P    E ++   F + G +          ++    KG  ++ F +  
Sbjct: 4   GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63

Query: 274 SVPMAIALSGQLLLGQPVMVKPSEAEKNLVQ 304
           SV   I    +      + V     +   VQ
Sbjct: 64  SVQALIDACLEEDGKLYLCVSSPTIKDKPVQ 94

>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 = 8e-08
 Identities = 18/97 (18%), Positives = 41/97 (42%), Gaps = 16/97 (16%)

Query: 315 GPYGAIDRKLYVGNLHFN---------MTETQLRKLFEPFGPVELVQLPLDIETGQCKGF 365
           G +   ++ LYVG +              E+++R +F   G ++ ++        + K  
Sbjct: 128 GSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNC 181

Query: 366 GFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH 402
           GFV+F    +A+ A+ A++ +  ++  + K       
Sbjct: 182 GFVKFKYQANAEFAKEAMSNQ-TLLLPSDKEWDDRRE 217

>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 = 48.0 bits (114), Expect = 3e-07
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 8/78 (10%)

Query: 322 RKLYVGNL-HFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           R +++ NL H   +++ + KL EP+G ++   L       + K   F++    E A A  
Sbjct: 26  RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL------MRMKSQAFIEMETREDAMAMV 79

Query: 381 SALNGK-LEIVGRTLKVS 397
                K L   GR +KV 
Sbjct: 80  DHCLKKALWFQGRCVKVD 97

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 38.4 bits (89), Expect = 8e-04
 Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 9/80 (11%)

Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI---ALSGQLLLGQ 289
           ++  V +     GK+++  L+      R K   +IE          +           G+
Sbjct: 39  SDSAVLKLAEPYGKIKNYILM------RMKSQAFIEMETREDAMAMVDHCLKKALWFQGR 92

Query: 290 PVMVKPSEAEKNLVQSNTSA 309
            V V  SE  K LV   +S 
Sbjct: 93  CVKVDLSEKYKKLVSGPSSG 112

>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A {Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A* Length = 995

 Score = 50.8 bits (122), Expect = 1e-06
 Identities = 15/166 (9%), Positives = 47/166 (28%)

Query: 14  EEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSR 73
           + +  +++   + +       + +  +  K E    E    + +  K+      + N   
Sbjct: 828 KLRLIKREPFVAPAGLTPNEIDSTWSALEKAEQEHAEALRIELKRQKKIAVLLQKYNRIL 887

Query: 74  RDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRDREKE 133
           +  +            +   D     + + +     +   +  E +   +      +  E
Sbjct: 888 KKLENWATTKSVYLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTE 947

Query: 134 RERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELE 179
                  E      +  +   +   SS    +    +E ER  ++E
Sbjct: 948 LNYNGVPELTERKDTFFAQQWTGVKSSAETYKNTLLAELERLQKIE 993

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 46.0 bits (109), Expect = 2e-06
 Identities = 18/92 (19%), Positives = 28/92 (30%), Gaps = 4/92 (4%)

Query: 305 SNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKG 364
           S     G+      A   ++ + NL    +   L+ L               + T    G
Sbjct: 12  SGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDG 68

Query: 365 FGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
            G ++F   E    A   LN   E  G  + V
Sbjct: 69  TGALEFPSEEILVEALERLNNI-EFRGSVITV 99

>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 = 45.9 bits (109), Expect = 2e-06
 Identities = 16/92 (17%), Positives = 32/92 (34%), Gaps = 8/92 (8%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +   P    + ++ V  L  + +   L+      G V    +  D       G G 
Sbjct: 2   SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 54

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV 399
           V+F + E    A   L+   +      + + +
Sbjct: 55  VEFVRKEDMTYAVRKLDNT-KFRSHEGETAYI 85

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 7/79 (8%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L + NL   +    LR L    GP+      L+      +G    ++   E A  AQ AL
Sbjct: 10  LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN------QGIALCKYTTREEANKAQMAL 63

Query: 384 NGKLEIVGRTLKVSSVTDH 402
           N  + +   T+   S +++
Sbjct: 64  NNCV-LANTTIFAESPSEN 81

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 15/95 (15%)

Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVK--HIYVDKRSAGFVYLRF 552
              S  LLLKN+           D      +   C ++G +   H Y+++   G    ++
Sbjct: 4   AWGSSWLLLKNL-------TAQIDGP---TLRTLCMQHGPLVSFHPYLNQ---GIALCKY 50

Query: 553 ESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEA 587
            + E A  AQ A++    A   I A      + ++
Sbjct: 51  TTREEANKAQMALNNCVLANTTIFAESPSENEVQS 85

>2i1j_A Moesin; FERM, coiled-coil, C-ermad, ERM, radixin, ezrin, MER actin binding, masking, regulation, SELF-inhibition, cell A membrane protein; 2.10A {Spodoptera frugiperda} PDB: 2i1k_A 1e5w_A Length = 575

 Score = 46.8 bits (110), Expect = 2e-05
 Identities = 27/197 (13%), Positives = 69/197 (35%), Gaps = 3/197 (1%)

Query: 10  EKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEE 69
           +  +    +Q +   ++ ++  +R+ + +   ++ E+++  E  E+ +     R  ++E 
Sbjct: 362 QDMILRLEEQLRQLQAAKEELEQRQNELQAMMQRLEETKNMEAAERQKLEDEIRAKQEEV 421

Query: 70  NGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRD 129
           +   R +     +D E  R   + +  R ++ E         + +     +  +     D
Sbjct: 422 S---RIQQEVELKDSETRRLQEEVEDARRKQDEAAAALLAATTPQHHHVAERADTDPDHD 478

Query: 130 REKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELR 189
              +   E  G   +          + R +   R ER     +  + +L R  +  +E  
Sbjct: 479 NASDAGSESGGGDLARGPDDLVDPVADRRTLAERNERLHNQLKALKQDLARSCDETKETA 538

Query: 190 ERERDLEMRESRRYKEK 206
             +   E     R K K
Sbjct: 539 MDKIHRENVRQGRDKYK 555

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 43.1 bits (101), Expect = 2e-05
 Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 5/63 (7%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           L + N  + +T   L  +  P G V+ +     +   +      V+F  +  A+ A++AL
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQRI-----VIFKRNGIQAMVEFESVLCAQKAKAAL 82

Query: 384 NGK 386
           NG 
Sbjct: 83  NGA 85

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 44.4 bits (104), Expect = 2e-05
 Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 5   EYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRR 64
           E E + K  EEQR++ Q+ D++SK     +E  E++ +  E+  + + E+  ++ K + R
Sbjct: 83  EPESIRKWREEQRKRLQELDAASKVM--EQEWREKAKKDLEEWNQRQSEQVEKN-KINNR 139

Query: 65  DEDEENGSRRDRD 77
             D+    + D D
Sbjct: 140 IADKAFYQQPDAD 152

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 43.6 bits (102), Expect = 5e-05
 Identities = 13/70 (18%), Positives = 30/70 (42%), Gaps = 11/70 (15%)

Query: 83  DKERHRRDRDRDRDRGRERERETERDRERSRE-----------RREKEKERERRERRDRE 131
           + E  R+ R+  R R +E +  ++   +  RE           R+ ++ E+ +   R  +
Sbjct: 83  EPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIAD 142

Query: 132 KERERERDGE 141
           K   ++ D +
Sbjct: 143 KAFYQQPDAD 152

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 43.2 bits (101), Expect = 7e-05
 Identities = 13/84 (15%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 112 SRERREKEKERERRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESE 171
            R  +E E  R+ RE +   ++R +E D      S+      + +         + +  +
Sbjct: 78  DRLTQEPESIRKWREEQ---RKRLQELDAA----SKVMEQEWREKAKKDLEEWNQRQSEQ 130

Query: 172 RERELELERERERERELRERERDL 195
            E+     R  + +   ++ + D+
Sbjct: 131 VEKNKINNRIAD-KAFYQQPDADI 153

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 41.7 bits (97), Expect = 2e-04
 Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 3/76 (3%)

Query: 96  DRGRERERETERD-RERSRER-REKEKERERRERRDREKERERERDGERRSSSRSRRSSS 153
           DR  + E E+ R  RE  R+R +E +   +  E+  REK ++   +  +R S +  ++  
Sbjct: 78  DRLTQ-EPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKI 136

Query: 154 QSRRSSSRSRRERERE 169
            +R +     ++ + +
Sbjct: 137 NNRIADKAFYQQPDAD 152

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 40.1 bits (93), Expect = 7e-04
 Identities = 12/86 (13%), Positives = 36/86 (41%), Gaps = 10/86 (11%)

Query: 101 RERETERDRERSRERREKEKER-ERRERRDREKERERERDGERRSSSRSRRSSSQSRRSS 159
           +     ++ E  R+ RE++++R +  +   +  E+E     ++     ++R S Q     
Sbjct: 76  QADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQ----- 130

Query: 160 SRSRRERERESERERELELERERERE 185
                E+ + + R  +    ++ + +
Sbjct: 131 ----VEKNKINNRIADKAFYQQPDAD 152

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 46.1 bits (108), Expect = 3e-05
 Identities = 32/207 (15%), Positives = 76/207 (36%), Gaps = 5/207 (2%)

Query: 15  EQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEENGSRR 74
            +   K  D    K+ A + EK    + K+      +          S  +E+ + G   
Sbjct: 369 IRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSDRCSGLLQVIFSPLEEEVKAGIYS 428

Query: 75  DRDRDRDRDKERHRRDRDRDRDRGRERERETERDRE-RSRERREKEKERERRERRDREKE 133
                R   ++     +    +  +  + E       +S+E       +  +   ++EKE
Sbjct: 429 KPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKE 488

Query: 134 RERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELRERER 193
            E ER     + + ++      R++     ++     E  ++L  + E +R + L+E+ER
Sbjct: 489 IEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQER 548

Query: 194 DLEMRESRRYKEKKEVVEPEADPERDQ 220
            L      + +E++++++     E   
Sbjct: 549 TLA----LKLQEQEQLLKEGFQKESRI 571

>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 = 42.3 bits (99), Expect = 3e-05
 Identities = 20/95 (21%), Positives = 41/95 (43%), Gaps = 10/95 (10%)

Query: 311 GTATGPYGAIDRKLYVGNLHFNMTETQLRK----LFEPFGPVELVQLPLDIETGQCKGFG 366
           G++       D  + V N+ + ++  +L++     F   G V+ V+L    +    +   
Sbjct: 1   GSSGSSGNGAD--VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKA 55

Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD 401
            VQ   L+ A  A ++L+   +I  + + VS  T 
Sbjct: 56  VVQMENLQDAIGAVNSLHRY-KIGSKKILVSLATG 89

>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 = 41.8 bits (98), Expect = 5e-05
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 8/78 (10%)

Query: 322 RKLYVGNLHFNM-TETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           R +++ +         QL +L EPFG +       +          F++ A  E A+AA 
Sbjct: 16  RVVHIMDFQRGKNLRYQLLQLVEPFGVIS------NHLILNKINEAFIEMATTEDAQAAV 69

Query: 381 SALNGK-LEIVGRTLKVS 397
                    + G+ ++V 
Sbjct: 70  DYYTTTPALVFGKPVRVH 87

>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 = 41.3 bits (97), Expect = 9e-05
 Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 8/85 (9%)

Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
            P    + ++ V  L  + +   L+      G V    +  D       G G V+F + E
Sbjct: 10  PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKE 62

Query: 375 HAKAAQSALNGKLEIVGRTLKVSSV 399
               A   L+   +      + + +
Sbjct: 63  DMTYAVRKLDNT-KFRSHEGETAYI 86

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.1 bits (98), Expect = 5e-04
 Identities = 70/478 (14%), Positives = 143/478 (29%), Gaps = 132/478 (27%)

Query: 193 RDLEMRE----SRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVR 248
            + + ++     +    K+E+       +    T+  +   L   E  V +F  +  +  
Sbjct: 31  DNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLR-I 89

Query: 249 DVRLIMDRNSRRSKG-----VGYIEFYDVMSVPMAIALSGQLLLGQPVM-VKPSEAEKNL 302
           + + +M       +        YIE  D +          Q+     V  ++P    +  
Sbjct: 90  NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN------DNQVFAKYNVSRLQPYLKLRQA 143

Query: 303 VQSNTSAGGTAT-GPYGA------------------IDRKLY---VGNLH-----FNMTE 335
           +     A      G  G+                  +D K++   + N +       M +
Sbjct: 144 LLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQ 203

Query: 336 TQLRKLFEPF--GPVELVQLPLDIETGQCKGFGFVQFAQLEHA---------KAAQSALN 384
             L ++   +         + L I + Q +    ++    E+            A +A N
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN 263

Query: 385 GKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALL-------MQKL 437
              +I+  T +   VTD +    T   S    D     L    + ++LL        Q L
Sbjct: 264 LSCKIL-LTTRFKQVTDFLSAATTTHISL---DHHSMTLTP-DEVKSLLLKYLDCRPQDL 318

Query: 438 DRTGIATS------IAGSLGVAPA-------VNGSAVNQ-QAISL----P---------- 469
            R  + T+      IA S+    A       VN   +      SL    P          
Sbjct: 319 PREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL 378

Query: 470 VVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEEC 529
            V  P+  +P     ++              L+  ++    +++D          V  + 
Sbjct: 379 SVFPPSAHIP---TILL-------------SLIWFDV----IKSDVM-------VVVNKL 411

Query: 530 SKYGRV-KHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYE 586
            KY  V K     K S   +   +   +     + A+H     R ++   +  P+ ++
Sbjct: 412 HKYSLVEKQ---PKESTISIPSIYLELKVKLENEYALH-----RSIVDH-YNIPKTFD 460

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	591
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.96
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.95
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.95
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.95
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.95
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.95
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.94
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.94
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.94
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.94
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.94
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.94
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.94
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.93
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.93
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.93
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.93
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.93
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.93
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.93
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.92
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.92
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.9
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.82
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.82
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.79
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.78
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.77
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.76
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.72
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.72
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.71
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.7
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.7
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.69
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.69
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.68
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.68
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.68
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.68
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.68
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.67
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.67
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.67
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.67
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.67
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.67
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.67
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.66
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.66
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.66
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.66
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.66
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.66
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.66
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.66
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.66
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.66
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.66
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.66
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.66
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.66
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.66
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.65
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.65
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.65
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.65
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.65
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.65
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.65
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.65
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.65
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.65
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.65
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.65
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.65
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.65
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.65
2div_A	99	TRNA selenocysteine associated protein; structural	99.64
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.64
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.64
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.64
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.64
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.64
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.64
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.64
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.63
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.63
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.63
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.63
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.63
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.63
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.63
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.63
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.63
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.63
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.63
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.62
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.62
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.62
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.62
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.62
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.62
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.62
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.62
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.62
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.62
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.62
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.62
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.62
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.61
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.61
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.61
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.61
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.61
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.61
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.61
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.61
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.61
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.61
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.61
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.6
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.6
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.6
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.6
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.6
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.6
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.6
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.6
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.6
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.6
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.6
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.6
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.6
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.6
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.59
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.59
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.59
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.59
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.59
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.59
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.59
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.59
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.59
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.59
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.59
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.59
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.59
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.59
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.59
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.59
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.59
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.59
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.58
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.58
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.58
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.58
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.58
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.58
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.58
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.58
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.58
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.58
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.57
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.57
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.57
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.57
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.57
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.57
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.57
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.57
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.57
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.57
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.57
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.57
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.57
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.56
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.56
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.56
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.56
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.56
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.56
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.56
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.56
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.56
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.56
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.56
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.56
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.56
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.56
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.56
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.55
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.55
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.55
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.55
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.55
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.55
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.55
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.55
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.55
2div_A	99	TRNA selenocysteine associated protein; structural	99.55
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.55
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.55
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.54
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.54
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.54
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.54
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.54
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.54
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.54
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.54
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.54
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.54
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.54
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.53
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.53
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.53
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.53
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.53
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.53
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.53
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.53
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.53
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.53
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.52
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.52
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.52
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.52
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.52
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.52
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.52
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.52
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.52
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.52
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.52
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.52
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.52
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.52
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.52
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.52
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.52
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.52
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.51
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.27
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.51
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.51
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.51
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.51
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.51
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.51
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.51
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.51
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.51
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.5
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.5
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.5
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.5
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.5
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.5
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.5
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.5
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.5
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.5
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.5
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.5
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.5
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.5
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.5
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.5
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.5
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.5
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.49
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.49
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.49
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.49
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.49
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.49
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.48
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.48
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.48
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.48
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.48
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.48
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.48
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.47
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.47
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.47
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.47
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.47
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.47
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.47
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.47
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.47
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.46
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.46
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.46
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.46
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.46
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.46
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.46
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.46
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.45
1x5p_A	97	Negative elongation factor E; structure genomics,	99.45
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.45
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.45
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.45
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.45
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.45
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.45
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.45
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.44
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.44
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.44
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.44
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.44
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.43
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.43
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.42
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.42
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.42
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.42
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.42
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.41
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.41
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.41
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.41
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.41
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.41
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.41
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.4
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.4
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.4
1x5p_A	97	Negative elongation factor E; structure genomics,	99.4
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.39
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.38
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.37
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.37
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.36
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.36
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.36
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.35
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.35
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.35
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.34
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.32
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.31
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.28
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.28
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.27
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.26
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.23
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.22
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.17
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.17
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.15
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.14
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.09
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.09
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.98
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.92
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.82
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.76
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.74
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.6
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.55
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.46
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.37
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.87
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.77
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.3
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.2
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.07
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.04
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.9
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.67
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.54
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.51
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.49
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.42
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.0
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.33
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.43
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	93.87
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	93.33
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	91.96

>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=2.3e-39  Score=319.89  Aligned_cols=240  Identities=24%  Similarity=0.305  Sum_probs=213.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +.++|||+|||+.+|+++|.++|..|| |..|.+      +.++|||||+|.+.++|..|+ .+||..|.|+.|.|.+..
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~   93 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP   93 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC
Confidence            458999999999999999999999999 988887      457899999999999999999 699999999999998743


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHH
Q 007742          298 AEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK  377 (591)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~  377 (591)
                      .                      ..+|||+|||+.+++++|.++|..||.|..|.++.+..++.++|||||+|.+.++|.
T Consensus        94 ~----------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~  151 (284)
T 3smz_A           94 T----------------------DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAA  151 (284)
T ss_dssp             C----------------------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             C----------------------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHH
Confidence            1                      269999999999999999999999999999999998889999999999999999999


Q ss_pred             HHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCccc
Q 007742          378 AAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVN  457 (591)
Q Consensus       378 ~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  457 (591)
                      .|+..|+|. .|.|+.|.|.++......                                                    
T Consensus       152 ~A~~~l~~~-~~~g~~i~v~~a~~~~~~----------------------------------------------------  178 (284)
T 3smz_A          152 RAKSDLLGK-PLGPRTLYVHWTDAGQLT----------------------------------------------------  178 (284)
T ss_dssp             HHHHHHTTC-EETTEECEEEECCGGGCC----------------------------------------------------
T ss_pred             HHHHHhCCC-EeCCcEEEEEECCCCCCC----------------------------------------------------
Confidence            999999996 699999999987431000                                                    


Q ss_pred             CccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCC-CCchhhhhHHHHHHHHhccccceE
Q 007742          458 GSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAME-TDPDFDLEIQGDVEEECSKYGRVK  536 (591)
Q Consensus       458 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~-~~~~~~~~~~edl~~~f~~~G~V~  536 (591)
                                                         ....+..+|+|.||  |..+ +        +++|.++|+.||.|.
T Consensus       179 -----------------------------------~~~~~~~~l~v~nl--p~~~~~--------~~~l~~~f~~~G~i~  213 (284)
T 3smz_A          179 -----------------------------------PALLHSRCLCVDRL--PPGFND--------VDALCRALSAVHSPT  213 (284)
T ss_dssp             -----------------------------------TTTTSCSEEEEECC--CTTCCC--------HHHHHHHTCSSSCCS
T ss_pred             -----------------------------------cccCCccEEEEecC--CcccCC--------HHHHHHHhhCCCCeE
Confidence                                               01134568999999  7774 6        899999999999999


Q ss_pred             EEEEecC----CCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchhh
Q 007742          537 HIYVDKR----SAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDY  585 (591)
Q Consensus       537 ~v~l~~~----~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  585 (591)
                      .+.|..+    ++|+|||+|.+.++|.+|+..|||..|+|+.|.|.|+.+...
T Consensus       214 ~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          214 FCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             EEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             EEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            9988654    478999999999999999999999999999999999987654

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=100.00  E-value=1.5e-39  Score=322.57  Aligned_cols=246  Identities=18%  Similarity=0.284  Sum_probs=208.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      ....++|||+|||+.+|+++|.++|..||.|..|.++.+..+  ++|||||+|.+.++|..|+.++|..+.|+.|.|.++
T Consensus        38 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~  115 (292)
T 2ghp_A           38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL  115 (292)
T ss_dssp             ----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEEC
Confidence            345799999999999999999999999999999999998754  589999999999999999999999999999999875


Q ss_pred             ccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeccCCCCCcccEEEEEeCCHHH
Q 007742          297 EAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG-PVELVQLPLDIETGQCKGFGFVQFAQLEH  375 (591)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~v~i~~~~~~~~~~g~a~Vef~~~~~  375 (591)
                      .                       ..+|||+|||+.+++++|.++|..|| .|..|.++.+. .+.++|||||+|.+.++
T Consensus       116 ~-----------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~  171 (292)
T 2ghp_A          116 T-----------------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKED  171 (292)
T ss_dssp             C-----------------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHH
T ss_pred             C-----------------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHH
Confidence            2                       27999999999999999999999999 99999998876 47789999999999999


Q ss_pred             HHHHHHHhcCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCc
Q 007742          376 AKAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPA  455 (591)
Q Consensus       376 a~~a~~~l~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  455 (591)
                      |..|+..|+|. .|.|+.|.|.++.+.......                                               
T Consensus       172 a~~A~~~l~g~-~~~g~~l~v~~a~~~~~~~~~-----------------------------------------------  203 (292)
T 2ghp_A          172 ARYCVEKLNGL-KIEGYTLVTKVSNPLEKSKRT-----------------------------------------------  203 (292)
T ss_dssp             HHHHHHHHTTC-EETTEECEEEECCCC-----------------------------------------------------
T ss_pred             HHHHHHHhCCC-EeCCcEEEEEECCCCcccccc-----------------------------------------------
Confidence            99999999996 699999999987532110000                                               


Q ss_pred             ccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCC-CCCchhhhhHHHHHHHHhccccc
Q 007742          456 VNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAM-ETDPDFDLEIQGDVEEECSKYGR  534 (591)
Q Consensus       456 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~-~~~~~~~~~~~edl~~~f~~~G~  534 (591)
                                                          .....+..+|+|.||  |.. ++        +++|.++|+.||.
T Consensus       204 ------------------------------------~~~~~~~~~l~v~nl--p~~~~t--------~~~l~~~F~~~G~  237 (292)
T 2ghp_A          204 ------------------------------------DSATLEGREIMIRNL--STELLD--------ENLLRESFEGFGS  237 (292)
T ss_dssp             ---------------------------------------CCTTTEEEEEEE--CTTTCC--------HHHHHHHHGGGSC
T ss_pred             ------------------------------------cccCCCCceEEEECC--CcccCC--------HHHHHHHHhccCC
Confidence                                                001245568999999  877 77        8999999999999


Q ss_pred             eEEEEEec------CCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          535 VKHIYVDK------RSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       535 V~~v~l~~------~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      |..|.|..      .++|+|||+|.+.++|.+|+ .|||..|+|+.|.|.|+.++
T Consensus       238 v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          238 IEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             EEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             eeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            99998853      35799999999999999999 99999999999999999865

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.97  E-value=1.1e-30  Score=245.72  Aligned_cols=168  Identities=26%  Similarity=0.405  Sum_probs=149.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|+++|.+||.|.+|.|+.++.+|.++|||||+|.+.++|..|| .+|+..+.|+.|.+.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            445689999999999999999999999999999999999999999999999999999999999 6999999999999988


Q ss_pred             CccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHH
Q 007742          296 SEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH  375 (591)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~  375 (591)
                      +..........              ..+|||+|||+.+++++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++
T Consensus        92 ~~~~~~~~~~~--------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~  155 (213)
T 4f02_A           92 SQRDPSLRKSG--------------VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEA  155 (213)
T ss_dssp             CCCCTHHHHHC--------------TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHH
T ss_pred             ccccccccccc--------------cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHH
Confidence            76543322221              2689999999999999999999999999999999874  4579999999999999


Q ss_pred             HHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          376 AKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       376 a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      |.+|+..|||. .|.|+.|.|.++.+
T Consensus       156 a~~Ai~~lng~-~~~g~~i~V~~a~~  180 (213)
T 4f02_A          156 AERAIEKMNGM-LLNDRKVFVGRFKS  180 (213)
T ss_dssp             HHHHHHHHTTC-EETTEECEEEECCC
T ss_pred             HHHHHHHhCCC-EECCEEEEEEEcCC
Confidence            99999999996 69999999998754

>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=99.97  E-value=8.4e-30  Score=236.91  Aligned_cols=176  Identities=21%  Similarity=0.392  Sum_probs=151.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      ....++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|.+||.+++..|.|+.|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA   89 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecc
Confidence            34569999999999999999999999999999999999999999999999999999999999988999999999999987


Q ss_pred             ccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHH
Q 007742          297 EAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHA  376 (591)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a  376 (591)
                      .........          .......+|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|
T Consensus        90 ~~~~~~~~~----------~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A  159 (196)
T 1l3k_A           90 VSREDSQRP----------GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV  159 (196)
T ss_dssp             CC---------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             cCccccccc----------ccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHH
Confidence            654322111          1122348999999999999999999999999999999999988899999999999999999


Q ss_pred             HHHHHHhcCCeeeCCeEEEEEEecCCCC
Q 007742          377 KAAQSALNGKLEIVGRTLKVSSVTDHVG  404 (591)
Q Consensus       377 ~~a~~~l~g~~~~~g~~l~v~~~~~~~~  404 (591)
                      .+|+.. +|. .|.|+.|.|.++.+...
T Consensus       160 ~~A~~~-~~~-~~~G~~i~v~~a~~k~~  185 (196)
T 1l3k_A          160 DKIVIQ-KYH-TVNGHNCEVRKALSKQE  185 (196)
T ss_dssp             HHHHHC-SCC-EETTEECEEEECC----
T ss_pred             HHHHHh-CCc-EECCEEEEEEecCChhH
Confidence            999965 775 79999999999876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.97  E-value=1.7e-29  Score=228.14  Aligned_cols=164  Identities=21%  Similarity=0.469  Sum_probs=149.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      ++|||+|||+.+|+++|.++|..||.|..|.++.++. |.++|||||+|.+.++|..|+ .++|..+.|+.|.|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            5899999999999999999999999999999999875 779999999999999999999 79999999999999987543


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHH
Q 007742          300 KNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA  379 (591)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a  379 (591)
                      ..              .......+|+|+|||..+++++|+++|++||.|..+.++.+..++.++|+|||+|.+.++|..|
T Consensus        80 ~~--------------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A  145 (166)
T 3md3_A           80 QQ--------------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA  145 (166)
T ss_dssp             CC--------------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHH
T ss_pred             CC--------------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHH
Confidence            32              1122347999999999999999999999999999999999988899999999999999999999


Q ss_pred             HHHhcCCeeeCCeEEEEEEec
Q 007742          380 QSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       380 ~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +..|||. .|.|+.|.|.+++
T Consensus       146 ~~~l~g~-~~~g~~i~v~~a~  165 (166)
T 3md3_A          146 MDSMQGQ-DLNGRPLRINWAA  165 (166)
T ss_dssp             HHHHTTC-EETTEECEEEESC
T ss_pred             HHHhCCC-ccCCcEEEEEecC
Confidence            9999997 6999999999874

>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=99.97  E-value=1.4e-29  Score=229.17  Aligned_cols=164  Identities=27%  Similarity=0.430  Sum_probs=150.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +.++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|..|+ .++|..+.|+.|.|.++.
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            3589999999999999999999999999999999999999999999999999999999999 599999999999999886


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHH
Q 007742          298 AEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK  377 (591)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~  377 (591)
                      +...                .....+|+|.|||..+++++|+++|++||.|..+.++.+..++.++|+|||+|.+.++|.
T Consensus        82 ~~~~----------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~  145 (168)
T 1b7f_A           82 PGGE----------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ  145 (168)
T ss_dssp             CCSS----------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCcc----------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHH
Confidence            4322                122479999999999999999999999999999999998878999999999999999999


Q ss_pred             HHHHHhcCCeeeCC--eEEEEEEe
Q 007742          378 AAQSALNGKLEIVG--RTLKVSSV  399 (591)
Q Consensus       378 ~a~~~l~g~~~~~g--~~l~v~~~  399 (591)
                      .|+..|||. .|.|  ++|.|.++
T Consensus       146 ~A~~~l~g~-~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          146 EAISALNNV-IPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHTTC-CCTTCSSCCEEEEC
T ss_pred             HHHHHhcCC-EecCCCeEEEEEeC
Confidence            999999997 6877  99999874

>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=99.97  E-value=2.8e-29  Score=226.91  Aligned_cols=163  Identities=26%  Similarity=0.461  Sum_probs=149.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      .++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|..|+ .++|..+.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            489999999999999999999999999999999999989999999999999999999999 5999999999999998865


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA  378 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~  378 (591)
                      ....                ....+|+|+|||..+++++|+++|++||.|..+.++.+..++.++|+|||+|.+.++|..
T Consensus        82 ~~~~----------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~  145 (167)
T 1fxl_A           82 SSAS----------------IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE  145 (167)
T ss_dssp             CCGG----------------GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             Cccc----------------CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHH
Confidence            4321                123789999999999999999999999999999999988789999999999999999999


Q ss_pred             HHHHhcCCeeeCCeE--EEEEEe
Q 007742          379 AQSALNGKLEIVGRT--LKVSSV  399 (591)
Q Consensus       379 a~~~l~g~~~~~g~~--l~v~~~  399 (591)
                      |+..|||. .|.|+.  |.|.|+
T Consensus       146 A~~~l~g~-~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          146 AIKGLNGQ-KPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHTTC-CCTTCSSCCEEEEC
T ss_pred             HHHHhcCC-ccCCCccceEEEeC
Confidence            99999997 699964  888764

>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=99.96  E-value=1.1e-29  Score=229.59  Aligned_cols=164  Identities=23%  Similarity=0.435  Sum_probs=149.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      ++++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|..|+. ++..+.|+.|.|.++..
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCEETTEECCCEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh-cccccCCeEcccccccc
Confidence            45899999999999999999999999999999999999999999999999999999999997 36789999999988765


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA  378 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~  378 (591)
                      ......                ..+|||+|||..+++++|.++|++||.|..|.++.+..++.++|||||+|.+.++|..
T Consensus        81 ~~~~~~----------------~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~  144 (167)
T 2cjk_A           81 RDEQDK----------------TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR  144 (167)
T ss_dssp             HHHHHH----------------CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHH
T ss_pred             hhhccC----------------CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHH
Confidence            433211                2689999999999999999999999999999999988789999999999999999999


Q ss_pred             HHHHhcCCeeeCCeEEEEEEecC
Q 007742          379 AQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       379 a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      |++ ++|. .|.|+.|.|.++.+
T Consensus       145 A~~-~~~~-~~~g~~i~V~~a~p  165 (167)
T 2cjk_A          145 VCQ-NKFI-DFKDRKIEIKRAEP  165 (167)
T ss_dssp             HHH-CSEE-CSSSSCEEEEECCC
T ss_pred             HHh-CCCE-EeCCeEEEEeecCC
Confidence            996 8884 79999999999865

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.96  E-value=2.5e-29  Score=237.52  Aligned_cols=177  Identities=19%  Similarity=0.374  Sum_probs=151.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~~~~  298 (591)
                      .++|||+|||+.+|+++|+++|..||.|..|.++.+..+|.++|||||+|.+.++|..||. |++..|.|+.|.|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            4899999999999999999999999999999999999899999999999999999999995 999999999999987654


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA  378 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~  378 (591)
                      ...........     ........+|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|..
T Consensus       108 ~~~~~~~~~~~-----~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~  182 (216)
T 2qfj_A          108 IGQAQPIIDQL-----AEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQD  182 (216)
T ss_dssp             CGGGHHHHHHH-----HHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             ccccchhhhhh-----hcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHH
Confidence            33211100000     0001123799999999999999999999999999999999998889999999999999999999


Q ss_pred             HHHHhcCCeeeCCeEEEEEEecCC
Q 007742          379 AQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       379 a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      |+..|||. .|.|+.|.|.++...
T Consensus       183 A~~~l~g~-~~~g~~i~V~~a~~~  205 (216)
T 2qfj_A          183 AVSSMNLF-DLGGQYLRVGKAVTP  205 (216)
T ss_dssp             HHHHHTTC-BCSSSBCEEEECSSC
T ss_pred             HHHHccCC-EeCCcEEEEEEecCC
Confidence            99999996 699999999998754

>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=99.96  E-value=2.6e-28  Score=222.38  Aligned_cols=165  Identities=29%  Similarity=0.489  Sum_probs=144.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCC--CccceEEEEecCcchHHHHH-HHcCCccC---CeeEE
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSR--RSKGVGYIEFYDVMSVPMAI-ALSGQLLL---GQPVM  292 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g--~~~G~afV~F~~~e~A~~Al-~l~g~~i~---g~~i~  292 (591)
                      ++++|||+|||+.+|+++|.++|.+||.|..|.++.+..+|  .++|||||+|.+.++|..|+ .|++..+.   +..+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            46899999999999999999999999999999999999887  89999999999999999999 59998876   57777


Q ss_pred             eccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCC
Q 007742          293 VKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ  372 (591)
Q Consensus       293 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~  372 (591)
                      +.++......               .....+|||+|||..+++++|+++|++||.|..|.++.+. ++.++|||||+|.+
T Consensus        82 ~~~~~~~~~~---------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~  145 (175)
T 3nmr_A           82 MKPADSEKNN---------------AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTT  145 (175)
T ss_dssp             EEECGGGCCS---------------CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESS
T ss_pred             Eccccccccc---------------cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECC
Confidence            7766543321               1124799999999999999999999999999999999886 68899999999999


Q ss_pred             HHHHHHHHHHhcCCeeeC--CeEEEEEEe
Q 007742          373 LEHAKAAQSALNGKLEIV--GRTLKVSSV  399 (591)
Q Consensus       373 ~~~a~~a~~~l~g~~~~~--g~~l~v~~~  399 (591)
                      .++|..|+..|||...+.  |++|.|.++
T Consensus       146 ~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          146 RAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             HHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            999999999999964344  499999886

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.96  E-value=4.5e-28  Score=227.73  Aligned_cols=166  Identities=25%  Similarity=0.336  Sum_probs=145.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +.++|||+|||+.+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|..|+..|++. .+.|+.|.+.++
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~-~~~g~~i~~~~~   92 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFD-VIKGKPVRIMWS   92 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhh-hcCCcccccccc
Confidence            3579999999999999999999999999999999999889999999999999999999999999997 699999999876


Q ss_pred             cCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCC
Q 007742          400 TDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVP  479 (591)
Q Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  479 (591)
                      .....                       .                                                   
T Consensus        93 ~~~~~-----------------------~---------------------------------------------------   98 (213)
T 4f02_A           93 QRDPS-----------------------L---------------------------------------------------   98 (213)
T ss_dssp             CCCTH-----------------------H---------------------------------------------------
T ss_pred             ccccc-----------------------c---------------------------------------------------
Confidence            32100                       0                                                   


Q ss_pred             CCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC---CCeeEEEEeCCHH
Q 007742          480 AVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR---SAGFVYLRFESTE  556 (591)
Q Consensus       480 ~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~---~~g~afV~F~~~e  556 (591)
                                    .......|+|.||  |..++        +++|.++|+.||.|..|.|..+   ++|+|||+|.+.+
T Consensus        99 --------------~~~~~~~l~v~nl--~~~~t--------~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~  154 (213)
T 4f02_A           99 --------------RKSGVGNIFIKNL--DKSID--------NKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQE  154 (213)
T ss_dssp             --------------HHHCTTEEEEESC--CTTCC--------HHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHH
T ss_pred             --------------cccccccceECCc--ccccH--------HHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHH
Confidence                          0012346999999  88888        8999999999999999988543   5799999999999


Q ss_pred             HHHHHHHHhcccccCCeEEEEEEeCchh
Q 007742          557 AAASAQRAMHMRWFARRLISAIFMKPED  584 (591)
Q Consensus       557 ~A~~A~~~l~g~~~~g~~l~v~~~~~~~  584 (591)
                      +|.+|+..|||..|+|+.|.|.|+.++.
T Consensus       155 ~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          155 AAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             HHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            9999999999999999999999998653

>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=99.95  E-value=9.6e-27  Score=229.15  Aligned_cols=247  Identities=15%  Similarity=0.259  Sum_probs=152.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLR----KLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRT  393 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~----~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~  393 (591)
                      ..++++|||+|||..+++++|+    ++|..||.|..|.|..   ++.++|||||+|.+.++|..|+..|||. .|.|+.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~   81 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGF-PFYDKP   81 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCC-eeCCcE
Confidence            3446899999999999999966    9999999999998875   6778999999999999999999999996 799999


Q ss_pred             EEEEEecCCCCCCcccccCCCCCCCCC--CCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcC
Q 007742          394 LKVSSVTDHVGTQDTAAKSADFDDDDG--GGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVV  471 (591)
Q Consensus       394 l~v~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  471 (591)
                      |.|.++............  .......  ..............................+........... ........
T Consensus        82 l~v~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~  158 (282)
T 3pgw_A           82 MRIQYAKTDSDIIAKMKG--TFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQA-PRIMHHMP  158 (282)
T ss_pred             EEEEEeccCcchhhhhcC--CcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCccccc-ccccccCC
Confidence            999998654421111100  0000000  000000000000000000000000000000000000000000 00000000


Q ss_pred             CCCCC----------------------CCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHh
Q 007742          472 GQPAV----------------------PVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEEC  529 (591)
Q Consensus       472 ~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f  529 (591)
                      |..+.                      ..........+.........++++|+|.||  |..++        +++|+++|
T Consensus       159 g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl--~~~~~--------~~~l~~~F  228 (282)
T 3pgw_A          159 GQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNL--PEETN--------ELMLSMLF  228 (282)
T ss_pred             CCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCC--CCcCC--------HHHHHHHH
Confidence            00000                      000000001111112234567789999999  87777        89999999


Q ss_pred             ccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccC-CeEEEEEEeC
Q 007742          530 SKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFA-RRLISAIFMK  581 (591)
Q Consensus       530 ~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~-g~~l~v~~~~  581 (591)
                      +.||.|..|.|....+|+|||+|.+.++|.+|+..|||..|+ |+.|.|.|++
T Consensus       229 ~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          229 NQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             HhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            999999999998777799999999999999999999999999 9999999986

>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=99.95  E-value=8.2e-28  Score=218.42  Aligned_cols=158  Identities=26%  Similarity=0.513  Sum_probs=142.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcC----C-------CeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccC
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKA----G-------KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLL  287 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~----G-------~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~  287 (591)
                      +.++|||+|||+.+|+++|.++|.+|    |       .|..+.+.      .++|||||+|.+.++|.+|+.+||..+.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~~~~~~~~~   76 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAMAFDGIIFQ   76 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHGGGTTCEET
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHHHhCCcEec
Confidence            46899999999999999999999999    6       77777664      4589999999999999999999999999


Q ss_pred             CeeEEeccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEE
Q 007742          288 GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF  367 (591)
Q Consensus       288 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~  367 (591)
                      |++|.|.++......                ....+|+|+|||..+++++|+++|++||.|..|.++.+..++.++|+||
T Consensus        77 g~~i~v~~~~~~~~~----------------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~af  140 (172)
T 2g4b_A           77 GQSLKIRRPHDYQPL----------------PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF  140 (172)
T ss_dssp             TEECEEECCSSCCCC----------------TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEE
T ss_pred             CceeeecCCcccCCC----------------CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEE
Confidence            999999876543211                1148999999999999999999999999999999999987899999999


Q ss_pred             EEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       368 Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      |+|.+.++|..|+..|||. .|.|+.|.|.++
T Consensus       141 V~f~~~~~A~~A~~~l~g~-~~~g~~l~V~~A  171 (172)
T 2g4b_A          141 CEYVDINVTDQAIAGLNGM-QLGDKKLLVQRA  171 (172)
T ss_dssp             EEESSTTHHHHHHHHHTTC-EETTEECEEEEC
T ss_pred             EEeCCHHHHHHHHHHcCCC-EECCeEEEEEeC
Confidence            9999999999999999996 699999999986

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.95  E-value=2.5e-27  Score=220.57  Aligned_cols=177  Identities=24%  Similarity=0.454  Sum_probs=147.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcC----C-------CeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccC
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKA----G-------KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLL  287 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~----G-------~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~  287 (591)
                      .+++|||+|||+.+|+++|.++|..|    |       .|..+.+      +.++|||||+|.+.++|.+||.|||..|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAMAFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHGGGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHHHhcCCEEc
Confidence            46899999999999999999999999    5       5666655      45689999999999999999999999999


Q ss_pred             CeeEEeccCccccccccccCCC----CCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcc
Q 007742          288 GQPVMVKPSEAEKNLVQSNTSA----GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK  363 (591)
Q Consensus       288 g~~i~v~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~  363 (591)
                      |+.|.|.++.............    .............+|||+|||..+++++|+++|++||.|..|.++.+..++.++
T Consensus        77 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~  156 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK  156 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEE
T ss_pred             CceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcc
Confidence            9999999876543221111100    011111222446899999999999999999999999999999999988789999


Q ss_pred             cEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       364 g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      |||||+|.+.++|..|+..|||. .|.|+.|.|.++.+.
T Consensus       157 g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~a~~~  194 (198)
T 2yh0_A          157 GYAFCEYVDINVTDQAIAGLNGM-QLGDKKLLVQRASVG  194 (198)
T ss_dssp             EEEEEEESSSSHHHHHHHHHTTC-EETTEECEEEESCCC
T ss_pred             eEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEECCCC
Confidence            99999999999999999999996 699999999998653

>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=99.95  E-value=1.8e-28  Score=223.46  Aligned_cols=166  Identities=20%  Similarity=0.348  Sum_probs=143.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEecc
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP  295 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~  295 (591)
                      .....++|||+|||+.+|+++|+++|..||.+.. .++.+..+|.++|||||+|.+.++|.+||+|||..|.|++|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEec
Confidence            3456799999999999999999999999998766 344555678899999999999999999999999999999999998


Q ss_pred             CccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHH
Q 007742          296 SEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH  375 (591)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~  375 (591)
                      +......              ......+|||+|||..+++++|+++|++||.|..+     ..++.++|||||+|.+.++
T Consensus        88 ~~~~~~~--------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~  148 (175)
T 1fje_B           88 PKGRDSK--------------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEAD  148 (175)
T ss_dssp             CCCSSCS--------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHH
T ss_pred             CCCcccc--------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHH
Confidence            8654321              11234899999999999999999999999988766     3478889999999999999


Q ss_pred             HHHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          376 AKAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       376 a~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      |..|+..|||. .|.|+.|.|.++.++
T Consensus       149 A~~A~~~l~g~-~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          149 AEKNLEEKQGA-EIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHHHHHTEE-EETTEEEEEEECSSC
T ss_pred             HHHHHHHhCCC-EECCeEEEEEecCCC
Confidence            99999999995 799999999998653

>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=99.95  E-value=1.2e-26  Score=228.78  Aligned_cols=169  Identities=22%  Similarity=0.266  Sum_probs=153.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||+.+|+++|.++|..||.|..|.++.+..+|.++|||||+|.+.++|..|+ .|+|..|.|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            4589999999999999999999999999999999999999999999999999999999999 799999999999999987


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEcCCCCCC-CHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHH
Q 007742          298 AEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNM-TETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHA  376 (591)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~-~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a  376 (591)
                      ......             ......+|||.|||..+ ++++|+++|+.||.|..|.|+.+. +|.++|+|||+|.+.++|
T Consensus       174 ~~~~~~-------------~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A  239 (284)
T 3smz_A          174 AGQLTP-------------ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMA  239 (284)
T ss_dssp             GGGCCT-------------TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHH
T ss_pred             CCCCCc-------------ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHH
Confidence            643221             11234899999999995 999999999999999999999886 888999999999999999


Q ss_pred             HHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          377 KAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       377 ~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      ..|+..|||. .|.|+.|.|.++.+.
T Consensus       240 ~~A~~~l~g~-~~~g~~l~v~~a~~~  264 (284)
T 3smz_A          240 EEAQQQADGL-SLGGSHLRVSFCAPG  264 (284)
T ss_dssp             HHHHHHHTTC-EETTEECEEEECCSS
T ss_pred             HHHHHHhCCC-ccCCeEEEEEEecCC
Confidence            9999999996 699999999998653

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.95  E-value=1.4e-26  Score=208.99  Aligned_cols=161  Identities=22%  Similarity=0.307  Sum_probs=141.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||..+++++|+++|++||.|..|.++.+. .+.++|||||+|.+.++|..|+..|+|. .+.|+.|.|.++..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~-~~~g~~i~v~~~~~   78 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGK-QIENNIVKINWAFQ   78 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCC-ccCCCeeEEEEcCC
Confidence            579999999999999999999999999999999886 5778999999999999999999999996 69999999998743


Q ss_pred             CCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCC
Q 007742          402 HVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAV  481 (591)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (591)
                      ...                                                                             
T Consensus        79 ~~~-----------------------------------------------------------------------------   81 (166)
T 3md3_A           79 SQQ-----------------------------------------------------------------------------   81 (166)
T ss_dssp             CCC-----------------------------------------------------------------------------
T ss_pred             CCC-----------------------------------------------------------------------------
Confidence            110                                                                             


Q ss_pred             CCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----CCeeEEEEeCCHH
Q 007742          482 TAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----SAGFVYLRFESTE  556 (591)
Q Consensus       482 ~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~~g~afV~F~~~e  556 (591)
                                 ....++.+|+|.||  |..++        +++|.++|+.||.|..+.+..+     ++|+|||+|.+.+
T Consensus        82 -----------~~~~~~~~l~v~nl--~~~~t--------~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~  140 (166)
T 3md3_A           82 -----------SSSDDTFNLFVGDL--NVNVD--------DETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQD  140 (166)
T ss_dssp             -----------CCCTTCEEEEEESC--CTTCC--------HHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHH
T ss_pred             -----------CCCCCCceEEECCC--CCCCC--------HHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHH
Confidence                       01234568999999  88887        8999999999999999988533     4789999999999


Q ss_pred             HHHHHHHHhcccccCCeEEEEEEeCc
Q 007742          557 AAASAQRAMHMRWFARRLISAIFMKP  582 (591)
Q Consensus       557 ~A~~A~~~l~g~~~~g~~l~v~~~~~  582 (591)
                      +|.+|+..|||..|+|+.|.|.|+.+
T Consensus       141 ~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          141 DAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             HHHHHHHHhCCCccCCcEEEEEecCC
Confidence            99999999999999999999999864

>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=99.95  E-value=7.5e-27  Score=216.78  Aligned_cols=173  Identities=17%  Similarity=0.231  Sum_probs=139.0

Q ss_pred             CCcEEEEeCCC-CCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          219 DQRTVFAYQMP-LKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       219 ~~~~l~V~nLp-~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ++++|||+||| +.+|+++|.++|..||.|..|.++.+     .+|||||+|.+.++|..|| .|||..+.|++|.|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            46899999999 89999999999999999999999865     4799999999999999999 69999999999999987


Q ss_pred             cccccccccc------CC------CC-CC--------CCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCe--eEEEE
Q 007742          297 EAEKNLVQSN------TS------AG-GT--------ATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPV--ELVQL  353 (591)
Q Consensus       297 ~~~~~~~~~~------~~------~~-~~--------~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i--~~v~i  353 (591)
                      ..........      .+      .. ..        ......+++.+|||.|||+.+++++|+++|++||.|  ..|.+
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~  157 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV  157 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEE
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE
Confidence            6432211000      00      00 00        000112446799999999999999999999999998  88988


Q ss_pred             eccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCe----EEEEEEe
Q 007742          354 PLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGR----TLKVSSV  399 (591)
Q Consensus       354 ~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~----~l~v~~~  399 (591)
                      +.+.  +..+|+|||+|.+.++|..||..|||. .|.|.    ++.|.++
T Consensus       158 ~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~-~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          158 FSGK--SERSSSGLLEWDSKSDALETLGFLNHY-QMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CSCC--SSSSEEEEEECSSHHHHHHHHHHHTTC-EECCSSSSSCEECEEE
T ss_pred             EcCC--CCCceEEEEEeCCHHHHHHHHHHhCCC-CccCCCCCcceEEEec
Confidence            8764  445699999999999999999999996 68876    5655543

>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=99.95  E-value=2.2e-26  Score=208.15  Aligned_cols=159  Identities=25%  Similarity=0.374  Sum_probs=142.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +++|||+|||+.+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|..|+..|+|. .+.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~-~~~g~~l~v~~~~   81 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGI-TVRNKRLKVSYAR   81 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCC-EeCCcEEEEEecC
Confidence            489999999999999999999999999999999998888999999999999999999999999996 7999999999874


Q ss_pred             CCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCC
Q 007742          401 DHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPA  480 (591)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (591)
                      +..                                                                             
T Consensus        82 ~~~-----------------------------------------------------------------------------   84 (168)
T 1b7f_A           82 PGG-----------------------------------------------------------------------------   84 (168)
T ss_dssp             CCS-----------------------------------------------------------------------------
T ss_pred             CCc-----------------------------------------------------------------------------
Confidence            210                                                                             


Q ss_pred             CCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCC-----CeeEEEEeCCH
Q 007742          481 VTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRS-----AGFVYLRFEST  555 (591)
Q Consensus       481 ~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~-----~g~afV~F~~~  555 (591)
                                   ...+..+|+|.||  |..++        +++|.++|+.||.|..+.+..+.     +|+|||+|.+.
T Consensus        85 -------------~~~~~~~l~v~nl--~~~~t--------~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~  141 (168)
T 1b7f_A           85 -------------ESIKDTNLYVTNL--PRTIT--------DDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR  141 (168)
T ss_dssp             -------------STTTTCEEEEESC--CTTCC--------HHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             -------------ccCCCCCEEEeCC--CCCCC--------HHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCH
Confidence                         0123458999999  88777        89999999999999999886543     68999999999


Q ss_pred             HHHHHHHHHhcccccCC--eEEEEEEe
Q 007742          556 EAAASAQRAMHMRWFAR--RLISAIFM  580 (591)
Q Consensus       556 e~A~~A~~~l~g~~~~g--~~l~v~~~  580 (591)
                      ++|.+|+..|||..|.|  ++|.|.|+
T Consensus       142 ~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          142 EEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            99999999999999988  99999985

>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=99.94  E-value=5.1e-26  Score=205.44  Aligned_cols=159  Identities=29%  Similarity=0.413  Sum_probs=141.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||+.+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|..|+..|+|. .+.|+.|.|.++.
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 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGL-RLQTKTIKVSYAR   80 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCC-ccCCceEEEEecC
Confidence            379999999999999999999999999999999998888999999999999999999999999996 7999999998874


Q ss_pred             CCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCC
Q 007742          401 DHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPA  480 (591)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (591)
                      +..                                                                             
T Consensus        81 ~~~-----------------------------------------------------------------------------   83 (167)
T 1fxl_A           81 PSS-----------------------------------------------------------------------------   83 (167)
T ss_dssp             CCC-----------------------------------------------------------------------------
T ss_pred             CCc-----------------------------------------------------------------------------
Confidence            210                                                                             


Q ss_pred             CCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----CCeeEEEEeCCH
Q 007742          481 VTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----SAGFVYLRFEST  555 (591)
Q Consensus       481 ~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~~g~afV~F~~~  555 (591)
                                   ...+..+|+|.||  |..++        +++|.++|+.||.|..+.+..+     ++|+|||+|.+.
T Consensus        84 -------------~~~~~~~l~v~nl--~~~~t--------~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~  140 (167)
T 1fxl_A           84 -------------ASIRDANLYVSGL--PKTMT--------QKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR  140 (167)
T ss_dssp             -------------GGGTTCEEEEESC--CTTCC--------HHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             -------------ccCCCCcEEECCC--CCcCC--------HHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCH
Confidence                         0112347999999  88777        8999999999999999988644     379999999999


Q ss_pred             HHHHHHHHHhcccccCCeE--EEEEEe
Q 007742          556 EAAASAQRAMHMRWFARRL--ISAIFM  580 (591)
Q Consensus       556 e~A~~A~~~l~g~~~~g~~--l~v~~~  580 (591)
                      ++|.+|+..|||..|.|+.  |.|.|+
T Consensus       141 ~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          141 IEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHHhcCCccCCCccceEEEeC
Confidence            9999999999999999965  888885

>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=99.94  E-value=2.4e-26  Score=218.47  Aligned_cols=174  Identities=18%  Similarity=0.293  Sum_probs=144.0

Q ss_pred             CCCCcEEEEeCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          217 ERDQRTVFAYQMPL-KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       217 ~~~~~~l~V~nLp~-~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      ..++++|||+|||+ .+|+++|.++|..||.|..|.++.++     +|||||+|.+.++|.+|+ .|||..|.|+.|.|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            44679999999999 99999999999999999999999764     789999999999999999 599999999999998


Q ss_pred             cCccccccccccC-------------------CCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEe
Q 007742          295 PSEAEKNLVQSNT-------------------SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG-PVELVQLP  354 (591)
Q Consensus       295 ~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~v~i~  354 (591)
                      ++...........                   ...........+++.+|||+|||..+++++|+++|.+|| .|..|.++
T Consensus       106 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~  185 (229)
T 2adc_A          106 LSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF  185 (229)
T ss_dssp             CCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC
T ss_pred             EecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEE
Confidence            8765421111100                   000000011234468999999999999999999999999 99999986


Q ss_pred             ccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC-CeEEEEEEecC
Q 007742          355 LDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV-GRTLKVSSVTD  401 (591)
Q Consensus       355 ~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~-g~~l~v~~~~~  401 (591)
                      ..     .+|+|||+|.+.++|..|+..|+|. .|. |+.|.|.|+++
T Consensus       186 ~~-----~~g~afV~f~~~~~A~~Ai~~l~g~-~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          186 QK-----DRKMALIQMGSVEEAVQALIDLHNH-DLGENHHLRVSFSKS  227 (229)
T ss_dssp             SS-----STTCEEEEESSHHHHHHHHHHHTTC-BSSSSCBCEEEECSS
T ss_pred             EC-----CCcEEEEEECCHHHHHHHHHHHCCC-ccCCCCeEEEEEecC
Confidence            43     3789999999999999999999996 688 99999999865

>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=99.94  E-value=5.2e-26  Score=223.91  Aligned_cols=175  Identities=22%  Similarity=0.356  Sum_probs=143.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeE
Q 007742          217 ERDQRTVFAYQMPLKATERDVY----EFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV  291 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~----~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i  291 (591)
                      ..+.++|||+|||+.+|+++|+    ++|..||.|..|.++.   +|.++|||||+|.+.++|..|+ .|||..|.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            3467999999999999999966    8999999999999886   5789999999999999999999 799999999999


Q ss_pred             EeccCcccccccccc---------------------------------C-------------------------------
Q 007742          292 MVKPSEAEKNLVQSN---------------------------------T-------------------------------  307 (591)
Q Consensus       292 ~v~~~~~~~~~~~~~---------------------------------~-------------------------------  307 (591)
                      .|.++..........                                 .                               
T Consensus        83 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  162 (282)
T 3pgw_A           83 RIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPP  162 (282)
T ss_pred             EEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCC
Confidence            998775433200000                                 0                               


Q ss_pred             --------CCCCC-----------------------CCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecc
Q 007742          308 --------SAGGT-----------------------ATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLD  356 (591)
Q Consensus       308 --------~~~~~-----------------------~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~  356 (591)
                              +..+.                       ......+.+++|||+|||..+++++|+++|+.||.|..|.|+.+
T Consensus       163 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~  242 (282)
T 3pgw_A          163 YMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG  242 (282)
T ss_pred             CCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecC
Confidence                    00000                       00012234688999999999999999999999999999999855


Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC-CeEEEEEEec
Q 007742          357 IETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV-GRTLKVSSVT  400 (591)
Q Consensus       357 ~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~-g~~l~v~~~~  400 (591)
                      .     +|||||+|.+.++|..|+..|||. .|. |+.|.|.|++
T Consensus       243 ~-----~g~afV~f~~~~~A~~A~~~l~g~-~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          243 R-----HDIAFVEFDNEVQAGAARDALQGF-KITQNNAMKISFAK  281 (282)
T ss_pred             C-----CcEEEEEeCCHHHHHHHHHHcCCc-EeCCCCEEEEEEec
Confidence            3     589999999999999999999996 688 9999999974

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.94  E-value=9.9e-26  Score=212.77  Aligned_cols=176  Identities=19%  Similarity=0.383  Sum_probs=145.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|++. .|.|+.|.|.++..
T Consensus        29 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~-~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSV-MLGGRNIKVGRPSN  107 (216)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSC-CCC-CCCEEECCSC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCC-eeCCeeEEEecCCC
Confidence            79999999999999999999999999999999998878899999999999999999999999996 69999999976542


Q ss_pred             CCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCC
Q 007742          402 HVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAV  481 (591)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (591)
                      ....                     .    ........                                          
T Consensus       108 ~~~~---------------------~----~~~~~~~~------------------------------------------  120 (216)
T 2qfj_A          108 IGQA---------------------Q----PIIDQLAE------------------------------------------  120 (216)
T ss_dssp             CGGG---------------------H----HHHHHHHH------------------------------------------
T ss_pred             cccc---------------------c----hhhhhhhc------------------------------------------
Confidence            1100                     0    00000000                                          


Q ss_pred             CCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----CCeeEEEEeCCHH
Q 007742          482 TAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----SAGFVYLRFESTE  556 (591)
Q Consensus       482 ~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~~g~afV~F~~~e  556 (591)
                                  ...+..+|+|.||  |..++        +++|.++|+.||.|..|.+..+     ++|+|||+|.+.+
T Consensus       121 ------------~~~~~~~l~v~nl--p~~~t--------~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~  178 (216)
T 2qfj_A          121 ------------EARAFNRIYVASV--HQDLS--------DDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQ  178 (216)
T ss_dssp             ------------HHTTSCEEEEECC--CTTCC--------HHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             ------------ccCCCcEEEEeCC--CCcCC--------HHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHH
Confidence                        0134568999999  88887        8999999999999999988654     3789999999999


Q ss_pred             HHHHHHHHhcccccCCeEEEEEEeCchhhhh
Q 007742          557 AAASAQRAMHMRWFARRLISAIFMKPEDYEA  587 (591)
Q Consensus       557 ~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  587 (591)
                      +|.+|+..|||..|+|+.|.|.|+.+.....
T Consensus       179 ~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~~  209 (216)
T 2qfj_A          179 SSQDAVSSMNLFDLGGQYLRVGKAVTPPMPL  209 (216)
T ss_dssp             HHHHHHHHHTTCBCSSSBCEEEECSSCSSTT
T ss_pred             HHHHHHHHccCCEeCCcEEEEEEecCCCCCC
Confidence            9999999999999999999999998775443

>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=99.94  E-value=1e-25  Score=209.17  Aligned_cols=169  Identities=20%  Similarity=0.326  Sum_probs=140.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||+.+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..||.. ++. .|.|+.|.|.++.
T Consensus        13 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~-~~~g~~l~v~~~~   90 (196)
T 1l3k_A           13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPH-KVDGRVVEPKRAV   90 (196)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSC-EETTEECEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCC-EECCEEeeeeccc
Confidence            48999999999999999999999999999999999988899999999999999999999954 774 7999999999874


Q ss_pred             CCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCC
Q 007742          401 DHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPA  480 (591)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (591)
                      .......                                                                         
T Consensus        91 ~~~~~~~-------------------------------------------------------------------------   97 (196)
T 1l3k_A           91 SREDSQR-------------------------------------------------------------------------   97 (196)
T ss_dssp             C-------------------------------------------------------------------------------
T ss_pred             Ccccccc-------------------------------------------------------------------------
Confidence            3210000                                                                         


Q ss_pred             CCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----CCeeEEEEeCCH
Q 007742          481 VTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----SAGFVYLRFEST  555 (591)
Q Consensus       481 ~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~~g~afV~F~~~  555 (591)
                                 .....+..+|+|.||  |..++        +++|.++|+.||.|..|.+..+     ++|+|||+|.+.
T Consensus        98 -----------~~~~~~~~~l~V~nL--p~~~t--------~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~  156 (196)
T 1l3k_A           98 -----------PGAHLTVKKIFVGGI--KEDTE--------EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH  156 (196)
T ss_dssp             ----------------CCSEEEEECC--TTTCC--------HHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             -----------cccCCCcceEEEeCC--CCCCC--------HHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCH
Confidence                       001234468999999  88888        8999999999999999988643     478999999999


Q ss_pred             HHHHHHHHHhcccccCCeEEEEEEeCchhhh
Q 007742          556 EAAASAQRAMHMRWFARRLISAIFMKPEDYE  586 (591)
Q Consensus       556 e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~  586 (591)
                      ++|.+|+.. +|..|+|+.|.|.|+.++.-.
T Consensus       157 ~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          157 DSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             HHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             HHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            999999986 799999999999999877643

>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=99.94  E-value=3.3e-26  Score=226.56  Aligned_cols=172  Identities=20%  Similarity=0.311  Sum_probs=143.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCC-CeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEeccC
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAG-KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKPS  296 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G-~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~~  296 (591)
                      ..++|||+|||+.+|+++|.++|..|| .|..|.++.+.. |.++|||||+|.+.++|..|+. |+|..|.|+.|.|.++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            468999999999999999999999999 999999998876 7899999999999999999995 9999999999999988


Q ss_pred             ccccccccccCCCCCCCCCCCCCCCceEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeccCC-CCCcccEEEEEeCCHH
Q 007742          297 EAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFN-MTETQLRKLFEPFGPVELVQLPLDIE-TGQCKGFGFVQFAQLE  374 (591)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~-~~~~~l~~~f~~~g~i~~v~i~~~~~-~~~~~g~a~Vef~~~~  374 (591)
                      .+.......         ........+|||.|||.. +++++|+++|++||.|..|.|+.+.. ++.++|||||+|.+.+
T Consensus       195 ~~~~~~~~~---------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~  265 (292)
T 2ghp_A          195 NPLEKSKRT---------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKD  265 (292)
T ss_dssp             CCC------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHH
T ss_pred             CCCcccccc---------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHH
Confidence            654432211         112233589999999999 99999999999999999999998764 4889999999999999


Q ss_pred             HHHHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          375 HAKAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       375 ~a~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      +|..|+ .|||. .|.|+.|.|.++.++
T Consensus       266 ~A~~A~-~l~g~-~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          266 SAERAL-QMNRS-LLGNREISVSLADKK  291 (292)
T ss_dssp             HHHHHG-GGTTE-EETTEEEEEEECCCC
T ss_pred             HHHHHH-HhcCC-EECCcEEEEEEecCC
Confidence            999999 99996 699999999998653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.94  E-value=4.3e-26  Score=212.07  Aligned_cols=171  Identities=18%  Similarity=0.301  Sum_probs=142.4

Q ss_pred             CcEEEEeCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          220 QRTVFAYQMPL-KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       220 ~~~l~V~nLp~-~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +++|||+|||+ .+|+++|.++|..||.|..|.++.++     +|||||+|.+.++|..|+ .|||..+.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            58999999999 99999999999999999999998764     789999999999999999 599999999999998876


Q ss_pred             cccccccccC-------------------CCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeccC
Q 007742          298 AEKNLVQSNT-------------------SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG-PVELVQLPLDI  357 (591)
Q Consensus       298 ~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~v~i~~~~  357 (591)
                      ..........                   ...........+++.+|||+|||..+++++|+++|.+|| .|..|.+..+ 
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-  156 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-  156 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-
T ss_pred             CCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-
Confidence            5422111100                   000011112234578999999999999999999999999 9999998653 


Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC-CeEEEEEEecC
Q 007742          358 ETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV-GRTLKVSSVTD  401 (591)
Q Consensus       358 ~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~-g~~l~v~~~~~  401 (591)
                          .+|+|||+|.+.++|..|+..|||. .|. |+.|.|.++++
T Consensus       157 ----~~g~afV~f~~~~~A~~A~~~l~g~-~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          157 ----DRKMALIQMGSVEEAVQALIDLHNH-DLGENHHLRVSFSKS  196 (198)
T ss_dssp             ----TSSCEEEECSSHHHHHHHHHHHTSS-CCSSCCSCCEEEECC
T ss_pred             ----CCcEEEEEeCCHHHHHHHHHHhcCC-ccCCCCeEEEEeecc
Confidence                2789999999999999999999997 588 99999999865

>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=99.93  E-value=1.2e-25  Score=218.20  Aligned_cols=157  Identities=25%  Similarity=0.390  Sum_probs=141.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|..||.|..|.+..      ++|||||+|.+.++|..|+ .+||..|.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            34568999999999999999999999999999999863      4799999999999999999 5999999999999998


Q ss_pred             CccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHH
Q 007742          296 SEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH  375 (591)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~  375 (591)
                      +.+                      ..+|||+|||+.+++++|.++|..||.|..|.|+.+. +|.++|||||+|.+.++
T Consensus        93 a~~----------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~  149 (261)
T 3sde_A           93 ATH----------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPP  149 (261)
T ss_dssp             CCC----------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEEEEEEEEESSHHH
T ss_pred             ccc----------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcCcEEEEEeCCHHH
Confidence            753                      2689999999999999999999999999999999984 89999999999999999


Q ss_pred             HHHHHHHhcCCeeeC---CeEEEEEEecCC
Q 007742          376 AKAAQSALNGKLEIV---GRTLKVSSVTDH  402 (591)
Q Consensus       376 a~~a~~~l~g~~~~~---g~~l~v~~~~~~  402 (591)
                      |..|+..|++...+.   |++|.|.++...
T Consensus       150 A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          150 ARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             HHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             HHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            999999995433355   899999987643

>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=99.93  E-value=4e-25  Score=210.07  Aligned_cols=194  Identities=25%  Similarity=0.322  Sum_probs=146.3

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          319 AIDRKLYVGNLHF-NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       319 ~~~~~l~v~nl~~-~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      +.+++|||+|||+ .+++++|+++|+.||.|..|.|+.+.     +|||||+|.+.++|..|+..|+|. .|.|+.|.|.
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~-~~~g~~l~v~  105 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGH-KLHGKPIRIT  105 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTC-BCSSSBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEE
Confidence            3458999999999 99999999999999999999998764     789999999999999999999996 6999999999


Q ss_pred             EecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCC
Q 007742          398 SVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVP  477 (591)
Q Consensus       398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  477 (591)
                      ++...............       ...                   .    ......             ......    
T Consensus       106 ~a~~~~~~~~~~~~~~~-------~~~-------------------~----~~~~~~-------------~~~~~~----  138 (229)
T 2adc_A          106 LSKHQNVQLPREGQEDQ-------GLT-------------------K----DYGNSP-------------LHRFKK----  138 (229)
T ss_dssp             CCSCCCCCCCCSSSSTT-------TTE-------------------E----ECTTCS-------------SCCCCS----
T ss_pred             EecCccccCcccccccc-------ccc-------------------c----ccccCc-------------ccccCC----
Confidence            88654221110000000       000                   0    000000             000000    


Q ss_pred             CCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhcccc-ceEEEEEecCCCeeEEEEeCCHH
Q 007742          478 VPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYG-RVKHIYVDKRSAGFVYLRFESTE  556 (591)
Q Consensus       478 ~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G-~V~~v~l~~~~~g~afV~F~~~e  556 (591)
                       +.      .. .......++.+|+|.||  |..++        +++|.++|+.|| .|..|.+....+|+|||+|.+.+
T Consensus       139 -~~------~~-~~~~~~~~~~~l~V~nl--p~~~t--------~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~  200 (229)
T 2adc_A          139 -PG------SK-NFQNIFPPSATLHLSNI--PPSVS--------EEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVE  200 (229)
T ss_dssp             -TT------SG-GGTTCCCSCSEEEEECC--CTTCC--------HHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHH
T ss_pred             -cc------cc-ccccCCCCCCEEEEeCC--CccCC--------HHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHH
Confidence             00      00 00112356789999999  88777        899999999999 99999996667899999999999


Q ss_pred             HHHHHHHHhcccccC-CeEEEEEEeCch
Q 007742          557 AAASAQRAMHMRWFA-RRLISAIFMKPE  583 (591)
Q Consensus       557 ~A~~A~~~l~g~~~~-g~~l~v~~~~~~  583 (591)
                      +|.+|+..|||..|+ |+.|.|.|+.+.
T Consensus       201 ~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          201 EAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             HHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             HHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            999999999999999 999999998764

>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=99.93  E-value=2.8e-25  Score=202.19  Aligned_cols=161  Identities=23%  Similarity=0.353  Sum_probs=136.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCC--CcccEEEEEeCCHHHHHHHHHHhcCCeeeC---CeEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAAQSALNGKLEIV---GRTLK  395 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~--~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~---g~~l~  395 (591)
                      .++|||+|||+.+++++|+++|++||.|..|.|+.+..++  .++|||||+|.+.++|..|+..|+|. .+.   ++.+.
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~-~~~~~~~~~~~   81 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNM-KVLPGMHHPIQ   81 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTT-CCCTTCSSCCE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCc-EEccCCccceE
Confidence            3799999999999999999999999999999999988666  78999999999999999999999996 343   45666


Q ss_pred             EEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCC
Q 007742          396 VSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPA  475 (591)
Q Consensus       396 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  475 (591)
                      +.++.....                                                                       
T Consensus        82 ~~~~~~~~~-----------------------------------------------------------------------   90 (175)
T 3nmr_A           82 MKPADSEKN-----------------------------------------------------------------------   90 (175)
T ss_dssp             EEECGGGCC-----------------------------------------------------------------------
T ss_pred             Ecccccccc-----------------------------------------------------------------------
Confidence            655421100                                                                       


Q ss_pred             CCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC----CCeeEEEE
Q 007742          476 VPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR----SAGFVYLR  551 (591)
Q Consensus       476 ~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~----~~g~afV~  551 (591)
                                        ...+..+|+|.||  |..++        +++|.++|+.||.|..+.+..+    ++|+|||+
T Consensus        91 ------------------~~~~~~~l~v~nl--~~~~t--------~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~  142 (175)
T 3nmr_A           91 ------------------NAVEDRKLFIGMI--SKKCT--------ENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVT  142 (175)
T ss_dssp             ------------------SCGGGSEEEEESC--CTTCC--------HHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEE
T ss_pred             ------------------ccCCCCeEEEcCC--CCcCC--------HHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEE
Confidence                              0123457999999  88887        8999999999999999988654    47899999


Q ss_pred             eCCHHHHHHHHHHhcccccC---CeEEEEEEeC
Q 007742          552 FESTEAAASAQRAMHMRWFA---RRLISAIFMK  581 (591)
Q Consensus       552 F~~~e~A~~A~~~l~g~~~~---g~~l~v~~~~  581 (591)
                      |.+.++|.+|+..|||..+.   |++|.|.|+.
T Consensus       143 f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          143 FTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             ESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             ECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            99999999999999998875   4999999974

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.93  E-value=5e-25  Score=204.83  Aligned_cols=192  Identities=24%  Similarity=0.312  Sum_probs=145.3

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          321 DRKLYVGNLHF-NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       321 ~~~l~v~nl~~-~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +++|||+|||+ .+++++|+++|+.||.|..|.++.+.     +|||||+|.+.++|..|+..|+|. .|.|+.|.|.++
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~-~~~g~~l~v~~a   76 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGH-KLHGKPIRITLS   76 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTC-CCSSCCCEEEEC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCC-eecCeEEEEEEe
Confidence            37999999999 99999999999999999999998764     789999999999999999999996 699999999998


Q ss_pred             cCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCC
Q 007742          400 TDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVP  479 (591)
Q Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  479 (591)
                      ...............       ..                       ....+....             ..+..     +
T Consensus        77 ~~~~~~~~~~~~~~~-------~~-----------------------~~~~~~~~~-------------~r~~~-----~  108 (198)
T 1qm9_A           77 KHQNVQLPREGQEDQ-------GL-----------------------TKDYGNSPL-------------HRFKK-----P  108 (198)
T ss_dssp             CCCSCCCSSSSSSSS-------SC-----------------------EEESSCCCT-------------TSSSS-----C
T ss_pred             cCCCcCCCCcCCccc-------cc-----------------------cccccCCch-------------hhccC-----c
Confidence            654321110000000       00                       000000000             00000     0


Q ss_pred             CCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhcccc-ceEEEEEecCCCeeEEEEeCCHHHH
Q 007742          480 AVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYG-RVKHIYVDKRSAGFVYLRFESTEAA  558 (591)
Q Consensus       480 ~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G-~V~~v~l~~~~~g~afV~F~~~e~A  558 (591)
                      .     ..  ......+++.+|+|.||  |..++        +++|.++|+.|| .|..|.+....+|+|||+|.+.++|
T Consensus       109 ~-----~~--~~~~~~~~~~~l~v~nl--~~~~~--------~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A  171 (198)
T 1qm9_A          109 G-----SK--NFQNIFPPSATLHLSNI--PPSVS--------EEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEA  171 (198)
T ss_dssp             C-----CC--CCSCCCCCCCEEEECCC--CTTCC--------HHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHH
T ss_pred             c-----cc--ccccCCCCccEEEEeCC--CCCCC--------HHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHH
Confidence            0     00  00012356789999999  88777        899999999999 9999999666799999999999999


Q ss_pred             HHHHHHhcccccC-CeEEEEEEeCch
Q 007742          559 ASAQRAMHMRWFA-RRLISAIFMKPE  583 (591)
Q Consensus       559 ~~A~~~l~g~~~~-g~~l~v~~~~~~  583 (591)
                      .+|+..|||..|+ |+.|.|.|+.+.
T Consensus       172 ~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          172 VQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             HHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             HHHHHHhcCCccCCCCeEEEEeeccc
Confidence            9999999999999 999999998764

>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=99.93  E-value=1.2e-25  Score=204.73  Aligned_cols=163  Identities=21%  Similarity=0.310  Sum_probs=137.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ..++|||+|||..+++++|+++|..||.+..+ ++.+..++.++|||||+|.+.++|..|+ .|+|. .|.|+.|.|.++
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~-~~~g~~l~v~~~   88 (175)
T 1fje_B           12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGL-KVFGNEIKLEKP   88 (175)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGE-EETTEEEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHH-hcCCC-EeCCeEEEEecC
Confidence            35899999999999999999999999877652 3334447788999999999999999999 69995 799999999887


Q ss_pred             cCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCC
Q 007742          400 TDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVP  479 (591)
Q Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  479 (591)
                      ......                                                                          
T Consensus        89 ~~~~~~--------------------------------------------------------------------------   94 (175)
T 1fje_B           89 KGRDSK--------------------------------------------------------------------------   94 (175)
T ss_dssp             CCSSCS--------------------------------------------------------------------------
T ss_pred             CCcccc--------------------------------------------------------------------------
Confidence            532100                                                                          


Q ss_pred             CCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHH
Q 007742          480 AVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAA  559 (591)
Q Consensus       480 ~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~  559 (591)
                                    ...+..+|+|.||  |..++        +++|.++|+.||.|..+.....++|+|||+|.+.++|.
T Consensus        95 --------------~~~~~~~l~v~nl--p~~~t--------~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~  150 (175)
T 1fje_B           95 --------------KVRAARTLLAKNL--SFNIT--------EDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAE  150 (175)
T ss_dssp             --------------TTGGGGEEEEESC--CSSCC--------HHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHH
T ss_pred             --------------ccccCCEEEEeCC--CCCCC--------HHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHH
Confidence                          0123468999999  88887        89999999999999888223457899999999999999


Q ss_pred             HHHHHhcccccCCeEEEEEEeCch
Q 007742          560 SAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       560 ~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      +|+..|||..|+|+.|.|.|+.++
T Consensus       151 ~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          151 KNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHHhCCCEECCeEEEEEecCCC
Confidence            999999999999999999999764

>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=99.93  E-value=2.5e-25  Score=200.92  Aligned_cols=159  Identities=20%  Similarity=0.358  Sum_probs=138.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +++|||+|||+.+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..  +. .+.|+.|.|.++.
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~-~~~g~~i~v~~~~   79 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QH-ILDGKVIDPKRAI   79 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CC-EETTEECCCEECC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--cc-ccCCeEccccccc
Confidence            37999999999999999999999999999999999988899999999999999999999963  43 6999999887753


Q ss_pred             CCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCC
Q 007742          401 DHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPA  480 (591)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (591)
                      ...                                                                             
T Consensus        80 ~~~-----------------------------------------------------------------------------   82 (167)
T 2cjk_A           80 PRD-----------------------------------------------------------------------------   82 (167)
T ss_dssp             CHH-----------------------------------------------------------------------------
T ss_pred             chh-----------------------------------------------------------------------------
Confidence            200                                                                             


Q ss_pred             CCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----CCeeEEEEeCCH
Q 007742          481 VTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----SAGFVYLRFEST  555 (591)
Q Consensus       481 ~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~~g~afV~F~~~  555 (591)
                                   ...++.+|+|.||  |..++        +++|.++|+.||.|..+.+..+     ++|+|||+|.+.
T Consensus        83 -------------~~~~~~~l~V~nl--p~~~t--------~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~  139 (167)
T 2cjk_A           83 -------------EQDKTGKIFVGGI--GPDVR--------PKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA  139 (167)
T ss_dssp             -------------HHHHCEEEEEEEE--CTTCC--------HHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSH
T ss_pred             -------------hccCCCeEEECCC--CCCCC--------HHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCH
Confidence                         0012347999999  88887        8999999999999999988543     579999999999


Q ss_pred             HHHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          556 EAAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       556 e~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                      ++|.+|++ |+|..|+|+.|.|.|+.++
T Consensus       140 ~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          140 DAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             HHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            99999998 8999999999999999875

>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=99.93  E-value=1.9e-24  Score=200.58  Aligned_cols=191  Identities=18%  Similarity=0.167  Sum_probs=136.5

Q ss_pred             CCceEEEcCCC-CCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          320 IDRKLYVGNLH-FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       320 ~~~~l~v~nl~-~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      .+.+|||+||| ..+++++|+++|++||.|..|.|+.+.     +|||||+|.+.++|..||+.|||. .|.|+.|.|.+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~-~~~g~~l~v~~   76 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNN-FMFGQKMNVCV   76 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCC-EECCceEEEEE
Confidence            35899999999 799999999999999999999997653     799999999999999999999996 79999999999


Q ss_pred             ecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCC
Q 007742          399 VTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPV  478 (591)
Q Consensus       399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  478 (591)
                      ++.......   ..  ..... +...                     . .......             ...       .
T Consensus        77 s~~~~~~p~---~~--~~~~~-~~~~---------------------~-~~~~~~~-------------~~r-------~  108 (205)
T 3tyt_A           77 SKQPAIMPG---QS--YGLED-GSCS---------------------Y-KDFSESR-------------NNR-------F  108 (205)
T ss_dssp             CSCSCCCCC---SC--CBCTT-SCBS---------------------E-EECTTCT-------------TCS-------C
T ss_pred             ccCCccCCC---cc--ccccc-CCcc---------------------c-cccCCCc-------------ccc-------c
Confidence            864321000   00  00000 0000                     0 0000000             000       0


Q ss_pred             CCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccce--EEEEEecC---CCeeEEEEeC
Q 007742          479 PAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRV--KHIYVDKR---SAGFVYLRFE  553 (591)
Q Consensus       479 ~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V--~~v~l~~~---~~g~afV~F~  553 (591)
                      ...    ... .......|+.+|+|.||  |..++        +++|.++|+.||.|  ..|.+...   .+|+|||+|.
T Consensus       109 ~~~----~~~-~~~~~~~p~~~l~v~NL--p~~~t--------~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~  173 (205)
T 3tyt_A          109 STP----EQA-AKNRIQHPSNVLHFFNA--PLEVT--------EENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWD  173 (205)
T ss_dssp             SSH----HHH-TTSCCCCCCSEEEEEEE--CTTCC--------HHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECS
T ss_pred             cCc----ccc-cccccCCCcceEEEeCC--CCCCC--------HHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeC
Confidence            000    000 00012356788999999  88888        89999999999999  88887543   3699999999


Q ss_pred             CHHHHHHHHHHhcccccCCe----EEEEEE
Q 007742          554 STEAAASAQRAMHMRWFARR----LISAIF  579 (591)
Q Consensus       554 ~~e~A~~A~~~l~g~~~~g~----~l~v~~  579 (591)
                      +.++|.+|+..|||..|.|.    ++.|.|
T Consensus       174 ~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~  203 (205)
T 3tyt_A          174 SKSDALETLGFLNHYQMKNPNGPYPYTLKL  203 (205)
T ss_dssp             SHHHHHHHHHHHTTCEECCSSSSSCEECEE
T ss_pred             CHHHHHHHHHHhCCCCccCCCCCcceEEEe
Confidence            99999999999999999888    455544

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.92  E-value=3.1e-24  Score=199.52  Aligned_cols=176  Identities=22%  Similarity=0.404  Sum_probs=138.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccC----C-------CeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeee
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPF----G-------PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI  389 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~----g-------~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~  389 (591)
                      .++|||+|||+.+++++|+++|+.|    |       .|..+.+.      .++|||||+|.+.++|..|+ .|+|. .|
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~l~g~-~~   75 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGI-IF   75 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTTE-EE
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcCC-EE
Confidence            4899999999999999999999999    5       56555553      35899999999999999999 89995 79


Q ss_pred             CCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccC
Q 007742          390 VGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLP  469 (591)
Q Consensus       390 ~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  469 (591)
                      .|+.|.|.++.............                                    .                .   
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~~------------------------------------~----------------~---  100 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSENP------------------------------------S----------------V---  100 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSCS------------------------------------S----------------C---
T ss_pred             cCceEEEeCCCCCCCCCCCcCCC------------------------------------c----------------C---
Confidence            99999999875432111000000                                    0                0   


Q ss_pred             cCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCC-----
Q 007742          470 VVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRS-----  544 (591)
Q Consensus       470 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~-----  544 (591)
                                     ..+.........+..+|+|.||  |..++        +++|.++|+.||.|..|.+..+.     
T Consensus       101 ---------------~~~~~~~~~~~~~~~~l~v~nl--~~~~~--------~~~l~~~f~~~G~v~~~~~~~~~~~~~~  155 (198)
T 2yh0_A          101 ---------------YVPGVVSTVVPDSAHKLFIGGL--PNYLN--------DDQVKELLTSFGPLKAFNLVKDSATGLS  155 (198)
T ss_dssp             ---------------CCTTSSCCCSSCCCCEEEEECC--CTTCC--------HHHHHHHHHTBSCEEEEEEEECTTTCSE
T ss_pred             ---------------CCCCCccCCCCCCCCEEEEeCC--CCCCC--------HHHHHHHHHHcCCccEEEEeecCCCCCc
Confidence                           0000011112356678999999  88877        89999999999999999886543     


Q ss_pred             CeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchh
Q 007742          545 AGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPED  584 (591)
Q Consensus       545 ~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~  584 (591)
                      +|+|||+|.+.++|.+|+..|||..|+|+.|.|.|+.+..
T Consensus       156 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          156 KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             EEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            7899999999999999999999999999999999988753

>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=99.92  E-value=4.6e-24  Score=193.58  Aligned_cols=153  Identities=24%  Similarity=0.404  Sum_probs=132.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccC----C-------CeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeee
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPF----G-------PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI  389 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~----g-------~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~  389 (591)
                      .++|||+|||+.+++++|+++|++|    |       .|..+.+..      ++|||||+|.+.++|..|+ .|+|. .+
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~-~~   75 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGI-IF   75 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTC-EE
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCc-Ee
Confidence            3799999999999999999999999    6       677776643      4799999999999999999 89996 69


Q ss_pred             CCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccC
Q 007742          390 VGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLP  469 (591)
Q Consensus       390 ~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  469 (591)
                      .|+.|.|.++.....                                                                 
T Consensus        76 ~g~~i~v~~~~~~~~-----------------------------------------------------------------   90 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQP-----------------------------------------------------------------   90 (172)
T ss_dssp             TTEECEEECCSSCCC-----------------------------------------------------------------
T ss_pred             cCceeeecCCcccCC-----------------------------------------------------------------
Confidence            999999987532100                                                                 


Q ss_pred             cCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----C
Q 007742          470 VVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----S  544 (591)
Q Consensus       470 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~  544 (591)
                                               .....+|+|.||  |..++        +++|.++|+.||.|..+.+..+     +
T Consensus        91 -------------------------~~~~~~l~v~nl--p~~~t--------~~~l~~~f~~~G~v~~v~i~~~~~~g~~  135 (172)
T 2g4b_A           91 -------------------------LPGAHKLFIGGL--PNYLN--------DDQVKELLTSFGPLKAFNLVKDSATGLS  135 (172)
T ss_dssp             -------------------------CTTTTCEEEECC--CTTCC--------HHHHHHHHHTTSCEEEEEEEECTTTCSE
T ss_pred             -------------------------CCCCCEEEEEcC--CCcCC--------HHHHHHHHHhcCCceEEEEEecCCCCCc
Confidence                                     112457999999  88877        8999999999999999988654     3


Q ss_pred             CeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeC
Q 007742          545 AGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMK  581 (591)
Q Consensus       545 ~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~  581 (591)
                      +|+|||+|.+.++|.+|+..|||..|+|+.|.|.|+.
T Consensus       136 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          136 KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            7899999999999999999999999999999999974

>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=99.90  E-value=4.2e-23  Score=200.13  Aligned_cols=151  Identities=26%  Similarity=0.403  Sum_probs=133.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||+.+|+++|.++|+.||.|..|.|..+      +|||||+|.+.++|..|+..|+|. .|.|+.|.|.++.
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~-~i~g~~l~v~~a~   94 (261)
T 3sde_A           22 RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGT-ILKSRPLRIRFAT   94 (261)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTC-EETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCc-EECCceeEeeecc
Confidence            479999999999999999999999999999998643      789999999999999999999996 6999999998863


Q ss_pred             CCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCC
Q 007742          401 DHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPA  480 (591)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  480 (591)
                                                                                                      
T Consensus        95 --------------------------------------------------------------------------------   94 (261)
T 3sde_A           95 --------------------------------------------------------------------------------   94 (261)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC----CCeeEEEEeCCHH
Q 007742          481 VTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR----SAGFVYLRFESTE  556 (591)
Q Consensus       481 ~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~----~~g~afV~F~~~e  556 (591)
                                      ++.+|+|.||  |..++        +++|.++|+.||.|..|.|..+    ++|+|||+|.+.+
T Consensus        95 ----------------~~~~l~v~nl--~~~~t--------~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~  148 (261)
T 3sde_A           95 ----------------HGAALTVKNL--SPVVS--------NELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKP  148 (261)
T ss_dssp             ----------------CSSEEEEESC--CTTCC--------HHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHH
T ss_pred             ----------------cCCcccccCC--CCCCC--------HHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHH
Confidence                            1237999999  88877        8999999999999999988543    4789999999999


Q ss_pred             HHHHHHHHhcccc-cC---CeEEEEEEeCchh
Q 007742          557 AAASAQRAMHMRW-FA---RRLISAIFMKPED  584 (591)
Q Consensus       557 ~A~~A~~~l~g~~-~~---g~~l~v~~~~~~~  584 (591)
                      +|.+|+..||+.. +.   |++|.|.++.+..
T Consensus       149 ~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          149 PARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             HHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             HHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            9999999996544 44   9999999987654

>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=99.82  E-value=1.4e-19  Score=161.18  Aligned_cols=148  Identities=22%  Similarity=0.284  Sum_probs=112.7

Q ss_pred             EEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccccccccccCCCCCCCCCCCCCCCceEEEc
Q 007742          249 DVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVG  327 (591)
Q Consensus       249 ~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~  327 (591)
                      .+.|+.+..  .++|||||+|.+.++|.+|+ .+++.......+.+............   ..............+|||+
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~l~v~   76 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEG---SHHHHHHMDVEGMTSLKVD   76 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECC---CCCSSCCCCCCBCCEEEEE
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCcccccccccc---ccccccccCCCCCCEEEEe
Confidence            456777665  58999999999999999999 56654433333333222111111110   0111111222345899999


Q ss_pred             CCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          328 NLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       328 nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      |||+.+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++...
T Consensus        77 nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~a~~~  150 (158)
T 2kn4_A           77 NLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA-VLDGRELRVQMARYG  150 (158)
T ss_dssp             SCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTE-ESSSSEEEEEEECCS
T ss_pred             CCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEEECCCC
Confidence            99999999999999999999999999999888999999999999999999999999995 799999999998754

>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=99.82  E-value=5.2e-20  Score=151.92  Aligned_cols=97  Identities=42%  Similarity=0.733  Sum_probs=92.1

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-CCeeEEEEeCCHHHHHHHHHHhcccccCCe
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-SAGFVYLRFESTEAAASAQRAMHMRWFARR  573 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-~~g~afV~F~~~e~A~~A~~~l~g~~~~g~  573 (591)
                      +.+++||+|.||++|..+.+++++.+|+++|+++|++||.|..|.|+.+ ++|+|||+|.+.++|.+|+..|||+.|+|+
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR   83 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGK   83 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            4688999999999999999999999999999999999999999999765 489999999999999999999999999999


Q ss_pred             EEEEEEeCchhhhhccCC
Q 007742          574 LISAIFMKPEDYEAKFKS  591 (591)
Q Consensus       574 ~l~v~~~~~~~~~~~~~~  591 (591)
                      .|.|.|+++..|..+||+
T Consensus        84 ~i~v~~~~~~~y~~~fp~  101 (114)
T 3s6e_A           84 MITAAYVPLPTYHNLFPD  101 (114)
T ss_dssp             ECEEEEECHHHHHHHCGG
T ss_pred             EEEEEEEcHHHHHHhCcc
Confidence            999999999999999985

>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=99.79  E-value=1.7e-19  Score=150.87  Aligned_cols=107  Identities=22%  Similarity=0.356  Sum_probs=73.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      ..+|||+|||+.+|+++|+++|.+||.|.+|.|+.+..  .++|||||+|.+.++|..|| .|+|..|.|+.|.|.++..
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~--~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT--EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC--CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            57899999999999999999999999999999999864  48999999999999999999 6999999999999998765


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHH
Q 007742          299 EKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTET  336 (591)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~  336 (591)
                      ........        .........|||.|||+.+|++
T Consensus        83 ~~~~~~~~--------~~~~~~~~~lyv~Nl~~~~T~~  112 (115)
T 4f25_A           83 RKEREAEL--------GARAKEFTNVYIKNFGPGSTRA  112 (115)
T ss_dssp             CCC-----------------------------------
T ss_pred             cccccccc--------ccccCCCCceEeCCCCCCcccc
Confidence            43221111        0111123679999999999876

>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=99.78  E-value=7.9e-19  Score=143.33  Aligned_cols=94  Identities=34%  Similarity=0.548  Sum_probs=87.9

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-------CCeeEEEEeCCHHHHHHHHHHhcc
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-------SAGFVYLRFESTEAAASAQRAMHM  567 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-------~~g~afV~F~~~e~A~~A~~~l~g  567 (591)
                      +.|+++|+|.||++|..+.++.++.++.++|+++|++||.|.+|.|+.+       ++|+|||+|.+.++|.+|+..|||
T Consensus         2 g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            2 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             CSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            4688999999999999999989999999999999999999999998643       579999999999999999999999


Q ss_pred             cccCCeEEEEEEeCchhhhhc
Q 007742          568 RWFARRLISAIFMKPEDYEAK  588 (591)
Q Consensus       568 ~~~~g~~l~v~~~~~~~~~~~  588 (591)
                      +.|+|+.|.|.|++++.|.+.
T Consensus        82 ~~f~GR~i~v~~~~~~~f~~~  102 (105)
T 3v4m_A           82 RKFANRVVVTKYCDPDSYHRR  102 (105)
T ss_dssp             CEETTEECEEEEECHHHHHTT
T ss_pred             CEeCCCEEEEEEeCHHHHhhc
Confidence            999999999999999999864

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.77  E-value=1.1e-18  Score=153.67  Aligned_cols=136  Identities=22%  Similarity=0.311  Sum_probs=112.1

Q ss_pred             CCccceEEEEecCcchHHHHH-HH-cCCccCCeeEEeccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHH
Q 007742          259 RRSKGVGYIEFYDVMSVPMAI-AL-SGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTET  336 (591)
Q Consensus       259 g~~~G~afV~F~~~e~A~~Al-~l-~g~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~  336 (591)
                      ...+|+++|+|.+.++|.+|+ .+ ||..+.| .+.+.++.........................++|||+|||+.++++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~   88 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKT   88 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            357899999999999999999 68 9999999 99998876544332221222222223334456899999999999999


Q ss_pred             HHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          337 QLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       337 ~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      +|+++|+.||.|..|.|+.+     ++|||||+|.+.++|..|+..|||. .|.|++|.|.++.+
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~a~~  147 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGR-TLCGCRVRVELSNG  147 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSS-CSSSSCCEEEECCC
T ss_pred             HHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEEEcCC
Confidence            99999999999999999865     5899999999999999999999996 69999999999864

>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=99.76  E-value=1.8e-18  Score=140.15  Aligned_cols=80  Identities=23%  Similarity=0.412  Sum_probs=76.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ++++|||+|||+.+|+++|+++|.+||.|..|.++.++.+|.++|||||+|.+.++|.+|+ .|||..|.|++|.|.++.
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            5689999999999999999999999999999999999999999999999999999999999 699999999999999885


Q ss_pred             c
Q 007742          298 A  298 (591)
Q Consensus       298 ~  298 (591)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            4

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.72  E-value=1.4e-17  Score=146.68  Aligned_cols=139  Identities=15%  Similarity=0.191  Sum_probs=108.7

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHh-cCCeeeCCeEEEEEEecCCCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHh
Q 007742          359 TGQCKGFGFVQFAQLEHAKAAQSAL-NGKLEIVGRTLKVSSVTDHVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKL  437 (591)
Q Consensus       359 ~~~~~g~a~Vef~~~~~a~~a~~~l-~g~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  437 (591)
                      ....+|+++|+|.+.++|.+|+..| ||. .+.| .+.+.++...........                           
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~-~~~G-~~~~~~a~~~~~~~~~~~---------------------------   59 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDN-GVDG-EWTYDDATKTFTVTEGSH---------------------------   59 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHH-TCCC-EEEEETTTTEEEEECSSS---------------------------
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCC-CCCC-ceecccccCccccccccc---------------------------
Confidence            3456899999999999999999999 896 6999 888876532100000000                           


Q ss_pred             hhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCCCCCccccccccccCCCcceEEEeccCCCCCCCCchh
Q 007742          438 DRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAVTAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDF  517 (591)
Q Consensus       438 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~  517 (591)
                                                     .                ...........+.++|+|+||  |..++    
T Consensus        60 -------------------------------~----------------~~~~~~~~~~~~~~~l~V~nl--~~~~t----   86 (150)
T 2i2y_A           60 -------------------------------H----------------HHHHMHRDSCPLDCKVYVGNL--GNNGN----   86 (150)
T ss_dssp             -------------------------------S----------------CCCCSCSSSSTTSCEEEEESC--CSCCS----
T ss_pred             -------------------------------c----------------ccccccccCCCCCCEEEEeCC--CCCCC----
Confidence                                           0                000000112345678999999  88777    


Q ss_pred             hhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCch
Q 007742          518 DLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       518 ~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~  583 (591)
                          +++|.++|+.||.|..|.+..+++|+|||+|.+.++|..|+..|||..|+|+.|.|.|+.+.
T Consensus        87 ----~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           87 ----KTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             ----CHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             ----HHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence                78999999999999999998888999999999999999999999999999999999998764

>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=99.72  E-value=2.6e-17  Score=146.46  Aligned_cols=79  Identities=23%  Similarity=0.375  Sum_probs=71.5

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-----CCeeEEEEeCCHHHHHHHHHHhccccc
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-----SAGFVYLRFESTEAAASAQRAMHMRWF  570 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-----~~g~afV~F~~~e~A~~A~~~l~g~~~  570 (591)
                      .+..+|||.||  |..++        +++|.++|+.||.|..|.|..+     ++|+|||+|.+.++|..|+..|||..|
T Consensus        68 ~~~~~l~v~nl--~~~~~--------~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~  137 (158)
T 2kn4_A           68 EGMTSLKVDNL--TYRTS--------PDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL  137 (158)
T ss_dssp             CBCCEEEEESC--CTTCC--------HHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEES
T ss_pred             CCCCEEEEeCC--CCCCC--------HHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            44578999999  88888        8999999999999999998543     689999999999999999999999999


Q ss_pred             CCeEEEEEEeCchh
Q 007742          571 ARRLISAIFMKPED  584 (591)
Q Consensus       571 ~g~~l~v~~~~~~~  584 (591)
                      +|+.|.|.|+.+..
T Consensus       138 ~g~~l~v~~a~~~~  151 (158)
T 2kn4_A          138 DGRELRVQMARYGR  151 (158)
T ss_dssp             SSSEEEEEEECCSS
T ss_pred             CCeEEEEEECCCCC
Confidence            99999999998753

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.71  E-value=3.7e-17  Score=134.97  Aligned_cols=83  Identities=13%  Similarity=0.198  Sum_probs=77.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      .+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.||.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.++
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            35689999999999999999999999999999999999999999999999999999999999 69999999999999887


Q ss_pred             cccc
Q 007742          297 EAEK  300 (591)
Q Consensus       297 ~~~~  300 (591)
                      ....
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            6443

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.70  E-value=7.5e-18  Score=134.25  Aligned_cols=81  Identities=26%  Similarity=0.420  Sum_probs=74.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCC-CeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-H-cCCccCCeeEEeccC
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAG-KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L-SGQLLLGQPVMVKPS  296 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G-~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l-~g~~i~g~~i~v~~~  296 (591)
                      +++|||+|||+.+|+++|+++|.+|| .|.+|.|+.++.+|.++|||||+|.+.++|.+||. + ++..+.|++|.|.++
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 89999999999999999999999999999999995 5 456799999999998


Q ss_pred             cccc
Q 007742          297 EAEK  300 (591)
Q Consensus       297 ~~~~  300 (591)
                      .+..
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7644

>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=99.70  E-value=8.4e-17  Score=130.19  Aligned_cols=80  Identities=36%  Similarity=0.540  Sum_probs=76.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +++|||+|||+.+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..|+..|||. .|.|++|.|.+++
T Consensus        19 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           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGL-RLQSKTIKVSYAR   97 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEee
Confidence            378999999999999999999999999999999999889999999999999999999999999996 7999999999986


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            4

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.4e-16  Score=129.54  Aligned_cols=84  Identities=30%  Similarity=0.508  Sum_probs=79.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      ..+.++|||+|||+.+|+++|+++|.+||.|..|.++.++.+|.++|||||+|.+.++|.+||.||+..|.|+.|.|.++
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccc
Q 007742          297 EAEK  300 (591)
Q Consensus       297 ~~~~  300 (591)
                      .+..
T Consensus        87 ~~~~   90 (99)
T 2dgs_A           87 EPRD   90 (99)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            7644

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.69  E-value=5.7e-17  Score=129.51  Aligned_cols=80  Identities=15%  Similarity=0.317  Sum_probs=73.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCC--eeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCC----ccCCee
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGK--VRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQ----LLLGQP  290 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~--i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~----~i~g~~  290 (591)
                      ..-.+|||+|||+.+|+++|.++|.+||.  |.+|.+++|+.||.++|||||+|.+.++|.+|+ .|||.    .|.|++
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            34479999999999999999999999995  679999999999999999999999999999999 68987    489999


Q ss_pred             EEeccCc
Q 007742          291 VMVKPSE  297 (591)
Q Consensus       291 i~v~~~~  297 (591)
                      |.|.++.
T Consensus        87 i~V~~Ak   93 (95)
T 2lkz_A           87 IGVDFAK   93 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEEcc
Confidence            9999875

>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=99.68  E-value=9.9e-17  Score=127.03  Aligned_cols=82  Identities=23%  Similarity=0.416  Sum_probs=75.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      .+.++|||+|||+.+|+++|+++|.+||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..+.|+.|.|.++
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            45689999999999999999999999999999999999989999999999999999999999 59999999999999987


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      ..+
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            653

>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=99.68  E-value=1.3e-16  Score=126.36  Aligned_cols=80  Identities=30%  Similarity=0.493  Sum_probs=75.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      ..+.++|||+|||+.+|+++|.++|.+||.|..|.++.++.+|.++|||||+|.+.++|.+|+.+++..|.|+.|.|.++
T Consensus         8 ~~~~~~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            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45679999999999999999999999999999999999999999999999999999999999998999999999999764

>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=99.68  E-value=1.6e-16  Score=129.16  Aligned_cols=85  Identities=21%  Similarity=0.404  Sum_probs=79.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|..|| .||+..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345799999999999999999999999999999999999989999999999999999999999 7999999999999999


Q ss_pred             Cccccc
Q 007742          296 SEAEKN  301 (591)
Q Consensus       296 ~~~~~~  301 (591)
                      +.....
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            877554

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.68  E-value=3.4e-16  Score=131.03  Aligned_cols=86  Identities=23%  Similarity=0.419  Sum_probs=80.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|+++|..||.|..|.|+.++.+|.++|||||+|.+.++|.+|| .||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            446799999999999999999999999999999999999989999999999999999999999 5999999999999999


Q ss_pred             Ccccccc
Q 007742          296 SEAEKNL  302 (591)
Q Consensus       296 ~~~~~~~  302 (591)
                      +......
T Consensus        92 a~~~~~~   98 (115)
T 2dgo_A           92 ATRKPPA   98 (115)
T ss_dssp             SSCCCCC
T ss_pred             ccCCCCC
Confidence            8765543

>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=99.68  E-value=4.4e-17  Score=129.80  Aligned_cols=80  Identities=20%  Similarity=0.288  Sum_probs=71.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAG--KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G--~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      .+|||+|||+.+|+++|+++|.+||  .|..|.++.++.+|.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  9999999999999999999999999999999999 699999999999999887


Q ss_pred             ccc
Q 007742          298 AEK  300 (591)
Q Consensus       298 ~~~  300 (591)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.8e-16  Score=128.68  Aligned_cols=84  Identities=19%  Similarity=0.302  Sum_probs=78.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|.+|+. ||+..|.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3457999999999999999999999999999999999999999999999999999999999995 999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +....
T Consensus        90 a~~~~   94 (103)
T 2dnm_A           90 ARYGR   94 (103)
T ss_dssp             CSSCC
T ss_pred             CCcCC
Confidence            87543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.9e-16  Score=126.60  Aligned_cols=83  Identities=27%  Similarity=0.422  Sum_probs=78.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ..+++|||+|||+.+|+++|.++|.+||.|..|.++.++.++.++|||||+|.+.++|..|+ .||+..|.|+.|.|.++
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            35689999999999999999999999999999999999999999999999999999999999 59999999999999998


Q ss_pred             cccc
Q 007742          297 EAEK  300 (591)
Q Consensus       297 ~~~~  300 (591)
                      ....
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            6544

>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=99.67  E-value=1.5e-16  Score=132.12  Aligned_cols=88  Identities=27%  Similarity=0.535  Sum_probs=78.0

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC---------CCeeEEEEeCCHHHHHHHHHHhc
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR---------SAGFVYLRFESTEAAASAQRAMH  566 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~---------~~g~afV~F~~~e~A~~A~~~l~  566 (591)
                      +|++||+|.||++|..+.     .+|+++|+++|++||.|.+|.|+.+         ++|+|||+|.++++|.+|+..||
T Consensus        18 ~ps~vl~L~Nm~~~~el~-----ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~Ln   92 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDID-----DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN   92 (118)
T ss_dssp             HSCCEEEEESCSCGGGCC-----TTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCHHHHH-----HHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHC
Confidence            478899999998876543     4578999999999999999988643         24899999999999999999999


Q ss_pred             ccccCCeEEEEEEeCchhhhhc
Q 007742          567 MRWFARRLISAIFMKPEDYEAK  588 (591)
Q Consensus       567 g~~~~g~~l~v~~~~~~~~~~~  588 (591)
                      |+.|+|+.|.|.|+++..|.+.
T Consensus        93 Gr~f~GR~i~v~~~~~~~f~~~  114 (118)
T 3ue2_A           93 GRWFAGRKVVAEVYDQERFDNS  114 (118)
T ss_dssp             TCEETTEECEEEEECHHHHHTT
T ss_pred             CCEECCcEEEEEEcChHhcccc
Confidence            9999999999999999999763

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.67  E-value=3e-16  Score=127.87  Aligned_cols=90  Identities=27%  Similarity=0.482  Sum_probs=77.8

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEec------CCCeeEEEEeCCHHHHHHHHHHhcc
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK------RSAGFVYLRFESTEAAASAQRAMHM  567 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~------~~~g~afV~F~~~e~A~~A~~~l~g  567 (591)
                      .+.++++|+|.||++|..+.     .+++++|+++|++||.|..|.|+.      .++|+|||+|.+.++|.+|+..|||
T Consensus         4 ~~~~s~~l~l~Nm~~~~~l~-----dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG   78 (105)
T 2pe8_A            4 GKCPTKVVLLRNMVGAGEVD-----EDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNG   78 (105)
T ss_dssp             GGSCCSEEEEESSSCSCCC--------CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEEcCCChHHhh-----HHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCC
Confidence            35688999999998776543     345899999999999999999864      3589999999999999999999999


Q ss_pred             cccCCeEEEEEEeCchhhhhc
Q 007742          568 RWFARRLISAIFMKPEDYEAK  588 (591)
Q Consensus       568 ~~~~g~~l~v~~~~~~~~~~~  588 (591)
                      +.|+|+.|.|.|+.+..|...
T Consensus        79 ~~~~Gr~i~v~~a~~~~f~~~   99 (105)
T 2pe8_A           79 RYFGGRVVKACFYNLDKFRVL   99 (105)
T ss_dssp             CEETTEECEEEECCHHHHHTT
T ss_pred             CEECCcEEEEEEcCHHHhhhh
Confidence            999999999999999998753

>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=99.67  E-value=2.3e-16  Score=123.63  Aligned_cols=79  Identities=16%  Similarity=0.287  Sum_probs=75.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      .+|||+|||+.+|+++|.++|..||.|..|.++.+..+|.++|||||+|.+.++|..|+ .|||..+.|+.|.|.++.+.
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            68999999999999999999999999999999999999999999999999999999999 59999999999999988653

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=2.2e-16  Score=130.10  Aligned_cols=83  Identities=27%  Similarity=0.417  Sum_probs=78.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|.|+.|.|.+
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            345689999999999999999999999999999999999999999999999999999999999 5999999999999999


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +...
T Consensus       100 a~~~  103 (106)
T 1p27_B          100 CFVR  103 (106)
T ss_dssp             SEES
T ss_pred             ecCC
Confidence            8654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.67  E-value=8.8e-17  Score=128.00  Aligned_cols=81  Identities=25%  Similarity=0.384  Sum_probs=75.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCC-CeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFG-PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ++|||+|||+.+|+++|+++|++|| .|..|.|+.++.++.++|||||+|.+.++|..||+.|++.+.|.|++|.|.++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            6899999999999999999999999 899999999988999999999999999999999988865567999999999986


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      +.
T Consensus        82 ~~   83 (91)
T 2lxi_A           82 PK   83 (91)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.67  E-value=3.4e-16  Score=128.76  Aligned_cols=86  Identities=26%  Similarity=0.423  Sum_probs=79.6

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEe
Q 007742          215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV  293 (591)
Q Consensus       215 ~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v  293 (591)
                      ......++|||+|||+.+|+++|.++|.+||.|..|.++.++.++.++|||||+|.+.++|.+|+ .||+..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            33456799999999999999999999999999999999999989999999999999999999999 59999999999999


Q ss_pred             ccCcccc
Q 007742          294 KPSEAEK  300 (591)
Q Consensus       294 ~~~~~~~  300 (591)
                      .++....
T Consensus        90 ~~a~~~~   96 (105)
T 1x5u_A           90 NKASAHN   96 (105)
T ss_dssp             EETTTTS
T ss_pred             EECCCCC
Confidence            9987654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.66  E-value=2.1e-16  Score=126.25  Aligned_cols=80  Identities=24%  Similarity=0.356  Sum_probs=74.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCC--eeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCC---eeeCCeEEEE
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGP--VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK---LEIVGRTLKV  396 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~--i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~---~~~~g~~l~v  396 (591)
                      .+|||+|||+.+|+++|+++|++||.  |..|.++.++.++.++|||||+|.+.++|..|++.|||.   +.|+|++|.|
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            79999999999999999999999995  678999999989999999999999999999999999985   4699999999


Q ss_pred             EEecC
Q 007742          397 SSVTD  401 (591)
Q Consensus       397 ~~~~~  401 (591)
                      .++++
T Consensus        90 ~~Aks   94 (95)
T 2lkz_A           90 DFAKS   94 (95)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            99864

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.66  E-value=3.5e-16  Score=127.09  Aligned_cols=84  Identities=25%  Similarity=0.415  Sum_probs=77.9

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeE--------EEEeecCCCCCccceEEEEecCcchHHHHH-HHcC
Q 007742          213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRD--------VRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSG  283 (591)
Q Consensus       213 ~~~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~--------v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g  283 (591)
                      ...+....++|||+|||+.+|+++|+++|.+||.|..        |.++.++.+|.++|||||+|.+.++|..|+ .|||
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g   85 (99)
T 2la6_A            6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG   85 (99)
T ss_dssp             SCCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCC
Confidence            3444556799999999999999999999999999999        999999999999999999999999999999 5999


Q ss_pred             CccCCeeEEeccC
Q 007742          284 QLLLGQPVMVKPS  296 (591)
Q Consensus       284 ~~i~g~~i~v~~~  296 (591)
                      ..|.|+.|.|.++
T Consensus        86 ~~~~g~~l~V~~A   98 (99)
T 2la6_A           86 KEFSGNPIKVSFA   98 (99)
T ss_dssp             CBSSSSBCEEEEC
T ss_pred             CEeCCcEEEEEec
Confidence            9999999999876

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.66  E-value=3.2e-16  Score=128.30  Aligned_cols=85  Identities=28%  Similarity=0.491  Sum_probs=78.8

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEec
Q 007742          215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK  294 (591)
Q Consensus       215 ~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~  294 (591)
                      .+..+.++|||+|||+.+|+++|.++|..|| |..|.++.++.+|.++|||||+|.+.++|.+||.||+..|.|+.|.|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVD   88 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEE
Confidence            3445679999999999999999999999997 999999999999999999999999999999999999999999999999


Q ss_pred             cCcccc
Q 007742          295 PSEAEK  300 (591)
Q Consensus       295 ~~~~~~  300 (591)
                      ++....
T Consensus        89 ~a~~~~   94 (103)
T 2dng_A           89 IAEGRK   94 (103)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            987644

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.4e-16  Score=129.58  Aligned_cols=79  Identities=19%  Similarity=0.318  Sum_probs=74.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      ..++|||+|||+.+|+++|.++|.+||.|.+|.|+.+.. |.++|||||+|.+.++|..||.+++..|.|+.|.|.+...
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEchH
Confidence            458999999999999999999999999999999999987 9999999999999999999999999999999999987654

>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=99.66  E-value=2.6e-16  Score=123.99  Aligned_cols=79  Identities=16%  Similarity=0.370  Sum_probs=75.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      .+.++|||+|||+.+|+++|.++|.+||.|..|.++.+..+|.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++
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            45699999999999999999999999999999999999999999999999999999999999 79999999999999876

>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=99.66  E-value=1.3e-16  Score=133.34  Aligned_cols=83  Identities=59%  Similarity=0.969  Sum_probs=78.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      ..++|||+|||+.+|+++|+++|..||.|..|.|+.++.+|.++|||||+|.+.++|.+||.||+..|.|+.|.|.++..
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~~  103 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecCC
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             ccc
Q 007742          299 EKN  301 (591)
Q Consensus       299 ~~~  301 (591)
                      ...
T Consensus       104 ~~~  106 (114)
T 2cq4_A          104 EKN  106 (114)
T ss_dssp             HHH
T ss_pred             Ccc
Confidence            554

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.66  E-value=8.6e-17  Score=130.71  Aligned_cols=82  Identities=18%  Similarity=0.314  Sum_probs=77.4

Q ss_pred             CCcEEEEeCCCC------CCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC-ee
Q 007742          219 DQRTVFAYQMPL------KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG-QP  290 (591)
Q Consensus       219 ~~~~l~V~nLp~------~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g-~~  290 (591)
                      ..++|||+|||+      .+++++|.++|.+||.|..|.|+.++.||.++|||||+|.+.++|.+|+ .|||..|.| +.
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            458999999999      9999999999999999999999999999999999999999999999999 699999999 99


Q ss_pred             EEeccCcccc
Q 007742          291 VMVKPSEAEK  300 (591)
Q Consensus       291 i~v~~~~~~~  300 (591)
                      |.|.++.+..
T Consensus        85 l~V~~a~~~~   94 (100)
T 3ns6_A           85 LFLYTMKDVE   94 (100)
T ss_dssp             CEEEESHHHH
T ss_pred             EEEEECchhh
Confidence            9999886643

>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=99.66  E-value=3.2e-16  Score=126.51  Aligned_cols=82  Identities=28%  Similarity=0.439  Sum_probs=77.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      +++|||+|||+.+|+++|.++|.+||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++..
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            589999999999999999999999999999999999999999999999999999999999 6999999999999998876


Q ss_pred             ccc
Q 007742          299 EKN  301 (591)
Q Consensus       299 ~~~  301 (591)
                      ...
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3.5e-16  Score=126.10  Aligned_cols=82  Identities=30%  Similarity=0.448  Sum_probs=77.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|+++|..||.|..|.++.++.+|.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            445699999999999999999999999999999999999999999999999999999999999 5999999999999998


Q ss_pred             Ccc
Q 007742          296 SEA  298 (591)
Q Consensus       296 ~~~  298 (591)
                      +..
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            753

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3.4e-16  Score=127.99  Aligned_cols=85  Identities=24%  Similarity=0.490  Sum_probs=79.1

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..|.++.++.++.++|||||+|.+.++|..|+ .||+..|.|+.|.|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3446799999999999999999999999999999999999999999999999999999999999 799999999999999


Q ss_pred             cCcccc
Q 007742          295 PSEAEK  300 (591)
Q Consensus       295 ~~~~~~  300 (591)
                      ++....
T Consensus        88 ~a~~~~   93 (102)
T 1x5s_A           88 QAGKSS   93 (102)
T ss_dssp             EEECCC
T ss_pred             ECCCCC
Confidence            886544

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.66  E-value=1.1e-16  Score=165.08  Aligned_cols=167  Identities=17%  Similarity=0.345  Sum_probs=110.1

Q ss_pred             HHHHHHhcCCCeeEEEEee----cC-CCCCccceE--EEEecCcchHHHHH-HHcCCccCCeeEEeccCcccccc-cccc
Q 007742          236 DVYEFFSKAGKVRDVRLIM----DR-NSRRSKGVG--YIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNL-VQSN  306 (591)
Q Consensus       236 ~l~~~f~~~G~i~~v~~~~----d~-~~g~~~G~a--fV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~~~~-~~~~  306 (591)
                      .|..+|.++|+|..|..+.    +. .+....|++  |+.|.....+..++ .++.....+.............. ....
T Consensus         8 ~L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~   87 (437)
T 3pgw_S            8 NLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELK   87 (437)
T ss_pred             cHHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            3788999999998773332    22 233344555  88888766655444 22222111110000000000000 0000


Q ss_pred             CCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCC
Q 007742          307 TSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK  386 (591)
Q Consensus       307 ~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~  386 (591)
                      .............+.++|||+|||+.+|+++|.++|.+||.|..|.|+.+..++.++|||||+|.+.++|..||..|||.
T Consensus        88 ~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  167 (437)
T 3pgw_S           88 MWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGK  167 (437)
T ss_pred             hcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCC
Confidence            00000111112233589999999999999999999999999999999999889999999999999999999999999996


Q ss_pred             eeeCCeEEEEEEecCCC
Q 007742          387 LEIVGRTLKVSSVTDHV  403 (591)
Q Consensus       387 ~~~~g~~l~v~~~~~~~  403 (591)
                       .|.|+.|.|.++....
T Consensus       168 -~i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          168 -KIDGRRVLVDVERGRT  183 (437)
T ss_pred             -EECCEEEEEEEeCCCC
Confidence             6999999999987543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.8e-16  Score=128.67  Aligned_cols=84  Identities=23%  Similarity=0.286  Sum_probs=78.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|.+||.|..|.++.++.+|.++|||||+|.+.++|.+|| .||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            345799999999999999999999999999999999999999999999999999999999999 5999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +.+..
T Consensus        92 a~~~~   96 (103)
T 2cq0_A           92 AKPST   96 (103)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            86644

>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=99.66  E-value=4.2e-16  Score=128.45  Aligned_cols=84  Identities=26%  Similarity=0.443  Sum_probs=78.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      +....++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|.|+.|.|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456799999999999999999999999999999999999999999999999999999999999 599999999999999


Q ss_pred             cCccc
Q 007742          295 PSEAE  299 (591)
Q Consensus       295 ~~~~~  299 (591)
                      ++.+.
T Consensus       102 ~a~~k  106 (108)
T 2jrs_A          102 HVTER  106 (108)
T ss_dssp             CSCSS
T ss_pred             EcccC
Confidence            88653

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=5.5e-16  Score=128.00  Aligned_cols=86  Identities=22%  Similarity=0.480  Sum_probs=79.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeec-CCCCCccceEEEEecCcchHHHHH-HH-cCCccCCeeEE
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMD-RNSRRSKGVGYIEFYDVMSVPMAI-AL-SGQLLLGQPVM  292 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d-~~~g~~~G~afV~F~~~e~A~~Al-~l-~g~~i~g~~i~  292 (591)
                      .....++|||+|||+.+|+++|+++|..||.|..|.|+.+ ..+|.++|||||+|.+.++|.+|| .| |+..|.|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3456799999999999999999999999999999999999 788999999999999999999999 58 89999999999


Q ss_pred             eccCccccc
Q 007742          293 VKPSEAEKN  301 (591)
Q Consensus       293 v~~~~~~~~  301 (591)
                      |.++.....
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999876543

>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=99.66  E-value=4.3e-16  Score=130.13  Aligned_cols=77  Identities=26%  Similarity=0.443  Sum_probs=71.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      .+|||+|||+.+++++|+++|+.||.|..|.|+.+.  +.++|||||+|.+.++|..||..|+|. .|.|+.|.|.++..
T Consensus         6 ~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~-~~~g~~i~V~~a~~   82 (115)
T 4f25_A            6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGM-LLNDRKVFVGRFKS   82 (115)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTC-EETTEECEEEESSC
T ss_pred             CEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEECCC
Confidence            689999999999999999999999999999999874  447999999999999999999999996 69999999998753

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=2.4e-16  Score=128.84  Aligned_cols=84  Identities=15%  Similarity=0.357  Sum_probs=78.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|..||.|..|.|+.++.++.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            346799999999999999999999999999999999999999999999999999999999999 6999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +.+..
T Consensus        89 a~~~~   93 (102)
T 2cqb_A           89 AKPMR   93 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87644

>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=99.65  E-value=4.3e-16  Score=130.37  Aligned_cols=85  Identities=19%  Similarity=0.422  Sum_probs=79.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+.+|+++|+++|..||.|..|.|+.++.+|.++|||||+|.+.++|.+|| .||+..|.|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999999999989999999999999999999999 7999999999999999


Q ss_pred             Cccccc
Q 007742          296 SEAEKN  301 (591)
Q Consensus       296 ~~~~~~  301 (591)
                      +.+...
T Consensus       102 a~~~~~  107 (115)
T 2cpz_A          102 KRSKND  107 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCc
Confidence            876543

>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=99.65  E-value=4.4e-16  Score=127.77  Aligned_cols=85  Identities=29%  Similarity=0.468  Sum_probs=78.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC-CCccceEEEEecCcchHHHHHHHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS-RRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~-g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~  294 (591)
                      +..+.++|||+|||+.+|+++|.++|..|| |..|.|+.++.+ |.++|||||+|.+.++|.+||.||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVD   89 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEE
Confidence            345669999999999999999999999999 999999999988 999999999999999999999999999999999999


Q ss_pred             cCccccc
Q 007742          295 PSEAEKN  301 (591)
Q Consensus       295 ~~~~~~~  301 (591)
                      ++.....
T Consensus        90 ~a~~~~~   96 (104)
T 1wi8_A           90 VADQAQD   96 (104)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9876543

>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=99.65  E-value=2.5e-16  Score=131.91  Aligned_cols=104  Identities=24%  Similarity=0.438  Sum_probs=92.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ...+++|||+|||+.+|+++|.++|..||.|..|.++.+   +.++|||||+|.+.++|..|+ .|||..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            345689999999999999999999999999999999976   446999999999999999999 5999999999999999


Q ss_pred             CccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCC
Q 007742          296 SEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGP  347 (591)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~  347 (591)
                      +.+....                        .+++...++++|.++|++||.
T Consensus        82 a~~~~~~------------------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           82 YNANRAF------------------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CCHHHHT------------------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             ecCChhh------------------------hhhhHhHhHHHHHHHHHHhCC
Confidence            8764431                        467778899999999999984

>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=99.65  E-value=6.3e-16  Score=128.55  Aligned_cols=84  Identities=21%  Similarity=0.386  Sum_probs=78.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHc------CCccCCe
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALS------GQLLLGQ  289 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~------g~~i~g~  289 (591)
                      ..+.++|||+|||+.+|+++|.++|..||.|..|.|+.++.+|.++|||||+|.+.++|.+|| .||      +..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            446789999999999999999999999999999999999999999999999999999999999 588      9999999


Q ss_pred             eEEeccCcccc
Q 007742          290 PVMVKPSEAEK  300 (591)
Q Consensus       290 ~i~v~~~~~~~  300 (591)
                      .|.|.++.+..
T Consensus        92 ~l~v~~a~~~~  102 (111)
T 1x4h_A           92 QLKVDLAVTRD  102 (111)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCc
Confidence            99999987654

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.65  E-value=1.3e-16  Score=122.36  Aligned_cols=75  Identities=24%  Similarity=0.409  Sum_probs=72.0

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       222 ~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      +|||+|||+.+|+++|.++|.+||.|..|.++.++.+|.++|||||+|.+.++|.+|+.+++..|.|+.|.|.++
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 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            589999999999999999999999999999999998999999999999999999999999999999999999764

>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=99.65  E-value=4.2e-16  Score=123.98  Aligned_cols=79  Identities=30%  Similarity=0.499  Sum_probs=75.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      .++|||+|||+.+|+++|.++|..||.|..|.++.+..+|.++|||||+|.+.++|.+|+.+||..|.|+.|.|.++.+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccC
Confidence            4899999999999999999999999999999999999999999999999999999999999999999999999998865

>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=99.65  E-value=4.3e-16  Score=129.27  Aligned_cols=83  Identities=24%  Similarity=0.362  Sum_probs=78.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|.|+.|.|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            445699999999999999999999999999999999999999999999999999999999999 5999999999999999


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +...
T Consensus       103 a~~~  106 (110)
T 1oo0_B          103 CFVK  106 (110)
T ss_dssp             SEES
T ss_pred             cccC
Confidence            8654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=9.2e-16  Score=128.56  Aligned_cols=84  Identities=18%  Similarity=0.356  Sum_probs=77.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~  294 (591)
                      .....++|||+|||+.+|+++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|.+||. +++ .|.|+.|.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            34567999999999999999999999999999999999999999999999999999999999995 776 8999999999


Q ss_pred             cCcccc
Q 007742          295 PSEAEK  300 (591)
Q Consensus       295 ~~~~~~  300 (591)
                      ++....
T Consensus        92 ~a~~~~   97 (116)
T 2cqd_A           92 LAYLGA   97 (116)
T ss_dssp             ESTTTC
T ss_pred             EcccCC
Confidence            986543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=6.5e-16  Score=125.75  Aligned_cols=82  Identities=22%  Similarity=0.464  Sum_probs=76.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|..||.|..|.++.+. +|.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.+
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4457899999999999999999999999999999999998 8999999999999999999999 7999999999999998


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +.+.
T Consensus        93 a~~~   96 (100)
T 2do4_A           93 SNSG   96 (100)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8654

>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=99.65  E-value=5e-16  Score=127.95  Aligned_cols=86  Identities=27%  Similarity=0.467  Sum_probs=79.1

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCcc---CCee
Q 007742          215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL---LGQP  290 (591)
Q Consensus       215 ~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i---~g~~  290 (591)
                      ......++|||+|||+.+|+++|+++|.+||.|..|.|+.++.+|.++|||||+|.+.++|.+|+ .||+..+   .|+.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            34456799999999999999999999999999999999999999999999999999999999999 5999987   8999


Q ss_pred             EEeccCcccc
Q 007742          291 VMVKPSEAEK  300 (591)
Q Consensus       291 i~v~~~~~~~  300 (591)
                      |.|.++....
T Consensus        88 l~v~~a~~~~   97 (106)
T 2dgp_A           88 IQVKPADSES   97 (106)
T ss_dssp             CEEEECCCCS
T ss_pred             EEEEECCccc
Confidence            9999987644

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=4.9e-16  Score=127.75  Aligned_cols=84  Identities=23%  Similarity=0.409  Sum_probs=78.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      ....++|||+|||+.+|+++|+++|..||.|..|.|+.++.+|.++|||||+|.+.++|.+||..++..|.|+.|.|.++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~a   92 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPC   92 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEc
Confidence            44679999999999999999999999999999999999999999999999999999999999966999999999999998


Q ss_pred             cccc
Q 007742          297 EAEK  300 (591)
Q Consensus       297 ~~~~  300 (591)
                      .+..
T Consensus        93 ~~~~   96 (105)
T 2dh8_A           93 TPRG   96 (105)
T ss_dssp             CCSS
T ss_pred             cCCC
Confidence            7654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.65  E-value=1e-15  Score=126.19  Aligned_cols=80  Identities=23%  Similarity=0.282  Sum_probs=76.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +.++|||+|||+.+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~-~~~gr~i~V~~a   83 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLT-SVMGNIIHAQLD   83 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEEC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEEEC
Confidence            3589999999999999999999999999999999999988999999999999999999999999996 799999999987


Q ss_pred             c
Q 007742          400 T  400 (591)
Q Consensus       400 ~  400 (591)
                      .
T Consensus        84 ~   84 (110)
T 3s8s_A           84 I   84 (110)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=3.8e-16  Score=126.63  Aligned_cols=84  Identities=23%  Similarity=0.381  Sum_probs=77.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCC---CCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEe
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRN---SRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMV  293 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~---~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v  293 (591)
                      .+.++|||+|||+.+|+++|+++|..||.|..|.++.+..   ++.++|||||+|.+.++|.+|+. ||+..|.|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3568999999999999999999999999999999999876   66899999999999999999995 9999999999999


Q ss_pred             ccCccccc
Q 007742          294 KPSEAEKN  301 (591)
Q Consensus       294 ~~~~~~~~  301 (591)
                      .++.....
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=3.5e-16  Score=126.39  Aligned_cols=83  Identities=23%  Similarity=0.399  Sum_probs=77.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEE-EEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEecc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDV-RLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKP  295 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v-~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~  295 (591)
                      .+.++|||+|||+.+|+++|.++|..||.|..| .++.++.+|.++|||||+|.+.++|.+|+. ||+..|.|+.|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            356999999999999999999999999999999 999998999999999999999999999995 999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +.+..
T Consensus        83 a~~~~   87 (96)
T 1x5t_A           83 AFKKD   87 (96)
T ss_dssp             SCCCC
T ss_pred             ecccC
Confidence            86644

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=2.9e-16  Score=127.59  Aligned_cols=83  Identities=16%  Similarity=0.260  Sum_probs=77.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCee-EEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCee----
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVR-DVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQP----  290 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~-~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~----  290 (591)
                      ..+.++|||+|||+.+|+++|+++|.+||.|. .|.++.++.+|.++|||||+|.+.++|.+|+. |||..|.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            44679999999999999999999999999999 99999999999999999999999999999995 9999999999    


Q ss_pred             EEeccCccc
Q 007742          291 VMVKPSEAE  299 (591)
Q Consensus       291 i~v~~~~~~  299 (591)
                      |.|.++.+.
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999887653

>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=99.64  E-value=7.9e-16  Score=128.59  Aligned_cols=82  Identities=23%  Similarity=0.415  Sum_probs=76.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ...++|||+|||+.+|+++|.++|.+||.|..|.++.+. +|.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            456899999999999999999999999999999999998 8999999999999999999999 59999999999999998


Q ss_pred             cccc
Q 007742          297 EAEK  300 (591)
Q Consensus       297 ~~~~  300 (591)
                      ....
T Consensus        84 ~~~~   87 (116)
T 2fy1_A           84 KKPS   87 (116)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7544

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=5.8e-16  Score=124.54  Aligned_cols=80  Identities=33%  Similarity=0.572  Sum_probs=75.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|.+||.|..|.++.++.+|.++|||||+|.+.++|..|+ .||+..|.|+.|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            345689999999999999999999999999999999999999999999999999999999999 6999999999999987


Q ss_pred             C
Q 007742          296 S  296 (591)
Q Consensus       296 ~  296 (591)
                      +
T Consensus        93 a   93 (94)
T 2e5h_A           93 A   93 (94)
T ss_dssp             C
T ss_pred             c
Confidence            6

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=7.8e-16  Score=126.30  Aligned_cols=84  Identities=23%  Similarity=0.419  Sum_probs=77.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhc-CCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCc-cCCeeEEe
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSK-AGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQL-LLGQPVMV  293 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~-~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~-i~g~~i~v  293 (591)
                      ..+.++|||+|||+.+|+++|.++|.. ||.|..|.|+.+. +|.++|||||+|.+.++|.+|| .||+.. |.|+.|.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            345699999999999999999999999 9999999999998 8999999999999999999999 599999 99999999


Q ss_pred             ccCccccc
Q 007742          294 KPSEAEKN  301 (591)
Q Consensus       294 ~~~~~~~~  301 (591)
                      .++.....
T Consensus        85 ~~a~~~~~   92 (104)
T 2dhg_A           85 SVAIPKAS   92 (104)
T ss_dssp             CBCCCCCS
T ss_pred             EEccCCCc
Confidence            99865543

>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=99.64  E-value=5.1e-16  Score=132.16  Aligned_cols=83  Identities=31%  Similarity=0.434  Sum_probs=78.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|.+||.|..|.++.++.+|.++|||||+|.+.++|.+|| .|||..|.|+.|.|.+
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            445689999999999999999999999999999999999999999999999999999999999 5999999999999999


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +...
T Consensus       123 a~~~  126 (129)
T 2kxn_B          123 SITK  126 (129)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            8654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=7.7e-16  Score=126.07  Aligned_cols=83  Identities=17%  Similarity=0.386  Sum_probs=76.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|+++|..||.|..|.++.+  +|.++|||||+|.+.++|..|+ .||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            446799999999999999999999999999999999998  7899999999999999999999 5999999999999999


Q ss_pred             Cccccc
Q 007742          296 SEAEKN  301 (591)
Q Consensus       296 ~~~~~~  301 (591)
                      +.....
T Consensus        90 a~~~~~   95 (103)
T 2d9p_A           90 AQRKEE   95 (103)
T ss_dssp             CSSCCC
T ss_pred             eccccc
Confidence            876543

>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=99.64  E-value=1.1e-15  Score=125.60  Aligned_cols=84  Identities=23%  Similarity=0.400  Sum_probs=77.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC---eeEE
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG---QPVM  292 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g---~~i~  292 (591)
                      ....++|||+|||+.+|+++|.++|..||.|..|.|+.++ +|.++|||||+|.+.++|.+|+ .||+..+.|   +.|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3457999999999999999999999999999999999997 6899999999999999999999 599999988   9999


Q ss_pred             eccCccccc
Q 007742          293 VKPSEAEKN  301 (591)
Q Consensus       293 v~~~~~~~~  301 (591)
                      |.++.....
T Consensus        91 V~~a~~~~~   99 (105)
T 2dnh_A           91 VKFADTDKE   99 (105)
T ss_dssp             EEESCSSCC
T ss_pred             EEECccCcc
Confidence            998876543

>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=99.64  E-value=2.9e-16  Score=131.03  Aligned_cols=84  Identities=17%  Similarity=0.240  Sum_probs=77.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCe-eEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKV-RDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i-~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~  294 (591)
                      ...+.++|||+|||+.+|+++|+++|..||.| ..|.|+.++ +|.++|||||+|.+.++|.+||.+|+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~   89 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVH   89 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEE
Confidence            34567999999999999999999999999999 899999998 8999999999999999999999889999999999999


Q ss_pred             cCcccc
Q 007742          295 PSEAEK  300 (591)
Q Consensus       295 ~~~~~~  300 (591)
                      ++....
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            887655

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.63  E-value=4.1e-16  Score=127.22  Aligned_cols=99  Identities=21%  Similarity=0.294  Sum_probs=81.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      ++|||+|||+.+|+++|+++|.+||.|..|.++.+     ++|||||+|.+.++|.+|+ .||+..+.|+.|.|.++...
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            48999999999999999999999999999999876     6899999999999999999 59999999999999998765


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEcCCC
Q 007742          300 KNLVQSNTSAGGTATGPYGAIDRKLYVGNLH  330 (591)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~  330 (591)
                      ........+      .........|||+||+
T Consensus        76 ~~~~~~~~~------~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           76 PRRSRFDRP------PARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSSCCCSC------CCSCCCCSCCCSCCCC
T ss_pred             CCcccCCCC------CccccCCCceecCCCC
Confidence            532211111      1112234789999996

>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=99.63  E-value=6.9e-16  Score=131.46  Aligned_cols=86  Identities=26%  Similarity=0.392  Sum_probs=79.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      ...+.++|||+|||+.+|+++|.++|..||.|..|.|+.++.+|.++|||||+|.+.++|.+|| .|||..|.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            3445789999999999999999999999999999999999999999999999999999999999 699999999999999


Q ss_pred             cCccccc
Q 007742          295 PSEAEKN  301 (591)
Q Consensus       295 ~~~~~~~  301 (591)
                      ++.....
T Consensus        98 ~a~~~~~  104 (126)
T 3ex7_B           98 WCFVRGP  104 (126)
T ss_dssp             ESEESSS
T ss_pred             EecCCCC
Confidence            9876543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2.3e-16  Score=124.30  Aligned_cols=80  Identities=18%  Similarity=0.330  Sum_probs=75.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      .+.++|||+|||+.+|+++|+++|.+||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|.|+.|++.++
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            45689999999999999999999999999999999999999999999999999999999999 59999999999988765


Q ss_pred             c
Q 007742          297 E  297 (591)
Q Consensus       297 ~  297 (591)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.63  E-value=5.6e-16  Score=128.02  Aligned_cols=86  Identities=21%  Similarity=0.349  Sum_probs=75.1

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEe
Q 007742          214 ADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMV  293 (591)
Q Consensus       214 ~~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v  293 (591)
                      .+.....++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|..||..++..|.|+.|.|
T Consensus        19 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V   98 (109)
T 2rs2_A           19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDP   98 (109)
T ss_dssp             -------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEE
Confidence            34455679999999999999999999999999999999999999999999999999999999999987778899999999


Q ss_pred             ccCccc
Q 007742          294 KPSEAE  299 (591)
Q Consensus       294 ~~~~~~  299 (591)
                      .++.+.
T Consensus        99 ~~a~~~  104 (109)
T 2rs2_A           99 KVAFPR  104 (109)
T ss_dssp             EECCCC
T ss_pred             EEccCC
Confidence            987653

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=9.7e-16  Score=127.81  Aligned_cols=85  Identities=18%  Similarity=0.364  Sum_probs=78.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCee--------EEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVR--------DVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL  287 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~--------~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~  287 (591)
                      ..+.++|||+|||+.+|+++|+++|..||.|.        .|.|+.++.+|.++|||||+|.+.++|.+|| .||+..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            44679999999999999999999999999999        6999999999999999999999999999999 59999999


Q ss_pred             CeeEEeccCccccc
Q 007742          288 GQPVMVKPSEAEKN  301 (591)
Q Consensus       288 g~~i~v~~~~~~~~  301 (591)
                      |+.|.|.++.....
T Consensus        92 g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           92 GSKLKVSLARKKPP  105 (113)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CCEEEEEECCCCCC
Confidence            99999999876543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=2.5e-15  Score=125.52  Aligned_cols=84  Identities=31%  Similarity=0.472  Sum_probs=76.9

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEe
Q 007742          215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV  293 (591)
Q Consensus       215 ~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v  293 (591)
                      ......++|||+|||+.+|+++|+++|..||.|..|.|+.++ +|.++|||||+|.+.++|..|| .||+..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   88 (114)
T 2do0_A           10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV   88 (114)
T ss_dssp             CCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEE
Confidence            344567999999999999999999999999999999999987 4899999999999999999999 59999999999999


Q ss_pred             ccCccc
Q 007742          294 KPSEAE  299 (591)
Q Consensus       294 ~~~~~~  299 (591)
                      .++...
T Consensus        89 ~~a~~~   94 (114)
T 2do0_A           89 KMDERA   94 (114)
T ss_dssp             EECSCC
T ss_pred             EEcccC
Confidence            987643

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=3.5e-15  Score=119.92  Aligned_cols=83  Identities=30%  Similarity=0.540  Sum_probs=76.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          317 YGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       317 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      ..+..++|||+|||..+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v   90 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNK-QLFGRVIKA   90 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTE-EETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCC-eeCCcEEEE
Confidence            3445689999999999999999999999999999999999888899999999999999999999999995 799999999


Q ss_pred             EEec
Q 007742          397 SSVT  400 (591)
Q Consensus       397 ~~~~  400 (591)
                      .+++
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9863

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=1.8e-15  Score=123.89  Aligned_cols=85  Identities=22%  Similarity=0.387  Sum_probs=77.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEecc
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP  295 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~  295 (591)
                      ...+.++|||+|||+.+|+++|+++|..||.|..|.|+.++.+|.++|||||+|.+.++|..||. ++..|.|+.|.|.+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEEC
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEEEEEe
Confidence            34467899999999999999999999999999999999999999999999999999999999998 57789999999999


Q ss_pred             Cccccc
Q 007742          296 SEAEKN  301 (591)
Q Consensus       296 ~~~~~~  301 (591)
                      +.....
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            876543

>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=99.63  E-value=3.7e-16  Score=127.18  Aligned_cols=80  Identities=23%  Similarity=0.275  Sum_probs=73.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      ....++|||+|||+.+|+++|+++|..||. +.|.|+.++ +|.++|||||+|.+.++|.+||.+|+..|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            445689999999999999999999999995 599999998 899999999999999999999999999999999999876


Q ss_pred             cc
Q 007742          297 EA  298 (591)
Q Consensus       297 ~~  298 (591)
                      ..
T Consensus        90 ~~   91 (102)
T 1wez_A           90 ST   91 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.63  E-value=2.7e-15  Score=122.81  Aligned_cols=85  Identities=22%  Similarity=0.475  Sum_probs=76.8

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEE
Q 007742          214 ADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVM  292 (591)
Q Consensus       214 ~~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~  292 (591)
                      .......++|||+|||+.+|+++|.++|..||.|..|.|+.+..  .++|||||+|.+.++|.+|+ .||+..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34455679999999999999999999999999999999998865  38999999999999999999 5999999999999


Q ss_pred             eccCcccc
Q 007742          293 VKPSEAEK  300 (591)
Q Consensus       293 v~~~~~~~  300 (591)
                      |.++....
T Consensus        87 v~~a~~~~   94 (103)
T 2cq3_A           87 VNNATARV   94 (103)
T ss_dssp             EEECCSSC
T ss_pred             EEEcccCC
Confidence            99987654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.63  E-value=7.4e-16  Score=135.57  Aligned_cols=81  Identities=21%  Similarity=0.350  Sum_probs=75.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAG--KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G--~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..++|||+|||+.+|+++|.++|..||  .|..|.|+.++.+|.++|||||+|.+.++|..|| .|||..|.|+.|.|.+
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            458999999999999999999999999  9999999999999999999999999999999999 5799999999999998


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +...
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.62  E-value=1.1e-15  Score=116.81  Aligned_cols=83  Identities=22%  Similarity=0.197  Sum_probs=73.8

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEE
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI  575 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l  575 (591)
                      ..+.-|+|+||  +..++        +++|+++|.+||.|.++.+.. ++|||||+|.+.++|.+|++.|||..|+|++|
T Consensus         5 ~~~~wL~VgNL--~~~~t--------e~~L~~lF~q~G~V~~~~l~~-~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I   73 (89)
T 2wbr_A            5 WGSSWLLLKNL--TAQID--------GPTLRTLCMQHGPLVSFHPYL-NQGIALCKYTTREEANKAQMALNNCVLANTTI   73 (89)
T ss_dssp             CCCCEEEEECC--CTTCC--------CHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CccceEEEeCC--CccCC--------HHHHHHHHHhhCCEEEEEEcC-CCcEEEEEECCHHHHHHHHHHhcCCEECCcEE
Confidence            34556999999  77777        799999999999999999864 79999999999999999999999999999999


Q ss_pred             EEEEeCchhhhhcc
Q 007742          576 SAIFMKPEDYEAKF  589 (591)
Q Consensus       576 ~v~~~~~~~~~~~~  589 (591)
                      .|.++++......+
T Consensus        74 ~V~~A~e~~~~~~~   87 (89)
T 2wbr_A           74 FAESPSENEVQSIM   87 (89)
T ss_dssp             EEECCCHHHHHHHH
T ss_pred             EEEECCHHHHHHHh
Confidence            99999987765443

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.62  E-value=6.4e-16  Score=132.41  Aligned_cols=85  Identities=15%  Similarity=0.298  Sum_probs=77.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeE--EEEeecCCCCCccceEEEEecCcchHHHHH-HHcCC----ccCC
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRD--VRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQ----LLLG  288 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~--v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~----~i~g  288 (591)
                      .....++|||+|||+.+|+++|+++|.+||.|..  |.|+.++.+|.++|||||+|.+. +|..|+ .|||.    .|.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3456789999999999999999999999999976  99999999999999999999999 999999 69999    9999


Q ss_pred             eeEEeccCccccc
Q 007742          289 QPVMVKPSEAEKN  301 (591)
Q Consensus       289 ~~i~v~~~~~~~~  301 (591)
                      +.|.|.++.+...
T Consensus        98 r~l~V~~a~~~~~  110 (131)
T 2m2b_A           98 KTINVEFAKGSKR  110 (131)
T ss_dssp             CCCCCEECCCSCC
T ss_pred             EEEEEEECCCCCC
Confidence            9999998876543

>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=99.62  E-value=1.2e-15  Score=125.80  Aligned_cols=80  Identities=20%  Similarity=0.342  Sum_probs=75.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+.+|+++|.++|..||.|..|.|+.+. +|.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.+
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3457999999999999999999999999999999999998 8999999999999999999999 5999999999999987


Q ss_pred             Cc
Q 007742          296 SE  297 (591)
Q Consensus       296 ~~  297 (591)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            63

>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=99.62  E-value=2.3e-15  Score=123.22  Aligned_cols=83  Identities=23%  Similarity=0.450  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      .....++|||+|||+.+|+++|+++|.+||.|..|.|+.+..+  ++|||||+|.+.++|.+|+ .||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            4456799999999999999999999999999999999998654  6899999999999999999 599999999999999


Q ss_pred             cCcccc
Q 007742          295 PSEAEK  300 (591)
Q Consensus       295 ~~~~~~  300 (591)
                      ++....
T Consensus        89 ~a~~~~   94 (103)
T 2cqi_A           89 WATTPS   94 (103)
T ss_dssp             ECCCTT
T ss_pred             ECCCCc
Confidence            987644

>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=99.62  E-value=1.3e-15  Score=122.76  Aligned_cols=80  Identities=35%  Similarity=0.555  Sum_probs=74.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+.+|+++|+++|.+||.|..|.++.++. |.++|||||+|.+.++|.+|+. ||+..|.|+.|.|.+
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            34569999999999999999999999999999999999986 8999999999999999999995 999999999999988


Q ss_pred             Cc
Q 007742          296 SE  297 (591)
Q Consensus       296 ~~  297 (591)
                      +.
T Consensus        92 a~   93 (95)
T 2ywk_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.62  E-value=8.1e-15  Score=122.60  Aligned_cols=85  Identities=27%  Similarity=0.493  Sum_probs=78.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||..+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~   91 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQ-WLGGRQIRTNW   91 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTC-EETTEECEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEE
Confidence            34589999999999999999999999999999999999878999999999999999999999999996 69999999999


Q ss_pred             ecCCCC
Q 007742          399 VTDHVG  404 (591)
Q Consensus       399 ~~~~~~  404 (591)
                      +.....
T Consensus        92 a~~~~~   97 (115)
T 2dgo_A           92 ATRKPP   97 (115)
T ss_dssp             SSCCCC
T ss_pred             ccCCCC
Confidence            876544

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.62  E-value=1.9e-15  Score=131.10  Aligned_cols=85  Identities=24%  Similarity=0.453  Sum_probs=79.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+.+|+++|.++|..||.|..|.|+.++.+|.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.+
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            445699999999999999999999999999999999999999999999999999999999999 5999999999999999


Q ss_pred             Cccccc
Q 007742          296 SEAEKN  301 (591)
Q Consensus       296 ~~~~~~  301 (591)
                      +.....
T Consensus       119 a~~~~~  124 (139)
T 1u6f_A          119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.62  E-value=8.1e-16  Score=122.02  Aligned_cols=81  Identities=23%  Similarity=0.367  Sum_probs=75.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCC-ccceEEEEecCcchHHHHHH-HcCCccCCeeEEeccC
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR-SKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKPS  296 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~-~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~~  296 (591)
                      ..++|||+|||+.+|+++|.++|.+||.|..|.++.+..++. ++|||||+|.+.++|.+|+. |||..|.|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            458999999999999999999999999999999999987766 89999999999999999994 9999999999999987


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.1e-15  Score=123.14  Aligned_cols=77  Identities=21%  Similarity=0.356  Sum_probs=69.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-Hc--CCccCCeeEEec
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LS--GQLLLGQPVMVK  294 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~--g~~i~g~~i~v~  294 (591)
                      .+.++|||+|||+.+|+++|+++|.+||.|.+|.|+.+      +|||||+|.+.++|..|+. ++  +..|.|++|.|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            35699999999999999999999999999999999864      7999999999999999995 75  478999999999


Q ss_pred             cCcccc
Q 007742          295 PSEAEK  300 (591)
Q Consensus       295 ~~~~~~  300 (591)
                      ++....
T Consensus        88 ~A~~~~   93 (105)
T 1sjq_A           88 FSNHKE   93 (105)
T ss_dssp             CCSSSS
T ss_pred             EcCCCC
Confidence            986544

>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=99.62  E-value=1.5e-15  Score=122.45  Aligned_cols=80  Identities=14%  Similarity=0.218  Sum_probs=73.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeE
Q 007742          217 ERDQRTVFAYQMPLKATERDVY----EFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV  291 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~----~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i  291 (591)
                      ....++|||+|||+.+|+++|+    ++|.+||.|..|.++.++.+   +|||||+|.+.++|.+|+ .|||..|.|+.|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            3456899999999999999999    99999999999999998775   899999999999999999 599999999999


Q ss_pred             EeccCccc
Q 007742          292 MVKPSEAE  299 (591)
Q Consensus       292 ~v~~~~~~  299 (591)
                      .|.++.+.
T Consensus        83 ~V~~a~~~   90 (96)
T 2dgx_A           83 LVSLATGA   90 (96)
T ss_dssp             EEEECCCS
T ss_pred             EEEEcCCC
Confidence            99988654

>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=99.62  E-value=1.3e-15  Score=124.83  Aligned_cols=81  Identities=17%  Similarity=0.233  Sum_probs=74.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeE-EEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRD-VRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~-v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+.+|+++|+++|..||.|.. |.|+.+ .+|.++|||||+|.+.++|.+||.+++..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEE
Confidence            345699999999999999999999999999987 888888 789999999999999999999997799999999999987


Q ss_pred             Ccc
Q 007742          296 SEA  298 (591)
Q Consensus       296 ~~~  298 (591)
                      +..
T Consensus        91 ~~~   93 (104)
T 1wg5_A           91 SSR   93 (104)
T ss_dssp             ECT
T ss_pred             CCH
Confidence            654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.62  E-value=1.2e-15  Score=128.38  Aligned_cols=80  Identities=24%  Similarity=0.398  Sum_probs=75.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|+++|.+||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|.|+.|.|.+
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            445699999999999999999999999999999999999999999999999999999999999 5999999999999987


Q ss_pred             C
Q 007742          296 S  296 (591)
Q Consensus       296 ~  296 (591)
                      +
T Consensus       117 a  117 (118)
T 2khc_A          117 K  117 (118)
T ss_dssp             C
T ss_pred             c
Confidence            5

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.62  E-value=2e-15  Score=120.31  Aligned_cols=77  Identities=21%  Similarity=0.255  Sum_probs=69.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCc--cCCeeEEe
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQL--LLGQPVMV  293 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~--i~g~~i~v  293 (591)
                      ..++++|||+|||+.+|+++|.++|.+||.|.+|.+++      .+|||||+|.+.++|..|+ .|++..  |.|++|.|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            44679999999999999999999999999999999984      4799999999999999999 688775  78999999


Q ss_pred             ccCccc
Q 007742          294 KPSEAE  299 (591)
Q Consensus       294 ~~~~~~  299 (591)
                      .++..+
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            998653

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=5.2e-15  Score=119.17  Aligned_cols=83  Identities=33%  Similarity=0.527  Sum_probs=76.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      .++.++|||+|||..+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~   90 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM-ELDGRRIRVS   90 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTE-EETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEE
Confidence            344689999999999999999999999999999999999888999999999999999999999999995 7999999999


Q ss_pred             EecC
Q 007742          398 SVTD  401 (591)
Q Consensus       398 ~~~~  401 (591)
                      +++.
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            8753

>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=99.61  E-value=3.5e-16  Score=127.21  Aligned_cols=82  Identities=32%  Similarity=0.480  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecC-CCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR-NSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~-~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~  294 (591)
                      .....++|||+|||+.+|+++|.++|..|| |..|.++.++ .+|.++|||||+|.+.++|..|+.|||..|.|+.|.|.
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVD   93 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEE
Confidence            344679999999999999999999999999 9999999998 68999999999999999999999999999999999999


Q ss_pred             cCcc
Q 007742          295 PSEA  298 (591)
Q Consensus       295 ~~~~  298 (591)
                      ++..
T Consensus        94 ~a~~   97 (100)
T 2j76_E           94 VADQ   97 (100)
T ss_dssp             ECCC
T ss_pred             eccC
Confidence            8764

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.61  E-value=4.7e-16  Score=133.66  Aligned_cols=121  Identities=25%  Similarity=0.353  Sum_probs=78.4

Q ss_pred             eEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHh
Q 007742          264 VGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLF  342 (591)
Q Consensus       264 ~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f  342 (591)
                      ++|++|.+...+..|| .++|....|... +.+..                ........++|||+|||..+++++|+++|
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~----------------~~~~~~~~~~l~V~nLp~~~te~~L~~~F   68 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGR----------------PPPDVEGMTSLKVDNLTYRTSPDTLRRVF   68 (135)
T ss_dssp             ------------------------------CCSCC----------------SCSSGGGCCCEEEECCCSSCHHHHHHHHH
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCC-CCcCC----------------CCCCCCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            5677777777788888 577766555431 11111                11112234899999999999999999999


Q ss_pred             ccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          343 EPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       343 ~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      +.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.++...
T Consensus        69 ~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~-~i~g~~l~V~~a~~~  127 (135)
T 2lea_A           69 EKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA-VLDGRELRVQMARYG  127 (135)
T ss_dssp             GGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTC-CSSSSCCEEEECCCC
T ss_pred             HhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEECCCC
Confidence            99999999999998888999999999999999999999999996 699999999998654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.61  E-value=3.2e-15  Score=119.06  Aligned_cols=80  Identities=13%  Similarity=0.116  Sum_probs=72.8

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccc--cC
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRW--FA  571 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~--~~  571 (591)
                      ..+|+++|+|+||  |..++        +++|.++|+.||.|.+|.+.+ .+|+|||+|.+.++|..|+..|+|..  |.
T Consensus        17 ~~~ps~~l~V~NL--p~~~t--------e~~L~~lF~~fG~V~~v~i~~-~kg~AFVef~~~~~A~~Av~~ln~~~~~i~   85 (100)
T 3r27_A           17 KTPASPVVHIRGL--IDGVV--------EADLVEALQEFGPISYVVVMP-KKRQALVEFEDVLGACNAVNYAADNQIYIA   85 (100)
T ss_dssp             CCCCCSEEEEESC--CTTCC--------HHHHHHHHGGGSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCEEET
T ss_pred             cCCCCcEEEEeCC--CCCCC--------HHHHHHHHhccCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHhcCCCceeC
Confidence            4578899999999  88888        899999999999999998874 68999999999999999999999986  78


Q ss_pred             CeEEEEEEeCchh
Q 007742          572 RRLISAIFMKPED  584 (591)
Q Consensus       572 g~~l~v~~~~~~~  584 (591)
                      |++|.|+|++.+.
T Consensus        86 Gr~i~V~~S~~k~   98 (100)
T 3r27_A           86 GHPAFVNYSTSQK   98 (100)
T ss_dssp             TEEEEEEECSCSC
T ss_pred             CcEEEEEeccccc
Confidence            9999999998754

>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=99.61  E-value=6.6e-15  Score=119.51  Aligned_cols=84  Identities=36%  Similarity=0.561  Sum_probs=78.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ..++|||+|||..+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++
T Consensus         7 ~~~~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            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQ-VFQGRMLHVLPS   85 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTE-ESSSCEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEEEc
Confidence            3589999999999999999999999999999999999888999999999999999999999999995 799999999998


Q ss_pred             cCCCC
Q 007742          400 TDHVG  404 (591)
Q Consensus       400 ~~~~~  404 (591)
                      .....
T Consensus        86 ~~~~~   90 (99)
T 1whw_A           86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCcc
Confidence            76543

>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=99.61  E-value=3.3e-15  Score=117.59  Aligned_cols=79  Identities=41%  Similarity=0.679  Sum_probs=74.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ..++|||+|||+.+++++|+++|++||.|..|.++.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++
T Consensus         6 ~~~~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            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVNLA   84 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEEEc
Confidence            3589999999999999999999999999999999998778999999999999999999999999996 699999999986

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=1.8e-15  Score=120.83  Aligned_cols=81  Identities=20%  Similarity=0.296  Sum_probs=75.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      ....++|||+|||+.+|+++|+++|..| .|..|.++.+ .+|.++|||||+|.+.++|.+||.||+..|.|+.|.|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEEC
Confidence            4467999999999999999999999999 9999999999 7799999999999999999999999999999999999987


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      ...
T Consensus        85 ~~~   87 (91)
T 2dgw_A           85 KSG   87 (91)
T ss_dssp             SSC
T ss_pred             CcC
Confidence            654

>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=99.61  E-value=4e-16  Score=119.65  Aligned_cols=75  Identities=19%  Similarity=0.309  Sum_probs=71.4

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       222 ~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      +|||+|||+.+|+++|.++|.+||.|..|.++.++.+|.++|||||+|.+.++|..|+.+++..+.|+.|.|.++
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999988999999999988753

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=9.5e-16  Score=125.73  Aligned_cols=80  Identities=29%  Similarity=0.423  Sum_probs=74.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      ...+|||+|||+.+|+++|+++|..| .|..|.|+.++. |.++|||||+|.+.++|.+||.+|+..|.|+.|.|..+..
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCc
Confidence            35899999999999999999999999 899999999976 9999999999999999999999999999999999987765


Q ss_pred             cc
Q 007742          299 EK  300 (591)
Q Consensus       299 ~~  300 (591)
                      ..
T Consensus        93 ~~   94 (109)
T 2dnn_A           93 RQ   94 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            43

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=5.9e-15  Score=120.56  Aligned_cols=84  Identities=38%  Similarity=0.626  Sum_probs=77.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||..+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.+
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~~   88 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVNL   88 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTE-EETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEEe
Confidence            34589999999999999999999999999999999998888999999999999999999999999995 79999999999


Q ss_pred             ecCCC
Q 007742          399 VTDHV  403 (591)
Q Consensus       399 ~~~~~  403 (591)
                      +.+..
T Consensus        89 a~~~~   93 (102)
T 2cqb_A           89 AKPMR   93 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87543

>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=99.61  E-value=3e-15  Score=133.78  Aligned_cols=135  Identities=24%  Similarity=0.286  Sum_probs=78.3

Q ss_pred             EEecCcchHHHHH-HHcCCccC--CeeEEeccCccccccc-ccc---CCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHH
Q 007742          267 IEFYDVMSVPMAI-ALSGQLLL--GQPVMVKPSEAEKNLV-QSN---TSAGGTATGPYGAIDRKLYVGNLHFNMTETQLR  339 (591)
Q Consensus       267 V~F~~~e~A~~Al-~l~g~~i~--g~~i~v~~~~~~~~~~-~~~---~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~  339 (591)
                      .+|...++|..|+ .+++....  |+.+.+.+........ ...   ...............++|||+|||+.+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            7888999999998 57766554  5555554432211000 000   000011112223445899999999999999999


Q ss_pred             HHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          340 KLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       340 ~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      ++|..||.|..|.|+.+..++.++|||||+|.+.++|..||..|||. .|.|+.|.|.++...
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~~a~~~  152 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA-EIMGQTIQVDWCFVK  152 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEESEEC
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEecCC
Confidence            99999999999999999889999999999999999999999999996 799999999998654

>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=99.60  E-value=6.9e-16  Score=126.65  Aligned_cols=84  Identities=33%  Similarity=0.568  Sum_probs=78.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.
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            3589999999999999999999999999999999999989999999999999999999999 599999999999999887


Q ss_pred             ccccc
Q 007742          298 AEKNL  302 (591)
Q Consensus       298 ~~~~~  302 (591)
                      .....
T Consensus        87 ~~~~~   91 (104)
T 1p1t_A           87 SEKNK   91 (104)
T ss_dssp             CTTHH
T ss_pred             Cccch
Confidence            65543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.8e-15  Score=126.82  Aligned_cols=82  Identities=26%  Similarity=0.439  Sum_probs=77.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCccc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~~  299 (591)
                      .++|||+|||+.+|+++|+++|..||.|..|.|+.++.+|.++|||||+|.+.++|..||.+++..|.|+.|.|.++.+.
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~~  106 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR  106 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECCCC
Confidence            48999999999999999999999999999999999999999999999999999999999977999999999999998765


Q ss_pred             cc
Q 007742          300 KN  301 (591)
Q Consensus       300 ~~  301 (591)
                      ..
T Consensus       107 ~~  108 (116)
T 1x4b_A          107 EE  108 (116)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.60  E-value=2.6e-15  Score=120.10  Aligned_cols=81  Identities=21%  Similarity=0.334  Sum_probs=74.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|+++|.+||.|..|.++.+  +|.++|||||+|.+.++|..|+ .||+..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345799999999999999999999999999999999974  6889999999999999999999 5999999999999998


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +...
T Consensus        83 a~~~   86 (92)
T 2dgv_A           83 DRNA   86 (92)
T ss_dssp             CSCC
T ss_pred             cCCC
Confidence            8654

>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=99.60  E-value=2.4e-15  Score=134.48  Aligned_cols=84  Identities=24%  Similarity=0.353  Sum_probs=78.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|..+|.+||.|..|.|+.++.+|.++|||||+|.+.++|..|| .|||..|.|+.|.|.+
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            445789999999999999999999999999999999999999999999999999999999999 5999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +....
T Consensus       149 a~~~~  153 (165)
T 1rk8_A          149 CFVKG  153 (165)
T ss_dssp             SEECC
T ss_pred             ecCCC
Confidence            86644

>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=99.60  E-value=5.6e-15  Score=115.68  Aligned_cols=80  Identities=29%  Similarity=0.597  Sum_probs=75.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      .+|||+|||..+++++|+++|..||.|..|.++.+..++.++|||||+|.+.++|..|+..|||. .+.|+.|.|.++.+
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 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ-DLNGRPLRINWAAK   80 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTC-EETTEECEEEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCC-eeCCcEEEEEecCc
Confidence            68999999999999999999999999999999999889999999999999999999999999996 69999999999865


Q ss_pred             C
Q 007742          402 H  402 (591)
Q Consensus       402 ~  402 (591)
                      .
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=8.2e-15  Score=119.89  Aligned_cols=84  Identities=32%  Similarity=0.456  Sum_probs=78.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ....++|||+|||..+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~   90 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGF-GYDHLILNVE   90 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCC-eeCCcEEEEE
Confidence            344689999999999999999999999999999999999888999999999999999999999999996 6999999999


Q ss_pred             EecCC
Q 007742          398 SVTDH  402 (591)
Q Consensus       398 ~~~~~  402 (591)
                      ++...
T Consensus        91 ~a~~~   95 (103)
T 2cq0_A           91 WAKPS   95 (103)
T ss_dssp             ESSCC
T ss_pred             ECCCC
Confidence            98654

>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=99.60  E-value=4.8e-15  Score=117.23  Aligned_cols=80  Identities=29%  Similarity=0.527  Sum_probs=75.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ..+|||+|||..+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++.
T Consensus         6 ~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~~a~   84 (87)
T 3bs9_A            6 HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQ-WLGGRQIRTNWAT   84 (87)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEEEC
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEEecC
Confidence            489999999999999999999999999999999998878999999999999999999999999996 6999999999986


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      .
T Consensus        85 ~   85 (87)
T 3bs9_A           85 R   85 (87)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.60  E-value=8.1e-16  Score=123.92  Aligned_cols=79  Identities=11%  Similarity=0.175  Sum_probs=74.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||+.+|+++|+++|.+||.|..+.++.+..+|.++|||||+|.+.++|.+|| .||+..|.|+.|.|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            4589999999999999999999999999999999999999999999999999999999999 599999999999998764

>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=99.60  E-value=1.1e-15  Score=123.99  Aligned_cols=81  Identities=11%  Similarity=0.156  Sum_probs=75.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ...++|||+|||+.+|+++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.++
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            34689999999999999999999999999998889999899999999999999999999999 79999999999999987


Q ss_pred             cc
Q 007742          297 EA  298 (591)
Q Consensus       297 ~~  298 (591)
                      ..
T Consensus        93 ~~   94 (98)
T 2cqp_A           93 SG   94 (98)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.60  E-value=2.4e-15  Score=123.38  Aligned_cols=80  Identities=18%  Similarity=0.192  Sum_probs=73.0

Q ss_pred             CCCCcEEEEeCCCCCC------CHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCe
Q 007742          217 ERDQRTVFAYQMPLKA------TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQ  289 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~------te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~  289 (591)
                      ....++|||+|||+.+      |+++|..+|.+||.|..|.++  ..+|.++|||||+|.+.++|..|+ .|||..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            4456899999999999      789999999999999999988  467899999999999999999999 5999999998


Q ss_pred             -eEEeccCcc
Q 007742          290 -PVMVKPSEA  298 (591)
Q Consensus       290 -~i~v~~~~~  298 (591)
                       +|.|.++..
T Consensus        90 ~~l~V~~a~~   99 (105)
T 2nlw_A           90 HTFRVNLFTD   99 (105)
T ss_dssp             CEEEEECSCC
T ss_pred             ceEEEEEcch
Confidence             999998754

>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=99.60  E-value=3.3e-15  Score=123.72  Aligned_cols=84  Identities=20%  Similarity=0.297  Sum_probs=76.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCC-eeEEEEe-ecCCCCCccceEEEEecCcchHHHHH-HHc--CCccCCeeEE
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGK-VRDVRLI-MDRNSRRSKGVGYIEFYDVMSVPMAI-ALS--GQLLLGQPVM  292 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~-i~~v~~~-~d~~~g~~~G~afV~F~~~e~A~~Al-~l~--g~~i~g~~i~  292 (591)
                      .+.++|||+|||+.+|+++|.++|..||. |..|.++ .+..+|.++|||||+|.+.++|..|+ .|+  +..|.|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            35689999999999999999999999998 9999998 78888999999999999999999999 585  5889999999


Q ss_pred             eccCccccc
Q 007742          293 VKPSEAEKN  301 (591)
Q Consensus       293 v~~~~~~~~  301 (591)
                      |.++.+...
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999876554

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.60  E-value=1.9e-15  Score=128.32  Aligned_cols=80  Identities=28%  Similarity=0.502  Sum_probs=76.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCccc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~~  299 (591)
                      .++|||+|||+.+|+++|.++|.+||.|..|.++.++.+|.++|||||+|.+.++|..|+.|||..|.|+.|.|.++...
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCCC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999988643

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=9.5e-15  Score=118.54  Aligned_cols=83  Identities=29%  Similarity=0.529  Sum_probs=76.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||..+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..|+. |++. .|.|+.|.|.+
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~-~~~g~~l~V~~   85 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFH-DIMGKKVEVKR   85 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCC-BSSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCC-EECCeEEEEEE
Confidence            345899999999999999999999999999999999998889999999999999999999997 9996 69999999999


Q ss_pred             ecCCC
Q 007742          399 VTDHV  403 (591)
Q Consensus       399 ~~~~~  403 (591)
                      +....
T Consensus        86 a~~~~   90 (99)
T 2dgs_A           86 AEPRD   90 (99)
T ss_dssp             CCCCC
T ss_pred             CCCCc
Confidence            87543

>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=99.60  E-value=5.1e-16  Score=131.73  Aligned_cols=84  Identities=21%  Similarity=0.342  Sum_probs=76.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      ....++|||+|||+.+|+++|.++|..||.|..+.++.+..+|.++|||||+|.+.++|.+||.||+..|.|+.|.|.++
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            44569999999999999999999999999999877777778899999999999999999999999999999999999887


Q ss_pred             cccc
Q 007742          297 EAEK  300 (591)
Q Consensus       297 ~~~~  300 (591)
                      ....
T Consensus       102 ~~~~  105 (124)
T 1wel_A          102 TKKG  105 (124)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            6544

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=6.7e-15  Score=118.48  Aligned_cols=83  Identities=46%  Similarity=0.814  Sum_probs=77.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      .+++|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++
T Consensus         4 ~~~~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            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGF-ELAGRPMRVGHV   82 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTC-CSSSSCCEEEES
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCC-eeCCcEEEEEEc
Confidence            3489999999999999999999999999999999999888999999999999999999999999996 699999999998


Q ss_pred             cCCC
Q 007742          400 TDHV  403 (591)
Q Consensus       400 ~~~~  403 (591)
                      .+..
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            7643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.59  E-value=1.3e-15  Score=127.66  Aligned_cols=83  Identities=20%  Similarity=0.247  Sum_probs=76.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCC---eeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEe
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGK---VRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMV  293 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~---i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v  293 (591)
                      ....++|||+|||+.+|+++|+++|..||.   |..|.|+.++. |.++|||||+|.+.++|.+||.+|+..|.|+.|.|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEE
Confidence            345799999999999999999999999999   89999999987 99999999999999999999999999999999999


Q ss_pred             ccCcccc
Q 007742          294 KPSEAEK  300 (591)
Q Consensus       294 ~~~~~~~  300 (591)
                      .++....
T Consensus        93 ~~a~~~~   99 (118)
T 2db1_A           93 FKSHRTE   99 (118)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            8876544

>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=99.59  E-value=6.7e-15  Score=118.69  Aligned_cols=81  Identities=32%  Similarity=0.591  Sum_probs=76.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +++|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.++.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~~a~   80 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGY-QLGSRFLKCGYSS   80 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECS
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEEEcC
Confidence            479999999999999999999999999999999999888999999999999999999999999996 7999999999986


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      +.
T Consensus        81 ~~   82 (96)
T 2x1f_A           81 NS   82 (96)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=1.5e-15  Score=117.14  Aligned_cols=75  Identities=23%  Similarity=0.417  Sum_probs=70.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEeccC
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKPS  296 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~~  296 (591)
                      ++|||+|||+.+|+++|+++|.+||.|..|.++.++.+|.++|||||+|.+.++|.+|+. ++ ..+.|+.|.|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999999999999999999999999999996 55 8999999999865

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=5.4e-15  Score=120.78  Aligned_cols=84  Identities=36%  Similarity=0.652  Sum_probs=78.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||+.+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..|+..||+. .|.|+.|.|.+
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~~   88 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGK-SVDGRQIRVDQ   88 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTC-CTTSCCCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEEE
Confidence            34589999999999999999999999999999999998888899999999999999999999999996 69999999999


Q ss_pred             ecCCC
Q 007742          399 VTDHV  403 (591)
Q Consensus       399 ~~~~~  403 (591)
                      +....
T Consensus        89 a~~~~   93 (102)
T 1x5s_A           89 AGKSS   93 (102)
T ss_dssp             EECCC
T ss_pred             CCCCC
Confidence            87654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.59  E-value=4.9e-15  Score=125.72  Aligned_cols=82  Identities=20%  Similarity=0.332  Sum_probs=76.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+.+|+++|.++|..||.|..|.++.+. +|.++|||||+|.+.++|..|+. |||..|.|+.|.|.+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4466999999999999999999999999999999999998 89999999999999999999994 999999999999998


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +...
T Consensus       111 a~~~  114 (124)
T 2kt5_A          111 VASQ  114 (124)
T ss_dssp             ECCT
T ss_pred             eCCC
Confidence            7653

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=3.7e-15  Score=123.13  Aligned_cols=85  Identities=22%  Similarity=0.471  Sum_probs=75.8

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCee
Q 007742          212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQP  290 (591)
Q Consensus       212 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~  290 (591)
                      .........++|||+|||..+|+++|.++|.+||.|..|.++.+..  .++|||||+|.+.++|.+|+ .|||..|.|+.
T Consensus        21 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~   98 (109)
T 2err_A           21 MNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRK   98 (109)
T ss_dssp             -CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT--BCTTEEEEECCCSHHHHHHHHHHTTCEETTEE
T ss_pred             CCccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC--CCceEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            3344455679999999999999999999999999999999998853  48999999999999999999 59999999999


Q ss_pred             EEeccCcc
Q 007742          291 VMVKPSEA  298 (591)
Q Consensus       291 i~v~~~~~  298 (591)
                      |.|.++..
T Consensus        99 l~V~~a~~  106 (109)
T 2err_A           99 IEVNNATA  106 (109)
T ss_dssp             CEEEECCC
T ss_pred             EEEEECCC
Confidence            99998765

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.59  E-value=5.3e-15  Score=113.12  Aligned_cols=73  Identities=26%  Similarity=0.324  Sum_probs=68.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +..|||+||++.+++++|+++|.+||+|..+.+..      ++|||||+|.+.++|..|++.||+ ..+.|++|.|.++.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~-~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNN-CVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTT-EEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcC-CEECCcEEEEEECC
Confidence            47899999999999999999999999999999865      589999999999999999999999 48999999999874

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=1.8e-14  Score=117.08  Aligned_cols=82  Identities=23%  Similarity=0.413  Sum_probs=76.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||..+++++|+++|..||.|..|.|+.+. ++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.+
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~   92 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGM-TIKENIIKVAI   92 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTE-ESSSCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEE
Confidence            335899999999999999999999999999999999987 8999999999999999999999999995 79999999999


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      +.+.
T Consensus        93 a~~~   96 (100)
T 2do4_A           93 SNSG   96 (100)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8653

>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=99.59  E-value=5.1e-16  Score=123.71  Aligned_cols=79  Identities=33%  Similarity=0.579  Sum_probs=72.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      ++|||+|||+.+|+++|.++|.+||.|..|.++.++.+|.++|||||+|.+.+ |..|+ .|||..+.|+.|.|.++...
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            68999999999999999999999999999999999999999999999999999 99999 59999999999999988664


Q ss_pred             c
Q 007742          300 K  300 (591)
Q Consensus       300 ~  300 (591)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.59  E-value=1.6e-14  Score=120.05  Aligned_cols=84  Identities=30%  Similarity=0.510  Sum_probs=77.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhc------CCeeeCCe
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN------GKLEIVGR  392 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~------g~~~~~g~  392 (591)
                      ...++|||+|||+.+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..||..|+      + ..|.|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~-~~~~g~   91 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGG-LKLDGR   91 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCC-EESSSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCC-cEEcCE
Confidence            345899999999999999999999999999999999998889999999999999999999999999      8 479999


Q ss_pred             EEEEEEecCCC
Q 007742          393 TLKVSSVTDHV  403 (591)
Q Consensus       393 ~l~v~~~~~~~  403 (591)
                      .|.|.++.+..
T Consensus        92 ~l~v~~a~~~~  102 (111)
T 1x4h_A           92 QLKVDLAVTRD  102 (111)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCc
Confidence            99999987643

>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=99.59  E-value=1.2e-15  Score=130.33  Aligned_cols=83  Identities=20%  Similarity=0.233  Sum_probs=76.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCC---eeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEe
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGK---VRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMV  293 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~---i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v  293 (591)
                      ....++|||+|||+.+|+++|+++|..||.   |..|.|+.++. |.++|||||+|.+.++|.+||.+|+..|.|+.|.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V  119 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEV  119 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEE
Confidence            345689999999999999999999999999   88999999987 99999999999999999999999999999999999


Q ss_pred             ccCcccc
Q 007742          294 KPSEAEK  300 (591)
Q Consensus       294 ~~~~~~~  300 (591)
                      .++....
T Consensus       120 ~~a~~~e  126 (136)
T 2hgl_A          120 FKSHRTE  126 (136)
T ss_dssp             EECCHHH
T ss_pred             EECChHH
Confidence            8875443

>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=99.59  E-value=9.7e-15  Score=119.95  Aligned_cols=84  Identities=33%  Similarity=0.545  Sum_probs=78.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|..|+..|++. .|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~   91 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMI-KLYGKPIRVNK   91 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSC-BCSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEEE
Confidence            34589999999999999999999999999999999999888999999999999999999999999996 69999999999


Q ss_pred             ecCCC
Q 007742          399 VTDHV  403 (591)
Q Consensus       399 ~~~~~  403 (591)
                      +....
T Consensus        92 a~~~~   96 (105)
T 1x5u_A           92 ASAHN   96 (105)
T ss_dssp             TTTTS
T ss_pred             CCCCC
Confidence            86543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=7.1e-15  Score=120.28  Aligned_cols=83  Identities=33%  Similarity=0.508  Sum_probs=77.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||..+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.+
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~~   89 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGA-ELDGRELRVQV   89 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSC-CBTTBCCEEEE
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCC-EECCcEEEEEE
Confidence            34589999999999999999999999999999999999888999999999999999999999999996 69999999999


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      +...
T Consensus        90 a~~~   93 (103)
T 2dnm_A           90 ARYG   93 (103)
T ss_dssp             CSSC
T ss_pred             CCcC
Confidence            8754

>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=99.59  E-value=8.3e-16  Score=126.62  Aligned_cols=83  Identities=22%  Similarity=0.266  Sum_probs=76.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCC---eeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEe
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGK---VRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMV  293 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~---i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v  293 (591)
                      ....++|||+|||+.+|+++|+++|..||.   |..|.|+.++. |.++|||||+|.+.++|.+||.+|+..|.|+.|.|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEE
Confidence            446799999999999999999999999998   89999999988 99999999999999999999999999999999999


Q ss_pred             ccCcccc
Q 007742          294 KPSEAEK  300 (591)
Q Consensus       294 ~~~~~~~  300 (591)
                      .++....
T Consensus        87 ~~a~~~~   93 (107)
T 2lmi_A           87 YEINNED   93 (107)
T ss_dssp             EECCHHH
T ss_pred             EECCHHH
Confidence            8876544

>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=99.59  E-value=7.1e-15  Score=119.47  Aligned_cols=78  Identities=18%  Similarity=0.177  Sum_probs=69.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcC--CccCCeeEEe
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSG--QLLLGQPVMV  293 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g--~~i~g~~i~v  293 (591)
                      ..++++|||+|||+.+|+++|.++|.+||.|..|.++.+      +|||||+|.+.++|..|+ .|++  ..|.|++|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345799999999999999999999999999999998753      799999999999999999 4765  4599999999


Q ss_pred             ccCcccc
Q 007742          294 KPSEAEK  300 (591)
Q Consensus       294 ~~~~~~~  300 (591)
                      .++....
T Consensus        86 ~~a~~~~   92 (104)
T 1wex_A           86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEccCcc
Confidence            9987644

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.59  E-value=1.6e-15  Score=118.11  Aligned_cols=72  Identities=19%  Similarity=0.245  Sum_probs=66.6

Q ss_pred             CcEEEEeCCCCCC------CHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCe-eE
Q 007742          220 QRTVFAYQMPLKA------TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQ-PV  291 (591)
Q Consensus       220 ~~~l~V~nLp~~~------te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~-~i  291 (591)
                      +++|||+|||+.+      |+++|.++|.+||.|..|.++  +.+|.++|||||+|.+.++|..|+ .|||..|.|+ +|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3789999999999      789999999999999999987  467899999999999999999999 5999999999 88


Q ss_pred             Ee
Q 007742          292 MV  293 (591)
Q Consensus       292 ~v  293 (591)
                      .|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>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=99.59  E-value=4.2e-15  Score=131.65  Aligned_cols=84  Identities=20%  Similarity=0.394  Sum_probs=78.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|..||.|..|.|+.++.++.++|||||+|.+.++|.+|| .||+..|.|+.|.|.+
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            345799999999999999999999999999999999999999999999999999999999999 4999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +....
T Consensus       116 a~~~~  120 (156)
T 1h2v_Z          116 DAGFK  120 (156)
T ss_dssp             ESCCC
T ss_pred             CCCCC
Confidence            86543

>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=99.58  E-value=6.3e-15  Score=121.91  Aligned_cols=78  Identities=21%  Similarity=0.340  Sum_probs=69.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHc--CCccCCeeEEe
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALS--GQLLLGQPVMV  293 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~--g~~i~g~~i~v  293 (591)
                      ..++++|||+|||+.+|+++|+++|.+||.|..|.|+.+      +|||||+|.+.++|.+|+ .++  +..|.|++|.|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            345789999999999999999999999999999999864      799999999999999999 466  56899999999


Q ss_pred             ccCcccc
Q 007742          294 KPSEAEK  300 (591)
Q Consensus       294 ~~~~~~~  300 (591)
                      .++....
T Consensus       102 ~~a~~k~  108 (119)
T 2ad9_A          102 QFSNHKE  108 (119)
T ss_dssp             EECSSSS
T ss_pred             EEccCCC
Confidence            9986544

>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=99.58  E-value=2.7e-15  Score=120.93  Aligned_cols=77  Identities=18%  Similarity=0.279  Sum_probs=68.8

Q ss_pred             CCCcEEEEeCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCC--ccCCeeEEe
Q 007742          218 RDQRTVFAYQMPL-KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQ--LLLGQPVMV  293 (591)
Q Consensus       218 ~~~~~l~V~nLp~-~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~--~i~g~~i~v  293 (591)
                      .++++|||+|||+ .+|+++|.++|.+||.|.+|.|+.+      +|||||+|.+.++|..|+ .||+.  .|.|++|.|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            3579999999999 9999999999999999999999864      589999999999999999 57754  599999999


Q ss_pred             ccCcccc
Q 007742          294 KPSEAEK  300 (591)
Q Consensus       294 ~~~~~~~  300 (591)
                      .++....
T Consensus        87 ~~a~~~~   93 (102)
T 1x4d_A           87 HLSQKYK   93 (102)
T ss_dssp             EEECCCT
T ss_pred             EECCCCC
Confidence            9987544

>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=99.58  E-value=2.4e-15  Score=126.26  Aligned_cols=80  Identities=16%  Similarity=0.243  Sum_probs=72.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCee--EEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEec
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVR--DVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK  294 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~--~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~  294 (591)
                      ....++|||+|||+.+|+++|+++|..| .|+  .|.|+.++. |.++|||||+|.+.++|.+||.+++..|.|+.|.|.
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~  116 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEVF  116 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEE
Confidence            3456899999999999999999999999 566  899999987 999999999999999999999888999999999998


Q ss_pred             cCcc
Q 007742          295 PSEA  298 (591)
Q Consensus       295 ~~~~  298 (591)
                      ++..
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            7654

>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=99.58  E-value=8.1e-15  Score=120.71  Aligned_cols=83  Identities=53%  Similarity=0.872  Sum_probs=77.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      +.+++|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.+
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~~  102 (108)
T 2jrs_A           24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGF-ELAGRPMKVGH  102 (108)
T ss_dssp             SSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTC-CSSSSCCEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEE
Confidence            34589999999999999999999999999999999999888999999999999999999999999996 69999999999


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      +++.
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            8654

>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=99.58  E-value=1.5e-14  Score=120.90  Aligned_cols=84  Identities=29%  Similarity=0.410  Sum_probs=78.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      +..++|||+|||..+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..|+..||+. .|.|+.|.|.+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~  101 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGF-QIGMKRLKVQL  101 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTC-EETTEECEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEE
Confidence            34589999999999999999999999999999999999888999999999999999999999999996 79999999999


Q ss_pred             ecCCC
Q 007742          399 VTDHV  403 (591)
Q Consensus       399 ~~~~~  403 (591)
                      +.+..
T Consensus       102 a~~~~  106 (115)
T 2cpz_A          102 KRSKN  106 (115)
T ss_dssp             CCCSC
T ss_pred             cCCCC
Confidence            87543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.58  E-value=9.5e-15  Score=118.52  Aligned_cols=80  Identities=33%  Similarity=0.426  Sum_probs=75.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVEL--------VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV  390 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~--------v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~  390 (591)
                      +...+|||+|||..+++++|+++|+.||.|..        |.|+.+..++.++|||||+|.+.++|..|+..|||. .|.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~-~~~   89 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK-EFS   89 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC-BSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC-EeC
Confidence            34589999999999999999999999999999        999998888999999999999999999999999996 799


Q ss_pred             CeEEEEEEe
Q 007742          391 GRTLKVSSV  399 (591)
Q Consensus       391 g~~l~v~~~  399 (591)
                      |+.|.|.++
T Consensus        90 g~~l~V~~A   98 (99)
T 2la6_A           90 GNPIKVSFA   98 (99)
T ss_dssp             SSBCEEEEC
T ss_pred             CcEEEEEec
Confidence            999999886

>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=99.58  E-value=4.1e-15  Score=123.49  Aligned_cols=91  Identities=29%  Similarity=0.490  Sum_probs=79.6

Q ss_pred             CCCcceEEEeccCCCCC-CCCchhhhhHHHHHHHHhccccceEEEEEe-cCCCeeEEEEeCCHHHHHHHHHHhcccccCC
Q 007742          495 GSPSECLLLKNMFDPAM-ETDPDFDLEIQGDVEEECSKYGRVKHIYVD-KRSAGFVYLRFESTEAAASAQRAMHMRWFAR  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~-~~~~~~~~~~~edl~~~f~~~G~V~~v~l~-~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g  572 (591)
                      +.++++|+|.||+.+.. ..++.++.+++++|.++|++||.|..|.|. ..++|+|||+|.+.++|.+|+..|||..|+|
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   91 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG   91 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            56788999999977764 335677888999999999999999999774 3478999999999999999999999999999


Q ss_pred             eEEEEEEeCchhh
Q 007742          573 RLISAIFMKPEDY  585 (591)
Q Consensus       573 ~~l~v~~~~~~~~  585 (591)
                      ++|.|.|+.+...
T Consensus        92 r~l~v~~a~~~~~  104 (112)
T 2dit_A           92 RQITAQAWDGTTD  104 (112)
T ss_dssp             EECEEEECCSCCC
T ss_pred             cEEEEEEeCCCCC
Confidence            9999999987543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=5e-14  Score=117.57  Aligned_cols=83  Identities=27%  Similarity=0.417  Sum_probs=76.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ....++|||+|||..+++++|+++|..||.|..|.|+.+. ++.++|||||+|.+.++|..|+..||+. .|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~   89 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQ-LLFDRPMHVK   89 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCC-EeCCCEEEEE
Confidence            3446899999999999999999999999999999999887 6889999999999999999999999996 6999999999


Q ss_pred             EecCC
Q 007742          398 SVTDH  402 (591)
Q Consensus       398 ~~~~~  402 (591)
                      ++...
T Consensus        90 ~a~~~   94 (114)
T 2do0_A           90 MDERA   94 (114)
T ss_dssp             ECSCC
T ss_pred             EcccC
Confidence            98653

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.58  E-value=5e-15  Score=124.93  Aligned_cols=82  Identities=20%  Similarity=0.323  Sum_probs=72.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeE
Q 007742          217 ERDQRTVFAYQMPLKATERDVY----EFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV  291 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~----~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i  291 (591)
                      ..+.++|||+|||+.+++++|+    ++|.+||.|..|.+..   +|.++|||||+|.+.++|..|+ .|||..|.|++|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            3457899999999999999876    6999999999988753   5788999999999999999999 699999999999


Q ss_pred             EeccCccccc
Q 007742          292 MVKPSEAEKN  301 (591)
Q Consensus       292 ~v~~~~~~~~  301 (591)
                      .|.++.....
T Consensus       103 ~V~~a~~~~~  112 (127)
T 2a3j_A          103 VITFSETPQS  112 (127)
T ss_dssp             EEEECCCCCH
T ss_pred             EEEEccCcch
Confidence            9999876543

>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=99.58  E-value=3.6e-15  Score=123.68  Aligned_cols=83  Identities=16%  Similarity=0.286  Sum_probs=75.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHH---HHHhcCCCeeEEEEeecCCCC---CccceEEEEecCcchHHHHH-HHcCCccCCee
Q 007742          218 RDQRTVFAYQMPLKATERDVY---EFFSKAGKVRDVRLIMDRNSR---RSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQP  290 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~---~~f~~~G~i~~v~~~~d~~~g---~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~  290 (591)
                      .+.++|||+|||+.+|+++|.   ++|.+||.|..|.++.+..++   .++|||||+|.+.++|.+|| .|||..|.|+.
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            356899999999999999999   999999999999999987754   45699999999999999999 58999999999


Q ss_pred             EEeccCcccc
Q 007742          291 VMVKPSEAEK  300 (591)
Q Consensus       291 i~v~~~~~~~  300 (591)
                      |.|.++.+..
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999987654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=1.6e-14  Score=119.07  Aligned_cols=85  Identities=34%  Similarity=0.594  Sum_probs=77.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEecc-CCCCCcccEEEEEeCCHHHHHHHHHHh-cCCeeeCCeEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLD-IETGQCKGFGFVQFAQLEHAKAAQSAL-NGKLEIVGRTLK  395 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~-~~~~~~~g~a~Vef~~~~~a~~a~~~l-~g~~~~~g~~l~  395 (591)
                      ....++|||+|||..+++++|+++|..||.|..|.|+.+ ..++.++|||||+|.+.++|..|+..| |+. .|.|+.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~-~~~g~~l~   90 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHST-HLYGRRLV   90 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCC-BSSSCBCE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCC-eECCCEEE
Confidence            344689999999999999999999999999999999988 678899999999999999999999999 885 69999999


Q ss_pred             EEEecCCC
Q 007742          396 VSSVTDHV  403 (591)
Q Consensus       396 v~~~~~~~  403 (591)
                      |.++....
T Consensus        91 v~~a~~~~   98 (107)
T 2cph_A           91 LEWADSEV   98 (107)
T ss_dssp             EEECCCCC
T ss_pred             EEeCCCCC
Confidence            99987643

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.57  E-value=2.3e-15  Score=122.24  Aligned_cols=80  Identities=28%  Similarity=0.429  Sum_probs=75.7

Q ss_pred             CceEEEcCCCC------CCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC-eE
Q 007742          321 DRKLYVGNLHF------NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG-RT  393 (591)
Q Consensus       321 ~~~l~v~nl~~------~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g-~~  393 (591)
                      +++|||+|||.      .+++++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.| +.
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~-~~~g~r~   84 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK-RLDLKHR   84 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC-BSSSSCB
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCc-ccCCCeE
Confidence            48999999999      9999999999999999999999999888999999999999999999999999996 6999 99


Q ss_pred             EEEEEecC
Q 007742          394 LKVSSVTD  401 (591)
Q Consensus       394 l~v~~~~~  401 (591)
                      |.|.++.+
T Consensus        85 l~V~~a~~   92 (100)
T 3ns6_A           85 LFLYTMKD   92 (100)
T ss_dssp             CEEEESHH
T ss_pred             EEEEECch
Confidence            99998754

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.57  E-value=7.3e-16  Score=125.70  Aligned_cols=82  Identities=13%  Similarity=0.251  Sum_probs=75.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      ....++|||+|||+.+|+++|+++|..||.|.. .++.+..+|.++|||||+|.+.++|.+||.||+..|.|+.|.|.++
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEc
Confidence            346799999999999999999999999999888 6777777889999999999999999999999999999999999988


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      ...
T Consensus        93 ~~~   95 (101)
T 1fj7_A           93 KGR   95 (101)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.57  E-value=1.7e-15  Score=130.09  Aligned_cols=84  Identities=21%  Similarity=0.375  Sum_probs=78.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|..||.|..|.|+.++.+|.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.+
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999999999999999999999999999999999 5999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +....
T Consensus       124 a~~~~  128 (135)
T 2lea_A          124 ARYGR  128 (135)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            86543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=8.5e-15  Score=118.14  Aligned_cols=82  Identities=29%  Similarity=0.529  Sum_probs=76.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELV-QLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v-~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      .++|||+|||..+++++|+++|+.||.|..| .|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++
T Consensus         5 ~~~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            5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQ-YLCNRPITVSYA   83 (96)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTC-EETTEECEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEEe
Confidence            4899999999999999999999999999999 99998778999999999999999999999999996 699999999998


Q ss_pred             cCCC
Q 007742          400 TDHV  403 (591)
Q Consensus       400 ~~~~  403 (591)
                      .+..
T Consensus        84 ~~~~   87 (96)
T 1x5t_A           84 FKKD   87 (96)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            6543

>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=99.57  E-value=1.7e-14  Score=119.30  Aligned_cols=81  Identities=20%  Similarity=0.319  Sum_probs=73.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+.+|+++|+++|.+||.|..|.|..+   +.++|||||+|.+.++|.+|| .||+..|.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            345699999999999999999999999999999999654   457999999999999999999 7999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +....
T Consensus        96 a~~~~  100 (109)
T 1x4a_A           96 PRSGR  100 (109)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            86643

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=3.4e-14  Score=118.94  Aligned_cols=84  Identities=33%  Similarity=0.472  Sum_probs=77.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          317 YGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       317 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      .....++|||.|||..+++++|+++|..||.|..|.|+.++.++.++|||||+|.+.++|..||..|++  .|.|+.|.|
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~--~~~g~~l~V   90 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP--IIDGRKANV   90 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC--EETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC--cCCCEEEEE
Confidence            344568999999999999999999999999999999999988899999999999999999999999998  499999999


Q ss_pred             EEecCC
Q 007742          397 SSVTDH  402 (591)
Q Consensus       397 ~~~~~~  402 (591)
                      .++...
T Consensus        91 ~~a~~~   96 (116)
T 2cqd_A           91 NLAYLG   96 (116)
T ss_dssp             EESTTT
T ss_pred             EEcccC
Confidence            998654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=1.1e-14  Score=118.01  Aligned_cols=83  Identities=27%  Similarity=0.456  Sum_probs=75.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCC---CCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE---TGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~---~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      ..++|||+|||..+++++|+++|+.||.|..|.|+.+..   ++.++|||||+|.+.++|..|+..|||. .|.|+.|.|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V   82 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGH-TVDGHKLEV   82 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTC-EETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCC-eeCCeEEEE
Confidence            358999999999999999999999999999999998765   5588999999999999999999999996 699999999


Q ss_pred             EEecCCC
Q 007742          397 SSVTDHV  403 (591)
Q Consensus       397 ~~~~~~~  403 (591)
                      .++....
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9986543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.57  E-value=3.4e-15  Score=121.97  Aligned_cols=81  Identities=27%  Similarity=0.521  Sum_probs=75.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~  297 (591)
                      ...++|||+|||+.+|+++|.++|..||.|..|.++.+. +|.++|||||+|.+.++|..|+. ++..|.|+.|.|.++.
T Consensus         7 ~~~~~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            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEECC
Confidence            356899999999999999999999999999999999998 89999999999999999999999 9999999999998876


Q ss_pred             ccc
Q 007742          298 AEK  300 (591)
Q Consensus       298 ~~~  300 (591)
                      ...
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.57  E-value=7.6e-15  Score=127.61  Aligned_cols=81  Identities=16%  Similarity=0.363  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      .....++|||+|||+.+|+++|+++|.+||.|..|.++.++.+|.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3446799999999999999999999999999999999999999999999999999999999999 699999999999997


Q ss_pred             cC
Q 007742          295 PS  296 (591)
Q Consensus       295 ~~  296 (591)
                      ++
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            64

>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=99.57  E-value=1e-14  Score=121.71  Aligned_cols=81  Identities=23%  Similarity=0.470  Sum_probs=73.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCcc--------C
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL--------L  287 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i--------~  287 (591)
                      ..+.++|||+|||+.+|+++|+++|..||.|..|.|+.+. +|.++|||||+|.+.++|..|+ .|||..|        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3456999999999999999999999999999999999998 8999999999999999999999 5999999        5


Q ss_pred             CeeEEeccCcc
Q 007742          288 GQPVMVKPSEA  298 (591)
Q Consensus       288 g~~i~v~~~~~  298 (591)
                      +++|.|.++.+
T Consensus       101 ~~~l~v~~a~p  111 (114)
T 1x5o_A          101 TEPLLCKFSGP  111 (114)
T ss_dssp             SSCBEEEECCC
T ss_pred             CCceeEEccCC
Confidence            66777777653

>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=99.57  E-value=1.3e-14  Score=116.80  Aligned_cols=80  Identities=38%  Similarity=0.557  Sum_probs=74.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.+
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~   91 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGI-RLYGRPINVSG   91 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTC-EETTEECEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCC-EECCCEEEEEE
Confidence            345899999999999999999999999999999999887 4889999999999999999999999996 69999999998


Q ss_pred             ec
Q 007742          399 VT  400 (591)
Q Consensus       399 ~~  400 (591)
                      ++
T Consensus        92 a~   93 (95)
T 2ywk_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=2.4e-14  Score=117.07  Aligned_cols=81  Identities=33%  Similarity=0.574  Sum_probs=75.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ..++|||+|||+.+++++|+++|..||.|..|.|+.+  ++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~~a   90 (103)
T 2d9p_A           14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGR-IVATKPLYVALA   90 (103)
T ss_dssp             SCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTC-BSSSSBCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCC-EeCCcEEEEEEe
Confidence            4589999999999999999999999999999999987  7889999999999999999999999996 699999999998


Q ss_pred             cCCC
Q 007742          400 TDHV  403 (591)
Q Consensus       400 ~~~~  403 (591)
                      ....
T Consensus        91 ~~~~   94 (103)
T 2d9p_A           91 QRKE   94 (103)
T ss_dssp             SSCC
T ss_pred             cccc
Confidence            7644

>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=99.56  E-value=1.9e-14  Score=118.70  Aligned_cols=80  Identities=29%  Similarity=0.487  Sum_probs=75.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||+.+++++|+++|.+||.|..|.|+.+. ++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.+
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~~  104 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGV-PLDGRPMNIQL  104 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCC-EeCCcEEEEEE
Confidence            445899999999999999999999999999999999998 8999999999999999999999999996 69999999998


Q ss_pred             ec
Q 007742          399 VT  400 (591)
Q Consensus       399 ~~  400 (591)
                      ++
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            74

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=1.2e-14  Score=119.69  Aligned_cols=82  Identities=28%  Similarity=0.503  Sum_probs=76.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      .+++|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++
T Consensus        22 ~~~~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           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ-DLMGQPISVDWC  100 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTC-BSSSSBCEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCC-EECCcEEEEEee
Confidence            3589999999999999999999999999999999999888999999999999999999999999996 699999999998


Q ss_pred             cCC
Q 007742          400 TDH  402 (591)
Q Consensus       400 ~~~  402 (591)
                      ...
T Consensus       101 ~~~  103 (106)
T 1p27_B          101 FVR  103 (106)
T ss_dssp             EES
T ss_pred             cCC
Confidence            653

>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=99.56  E-value=1.7e-14  Score=119.58  Aligned_cols=83  Identities=31%  Similarity=0.514  Sum_probs=77.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.+
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~~  102 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA-EIMGQTIQVDW  102 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC-EECCcEEEEEE
Confidence            34589999999999999999999999999999999998888999999999999999999999999996 69999999999


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      +...
T Consensus       103 a~~~  106 (110)
T 1oo0_B          103 CFVK  106 (110)
T ss_dssp             SEES
T ss_pred             cccC
Confidence            8653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=5.2e-15  Score=119.16  Aligned_cols=80  Identities=19%  Similarity=0.311  Sum_probs=71.8

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcc--cccCC
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHM--RWFAR  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g--~~~~g  572 (591)
                      +.+..+|+|+||  |+.++        +++|.++|+.||.|..|.|... +|||||+|.+.++|..|+..|++  ..|.|
T Consensus        13 ~~~~~~LfV~nL--p~~vt--------e~dL~~lF~~fG~V~~v~i~~~-kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~G   81 (105)
T 1sjq_A           13 GVPSRVIHIRKL--PIDVT--------EGEVISLGLPFGKVTNLLMLKG-KNQAFIEMNTEEAANTMVNYYTSVTPVLRG   81 (105)
T ss_dssp             CCCCCEEEECSC--CTTSC--------HHHHHHHHHHHCCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTSCCEETT
T ss_pred             CCCCCEEEEeCC--CCCCC--------HHHHHHHHHhcCCEEEEEEEcC-CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            456789999999  88888        8999999999999999998864 89999999999999999998864  78999


Q ss_pred             eEEEEEEeCchhh
Q 007742          573 RLISAIFMKPEDY  585 (591)
Q Consensus       573 ~~l~v~~~~~~~~  585 (591)
                      ++|.|.|+.++..
T Consensus        82 r~l~V~~A~~~~~   94 (105)
T 1sjq_A           82 QPIYIQFSNHKEL   94 (105)
T ss_dssp             EECCBCCCSSSSC
T ss_pred             EEEEEEEcCCCCC
Confidence            9999999987653

>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=99.56  E-value=1.1e-14  Score=117.93  Aligned_cols=82  Identities=21%  Similarity=0.195  Sum_probs=75.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      +...+|||+|||+.+++++|+++|..||.|..+.++.+..++.++|||||+|.+.++|.+|+..|||. .|.|+.|.|.+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~-~~~g~~l~V~~   91 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR-PIGSRKVKLVL   91 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTC-EETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCC-eeCCeEEEEEE
Confidence            34589999999999999999999999999988888877778999999999999999999999999996 79999999999


Q ss_pred             ecC
Q 007742          399 VTD  401 (591)
Q Consensus       399 ~~~  401 (591)
                      +.+
T Consensus        92 a~~   94 (98)
T 2cqp_A           92 GSG   94 (98)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            764

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.9e-14  Score=114.43  Aligned_cols=77  Identities=26%  Similarity=0.401  Sum_probs=70.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|.+||.|..|.++        +|||||+|.+.++|..|+ .||+..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            3457999999999999999999999999999999987        689999999999999999 6999999999999999


Q ss_pred             Cccccc
Q 007742          296 SEAEKN  301 (591)
Q Consensus       296 ~~~~~~  301 (591)
                      +.....
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.56  E-value=2.7e-14  Score=116.97  Aligned_cols=82  Identities=23%  Similarity=0.512  Sum_probs=75.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCC-CCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIET-GQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~-~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      .+.++|||+|||..+++++|+++|..|| |..|.|+.+..+ +.++|||||+|.+.++|.+|| .|++. .|.|+.|.|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~-~~~g~~l~V~   89 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE-SLGNKRIRVD   89 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTC-EETTEECEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCC-EeCCcEEEEE
Confidence            3458999999999999999999999999 999999998877 899999999999999999999 99996 6999999999


Q ss_pred             EecCCC
Q 007742          398 SVTDHV  403 (591)
Q Consensus       398 ~~~~~~  403 (591)
                      ++....
T Consensus        90 ~a~~~~   95 (104)
T 1wi8_A           90 VADQAQ   95 (104)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            987643

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=9.1e-15  Score=119.14  Aligned_cols=81  Identities=20%  Similarity=0.300  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~  294 (591)
                      .....++|||+|||+.+|+++|+++|.+||.|   .++.+ .+|.++|||||+|.+.++|.+||. ||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            44567999999999999999999999999977   45555 678999999999999999999995 99999999999999


Q ss_pred             cCcccc
Q 007742          295 PSEAEK  300 (591)
Q Consensus       295 ~~~~~~  300 (591)
                      ++....
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            987653

>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=99.56  E-value=5.8e-15  Score=138.81  Aligned_cols=81  Identities=19%  Similarity=0.293  Sum_probs=75.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAG--KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G--~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..++|||+|||+.+|+++|+++|..||  .|..|.|+.++.+|.++|||||+|.+.++|.+|| .||+..|.|+.|.|.+
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            568999999999999999999999999  9999999999999999999999999999999999 5999999999999998


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +...
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8654

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.56  E-value=3.9e-14  Score=115.81  Aligned_cols=81  Identities=28%  Similarity=0.502  Sum_probs=75.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||..+++++|+++|..|| |..|.|+.+..++.++|||||+|.+.++|..|+ .|||. .|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~-~~~g~~l~V~~   89 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGA-LLGDRSLRVDI   89 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTC-EETTEECEEEE
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCC-eECCeEEEEEE
Confidence            3458999999999999999999999997 999999999888999999999999999999999 89995 79999999999


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      +...
T Consensus        90 a~~~   93 (103)
T 2dng_A           90 AEGR   93 (103)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            8654

>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=99.56  E-value=5.2e-14  Score=115.06  Aligned_cols=82  Identities=33%  Similarity=0.536  Sum_probs=74.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.+..  .++|||||+|.+.++|..|+..|++. .|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~V~   88 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGR-KILGKEVKVN   88 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTE-EETTEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCC-CcCCCeEEEE
Confidence            34468999999999999999999999999999999998753  36899999999999999999999995 7999999999


Q ss_pred             EecCC
Q 007742          398 SVTDH  402 (591)
Q Consensus       398 ~~~~~  402 (591)
                      ++...
T Consensus        89 ~a~~~   93 (103)
T 2cqi_A           89 WATTP   93 (103)
T ss_dssp             ECCCT
T ss_pred             ECCCC
Confidence            98764

>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=99.56  E-value=3.3e-14  Score=116.75  Aligned_cols=83  Identities=33%  Similarity=0.512  Sum_probs=76.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC---eEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG---RTLK  395 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g---~~l~  395 (591)
                      +..++|||+|||..+++++|+++|..||.|..|.|+.+. ++.++|||||+|.+.++|..|+..|||. .|.|   +.|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~gg~~~~l~   90 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGS-QTMPGASSSLV   90 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSC-CCCTTCSSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCC-ccCCCCCccEE
Confidence            345899999999999999999999999999999999987 7899999999999999999999999996 5777   9999


Q ss_pred             EEEecCCC
Q 007742          396 VSSVTDHV  403 (591)
Q Consensus       396 v~~~~~~~  403 (591)
                      |.++....
T Consensus        91 V~~a~~~~   98 (105)
T 2dnh_A           91 VKFADTDK   98 (105)
T ss_dssp             EEESCSSC
T ss_pred             EEECccCc
Confidence            99987543

>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=99.56  E-value=6.6e-14  Score=114.45  Aligned_cols=83  Identities=31%  Similarity=0.587  Sum_probs=74.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ....++|||+|||..+++++|+++|..||.|..|.|+.+..  .++|||||+|.+.++|..|+..|+|. .|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~   88 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGT-VVEGRKIEVN   88 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEE
Confidence            34458999999999999999999999999999999998753  37999999999999999999999996 6999999999


Q ss_pred             EecCCC
Q 007742          398 SVTDHV  403 (591)
Q Consensus       398 ~~~~~~  403 (591)
                      ++....
T Consensus        89 ~a~~~~   94 (103)
T 2cq3_A           89 NATARV   94 (103)
T ss_dssp             ECCSSC
T ss_pred             EcccCC
Confidence            987643

>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=99.56  E-value=2.7e-15  Score=119.36  Aligned_cols=80  Identities=24%  Similarity=0.372  Sum_probs=71.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFG--PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g--~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      .+|||+|||..+++++|+++|+.||  .|..|.|+.+..+|.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~-~~~gr~i~V~~~   80 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR-ELHGQNPVVTPS   80 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGS-CSSSCCCEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCC-eeCCEEEEEEEC
Confidence            4799999999999999999999999  9999999999889999999999999999999999999996 699999999987


Q ss_pred             cCC
Q 007742          400 TDH  402 (591)
Q Consensus       400 ~~~  402 (591)
                      .+.
T Consensus        81 ~~~   83 (90)
T 3p5t_L           81 NKL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            653

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.56  E-value=2.1e-14  Score=120.73  Aligned_cols=81  Identities=33%  Similarity=0.482  Sum_probs=75.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      .+..++|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.
T Consensus        37 ~~~~~~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           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGF-QVGTKRLKVQ  115 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCC-EETTEECCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEE
Confidence            344689999999999999999999999999999999998878999999999999999999999999996 7999999998


Q ss_pred             Ee
Q 007742          398 SV  399 (591)
Q Consensus       398 ~~  399 (591)
                      ++
T Consensus       116 ~a  117 (118)
T 2khc_A          116 LK  117 (118)
T ss_dssp             EC
T ss_pred             ec
Confidence            86

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=3.4e-14  Score=118.36  Aligned_cols=84  Identities=32%  Similarity=0.443  Sum_probs=77.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCee--------EEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVE--------LVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV  390 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~--------~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~  390 (591)
                      ...++|||+|||..+++++|+++|..||.|.        .|.|+.+..++.++|||||+|.+.++|..||..|||. .|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~   91 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK-DFQ   91 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC-EET
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC-ccC
Confidence            3458999999999999999999999999998        6999998778999999999999999999999999996 699


Q ss_pred             CeEEEEEEecCCC
Q 007742          391 GRTLKVSSVTDHV  403 (591)
Q Consensus       391 g~~l~v~~~~~~~  403 (591)
                      |+.|.|.++....
T Consensus        92 g~~l~V~~a~~~~  104 (113)
T 2cpe_A           92 GSKLKVSLARKKP  104 (113)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CCEEEEEECCCCC
Confidence            9999999986543

>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=99.55  E-value=2e-14  Score=116.05  Aligned_cols=81  Identities=20%  Similarity=0.317  Sum_probs=72.4

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhc--ccccCC
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMH--MRWFAR  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~--g~~~~g  572 (591)
                      ..++++|+|+||  |..++        +++|.++|+.||.|..|.+... +|+|||+|.+.++|..|+..|+  +..|.|
T Consensus        12 ~~p~~~l~V~nL--p~~~t--------e~~L~~~F~~fG~v~~v~i~~~-kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G   80 (101)
T 2cq1_A           12 GAPSRVLHIRKL--PGEVT--------ETEVIALGLPFGKVTNILMLKG-KNQAFLELATEEAAITMVNYYSAVTPHLRN   80 (101)
T ss_dssp             SSCCSEEEEESC--CTTCC--------HHHHHHTTTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCCEEEEeCC--CCCCC--------HHHHHHHHHhcCCEEEEEEECC-CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            467789999999  88888        8999999999999999988754 8999999999999999999875  567999


Q ss_pred             eEEEEEEeCchhhh
Q 007742          573 RLISAIFMKPEDYE  586 (591)
Q Consensus       573 ~~l~v~~~~~~~~~  586 (591)
                      ++|.|.|+..+...
T Consensus        81 r~l~V~~a~~~~~~   94 (101)
T 2cq1_A           81 QPIYIQYSNHKELK   94 (101)
T ss_dssp             EECEEEECSCSSCC
T ss_pred             cEEEEEEcCcccCc
Confidence            99999999877654

>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=99.55  E-value=3.2e-14  Score=112.38  Aligned_cols=78  Identities=24%  Similarity=0.517  Sum_probs=72.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|..|+ .+++. .|.|+.|.|.++
T Consensus        10 ~~~~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           10 DAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVL-DQKEH-RLDGRVIDPKKA   87 (87)
T ss_dssp             CTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHH-HSSCE-EETTEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHH-HhCCC-EECCEEEEEEeC
Confidence            3589999999999999999999999999999999999888999999999999999999999 55775 699999999864

>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=99.55  E-value=1.8e-14  Score=118.51  Aligned_cols=83  Identities=31%  Similarity=0.480  Sum_probs=76.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeee---CCeEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI---VGRTLK  395 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~---~g~~l~  395 (591)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|..|+..||+. .+   .|+.|.
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~-~~~~~~g~~l~   89 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQ-KTLPGMNRPIQ   89 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTT-CCCTTCSSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCC-cccCCCCceEE
Confidence            34589999999999999999999999999999999999888999999999999999999999999996 46   889999


Q ss_pred             EEEecCC
Q 007742          396 VSSVTDH  402 (591)
Q Consensus       396 v~~~~~~  402 (591)
                      |.++...
T Consensus        90 v~~a~~~   96 (106)
T 2dgp_A           90 VKPADSE   96 (106)
T ss_dssp             EEECCCC
T ss_pred             EEECCcc
Confidence            9998654

>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=99.55  E-value=2.5e-14  Score=117.96  Aligned_cols=77  Identities=21%  Similarity=0.309  Sum_probs=70.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC-----ee
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG-----QP  290 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g-----~~  290 (591)
                      ....++|||+|||+.+|+++|+++|.+||.|..|.|+.+       |||||+|.+.++|.+|| .||+..|.|     +.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            456799999999999999999999999999999999865       89999999999999999 599999999     99


Q ss_pred             EEeccCcccc
Q 007742          291 VMVKPSEAEK  300 (591)
Q Consensus       291 i~v~~~~~~~  300 (591)
                      |.|.++.+..
T Consensus        85 i~V~~a~~~~   94 (108)
T 1x4c_A           85 IRVKVDGPRS   94 (108)
T ss_dssp             EEEEESSCCS
T ss_pred             EEEEeCCCCC
Confidence            9999887644

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.55  E-value=6.7e-15  Score=120.85  Aligned_cols=78  Identities=13%  Similarity=0.153  Sum_probs=70.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCC-CeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAG-KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G-~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ...++|||+|||+.+|+++|+++|.+|| .|..+.++.+    .++|||||+|.+.++|.+|| .|||..|.|+.|.|.+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3568999999999999999999999999 8999988643    47999999999999999999 6999999999999998


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +...
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            7543

>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=99.55  E-value=2e-14  Score=113.85  Aligned_cols=80  Identities=23%  Similarity=0.556  Sum_probs=73.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCC-cccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQ-CKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~-~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +++|||+|||..+++++|.++|++||.|..|.|+.+..++. ++|||||+|.+.++|..|+..|||. .|.|+.|.|.++
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~a   82 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGG-QIDGQEITATAV   82 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCC-eECCeEEEEEEC
Confidence            47999999999999999999999999999999998876655 8999999999999999999999996 799999999998


Q ss_pred             cC
Q 007742          400 TD  401 (591)
Q Consensus       400 ~~  401 (591)
                      .+
T Consensus        83 ~~   84 (88)
T 4a8x_A           83 LA   84 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.55  E-value=2.9e-14  Score=116.54  Aligned_cols=78  Identities=19%  Similarity=0.290  Sum_probs=70.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|.++|.+||.|..|.++        +|||||+|.+.++|.+|+ .||+..|.|+.|.|.+
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            3456999999999999999999999999999999886        569999999999999999 5999999999999999


Q ss_pred             Ccccccc
Q 007742          296 SEAEKNL  302 (591)
Q Consensus       296 ~~~~~~~  302 (591)
                      +.+....
T Consensus        80 a~~~~~~   86 (103)
T 2dgu_A           80 AKPPDQK   86 (103)
T ss_dssp             CCCCCCC
T ss_pred             cCCCccc
Confidence            8765543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=3e-15  Score=125.46  Aligned_cols=79  Identities=20%  Similarity=0.228  Sum_probs=72.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCe----eEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEec
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKV----RDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK  294 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i----~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~  294 (591)
                      ..++|||+|||+.+|+++|+++|.+||.|    ..|.|+.+ .+|.++|||||+|.+.++|.+||.+|++.|.|+.|.|.
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 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELF  100 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEE
Confidence            45899999999999999999999999975    68999988 47999999999999999999999889999999999997


Q ss_pred             cCcc
Q 007742          295 PSEA  298 (591)
Q Consensus       295 ~~~~  298 (591)
                      .+..
T Consensus       101 ~a~~  104 (123)
T 2dha_A          101 RSTA  104 (123)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            6654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=1.4e-14  Score=117.57  Aligned_cols=81  Identities=30%  Similarity=0.463  Sum_probs=75.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCee-EEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeE----E
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVE-LVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRT----L  394 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~-~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~----l  394 (591)
                      .+++|||+|||..+++++|+++|.+||.|. .|.|+.++.++.++|||||+|.+.++|..|+..|||. .|.|+.    |
T Consensus         8 ~~~~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            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGK-PLPGATPAKRF   86 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTS-EESSCSSCEEC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCC-ccCCCCcceeE
Confidence            358999999999999999999999999999 9999999889999999999999999999999999996 699999    9


Q ss_pred             EEEEecC
Q 007742          395 KVSSVTD  401 (591)
Q Consensus       395 ~v~~~~~  401 (591)
                      .|.++..
T Consensus        87 ~v~~a~~   93 (99)
T 2div_A           87 KLNYATY   93 (99)
T ss_dssp             CEEETTC
T ss_pred             EEeecCC
Confidence            9998764

>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=99.55  E-value=2.4e-14  Score=116.39  Aligned_cols=81  Identities=12%  Similarity=0.077  Sum_probs=72.6

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccc--cCC
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRW--FAR  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~--~~g  572 (591)
                      ..|+++|+|+||  |..++        +++|.++|++||.|..|.|.. .+|+|||+|.+.++|..|+..|+|..  |.|
T Consensus        12 ~~p~~~l~V~nL--p~~~t--------e~~L~~~F~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~G   80 (104)
T 1wex_A           12 VSVSPVVHVRGL--CESVV--------EADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVPVYIAG   80 (104)
T ss_dssp             CCCCSEEEEESC--CSSCC--------HHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCBSSS
T ss_pred             CCCCCEEEEeCC--CCCCC--------HHHHHHHHHhCCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            467789999999  88888        899999999999999998875 58999999999999999999998764  999


Q ss_pred             eEEEEEEeCchhhh
Q 007742          573 RLISAIFMKPEDYE  586 (591)
Q Consensus       573 ~~l~v~~~~~~~~~  586 (591)
                      ++|.|.|+..+...
T Consensus        81 r~l~V~~a~~~~~~   94 (104)
T 1wex_A           81 QQAFFNYSTSKRIT   94 (104)
T ss_dssp             SBCEEEECSSSSCC
T ss_pred             EEEEEEEccCcccc
Confidence            99999999876544

>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=99.55  E-value=3.3e-14  Score=118.72  Aligned_cols=81  Identities=32%  Similarity=0.569  Sum_probs=76.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||..+++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.+++
T Consensus         7 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~-~~~g~~l~V~~a~   84 (116)
T 2fy1_A            7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGK-SLHGKAIKVEQAK   84 (116)
T ss_dssp             CCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSC-BCSSSBCEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEECC
Confidence            4899999999999999999999999999999999987 8999999999999999999999999996 6999999999987


Q ss_pred             CCC
Q 007742          401 DHV  403 (591)
Q Consensus       401 ~~~  403 (591)
                      ...
T Consensus        85 ~~~   87 (116)
T 2fy1_A           85 KPS   87 (116)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            544

>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=99.54  E-value=7.4e-14  Score=112.67  Aligned_cols=80  Identities=23%  Similarity=0.243  Sum_probs=70.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcC-CeeeCCeEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG-KLEIVGRTLKV  396 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g-~~~~~g~~l~v  396 (591)
                      .+++++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|..|+..|++ ...|.|++|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            345689999999999999999999999999999988753      79999999999999999998752 24699999999


Q ss_pred             EEecCCC
Q 007742          397 SSVTDHV  403 (591)
Q Consensus       397 ~~~~~~~  403 (591)
                      .+++...
T Consensus        86 ~~a~~~~   92 (101)
T 2cq1_A           86 QYSNHKE   92 (101)
T ss_dssp             EECSCSS
T ss_pred             EEcCccc
Confidence            9987543

>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=99.54  E-value=8.3e-15  Score=117.95  Aligned_cols=80  Identities=23%  Similarity=0.229  Sum_probs=73.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ...+|||+|||+.+++++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|.+|+..||+. .|.|+.|.|.++
T Consensus        14 ~~~~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           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR-PIGSRKVKLSGP   92 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCC-eECCcEEEEEec
Confidence            3589999999999999999999999999988888888778899999999999999999999999996 799999999886


Q ss_pred             c
Q 007742          400 T  400 (591)
Q Consensus       400 ~  400 (591)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.54  E-value=1.6e-14  Score=122.93  Aligned_cols=83  Identities=31%  Similarity=0.509  Sum_probs=77.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      .+.++|||+|||..+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.+
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~~  122 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM-ELDGRRIRVDF  122 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTC-CSSSSCCEESC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEE
Confidence            34589999999999999999999999999999999999888999999999999999999999999996 69999999998


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      +.+.
T Consensus       123 a~~~  126 (129)
T 2kxn_B          123 SITK  126 (129)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            7653

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=3.4e-14  Score=116.62  Aligned_cols=84  Identities=27%  Similarity=0.425  Sum_probs=76.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ....++|||+|||+.+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..||.. ++ ..|.|+.|.|.
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~-~~~~g~~l~V~   90 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RP-HTLDGRNIDPK   90 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CS-EEETTEEEBCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CC-CeECCEEEEEE
Confidence            34468999999999999999999999999999999999988899999999999999999999977 88 57999999999


Q ss_pred             EecCCC
Q 007742          398 SVTDHV  403 (591)
Q Consensus       398 ~~~~~~  403 (591)
                      ++.+..
T Consensus        91 ~a~~~~   96 (105)
T 2dh8_A           91 PCTPRG   96 (105)
T ss_dssp             CSCCSS
T ss_pred             EccCCC
Confidence            886543

>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=99.54  E-value=1.8e-14  Score=119.17  Aligned_cols=82  Identities=18%  Similarity=0.305  Sum_probs=73.4

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcc--cccC
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHM--RWFA  571 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g--~~~~  571 (591)
                      ...++++|+|+||  |+.++        +++|.++|+.||.|..|.|... +|+|||+|.+.++|.+|+..|++  ..|.
T Consensus        27 ~~~ps~~LfVgNL--p~~vt--------e~dL~~lF~~fG~V~~v~i~~~-kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~   95 (119)
T 2ad9_A           27 AGVPSRVIHIRKL--PIDVT--------EGEVISLGLPFGKVTNLLMLKG-KNQAFIEMNTEEAANTMVNYYTSVTPVLR   95 (119)
T ss_dssp             CSSCCSEEEEESC--CTTCC--------HHHHHHHHTTTSCCCEEEEEGG-GTEEEEECSCHHHHHHHHHHHHHHCCCBT
T ss_pred             cCCCCCEEEEeCC--CCCCC--------HHHHHHHHHhcCCEEEEEEeCC-CCEEEEEECCHHHHHHHHHHhccCCceEC
Confidence            4567889999999  88888        8999999999999999998764 89999999999999999999985  5799


Q ss_pred             CeEEEEEEeCchhhh
Q 007742          572 RRLISAIFMKPEDYE  586 (591)
Q Consensus       572 g~~l~v~~~~~~~~~  586 (591)
                      |++|.|.|+..+...
T Consensus        96 Gr~l~V~~a~~k~~~  110 (119)
T 2ad9_A           96 GQPIYIQFSNHKELK  110 (119)
T ss_dssp             TBCCEEEECSSSSCC
T ss_pred             CeEEEEEEccCCCCC
Confidence            999999999876643

>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=99.54  E-value=1.8e-14  Score=116.09  Aligned_cols=79  Identities=6%  Similarity=0.058  Sum_probs=70.7

Q ss_pred             CCCcceEEEeccCCCC-CCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccc--cC
Q 007742          495 GSPSECLLLKNMFDPA-METDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRW--FA  571 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~-~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~--~~  571 (591)
                      ..++++|+|+||  |+ .++        +++|.++|+.||.|..|.|.. .+|+|||+|.+.++|..|+..|||..  |.
T Consensus        12 ~~p~~~l~V~nL--p~~~~t--------e~dL~~lF~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~   80 (102)
T 1x4d_A           12 VETRRVVHIMDF--QRGKNL--------RYQLLQLVEPFGVISNHLILN-KINEAFIEMATTEDAQAAVDYYTTTPALVF   80 (102)
T ss_dssp             CCCCCEEEEESC--CCSSSH--------HHHHHTTTGGGSCEEEEEECS-SSSCEEEEESSHHHHHHHHHHHHHSCCEET
T ss_pred             CCCCCEEEEeCC--CCCcCC--------HHHHHHHHHhcCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHHcCCCceEC
Confidence            347789999999  88 777        899999999999999999875 47999999999999999999999764  99


Q ss_pred             CeEEEEEEeCchh
Q 007742          572 RRLISAIFMKPED  584 (591)
Q Consensus       572 g~~l~v~~~~~~~  584 (591)
                      |++|.|.|+....
T Consensus        81 Gr~l~V~~a~~~~   93 (102)
T 1x4d_A           81 GKPVRVHLSQKYK   93 (102)
T ss_dssp             TEECEEEEECCCT
T ss_pred             CcEEEEEECCCCC
Confidence            9999999998644

>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=99.54  E-value=2.8e-14  Score=115.75  Aligned_cols=78  Identities=23%  Similarity=0.330  Sum_probs=71.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|+++|.+||.|..|.++.      .+|||||+|.+.++|.+|+ .||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~------~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET------TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            34668999999999999999999999999999999984      3789999999999999999 7999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +....
T Consensus        86 a~~~~   90 (99)
T 2cpj_A           86 ACHSA   90 (99)
T ss_dssp             SSCCS
T ss_pred             cCCCC
Confidence            86643

>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=99.54  E-value=2.4e-14  Score=118.37  Aligned_cols=78  Identities=21%  Similarity=0.319  Sum_probs=71.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ...++|||+|||+.+|+++|+.+|..||.|..|.++.+      +|||||+|.+.++|..|+ .|||..|.|+.|.|.++
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            34689999999999999999999999999999999865      789999999999999999 79999999999999998


Q ss_pred             ccccc
Q 007742          297 EAEKN  301 (591)
Q Consensus       297 ~~~~~  301 (591)
                      .....
T Consensus        97 ~~~~~  101 (109)
T 1x4g_A           97 KESPD  101 (109)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            76543

>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=99.54  E-value=1.7e-15  Score=129.72  Aligned_cols=81  Identities=21%  Similarity=0.266  Sum_probs=73.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      ....++|||+|||+.+|+++|+++|.+|| |+.|.|+.++. |.++|||||+|.+.++|.+||.+|+..|.|+.|.|.++
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLN  120 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEEC
Confidence            34568999999999999999999999999 77999999986 99999999999999999999999999999999999877


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      ...
T Consensus       121 ~~~  123 (139)
T 2hgn_A          121 STT  123 (139)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            543

>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=99.54  E-value=3e-14  Score=113.14  Aligned_cols=78  Identities=31%  Similarity=0.538  Sum_probs=74.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||..+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|..|+ .|+|. .|.|+.|.|.++.+
T Consensus         7 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~-~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDES-LFRGRQIKVIPKRT   84 (89)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTC-EETTEECEEEETTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCC-EECCcEEEEEEccC
Confidence            79999999999999999999999999999999998888999999999999999999999 99996 69999999998764

>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=99.54  E-value=2.3e-14  Score=122.02  Aligned_cols=84  Identities=27%  Similarity=0.478  Sum_probs=77.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||+.+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.+
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~   98 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ-DLMGQPISVDW   98 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTC-BSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCC-eeCCeEEEEEE
Confidence            34589999999999999999999999999999999999889999999999999999999999999996 69999999999


Q ss_pred             ecCCC
Q 007742          399 VTDHV  403 (591)
Q Consensus       399 ~~~~~  403 (591)
                      +....
T Consensus        99 a~~~~  103 (126)
T 3ex7_B           99 CFVRG  103 (126)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            87543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=2.2e-14  Score=115.89  Aligned_cols=79  Identities=18%  Similarity=0.254  Sum_probs=70.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      .....++|||+|||+.+|+++|+++|..||.|. +.++.    +.++|||||+|.+.++|..|+ .|||..|.|+.|.|.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            345579999999999999999999999999997 66664    357899999999999999999 799999999999999


Q ss_pred             cCccc
Q 007742          295 PSEAE  299 (591)
Q Consensus       295 ~~~~~  299 (591)
                      ++.+.
T Consensus        90 ~a~~~   94 (97)
T 2e5j_A           90 LARQQ   94 (97)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            88654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.53  E-value=1.7e-14  Score=117.84  Aligned_cols=77  Identities=18%  Similarity=0.259  Sum_probs=68.9

Q ss_pred             cEEEEeCC----CCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecC----cch----HHHHHH---HcCCc
Q 007742          221 RTVFAYQM----PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD----VMS----VPMAIA---LSGQL  285 (591)
Q Consensus       221 ~~l~V~nL----p~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~----~e~----A~~Al~---l~g~~  285 (591)
                      ..|||+||    |+.+++.+|+++|..||.|..|.++.|+.||.++|||||+|.+    +.+    |..|+.   ++|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999999999999999999996    544    677764   69999


Q ss_pred             cCCeeEEeccCc
Q 007742          286 LLGQPVMVKPSE  297 (591)
Q Consensus       286 i~g~~i~v~~~~  297 (591)
                      |.|++|+|....
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            999999997553

>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=99.53  E-value=3.2e-14  Score=114.91  Aligned_cols=77  Identities=12%  Similarity=0.194  Sum_probs=70.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccC--CeeEEe
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL--GQPVMV  293 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~--g~~i~v  293 (591)
                      ..+.++|||+|||+.+|+++|.++|.+||.|..|.++.+      +|||||+|.+.++|.+|+ .||+..|.  |+.|.|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            345689999999999999999999999999999998753      789999999999999999 59999999  999999


Q ss_pred             ccCccc
Q 007742          294 KPSEAE  299 (591)
Q Consensus       294 ~~~~~~  299 (591)
                      .++.+.
T Consensus        88 ~~a~~~   93 (97)
T 1why_A           88 DFAKSG   93 (97)
T ss_dssp             EECCCC
T ss_pred             EECCCC
Confidence            998664

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=2.2e-14  Score=117.15  Aligned_cols=82  Identities=22%  Similarity=0.350  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      ...+.++|||+|||+.+|+++|+++|..|+   .|.++.+..++.++|||||+|.+.++|.+|| .||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            345679999999999999999999999773   6788888889999999999999999999999 599999999999999


Q ss_pred             cCcccc
Q 007742          295 PSEAEK  300 (591)
Q Consensus       295 ~~~~~~  300 (591)
                      ++.+..
T Consensus        88 ~a~~~~   93 (102)
T 2fc8_A           88 WAKPKG   93 (102)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            987644

>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=99.53  E-value=4.9e-15  Score=123.94  Aligned_cols=81  Identities=19%  Similarity=0.369  Sum_probs=71.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCe----eEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeE
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKV----RDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV  291 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i----~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i  291 (591)
                      ..+.++|||+|||+.+|+++|.++|..||.|    ..+.++    +|.++|||||+|.+.++|..|| .|||..|.|+.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~----~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   97 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL   97 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE----CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC----CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            4467999999999999999999999999998    455544    6889999999999999999999 599999999999


Q ss_pred             EeccCccccc
Q 007742          292 MVKPSEAEKN  301 (591)
Q Consensus       292 ~v~~~~~~~~  301 (591)
                      .|.++.....
T Consensus        98 ~v~~a~~~~~  107 (115)
T 2cpx_A           98 VIEFGKNKKQ  107 (115)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEEccCCCC
Confidence            9999876543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=3.6e-14  Score=113.82  Aligned_cols=78  Identities=26%  Similarity=0.392  Sum_probs=69.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~  297 (591)
                      ...++|||+|||+.+|+++|.++|..||.|..|  +.++.+|.   ||||+|.+.++|.+|+.||+..|.|+.|.|.++.
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECC
Confidence            356899999999999999999999999999987  55666655   9999999999999999999999999999999875


Q ss_pred             ccc
Q 007742          298 AEK  300 (591)
Q Consensus       298 ~~~  300 (591)
                      ...
T Consensus        81 ~~~   83 (94)
T 2e5g_A           81 QKE   83 (94)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            443

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=1e-13  Score=110.52  Aligned_cols=79  Identities=22%  Similarity=0.325  Sum_probs=73.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ...+|||+|||+.+++++|+++|..| .|..|.|+.+ .++.++|||||+|.+.++|..|+. |||. .|.|+.|.|.++
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~-~~~gr~i~v~~a   84 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNRE-YMGGRYIEVFRE   84 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSE-EETTEEEEEEEE
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCc-eeCCcEEEEEEC
Confidence            34899999999999999999999999 9999999988 589999999999999999999998 9995 799999999998


Q ss_pred             cCC
Q 007742          400 TDH  402 (591)
Q Consensus       400 ~~~  402 (591)
                      ...
T Consensus        85 ~~~   87 (91)
T 2dgw_A           85 KSG   87 (91)
T ss_dssp             SSC
T ss_pred             CcC
Confidence            654

>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=99.53  E-value=2.6e-14  Score=112.41  Aligned_cols=74  Identities=18%  Similarity=0.300  Sum_probs=68.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-H-cCCccCCeeEEec
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L-SGQLLLGQPVMVK  294 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l-~g~~i~g~~i~v~  294 (591)
                      ....++|||+|||+.+|+++|+++|.+||.|..|.++.      ++|||||+|.+.++|..|+. | ++..+.|+.|.|.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~------~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC------CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            44568999999999999999999999999999999985      47999999999999999995 7 9999999999998


Q ss_pred             cC
Q 007742          295 PS  296 (591)
Q Consensus       295 ~~  296 (591)
                      ++
T Consensus        83 ~a   84 (85)
T 2ytc_A           83 WG   84 (85)
T ss_dssp             EC
T ss_pred             ec
Confidence            76

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.53  E-value=2.4e-14  Score=128.89  Aligned_cols=83  Identities=19%  Similarity=0.320  Sum_probs=77.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+.+|+++|.++|..||.|..|.|+.+. +|.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.+
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3457999999999999999999999999999999999998 8999999999999999999999 5999999999999998


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            76543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.53  E-value=2.5e-14  Score=117.72  Aligned_cols=76  Identities=26%  Similarity=0.498  Sum_probs=69.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      .....++|||+|||+.+|+++|.++|.+||.|..|.++        +|||||+|.+.++|.+|+ .|||..|.|+.|.|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34567999999999999999999999999999999987        689999999999999999 599999999999999


Q ss_pred             cCccc
Q 007742          295 PSEAE  299 (591)
Q Consensus       295 ~~~~~  299 (591)
                      ++...
T Consensus        99 ~a~~~  103 (108)
T 2jvo_A           99 YSKLP  103 (108)
T ss_dssp             SCSCC
T ss_pred             EecCC
Confidence            98654

>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=99.52  E-value=9.1e-15  Score=118.22  Aligned_cols=81  Identities=19%  Similarity=0.400  Sum_probs=72.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeE
Q 007742          217 ERDQRTVFAYQMPLKATERDVY----EFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV  291 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~----~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i  291 (591)
                      ..++++|||+|||+.+|+++|.    ++|.+||.|..|.++.   +|.++|||||+|.+.++|..|+ .|||..|.|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3457999999999999999999    9999999999998874   4678999999999999999999 599999999999


Q ss_pred             EeccCcccc
Q 007742          292 MVKPSEAEK  300 (591)
Q Consensus       292 ~v~~~~~~~  300 (591)
                      .|.++....
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999886643

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=5.4e-14  Score=108.48  Aligned_cols=76  Identities=16%  Similarity=0.336  Sum_probs=66.1

Q ss_pred             CCcE-EEEeCCCCCCCHHH----HHHHHhcC-CCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeE
Q 007742          219 DQRT-VFAYQMPLKATERD----VYEFFSKA-GKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV  291 (591)
Q Consensus       219 ~~~~-l~V~nLp~~~te~~----l~~~f~~~-G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i  291 (591)
                      ++.+ |||+|||+.+++++    |+++|.+| |+|.+|       +|   |+|||.|.+.++|..|+ .|+|..+.|++|
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i   76 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRI   76 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceE
Confidence            3455 99999999999988    55899999 599998       34   99999999999999999 699999999999


Q ss_pred             EeccCcccccccc
Q 007742          292 MVKPSEAEKNLVQ  304 (591)
Q Consensus       292 ~v~~~~~~~~~~~  304 (591)
                      +|.++........
T Consensus        77 ~v~~A~~~sd~~~   89 (96)
T 2diu_A           77 IVSFTPKNRELCE   89 (96)
T ss_dssp             EEESSCCSCCCCC
T ss_pred             EEEecCCCcceeE
Confidence            9999977655443

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=1.9e-14  Score=116.95  Aligned_cols=78  Identities=23%  Similarity=0.305  Sum_probs=72.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||+.+|+++|.++|++||+|..|.|+.+.. +.++|||||+|.+.++|..|+. +++. .|.|+.|.|.+..
T Consensus        11 ~~~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           11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQ-KYKETDLLILFKD   87 (103)
T ss_dssp             GGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCC-CCTTTTCEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCC-EECCEEEEEEEch
Confidence            48999999999999999999999999999999999875 8999999999999999999997 8885 7999999999875


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      +
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=1.6e-13  Score=112.15  Aligned_cols=83  Identities=33%  Similarity=0.474  Sum_probs=75.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||..+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..||.  ++ ..|.|+.|.|.+
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~-~~~~g~~l~v~~   89 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QR-HMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SC-EEETTEEEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cC-CeeCCeEEEEEe
Confidence            345899999999999999999999999999999999998889999999999999999999996  45 369999999999


Q ss_pred             ecCCCC
Q 007742          399 VTDHVG  404 (591)
Q Consensus       399 ~~~~~~  404 (591)
                      +.+...
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            876543

>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=2.6e-14  Score=116.28  Aligned_cols=84  Identities=29%  Similarity=0.448  Sum_probs=70.0

Q ss_pred             cceEEEeccC-CCCCCCC--------------chhhhhHHHHHHHHh-ccccceEEEEEecC----CCeeEEEEeCCHHH
Q 007742          498 SECLLLKNMF-DPAMETD--------------PDFDLEIQGDVEEEC-SKYGRVKHIYVDKR----SAGFVYLRFESTEA  557 (591)
Q Consensus       498 s~~l~v~Nl~-~p~~~~~--------------~~~~~~~~edl~~~f-~~~G~V~~v~l~~~----~~g~afV~F~~~e~  557 (591)
                      ++||+|.||+ +|...+.              .+.+.++.++|.++| ++||.|..|.|+.+    ++|+|||+|.+.++
T Consensus         1 s~~~~l~nm~~~p~~~~~~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~   80 (104)
T 1jmt_A            1 SQTIALLNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREED   80 (104)
T ss_dssp             CCEEEEEEEEECCC------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHH
T ss_pred             CcEEEEeeccCCccccccccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHH
Confidence            4689999998 5765443              123456789999999 99999999999754    48999999999999


Q ss_pred             HHHHHHHhcccccCCeEEEEEEeC
Q 007742          558 AASAQRAMHMRWFARRLISAIFMK  581 (591)
Q Consensus       558 A~~A~~~l~g~~~~g~~l~v~~~~  581 (591)
                      |.+|+..|||+.|+|+.|.|.|++
T Consensus        81 A~~A~~~lng~~~~Gr~i~v~~sp  104 (104)
T 1jmt_A           81 AEKAVIDLNNRWFNGQPIHAELSP  104 (104)
T ss_dssp             HHHHHHHHTTCEETTEECCEEECC
T ss_pred             HHHHHHHHCCCEECCEEEEEEEcC
Confidence            999999999999999999999975

>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=99.52  E-value=6.3e-14  Score=116.14  Aligned_cols=83  Identities=22%  Similarity=0.273  Sum_probs=74.7

Q ss_pred             CCceEEEcCCCCCCCHHHHH---HHhccCCCeeEEEEeccCCCC---CcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeE
Q 007742          320 IDRKLYVGNLHFNMTETQLR---KLFEPFGPVELVQLPLDIETG---QCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRT  393 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~---~~f~~~g~i~~v~i~~~~~~~---~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~  393 (591)
                      ...+|||+|||+.+++++|+   ++|.+||.|..|.|+.+..++   .++|||||+|.+.++|..|+..|||. .|.|+.
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~-~~~gr~   92 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNV-VVDGRT   92 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTE-EETTEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCC-EECCEE
Confidence            35899999999999999999   999999999999998886543   45699999999999999999999995 799999


Q ss_pred             EEEEEecCCC
Q 007742          394 LKVSSVTDHV  403 (591)
Q Consensus       394 l~v~~~~~~~  403 (591)
                      |.|.+++...
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999987654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.52  E-value=1.2e-13  Score=119.75  Aligned_cols=85  Identities=38%  Similarity=0.583  Sum_probs=78.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~  117 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF-NILNKRLKVA  117 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTE-ECSSCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEE
Confidence            334589999999999999999999999999999999999888999999999999999999999999995 7999999999


Q ss_pred             EecCCC
Q 007742          398 SVTDHV  403 (591)
Q Consensus       398 ~~~~~~  403 (591)
                      ++....
T Consensus       118 ~a~~~~  123 (139)
T 1u6f_A          118 LAASGH  123 (139)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            987643

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.52  E-value=5.1e-14  Score=112.54  Aligned_cols=80  Identities=29%  Similarity=0.472  Sum_probs=73.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ..++|||+|||..+++++|+++|..||.|..|.|..+  ++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.++
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~-~~~g~~l~v~~a   83 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGM-KLSGREIDVRID   83 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTC-CBTTBCCCCEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEEEc
Confidence            3589999999999999999999999999999999874  7889999999999999999999999996 699999999998


Q ss_pred             cCC
Q 007742          400 TDH  402 (591)
Q Consensus       400 ~~~  402 (591)
                      ...
T Consensus        84 ~~~   86 (92)
T 2dgv_A           84 RNA   86 (92)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.52  E-value=3e-14  Score=116.08  Aligned_cols=74  Identities=22%  Similarity=0.295  Sum_probs=68.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||..+|+++|+.+|..||.|..|.++      .++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            46899999999999999999999999999999997      35899999999999999999 699999999999999875


Q ss_pred             c
Q 007742          298 A  298 (591)
Q Consensus       298 ~  298 (591)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.52  E-value=1.2e-14  Score=118.92  Aligned_cols=78  Identities=19%  Similarity=0.218  Sum_probs=68.6

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHc--CCccCCeeEE
Q 007742          217 ERDQRTVFAYQMPLK-ATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALS--GQLLLGQPVM  292 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~-~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~--g~~i~g~~i~  292 (591)
                      ..++++|||+|||+. +|+++|.++|.+||.|..|.|+.      ++|||||+|.+.++|..|+ .|+  +..|.|++|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            345799999999998 99999999999999999999973      4799999999999999999 465  4569999999


Q ss_pred             eccCcccc
Q 007742          293 VKPSEAEK  300 (591)
Q Consensus       293 v~~~~~~~  300 (591)
                      |.++....
T Consensus        96 V~~a~~~~  103 (112)
T 1x4f_A           96 VDLSEKYK  103 (112)
T ss_dssp             EEEECSCS
T ss_pred             EEECcccc
Confidence            99986544

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.52  E-value=1.7e-14  Score=117.57  Aligned_cols=77  Identities=17%  Similarity=0.227  Sum_probs=70.8

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      ....++|+|+||  |..++        +++|.++|+.||.|..|.+. .++|+|||+|.+.++|..|+..|||..|+|+.
T Consensus        24 ~~~~~~l~V~nl--p~~~~--------~~~l~~~f~~~G~i~~~~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   92 (101)
T 2la4_A           24 PPRVTTAYIGNI--PHFAT--------EADLIPLFQNFGFILDFKHY-PEKGCCFIKYDTHEQAAVCIVALANFPFQGRN   92 (101)
T ss_dssp             CSSCCEEEEESC--CTTCC--------HHHHHHHHHTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCEEEEcCC--CcccC--------HHHHHHHHHhCCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            345678999999  88887        89999999999999999987 56899999999999999999999999999999


Q ss_pred             EEEEEeCc
Q 007742          575 ISAIFMKP  582 (591)
Q Consensus       575 l~v~~~~~  582 (591)
                      |.|.|+.+
T Consensus        93 l~V~~a~~  100 (101)
T 2la4_A           93 LRTGWGKE  100 (101)
T ss_dssp             CCCCBCCC
T ss_pred             EEEEeccC
Confidence            99999875

>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=99.52  E-value=8.3e-14  Score=112.09  Aligned_cols=78  Identities=23%  Similarity=0.328  Sum_probs=71.9

Q ss_pred             CceEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLR----KLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~----~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      ..+|||+|||..+++++|+    ++|++||.|..|.|+.+..+   +|||||+|.+.++|..|+..|||. .|.|+.|.|
T Consensus         9 ~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~-~~~gr~l~V   84 (96)
T 2dgx_A            9 GADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRY-KIGSKKILV   84 (96)
T ss_dssp             CEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTE-EETTEEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCC-EECCeEEEE
Confidence            4799999999999999999    99999999999999987644   889999999999999999999995 799999999


Q ss_pred             EEecCC
Q 007742          397 SSVTDH  402 (591)
Q Consensus       397 ~~~~~~  402 (591)
                      .++.+.
T Consensus        85 ~~a~~~   90 (96)
T 2dgx_A           85 SLATGA   90 (96)
T ss_dssp             EECCCS
T ss_pred             EEcCCC
Confidence            998653

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.52  E-value=3e-14  Score=121.91  Aligned_cols=84  Identities=21%  Similarity=0.332  Sum_probs=76.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeE--EEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCC---eeeCCe
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVEL--VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK---LEIVGR  392 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~--v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~---~~~~g~  392 (591)
                      ....++|||+|||+.+++++|+++|.+||.|..  |.|+.+..++.++|||||+|.+. +|..|+..|||.   +.|.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            345689999999999999999999999999977  99999988999999999999999 999999999994   259999


Q ss_pred             EEEEEEecCC
Q 007742          393 TLKVSSVTDH  402 (591)
Q Consensus       393 ~l~v~~~~~~  402 (591)
                      .|.|.++.+.
T Consensus        99 ~l~V~~a~~~  108 (131)
T 2m2b_A           99 TINVEFAKGS  108 (131)
T ss_dssp             CCCCEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999998764

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.52  E-value=4e-14  Score=124.45  Aligned_cols=80  Identities=25%  Similarity=0.378  Sum_probs=75.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFG--PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g--~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      .++|||+|||+.+++++|+++|..||  .|..|.|+.+..+|.++|||||+|.+.++|..||..|||. .|.|+.|.|.+
T Consensus        55 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~-~~~Gr~l~V~~  133 (156)
T 3n9u_C           55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGK-VLNGEKVDVRP  133 (156)
T ss_dssp             -CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTC-EETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC-EECCeEeEEEE
Confidence            47999999999999999999999999  9999999999889999999999999999999999999996 79999999998


Q ss_pred             ecC
Q 007742          399 VTD  401 (591)
Q Consensus       399 ~~~  401 (591)
                      +..
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            753

>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=99.52  E-value=4.6e-14  Score=113.73  Aligned_cols=75  Identities=23%  Similarity=0.453  Sum_probs=68.5

Q ss_pred             CCCCCcEEEEeCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEe
Q 007742          216 PERDQRTVFAYQMPL-KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV  293 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~-~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v  293 (591)
                      .....++|||+|||+ .+|+++|.++|..||.|..|.+.        +|||||+|.+.++|..|+ .|||..+.|+.|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345679999999998 99999999999999999999883        789999999999999999 59999999999999


Q ss_pred             ccCcc
Q 007742          294 KPSEA  298 (591)
Q Consensus       294 ~~~~~  298 (591)
                      .++..
T Consensus        90 ~~a~~   94 (97)
T 2xnq_A           90 EVSSS   94 (97)
T ss_dssp             EECCC
T ss_pred             EecCC
Confidence            98754

>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=99.52  E-value=4.4e-14  Score=115.44  Aligned_cols=81  Identities=16%  Similarity=0.279  Sum_probs=71.5

Q ss_pred             CCCcceEEEeccCCCCC-CCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccc--ccC
Q 007742          495 GSPSECLLLKNMFDPAM-ETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMR--WFA  571 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~-~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~--~~~  571 (591)
                      ..++++|+|+||  |+. ++        +++|.++|+.||.|..|.|.. ++|+|||+|.+.++|..|+..|++.  .|.
T Consensus        22 ~~p~~~l~V~NL--p~~~~t--------e~~L~~lF~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~   90 (112)
T 1x4f_A           22 QELGRVIHLSNL--PHSGYS--------DSAVLKLAEPYGKIKNYILMR-MKSQAFIEMETREDAMAMVDHCLKKALWFQ   90 (112)
T ss_dssp             SCCCCEEEEESC--CCSSCC--------SHHHHTTTTTTSCCSEEEEET-TTTEEEEECSSHHHHHHHHHHHHHSCCCSS
T ss_pred             CCCCCEEEEeCC--CCccCC--------HHHHHHHHHhcCCEEEEEEec-CCCEEEEEECCHHHHHHHHHHhccCCceEC
Confidence            457889999999  886 77        789999999999999999874 6899999999999999999999764  599


Q ss_pred             CeEEEEEEeCchhhh
Q 007742          572 RRLISAIFMKPEDYE  586 (591)
Q Consensus       572 g~~l~v~~~~~~~~~  586 (591)
                      |++|.|.|+....-.
T Consensus        91 Gr~l~V~~a~~~~~~  105 (112)
T 1x4f_A           91 GRCVKVDLSEKYKKL  105 (112)
T ss_dssp             SSCCEEEEECSCSSS
T ss_pred             CEEEEEEECcccccc
Confidence            999999999866544

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=4.3e-14  Score=115.83  Aligned_cols=82  Identities=24%  Similarity=0.412  Sum_probs=76.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhcc-CCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCee-eCCeEEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEP-FGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLE-IVGRTLKVS  397 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~-~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~-~~g~~l~v~  397 (591)
                      ...+|||+|||..+++++|+++|.. ||.|..|.|+.+. ++.++|||||+|.+.++|..|+..|++. . |.|+.|.|.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~~g~~l~v~   85 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGA-VGLGSKPVRLS   85 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTC-CSSSSSCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCC-cccCCEeEEEE
Confidence            3489999999999999999999999 9999999999998 8999999999999999999999999996 6 999999999


Q ss_pred             EecCCC
Q 007742          398 SVTDHV  403 (591)
Q Consensus       398 ~~~~~~  403 (591)
                      ++....
T Consensus        86 ~a~~~~   91 (104)
T 2dhg_A           86 VAIPKA   91 (104)
T ss_dssp             BCCCCC
T ss_pred             EccCCC
Confidence            886543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.52  E-value=8.4e-14  Score=120.95  Aligned_cols=81  Identities=40%  Similarity=0.667  Sum_probs=75.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ....++|||+|||..+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|.+|+..|||. .|.|+.|.|.
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~  138 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVN  138 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEE-EETTEEEEEE
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEE
Confidence            345689999999999999999999999999999999999888999999999999999999999999995 7999999998


Q ss_pred             Ee
Q 007742          398 SV  399 (591)
Q Consensus       398 ~~  399 (591)
                      ++
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            64

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=6.2e-14  Score=115.71  Aligned_cols=81  Identities=31%  Similarity=0.574  Sum_probs=73.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ....++|||+|||..+++++|+++|++||.|..|.|..+.  +.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~  102 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGT-VVEGRKIEVN  102 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCC-EECCEEEEEE
Confidence            3345899999999999999999999999999999998874  348999999999999999999999996 6999999999


Q ss_pred             EecC
Q 007742          398 SVTD  401 (591)
Q Consensus       398 ~~~~  401 (591)
                      +++.
T Consensus       103 ~a~~  106 (109)
T 2err_A          103 NATA  106 (109)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9865

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.27  E-value=1.1e-15  Score=128.14  Aligned_cols=85  Identities=25%  Similarity=0.421  Sum_probs=78.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeE--------EEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRD--------VRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG  288 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~--------v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g  288 (591)
                      .+.++|||+|||+.+|+++|+++|.+||.|..        |.++.++.+|.++|||||+|.+.++|.+|+ .||+..|.|
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            35689999999999999999999999999998        999999889999999999999999999999 599999999


Q ss_pred             eeEEeccCcccccc
Q 007742          289 QPVMVKPSEAEKNL  302 (591)
Q Consensus       289 ~~i~v~~~~~~~~~  302 (591)
                      +.|.|.++......
T Consensus        85 ~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           85 NPIKVSFATRRADF   98 (116)
Confidence            99999998765543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.51  E-value=6.6e-14  Score=117.18  Aligned_cols=81  Identities=17%  Similarity=0.215  Sum_probs=72.6

Q ss_pred             eEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCee-EEEEeCCHHHHHHHHHHhcccccCC--eEEE
Q 007742          500 CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGF-VYLRFESTEAAASAQRAMHMRWFAR--RLIS  576 (591)
Q Consensus       500 ~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~-afV~F~~~e~A~~A~~~l~g~~~~g--~~l~  576 (591)
                      .|+|.||  +..++        +++|.++|++||.|..|.+....+|+ |||+|.+.++|..|+..|||..|.|  ++|.
T Consensus        30 ~I~V~NL--~~~vt--------e~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~Lr   99 (130)
T 3zzy_A           30 RIIVENL--FYPVT--------LDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR   99 (130)
T ss_dssp             EEEEESC--CSCCC--------HHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEE
T ss_pred             EEEECCC--CCCCC--------HHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEE
Confidence            3669999  77777        89999999999999999987777888 9999999999999999999999988  9999


Q ss_pred             EEEeCchhhhhccC
Q 007742          577 AIFMKPEDYEAKFK  590 (591)
Q Consensus       577 v~~~~~~~~~~~~~  590 (591)
                      |.|+++..++-++.
T Consensus       100 I~~ak~~~l~v~~n  113 (130)
T 3zzy_A          100 IDFSKLTSLNVKYN  113 (130)
T ss_dssp             EEECSCSSCCCCCC
T ss_pred             EEecCCCceeEEec
Confidence            99999987765554

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=5.4e-14  Score=111.79  Aligned_cols=76  Identities=17%  Similarity=0.347  Sum_probs=69.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      .....++|||+|||+.+|+++|.++|.+||.|..|.++        +|||||+|.+.++|..|+ .|||..|.|+.|.|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567999999999999999999999999999999997        349999999999999999 599999999999999


Q ss_pred             cCccc
Q 007742          295 PSEAE  299 (591)
Q Consensus       295 ~~~~~  299 (591)
                      ++...
T Consensus        77 ~a~~~   81 (90)
T 2dnp_A           77 LSTKG   81 (90)
T ss_dssp             ESCCC
T ss_pred             ECCCC
Confidence            98664

>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=99.51  E-value=5.1e-14  Score=117.44  Aligned_cols=79  Identities=22%  Similarity=0.430  Sum_probs=74.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||..+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..|| .|||. .|.|+.|.|.++.
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~-~~~g~~l~V~~a~  102 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQ-RLLGVPIIVQASQ  102 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTE-EETTEEEEEEEHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCC-EeCCeEEEEEecC
Confidence            479999999999999999999999999999999999888999999999999999999999 99995 7999999999875


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      .
T Consensus       103 ~  103 (114)
T 2cq4_A          103 A  103 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.51  E-value=2.2e-13  Score=115.41  Aligned_cols=83  Identities=25%  Similarity=0.471  Sum_probs=77.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ..+++|||+|||..+++++|+++|..||.|..|.|+.+. ++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.+
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~l~V~~  110 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGV-PLDGRPMDIQL  110 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTE-ESSSCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCC-EECCcEEEEEE
Confidence            345899999999999999999999999999999999988 8999999999999999999999999995 79999999999


Q ss_pred             ecCCC
Q 007742          399 VTDHV  403 (591)
Q Consensus       399 ~~~~~  403 (591)
                      +....
T Consensus       111 a~~~~  115 (124)
T 2kt5_A          111 VASQI  115 (124)
T ss_dssp             ECCTT
T ss_pred             eCCCC
Confidence            87643

>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=99.51  E-value=3.2e-14  Score=121.45  Aligned_cols=78  Identities=14%  Similarity=0.158  Sum_probs=72.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGP---VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~---i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      ...+|||+|||+.+|+++|+++|+.||.   |..|.|+.+.. +.++|||||+|.+.++|.+||. ||+. .|.|+.|.|
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~-~l~gr~i~V  119 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRE-SMGHRYIEV  119 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEE-ESSSSEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCC-EECCEEEEE
Confidence            3589999999999999999999999999   88999999875 9999999999999999999997 9995 799999999


Q ss_pred             EEec
Q 007742          397 SSVT  400 (591)
Q Consensus       397 ~~~~  400 (591)
                      .++.
T Consensus       120 ~~a~  123 (136)
T 2hgl_A          120 FKSH  123 (136)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            8874

>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=99.51  E-value=3.7e-14  Score=117.39  Aligned_cols=80  Identities=18%  Similarity=0.243  Sum_probs=73.4

Q ss_pred             CcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEE
Q 007742          497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLIS  576 (591)
Q Consensus       497 ~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~  576 (591)
                      ..++|+|.||  |..++        +++|.++|+.||.|..|.|+. ++|+|||+|.+.++|..|+..|||..|+|+.|.
T Consensus         9 ~~~~l~V~nL--p~~~t--------e~~L~~~F~~~G~i~~v~i~~-~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   77 (111)
T 1whx_A            9 SKTVILAKNL--PAGTL--------AAEIQETFSRFGSLGRVLLPE-GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLY   77 (111)
T ss_dssp             EEEEEEEESC--CTTCC--------HHHHHHHHHTTSCEEEEECCS-SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCEEEEeCC--CCCCC--------HHHHHHHHHhcCCEEEEEEeC-CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEE
Confidence            4578999999  88887        899999999999999998874 789999999999999999999999999999999


Q ss_pred             EEEeCchhhhh
Q 007742          577 AIFMKPEDYEA  587 (591)
Q Consensus       577 v~~~~~~~~~~  587 (591)
                      |.|+....|..
T Consensus        78 V~~a~~~~~~~   88 (111)
T 1whx_A           78 LEWAPIGVFGA   88 (111)
T ss_dssp             EEEEETTTTCC
T ss_pred             EEECCCCccCC
Confidence            99998877754

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=8.7e-15  Score=115.09  Aligned_cols=78  Identities=32%  Similarity=0.526  Sum_probs=72.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..|+..|||. .|.|+.|++.+.
T Consensus         5 ~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~-~~~g~~~~~~~~   82 (85)
T 1x4e_A            5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS-GVQAQMAKQSGP   82 (85)
T ss_dssp             CCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHH-TCCEESCCSSCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCC-eEeeEEEeecCC
Confidence            489999999999999999999999999999999999888999999999999999999999999996 689988877543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=1.3e-13  Score=111.85  Aligned_cols=77  Identities=19%  Similarity=0.364  Sum_probs=69.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcC--CCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEE
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKA--GKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVM  292 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~--G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~  292 (591)
                      ...+.++|||+|||+.+|+++|+++|.+|  |.|..|.+.        +|||||+|.+.++|.+|+. ||+..|.|+.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIE   82 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            34467999999999999999999999999  999998764        6799999999999999994 999999999999


Q ss_pred             eccCcccc
Q 007742          293 VKPSEAEK  300 (591)
Q Consensus       293 v~~~~~~~  300 (591)
                      |.++.+..
T Consensus        83 v~~a~~~~   90 (99)
T 2cpd_A           83 VTLAKPVD   90 (99)
T ss_dssp             EECCCCCC
T ss_pred             EEECCCCC
Confidence            99987644

>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=99.51  E-value=3e-14  Score=116.78  Aligned_cols=80  Identities=40%  Similarity=0.709  Sum_probs=75.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++.
T Consensus         8 ~~~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            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGR-EFSGRALRVDNAA   86 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSB-SCSSSCBEEEETT
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCC-eeCCcEEEEEeCC
Confidence            379999999999999999999999999999999998878999999999999999999999999996 6999999999986


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      .
T Consensus        87 ~   87 (104)
T 1p1t_A           87 S   87 (104)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.50  E-value=6e-14  Score=144.57  Aligned_cols=83  Identities=18%  Similarity=0.360  Sum_probs=78.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      .+.++|||+|||+.+|+++|..+|.+||.|..|.|+.++.+|.++|||||+|.+.++|.+|| .|||..|.|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35689999999999999999999999999999999999999999999999999999999999 79999999999999988


Q ss_pred             cccc
Q 007742          297 EAEK  300 (591)
Q Consensus       297 ~~~~  300 (591)
                      ....
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            7543

>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=99.50  E-value=2.1e-13  Score=112.66  Aligned_cols=81  Identities=25%  Similarity=0.404  Sum_probs=72.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ....++|||+|||..+++++|+++|..||.|..|.|..+   +.++|||||+|.+.++|..|+..||+. .|.|+.|.|.
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~   94 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGY-DYDGYRLRVE   94 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCC-EECCeEEEEE
Confidence            334689999999999999999999999999999999653   457899999999999999999999996 7999999999


Q ss_pred             EecCC
Q 007742          398 SVTDH  402 (591)
Q Consensus       398 ~~~~~  402 (591)
                      +++..
T Consensus        95 ~a~~~   99 (109)
T 1x4a_A           95 FPRSG   99 (109)
T ss_dssp             CCCCC
T ss_pred             EcccC
Confidence            98654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.50  E-value=9.1e-14  Score=114.64  Aligned_cols=80  Identities=25%  Similarity=0.409  Sum_probs=73.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..+ + ..|.|+.|.|.++.
T Consensus        25 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~-~~l~g~~l~V~~a~  102 (109)
T 2rs2_A           25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-R-HELDSKTIDPKVAF  102 (109)
T ss_dssp             -CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-C-EEETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-C-CcCCCEEEEEEEcc
Confidence            489999999999999999999999999999999999888999999999999999999999765 5 57999999999986


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      ..
T Consensus       103 ~~  104 (109)
T 2rs2_A          103 PR  104 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.50  E-value=2e-14  Score=116.78  Aligned_cols=79  Identities=25%  Similarity=0.546  Sum_probs=72.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccC-CCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDI-ETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~-~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ..++|||+|||..+++++|+++|+.|| |..|.|+.+. .++.++|||||+|.+.++|..|+ .|+|. .|.|+.|.|.+
T Consensus        18 ~~~~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           18 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE-SLGNRRIRVDV   94 (100)
T ss_dssp             --CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTC-CBTTBCCCCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCC-EECCeEEEEEe
Confidence            358999999999999999999999999 9999999887 58899999999999999999999 99996 69999999998


Q ss_pred             ecC
Q 007742          399 VTD  401 (591)
Q Consensus       399 ~~~  401 (591)
                      +..
T Consensus        95 a~~   97 (100)
T 2j76_E           95 ADQ   97 (100)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            864

>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=99.50  E-value=6.5e-14  Score=113.06  Aligned_cols=78  Identities=22%  Similarity=0.334  Sum_probs=71.7

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccC--C
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFA--R  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~--g  572 (591)
                      ..++++|+|.||  |..++        +++|.++|+.||.|..|.+... +|+|||+|.+.++|.+|+..|||..|.  |
T Consensus        14 ~~~~~~l~V~nl--p~~~t--------~~~l~~~F~~~G~v~~v~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~~~g   82 (97)
T 1why_A           14 ANPTTRLWVGGL--GPNTS--------LAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPD   82 (97)
T ss_dssp             CCCCSCEEEECC--CSSCC--------HHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSS
T ss_pred             CCCCCEEEEeCC--CCCCC--------HHHHHHHHHhcCCeeEEEEeCC-CCEEEEEECCHHHHHHHHHHHCCCEeCCCC
Confidence            356678999999  88887        8999999999999999998754 899999999999999999999999999  9


Q ss_pred             eEEEEEEeCch
Q 007742          573 RLISAIFMKPE  583 (591)
Q Consensus       573 ~~l~v~~~~~~  583 (591)
                      +.|.|.|+.++
T Consensus        83 ~~l~V~~a~~~   93 (97)
T 1why_A           83 RRLRVDFAKSG   93 (97)
T ss_dssp             CBCEEEECCCC
T ss_pred             cEEEEEECCCC
Confidence            99999999875

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=8.8e-14  Score=111.07  Aligned_cols=76  Identities=14%  Similarity=0.234  Sum_probs=69.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+.+|+++|+++|.+||.|..|.++        ++||||+|.+.++|.+|+ .||+..|.|+.|.|.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            4467999999999999999999999999999999987        349999999999999999 6999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +....
T Consensus        79 a~~~~   83 (92)
T 2dgt_A           79 STSRL   83 (92)
T ss_dssp             SSCCC
T ss_pred             ccCCC
Confidence            86643

>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=99.50  E-value=9.3e-14  Score=111.92  Aligned_cols=77  Identities=14%  Similarity=0.219  Sum_probs=70.1

Q ss_pred             cCCCcceEEEeccCCCC-CCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCC
Q 007742          494 IGSPSECLLLKNMFDPA-METDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFAR  572 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~-~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g  572 (591)
                      ..+++++|+|+||  |. .++        +++|.++|+.||.|..|.+.   +|+|||+|.+.++|.+|+..|||..|+|
T Consensus        18 ~~~~~~~l~V~nL--p~~~~t--------~~~L~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (97)
T 2xnq_A           18 GSHMKSRLFIGNL--PLKNVS--------KEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIEXESQEMNFG   84 (97)
T ss_dssp             -CCTTCEEEEESC--CSSCCC--------HHHHHHHHGGGSCEEEEEEC---SSEEEEEESSHHHHHHHHHHHTTSEETT
T ss_pred             CCCCCCEEEEeCC--CcccCC--------HHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3567789999999  87 777        89999999999999999884   8999999999999999999999999999


Q ss_pred             eEEEEEEeCch
Q 007742          573 RLISAIFMKPE  583 (591)
Q Consensus       573 ~~l~v~~~~~~  583 (591)
                      +.|.|.|+...
T Consensus        85 ~~l~V~~a~~~   95 (97)
T 2xnq_A           85 KKLILEVSSSN   95 (97)
T ss_dssp             EECEEEECCCC
T ss_pred             EEEEEEecCCC
Confidence            99999998753

>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=99.50  E-value=1e-13  Score=113.34  Aligned_cols=81  Identities=26%  Similarity=0.349  Sum_probs=72.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeE-EEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVEL-VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~-v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ....+|||+|||+.+++++|+++|..||.|.. |.|+.+ .++.++|||||+|.+.++|..||.. ++. .|.|+.|.|.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~-~~~gr~i~v~   89 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKE-RIGHRYIEIF   89 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTC-CSSSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-Ccc-hhCCcEEEEE
Confidence            34589999999999999999999999999987 888888 5899999999999999999999976 886 6999999998


Q ss_pred             EecCC
Q 007742          398 SVTDH  402 (591)
Q Consensus       398 ~~~~~  402 (591)
                      ++...
T Consensus        90 ~~~~~   94 (104)
T 1wg5_A           90 KSSRA   94 (104)
T ss_dssp             EECTT
T ss_pred             ECCHH
Confidence            87643

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.50  E-value=4.9e-14  Score=115.92  Aligned_cols=78  Identities=22%  Similarity=0.398  Sum_probs=71.6

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCe
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARR  573 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~  573 (591)
                      ...++++|+|+||  |..++        +++|.++|+.||.|..|.+.   +|+|||+|.+.++|.+|+..|||..|+|+
T Consensus        27 ~~~~~~~l~V~nL--p~~~t--------~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~   93 (108)
T 2jvo_A           27 GELSNTRLFVRPF--PLDVQ--------ESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQ   93 (108)
T ss_dssp             -CCSCSEEEECSS--CTTCC--------HHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCEEEEECC--CCCCC--------HHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            4567789999999  88888        89999999999999999988   89999999999999999999999999999


Q ss_pred             EEEEEEeCchh
Q 007742          574 LISAIFMKPED  584 (591)
Q Consensus       574 ~l~v~~~~~~~  584 (591)
                      .|.|.|+.+..
T Consensus        94 ~l~V~~a~~~~  104 (108)
T 2jvo_A           94 PLEVVYSKLPA  104 (108)
T ss_dssp             ECEEESCSCCC
T ss_pred             EEEEEEecCCC
Confidence            99999987653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.50  E-value=2.1e-14  Score=109.95  Aligned_cols=75  Identities=29%  Similarity=0.519  Sum_probs=70.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       323 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|..|+. |+|. .|.|+.|.|.++
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-IHFH-EINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCC-CSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCC-EECCEEEEEEeC
Confidence            48999999999999999999999999999999988889999999999999999999996 9996 699999999764

>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=99.50  E-value=7.2e-14  Score=116.40  Aligned_cols=79  Identities=24%  Similarity=0.300  Sum_probs=72.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCe-eEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPV-ELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i-~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...+|||+|||+.+++++|+++|..||.| ..|.|+.+. ++.++|||||+|.+.++|.+||.. |+. .|.|+.|.|.+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~-~~~gr~i~v~~   90 (114)
T 2cpy_A           14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRK-KLNGREAFVHV   90 (114)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSE-EETTEEEEEEE
T ss_pred             CccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCC-ccCCeEEEEEE
Confidence            35899999999999999999999999999 889999988 899999999999999999999965 884 79999999999


Q ss_pred             ecC
Q 007742          399 VTD  401 (591)
Q Consensus       399 ~~~  401 (591)
                      +..
T Consensus        91 a~~   93 (114)
T 2cpy_A           91 VTL   93 (114)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            853

>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=99.50  E-value=3e-13  Score=110.49  Aligned_cols=76  Identities=29%  Similarity=0.451  Sum_probs=69.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ..++|||+|||..+++++|+++|.+||.|..|.|+        ++||||+|.+.++|..|+..|++. .|.|+.|.|.++
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~a   80 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGK-DLEGENIEIVFA   80 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTE-EETTEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCC-ccCCCEEEEEEc
Confidence            35899999999999999999999999999999886        459999999999999999999995 799999999998


Q ss_pred             cCCCC
Q 007742          400 TDHVG  404 (591)
Q Consensus       400 ~~~~~  404 (591)
                      .+...
T Consensus        81 ~~~~~   85 (103)
T 2dgu_A           81 KPPDQ   85 (103)
T ss_dssp             CCCCC
T ss_pred             CCCcc
Confidence            76543

>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=99.50  E-value=1.2e-13  Score=122.26  Aligned_cols=82  Identities=29%  Similarity=0.435  Sum_probs=77.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ..++|||.|||..+++++|.++|+.||.|..|.|+.+..++.++|||||+|.+.++|.+||..|++. .|.|+.|.|.++
T Consensus        38 ~~~~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           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGT-RLDDRIIRTDWD  116 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTS-EETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCC-EECCeEEEEEEC
Confidence            3589999999999999999999999999999999999888999999999999999999999999996 699999999999


Q ss_pred             cCC
Q 007742          400 TDH  402 (591)
Q Consensus       400 ~~~  402 (591)
                      ...
T Consensus       117 ~~~  119 (156)
T 1h2v_Z          117 AGF  119 (156)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            754

>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=99.50  E-value=2.4e-13  Score=112.00  Aligned_cols=77  Identities=18%  Similarity=0.208  Sum_probs=70.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC-----eE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG-----RT  393 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g-----~~  393 (591)
                      ....+|||+|||+.+++++|+++|.+||.|..|.|+.+       |||||+|.+.++|.+||..|||. .|.|     +.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~-~~~g~~~~~~~   84 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNT-KFRSHEGETAY   84 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSE-EEECTTSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcC-CccCCcCcceE
Confidence            34589999999999999999999999999999999865       89999999999999999999995 7999     99


Q ss_pred             EEEEEecCCC
Q 007742          394 LKVSSVTDHV  403 (591)
Q Consensus       394 l~v~~~~~~~  403 (591)
                      |.|.++.+..
T Consensus        85 i~V~~a~~~~   94 (108)
T 1x4c_A           85 IRVKVDGPRS   94 (108)
T ss_dssp             EEEEESSCCS
T ss_pred             EEEEeCCCCC
Confidence            9999987643

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.50  E-value=1.4e-14  Score=116.81  Aligned_cols=79  Identities=27%  Similarity=0.390  Sum_probs=70.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~  294 (591)
                      ...+.++|||+|||+.+|+++|.++|..||.|..+     ..+|.++|||||+|.+.++|..|+. |||..|.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34467999999999999999999999999988766     3467899999999999999999995 99999999999999


Q ss_pred             cCccc
Q 007742          295 PSEAE  299 (591)
Q Consensus       295 ~~~~~  299 (591)
                      ++.+.
T Consensus        87 ~a~~~   91 (96)
T 1fjc_A           87 YTGEK   91 (96)
T ss_dssp             ECSSS
T ss_pred             EcCCC
Confidence            88653

>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=99.50  E-value=8.8e-14  Score=113.03  Aligned_cols=80  Identities=23%  Similarity=0.333  Sum_probs=72.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ....+|||+|||+.+++++|+++|.+||.+ .|.|+.+. ++.++|||||+|.+.++|.+|| .+|+. .|.|+.|.|..
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~-~~~gr~i~V~~   88 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKA-NMQHRYVELFL   88 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSC-CSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCC-eECCcEEEEEE
Confidence            345899999999999999999999999955 99999987 8999999999999999999999 57886 69999999988


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      +...
T Consensus        89 ~~~~   92 (102)
T 1wez_A           89 NSTA   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            7643

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.50  E-value=3.6e-14  Score=114.28  Aligned_cols=76  Identities=22%  Similarity=0.452  Sum_probs=68.4

Q ss_pred             CCCCcEEEEeCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          217 ERDQRTVFAYQMPL-KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       217 ~~~~~~l~V~nLp~-~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      ..+.++|||+|||+ .+|+++|.++|.+||.|..|.+.        +|||||+|.+.++|..|+ .|||..+.|+.|.|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34579999999998 99999999999999999999884        789999999999999999 599999999999999


Q ss_pred             cCcccc
Q 007742          295 PSEAEK  300 (591)
Q Consensus       295 ~~~~~~  300 (591)
                      ++....
T Consensus        79 ~a~~~~   84 (96)
T 2kvi_A           79 VSSSNA   84 (96)
T ss_dssp             EEECCC
T ss_pred             EcCcCC
Confidence            886543

>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=99.50  E-value=4.9e-14  Score=116.63  Aligned_cols=74  Identities=18%  Similarity=0.243  Sum_probs=68.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||+.+|+++|+++|.+||.|..|.|+.      ++|||||+|.+.++|..|+ .|||..|.|+.|.|.|+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            358999999999999999999999999999998863      5789999999999999999 699999999999999875


Q ss_pred             c
Q 007742          298 A  298 (591)
Q Consensus       298 ~  298 (591)
                      .
T Consensus        83 ~   83 (111)
T 1whx_A           83 I   83 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.49  E-value=8e-14  Score=114.22  Aligned_cols=79  Identities=28%  Similarity=0.421  Sum_probs=72.3

Q ss_pred             CceEEEcCCCCCC------CHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCe-E
Q 007742          321 DRKLYVGNLHFNM------TETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGR-T  393 (591)
Q Consensus       321 ~~~l~v~nl~~~~------~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~-~  393 (591)
                      .++|||+|||+.+      ++++|.++|++||.|..|.|+.  .+|.++|||||+|.+.++|..|+..|||. .|.|+ .
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g~-~~~g~~~   91 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGY-KLDKQHT   91 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSSE-ECSTTCE
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCCc-ccCCCce
Confidence            4899999999999      7899999999999999999883  47889999999999999999999999995 79998 9


Q ss_pred             EEEEEecCC
Q 007742          394 LKVSSVTDH  402 (591)
Q Consensus       394 l~v~~~~~~  402 (591)
                      |.|.++.+.
T Consensus        92 l~V~~a~~~  100 (105)
T 2nlw_A           92 FRVNLFTDF  100 (105)
T ss_dssp             EEEECSCCC
T ss_pred             EEEEEcchH
Confidence            999988654

>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=99.49  E-value=9.4e-14  Score=114.97  Aligned_cols=76  Identities=22%  Similarity=0.389  Sum_probs=69.4

Q ss_pred             CCCCCcEEEEeCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEe
Q 007742          216 PERDQRTVFAYQMPLK-ATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV  293 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~-~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v  293 (591)
                      +....++|||+|||+. +|+++|+++|.+||.|..|.+        ++|||||+|.+.++|..|+ .||+..|.|+.|.|
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   94 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDI   94 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            3445689999999999 999999999999999999988        4799999999999999999 79999999999999


Q ss_pred             ccCccc
Q 007742          294 KPSEAE  299 (591)
Q Consensus       294 ~~~~~~  299 (591)
                      .++...
T Consensus        95 ~~a~~~  100 (110)
T 1wf1_A           95 NMAGEP  100 (110)
T ss_dssp             EESCCC
T ss_pred             EECCCC
Confidence            998643

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=3.2e-13  Score=109.92  Aligned_cols=79  Identities=30%  Similarity=0.578  Sum_probs=70.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||..+++++|+++|.+||.|   .++.+ .++.++|||||+|.+.++|..|+..||+. .|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~~   87 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKR-EIEGRAIRLEL   87 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSE-EETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCC-EeCCeEEEEEE
Confidence            346899999999999999999999999977   45555 47889999999999999999999999995 79999999999


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      +...
T Consensus        88 a~~~   91 (101)
T 2fc9_A           88 QGPR   91 (101)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8764

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=6.2e-14  Score=116.78  Aligned_cols=75  Identities=23%  Similarity=0.247  Sum_probs=64.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC---CCccceEEEEecCcchHHHHH-HHcCCccCCeeEEe
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS---RRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV  293 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~---g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v  293 (591)
                      ...++|||+|||+.+|+++|+++|.+||.|. +.++.+..+   |.++|||||+|.+.++|.+|| .|+  .+.|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4569999999999999999999999999999 888888877   799999999999999999999 463  256666665


Q ss_pred             cc
Q 007742          294 KP  295 (591)
Q Consensus       294 ~~  295 (591)
                      ..
T Consensus        83 ~~   84 (114)
T 2dnl_A           83 VS   84 (114)
T ss_dssp             EC
T ss_pred             cc
Confidence            43

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.49  E-value=7.3e-14  Score=114.66  Aligned_cols=78  Identities=17%  Similarity=0.132  Sum_probs=70.6

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhcccc-ceEEEEEe-cCCCeeEEEEeCCHHHHHHHHHHhcccccCCe
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYG-RVKHIYVD-KRSAGFVYLRFESTEAAASAQRAMHMRWFARR  573 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G-~V~~v~l~-~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~  573 (591)
                      .....|+|+||  |..++        +++|+++|+.|| .|..+.+. ..++|+|||+|.+.++|.+|+..|||..|+|+
T Consensus        26 ~~~~~l~VgnL--p~~~t--------e~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr   95 (111)
T 2jvr_A           26 AKRYRITMKNL--PEGCS--------WQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGS   95 (111)
T ss_dssp             CCCEEEEEECS--SCCCC--------HHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTE
T ss_pred             CCCCEEEEECC--CCCCC--------HHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            44568999999  88888        899999999999 89999884 56899999999999999999999999999999


Q ss_pred             EEEEEEeCch
Q 007742          574 LISAIFMKPE  583 (591)
Q Consensus       574 ~l~v~~~~~~  583 (591)
                      .|.|.++...
T Consensus        96 ~i~V~~a~~~  105 (111)
T 2jvr_A           96 VITVERDDNP  105 (111)
T ss_dssp             EEEEEESCC-
T ss_pred             EEEEEECCCC
Confidence            9999998654

>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=99.49  E-value=1.2e-13  Score=114.26  Aligned_cols=84  Identities=17%  Similarity=0.280  Sum_probs=75.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEe-ccCCCCCcccEEEEEeCCHHHHHHHHHHhc-CCeeeCCeEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGP-VELVQLP-LDIETGQCKGFGFVQFAQLEHAKAAQSALN-GKLEIVGRTLKV  396 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~v~i~-~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~-g~~~~~g~~l~v  396 (591)
                      ..++|||+|||..+++++|+++|..||. |..|.|+ .+..++.++|||||+|.+.++|..|+..|+ |.+.|.|+.|.|
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 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            3589999999999999999999999998 9999998 777778899999999999999999999996 324799999999


Q ss_pred             EEecCCC
Q 007742          397 SSVTDHV  403 (591)
Q Consensus       397 ~~~~~~~  403 (591)
                      .++.+..
T Consensus        87 ~~a~~~~   93 (109)
T 2dis_A           87 DWAEPEI   93 (109)
T ss_dssp             EESCSSC
T ss_pred             EEcCCCC
Confidence            9987654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.48  E-value=1.3e-13  Score=115.51  Aligned_cols=78  Identities=15%  Similarity=0.170  Sum_probs=72.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGP---VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~---i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      ...+|||+|||+.+++++|+++|..||.   |..|.|+.+.. +.++|||||+|.+.++|.+||. |++. .|.|+.|.|
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~-~~~gr~i~V   92 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRE-SMGHRYIEV   92 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTE-EETTEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCC-eECCeEEEE
Confidence            3589999999999999999999999998   89999998874 8999999999999999999997 9995 799999999


Q ss_pred             EEec
Q 007742          397 SSVT  400 (591)
Q Consensus       397 ~~~~  400 (591)
                      .++.
T Consensus        93 ~~a~   96 (118)
T 2db1_A           93 FKSH   96 (118)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9874

>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=99.48  E-value=1.4e-14  Score=124.10  Aligned_cols=122  Identities=16%  Similarity=0.146  Sum_probs=71.0

Q ss_pred             cceEEEEecCcchHHHHHHHcCCccCCeeEEeccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHH
Q 007742          262 KGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKL  341 (591)
Q Consensus       262 ~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~  341 (591)
                      +|+||.+|..++.+..++.-......|...--...              ............+|||+|||+.+++++|+++
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~gg~~~g~~~g--------------~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~   66 (139)
T 2hgn_A            1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSG--------------DSEFTVQSTTGHCVHMRGLPYKATENDIYNF   66 (139)
T ss_dssp             ----------------------------------------------------------CCCCEECCSCCTTCCHHHHHHH
T ss_pred             CCcccccccCccccchhcccchhccCCCCCCCCCC--------------CcccCCCCCCCCEEEEeCCCCCCCHHHHHHH
Confidence            36889999888887766621111122221100000              0001111223479999999999999999999


Q ss_pred             hccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          342 FEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       342 f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      |++|| |..|.|+.+. .+.++|||||+|.+.++|.+|| .+|+. .|.|+.|.|..+..
T Consensus        67 F~~~G-i~~v~i~~d~-~g~srGfaFV~F~~~e~A~~Al-~~~g~-~l~gR~i~V~~a~~  122 (139)
T 2hgn_A           67 FSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVAAM-SKDRA-NMQHRYIELFLNST  122 (139)
T ss_dssp             HCSCC-CSEEECCCSS-SSCSSCCCEEECSHHHHHHHHT-TCCSC-SSSSCCCCCEECCC
T ss_pred             HHhcC-CeEEEEEECC-CCCCceEEEEEeCCHHHHHHHH-hhCCC-EECCEEEEEEECCC
Confidence            99999 6699999987 4899999999999999999999 88986 69999999988754

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1.3e-13  Score=109.50  Aligned_cols=78  Identities=21%  Similarity=0.252  Sum_probs=71.8

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      ..+.++|+|.||  |..++        +++|.++|+.||.|..|.+.   +|+|||+|.+.++|.+|+..|||..|.|+.
T Consensus         5 ~~~~~~l~V~nl--p~~~t--------~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   71 (90)
T 2dnq_A            5 SSGMVKLFIGNL--PREAT--------EQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVN   71 (90)
T ss_dssp             SSCCEEEEEESC--CSSCC--------HHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCB
T ss_pred             CCCCeEEEEeCC--CCCCC--------HHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcE
Confidence            456788999999  88888        89999999999999999988   789999999999999999999999999999


Q ss_pred             EEEEEeCchhh
Q 007742          575 ISAIFMKPEDY  585 (591)
Q Consensus       575 l~v~~~~~~~~  585 (591)
                      |.|.|+.+..-
T Consensus        72 l~v~~a~~~~~   82 (90)
T 2dnq_A           72 INVEASKNKSK   82 (90)
T ss_dssp             CEEECSSCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999987654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=1.5e-13  Score=115.01  Aligned_cols=81  Identities=31%  Similarity=0.522  Sum_probs=75.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||..+++++|+++|..||.|..|.|+.+..++.++|||||+|.+.++|..||.. ++ ..|.|+.|.|.++.
T Consensus        27 ~~~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           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RP-HSIDGRVVEPKRAV  104 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CS-EEETTEEEEEECCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CC-cEECCEEEEEEECC
Confidence            48999999999999999999999999999999999988899999999999999999999976 88 47999999999987


Q ss_pred             CCC
Q 007742          401 DHV  403 (591)
Q Consensus       401 ~~~  403 (591)
                      ...
T Consensus       105 ~~~  107 (116)
T 1x4b_A          105 ARE  107 (116)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            653

>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=99.48  E-value=5.7e-14  Score=112.47  Aligned_cols=76  Identities=21%  Similarity=0.282  Sum_probs=67.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCC-eeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcC-CccCCeeEEec
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGK-VRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSG-QLLLGQPVMVK  294 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~-i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g-~~i~g~~i~v~  294 (591)
                      ...++|||+|||+.+|+++|+++|.+||. |..+.+.       ++|||||+|.+.++|.+|+ .||| ..|.|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45689999999999999999999999999 5555553       4799999999999999999 5999 99999999999


Q ss_pred             cCcccc
Q 007742          295 PSEAEK  300 (591)
Q Consensus       295 ~~~~~~  300 (591)
                      ++.+..
T Consensus        79 ~a~~~~   84 (93)
T 2cqh_A           79 YSVSKK   84 (93)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            987643

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1.7e-13  Score=112.27  Aligned_cols=76  Identities=28%  Similarity=0.381  Sum_probs=70.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ..+|||+|||+.+++++|+++|+.| .|..|.|+.+. .|.++|||||+|.+.++|.+|| .||+. .|.|+.|.|..+.
T Consensus        16 ~~~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           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRM-LMIQRYVEVSPAT   91 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTE-EETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCC-eECCeEEEEEECC
Confidence            4799999999999999999999999 89999999887 5889999999999999999999 79996 7999999998764

>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=99.48  E-value=2.5e-13  Score=106.73  Aligned_cols=75  Identities=32%  Similarity=0.412  Sum_probs=68.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHh-cCCeeeCCeEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL-NGKLEIVGRTLKV  396 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l-~g~~~~~g~~l~v  396 (591)
                      ....++|||+|||..+++++|+++|.+||.|..|.++.+      +|||||+|.+.++|..|+..| +|. .+.|+.|.|
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~-~~~g~~l~v   81 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKL-IVNGRRLNV   81 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTC-EETTEECCE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCe-eECCCEEEE
Confidence            344589999999999999999999999999999999863      789999999999999999988 885 799999999


Q ss_pred             EEe
Q 007742          397 SSV  399 (591)
Q Consensus       397 ~~~  399 (591)
                      .++
T Consensus        82 ~~a   84 (85)
T 2ytc_A           82 KWG   84 (85)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            886

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=1.2e-13  Score=116.52  Aligned_cols=85  Identities=21%  Similarity=0.266  Sum_probs=71.1

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEec--CCCeeEEEEeCCHHHHHHHHHHhcccccCC
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK--RSAGFVYLRFESTEAAASAQRAMHMRWFAR  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~--~~~g~afV~F~~~e~A~~A~~~l~g~~~~g  572 (591)
                      ..++++|||+||  |..++.    .+|.+.|.++|++||.|..|.+..  .++|+|||+|.+.++|..|+..|||..|.|
T Consensus        26 ~~p~~~LfV~nL--~~~~~e----~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~g   99 (127)
T 2a3j_A           26 TEPSQVVLITNI--NPEVPK----EKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQG   99 (127)
T ss_dssp             CSCCSEEEEESC--CTTSCH----HHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTT
T ss_pred             CCCCCEEEEeCC--CCCCCH----HHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            356778999999  777762    112344668999999999998853  568999999999999999999999999999


Q ss_pred             eEEEEEEeCchhh
Q 007742          573 RLISAIFMKPEDY  585 (591)
Q Consensus       573 ~~l~v~~~~~~~~  585 (591)
                      ++|.|.|+.....
T Consensus       100 r~l~V~~a~~~~~  112 (127)
T 2a3j_A          100 NPLVITFSETPQS  112 (127)
T ss_dssp             SCCEEEECCCCCH
T ss_pred             CEEEEEEccCcch
Confidence            9999999987654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.47  E-value=3.6e-14  Score=109.22  Aligned_cols=76  Identities=26%  Similarity=0.457  Sum_probs=71.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|..|+..++ . .+.|+.|.|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~-~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-H-ELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-C-CCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-C-ccCCEEEEEEec
Confidence            379999999999999999999999999999999988789999999999999999999998888 4 699999999875

>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=99.47  E-value=7.6e-14  Score=110.35  Aligned_cols=75  Identities=11%  Similarity=0.235  Sum_probs=68.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ...++|||+|||+.+|+++|+++|.+| .|..|.+.      .++|||||+|.+.++|..|+ .|||..+.|++|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   75 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEc
Confidence            346899999999999999999999999 99999884      57899999999999999999 59999999999999987


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      ...
T Consensus        76 ~~~   78 (88)
T 1wg1_A           76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            553

>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=99.47  E-value=2e-13  Score=114.05  Aligned_cols=81  Identities=19%  Similarity=0.312  Sum_probs=73.1

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEec--CCCeeEEEEeCCHHHHHHHHHHhcccccCC
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK--RSAGFVYLRFESTEAAASAQRAMHMRWFAR  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~--~~~g~afV~F~~~e~A~~A~~~l~g~~~~g  572 (591)
                      ..++++|+|.||  |..++        +++|.++|+.||.|..|.+..  .++|+|||+|.+.++|..|+..|||..|+|
T Consensus         5 ~~~~~~l~V~nl--p~~~t--------~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   74 (115)
T 3lqv_A            5 PEVNRILYIRNL--PYKIT--------AEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSN   74 (115)
T ss_dssp             TTCCSEEEEESC--CTTCC--------HHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCCEEEEeCC--CCCCC--------HHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            456789999999  88888        899999999999999998853  457999999999999999999999999999


Q ss_pred             eEEEEEEeCchhh
Q 007742          573 RLISAIFMKPEDY  585 (591)
Q Consensus       573 ~~l~v~~~~~~~~  585 (591)
                      +.|.|.|+.+..-
T Consensus        75 ~~l~v~~a~~~~~   87 (115)
T 3lqv_A           75 RYLVVLYYNANRA   87 (115)
T ss_dssp             CBCEEEECCHHHH
T ss_pred             eEEEEEEecCChh
Confidence            9999999987554

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.47  E-value=1.5e-13  Score=116.47  Aligned_cols=80  Identities=29%  Similarity=0.528  Sum_probs=75.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+ .|+|. .|.|+.|.|.++.
T Consensus        36 ~~~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           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDET-VFRGRTIKVLPKR  113 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTC-EETTEECEEEESS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCC-eECCeEEEEEECC
Confidence            379999999999999999999999999999999998878999999999999999999999 89996 6999999999986


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      ..
T Consensus       114 ~~  115 (124)
T 2jwn_A          114 TN  115 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.47  E-value=3.8e-13  Score=112.14  Aligned_cols=80  Identities=29%  Similarity=0.473  Sum_probs=74.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeee--------CC
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI--------VG  391 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~--------~g  391 (591)
                      ..++|||+|||..+++++|+++|..||.|..|.|+.+. ++.++|||||+|.+.++|..|+..|||. .|        .+
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~-~~~~~~~~~~~~  101 (114)
T 1x5o_A           24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGK-FIKTPPGVSAPT  101 (114)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTC-CCCCCTTSCCCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCC-EEcCCccccCCC
Confidence            35899999999999999999999999999999999998 8999999999999999999999999996 57        57


Q ss_pred             eEEEEEEecC
Q 007742          392 RTLKVSSVTD  401 (591)
Q Consensus       392 ~~l~v~~~~~  401 (591)
                      ++|.|.++.+
T Consensus       102 ~~l~v~~a~p  111 (114)
T 1x5o_A          102 EPLLCKFSGP  111 (114)
T ss_dssp             SCBEEEECCC
T ss_pred             CceeEEccCC
Confidence            8899998864

>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=99.47  E-value=1.5e-13  Score=113.58  Aligned_cols=80  Identities=16%  Similarity=0.225  Sum_probs=73.4

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      ..+.++|+|.||  |..++        +++|.++|+.||.|..|.|... +|+|||+|.+.++|.+|+..|+|..|+|+.
T Consensus        22 ~~~~~~l~V~nl--~~~~t--------~~~l~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   90 (109)
T 1x4g_A           22 SPKNCTVYCGGI--ASGLT--------DQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHV   90 (109)
T ss_dssp             CSSCCEEEEECC--SSCCC--------HHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCcEEEEeCC--CCCCC--------HHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHcCCCEECCcE
Confidence            456778999999  88887        8999999999999999999865 899999999999999999999999999999


Q ss_pred             EEEEEeCchhh
Q 007742          575 ISAIFMKPEDY  585 (591)
Q Consensus       575 l~v~~~~~~~~  585 (591)
                      |.|.|+.+..-
T Consensus        91 l~v~~a~~~~~  101 (109)
T 1x4g_A           91 VKCYWGKESPD  101 (109)
T ss_dssp             CEEECCCCCCS
T ss_pred             EEEEecCCCCC
Confidence            99999987653

>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=99.47  E-value=3.5e-13  Score=109.17  Aligned_cols=78  Identities=33%  Similarity=0.569  Sum_probs=71.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      +..++|||+|||..+++++|+++|..||.|..|.+..+      +|||||+|.+.++|..|+..|+|. .|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~-~~~g~~l~v~~   85 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNM-PLRGKQLRVRF   85 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTC-CBTTBCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCC-EeCCceEEEEE
Confidence            34589999999999999999999999999999999753      689999999999999999999996 69999999999


Q ss_pred             ecCCC
Q 007742          399 VTDHV  403 (591)
Q Consensus       399 ~~~~~  403 (591)
                      +.+..
T Consensus        86 a~~~~   90 (99)
T 2cpj_A           86 ACHSA   90 (99)
T ss_dssp             SSCCS
T ss_pred             cCCCC
Confidence            87643

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.47  E-value=3.1e-14  Score=110.69  Aligned_cols=72  Identities=26%  Similarity=0.413  Sum_probs=66.0

Q ss_pred             ceEEEcCCCCCC------CHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCe-EE
Q 007742          322 RKLYVGNLHFNM------TETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGR-TL  394 (591)
Q Consensus       322 ~~l~v~nl~~~~------~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~-~l  394 (591)
                      ++|||+|||..+      ++++|.++|++||.|..|.|+.  .++.++|||||+|.+.++|..|+..|||. .|.|+ +|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~-~~~g~~~l   78 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGY-KLDKQHTF   78 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSC-CCSSSSCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCc-ccCCceeE
Confidence            689999999999      7799999999999999999873  47889999999999999999999999996 69998 87


Q ss_pred             EE
Q 007742          395 KV  396 (591)
Q Consensus       395 ~v  396 (591)
                      .|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            65

>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=99.46  E-value=9.8e-14  Score=109.59  Aligned_cols=72  Identities=26%  Similarity=0.517  Sum_probs=66.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcC----C-------CeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCcc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKA----G-------KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLL  286 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~----G-------~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i  286 (591)
                      .+.++|||+|||+.+|+++|+++|.+|    |       .|..+.+..+      +|||||+|.+.++|.+|+.|||..|
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g~~~   77 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDGIIF   77 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCCCEE
Confidence            456999999999999999999999999    8       8999988743      7999999999999999999999999


Q ss_pred             CCeeEEecc
Q 007742          287 LGQPVMVKP  295 (591)
Q Consensus       287 ~g~~i~v~~  295 (591)
                      .|+.|.|..
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999864

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=4.7e-13  Score=109.15  Aligned_cols=80  Identities=34%  Similarity=0.479  Sum_probs=71.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ...++|||+|||..+++++|+++|..|+   .|.++.+..++.++|||||+|.+.++|..||..||+. .|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~V~~   88 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDG-EIDGNKVTLDW   88 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTC-EETTEECEEEE
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC-eECCeEEEEEE
Confidence            4458999999999999999999999874   5667777778899999999999999999999999996 79999999999


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      ++..
T Consensus        89 a~~~   92 (102)
T 2fc8_A           89 AKPK   92 (102)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            8754

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.46  E-value=2.8e-13  Score=113.01  Aligned_cols=83  Identities=20%  Similarity=0.226  Sum_probs=70.8

Q ss_pred             CCcce--EEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCee-EEEEeCCHHHHHHHHHHhcccccCC
Q 007742          496 SPSEC--LLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGF-VYLRFESTEAAASAQRAMHMRWFAR  572 (591)
Q Consensus       496 ~~s~~--l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~-afV~F~~~e~A~~A~~~l~g~~~~g  572 (591)
                      +++.+  |+|.||  ++.++        +++|.++|+.||.|..|.|... .|+ |||+|.+.++|..|+..|||..|.|
T Consensus        21 ~ps~vl~l~V~NL--~~~vt--------~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g   89 (124)
T 2e5i_A           21 GGNKVLLLSIQNP--LYPIT--------VDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYA   89 (124)
T ss_dssp             CCCSEEEEEEESC--CSCCC--------HHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBT
T ss_pred             CCCcEEEEEEcCc--CCCCC--------HHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecC
Confidence            34445  568999  77777        8999999999999999988654 586 9999999999999999999999987


Q ss_pred             --eEEEEEEeCchhhhhcc
Q 007742          573 --RLISAIFMKPEDYEAKF  589 (591)
Q Consensus       573 --~~l~v~~~~~~~~~~~~  589 (591)
                        +.|.|.|+.+.....++
T Consensus        90 ~~~~l~V~~Ak~~~l~v~~  108 (124)
T 2e5i_A           90 GCCTLKIEYARPTRLNVIR  108 (124)
T ss_dssp             TBSEEEEECCSCSCCCCSS
T ss_pred             CCeEEEEEEecCCcceeec
Confidence              69999999988755443

>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=99.46  E-value=2.1e-14  Score=125.12  Aligned_cols=80  Identities=19%  Similarity=0.368  Sum_probs=70.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEE--------EEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDV--------RLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLL  287 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v--------~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~  287 (591)
                      ..+.++|||+|||+.+|+++|..+|..||.|..+        .+.   .+|.++|||||+|.+.++|..|+ .|||..|.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~  118 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKALKEANGYVLF  118 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHHHHHHTTBEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeC
Confidence            4567999999999999999999999999998764        333   36889999999999999999999 59999999


Q ss_pred             CeeEEeccCccc
Q 007742          288 GQPVMVKPSEAE  299 (591)
Q Consensus       288 g~~i~v~~~~~~  299 (591)
                      |+.|.|.++...
T Consensus       119 g~~l~V~~a~~~  130 (143)
T 3egn_A          119 GKPMVVQFARSA  130 (143)
T ss_dssp             TEECEEEECCCS
T ss_pred             CcEEEEEECCCC
Confidence            999999988653

>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=99.46  E-value=1.3e-13  Score=111.29  Aligned_cols=80  Identities=18%  Similarity=0.400  Sum_probs=72.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLR----KLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTL  394 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~----~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l  394 (591)
                      +++++|||+|||..+++++|+    ++|.+||.|..|.+..   ++.++|||||+|.+.++|..|+..|||. .|.|+.|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l   81 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGF-PFYDKPM   81 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTC-EETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCC-EECCcEE
Confidence            345899999999999999999    9999999999998873   5667899999999999999999999996 6999999


Q ss_pred             EEEEecCC
Q 007742          395 KVSSVTDH  402 (591)
Q Consensus       395 ~v~~~~~~  402 (591)
                      .|.++...
T Consensus        82 ~v~~a~~~   89 (97)
T 1nu4_A           82 RIQYAKTD   89 (97)
T ss_dssp             EEEECSSC
T ss_pred             EEEEccCC
Confidence            99998654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=1.2e-13  Score=111.26  Aligned_cols=78  Identities=15%  Similarity=0.136  Sum_probs=70.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEE-EEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDV-RLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v-~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ...++|||+|||+.+|+++|+.+|..||.|..| .++.++.+    |.|||+|.+.++|..|+ .|||..|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            356899999999999999999999999999999 48877654    44999999999999999 5999999999999998


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +.+.
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            8664

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=2.3e-13  Score=109.78  Aligned_cols=79  Identities=11%  Similarity=0.166  Sum_probs=69.8

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      ...+++|+|.||  |..++        +++|.++|+.||.|....+...++|+|||+|.+.++|.+|+..|||..|+|+.
T Consensus        16 ~~~~~~l~V~nL--~~~~t--------~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   85 (97)
T 2e5j_A           16 APLAADVYVGNL--PRDAR--------VSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDT   85 (97)
T ss_dssp             SCCCCEEEEECC--CTTCC--------HHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCCCCEEEEeCC--CCcCc--------HHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            345678999999  88888        89999999999999733345567999999999999999999999999999999


Q ss_pred             EEEEEeCch
Q 007742          575 ISAIFMKPE  583 (591)
Q Consensus       575 l~v~~~~~~  583 (591)
                      |.|.|+.+.
T Consensus        86 l~V~~a~~~   94 (97)
T 2e5j_A           86 LRVALARQQ   94 (97)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEEcCCC
Confidence            999998775

>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=99.46  E-value=1.7e-13  Score=108.34  Aligned_cols=75  Identities=21%  Similarity=0.331  Sum_probs=62.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCc--cCCeeEEec
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQL--LLGQPVMVK  294 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~--i~g~~i~v~  294 (591)
                      ..+..+|||+|||+.+|+++|+++|.+||.|..|.|+.+     ++|||||+|.+.++|.+   +++..  +.|+.|.|.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~---~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS---LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH---HTTCEEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH---HcCCCcccCCEEEEEE
Confidence            445699999999999999999999999999999999864     78999999999999873   45555  469999998


Q ss_pred             cCccc
Q 007742          295 PSEAE  299 (591)
Q Consensus       295 ~~~~~  299 (591)
                      ++.+.
T Consensus        80 ~a~~k   84 (89)
T 3d2w_A           80 NAEPK   84 (89)
T ss_dssp             ECC--
T ss_pred             EcCCC
Confidence            87654

>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=99.45  E-value=2.2e-14  Score=114.19  Aligned_cols=79  Identities=38%  Similarity=0.654  Sum_probs=72.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||..+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.+ |..|+..|||. .+.|+.|.|.++..
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~-~~~g~~l~V~~a~~   79 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNT-DFMGRTIRVTEANP   79 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSS-CCSSSSCSEEEC--
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCC-EECCeEEEEEEcCC
Confidence            58999999999999999999999999999999999888999999999999999 99999999996 69999999999865


Q ss_pred             C
Q 007742          402 H  402 (591)
Q Consensus       402 ~  402 (591)
                      .
T Consensus        80 ~   80 (90)
T 2ki2_A           80 K   80 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=3.8e-13  Score=108.49  Aligned_cols=76  Identities=17%  Similarity=0.283  Sum_probs=68.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+||  .+|+++|+++|.+||.|..|.+.      .++|||||+|.+.++|.+|| .||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            446799999996  89999999999999999999884      46899999999999999999 7999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +....
T Consensus        84 a~~~~   88 (97)
T 1x5p_A           84 ARKQP   88 (97)
T ss_dssp             CSSCC
T ss_pred             CCCCC
Confidence            86644

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=3.7e-13  Score=107.41  Aligned_cols=77  Identities=18%  Similarity=0.276  Sum_probs=70.8

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      ..++++|+|.||  |..++        +++|.++|+.||.|..|.+.   +++|||+|.+.++|.+|+..|||..|.|+.
T Consensus         7 ~~~~~~l~V~nL--p~~~t--------~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~   73 (92)
T 2dgt_A            7 GKASTKLHVGNI--SPTCT--------NQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKR   73 (92)
T ss_dssp             CCSSEEEEEESC--CSSCC--------HHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCEEEEeCC--CCCCC--------HHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcE
Confidence            456789999999  88887        89999999999999999987   559999999999999999999999999999


Q ss_pred             EEEEEeCchh
Q 007742          575 ISAIFMKPED  584 (591)
Q Consensus       575 l~v~~~~~~~  584 (591)
                      |.|.|+.+..
T Consensus        74 l~V~~a~~~~   83 (92)
T 2dgt_A           74 MHVQLSTSRL   83 (92)
T ss_dssp             EEEEESSCCC
T ss_pred             EEEEEccCCC
Confidence            9999998754

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=1.5e-13  Score=105.93  Aligned_cols=78  Identities=22%  Similarity=0.255  Sum_probs=65.6

Q ss_pred             CCcce-EEEeccCCCCCCCCchhhhhHHHHHHHHhccc-cceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCe
Q 007742          496 SPSEC-LLLKNMFDPAMETDPDFDLEIQGDVEEECSKY-GRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARR  573 (591)
Q Consensus       496 ~~s~~-l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~-G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~  573 (591)
                      +|+.+ |+|.||  |+.++.    .+|...|.++|+.| |.|..|     ..|+|||.|.+.++|..|++.|+|..|.|+
T Consensus         6 ~p~~T~lYV~NL--~~~~~~----~~lk~~L~~lF~~yGG~Vl~V-----tgG~AfV~F~~~esA~~A~~~l~G~~l~gr   74 (96)
T 2diu_A            6 SGCHTLLYVYNL--PANKDG----KSVSNRLRRLSDNCGGKVLSI-----TGCSAILRFINQDSAERAQKRMENEDVFGN   74 (96)
T ss_dssp             CCSSEEEEEESC--CTTSCH----HHHHHHHHHHHHTTTCCEEEC-----CTTCEEEEESSHHHHHHHHHHHTTCCSSSS
T ss_pred             CCcceEEEEeCC--CCcCCH----HHHHHHHHHHHHHcCCeeEEE-----ecCEEEEEECCHHHHHHHHHHhcCCccCCc
Confidence            34555 889999  888762    22345688999999 599999     239999999999999999999999999999


Q ss_pred             EEEEEEeCchh
Q 007742          574 LISAIFMKPED  584 (591)
Q Consensus       574 ~l~v~~~~~~~  584 (591)
                      +|.|.|++...
T Consensus        75 ~i~v~~A~~~s   85 (96)
T 2diu_A           75 RIIVSFTPKNR   85 (96)
T ss_dssp             CCEEESSCCSC
T ss_pred             eEEEEecCCCc
Confidence            99999998753

>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=99.45  E-value=1.6e-13  Score=112.08  Aligned_cols=81  Identities=11%  Similarity=0.204  Sum_probs=71.2

Q ss_pred             CCCcceEEE--eccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccccc--
Q 007742          495 GSPSECLLL--KNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWF--  570 (591)
Q Consensus       495 ~~~s~~l~v--~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~--  570 (591)
                      ..|+.+|+|  .||  ++.++        +++|.++|++||.|..|.|+. .+|||||+|.+.++|.+|+..|||..|  
T Consensus        22 ~~pt~~L~V~Ng~L--~~~~t--------e~~L~~~F~~fG~v~~v~i~~-~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~   90 (114)
T 2cq2_A           22 SYATQSLVVANGGL--GNGVS--------RNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVVD   90 (114)
T ss_dssp             SSCCSEEEEETCTG--GGTCC--------HHHHHHHHHHHSCEEEEECCT-TCSCEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CCCCCEEEEECCCC--CCCCC--------HHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEEcc
Confidence            456788999  559  77777        899999999999999998874 589999999999999999999999988  


Q ss_pred             ---CCeEEEEEEeCchhhh
Q 007742          571 ---ARRLISAIFMKPEDYE  586 (591)
Q Consensus       571 ---~g~~l~v~~~~~~~~~  586 (591)
                         .|++|.|.|+..-.+.
T Consensus        91 ~lg~g~~l~v~~a~~~p~~  109 (114)
T 2cq2_A           91 DLGQKITLYLNFVEKVQWS  109 (114)
T ss_dssp             TTSCEEECEEEEESCCCCS
T ss_pred             ccCCCcEEEEEecccCccc
Confidence               7999999998765443

>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=99.45  E-value=1.2e-13  Score=115.09  Aligned_cols=73  Identities=22%  Similarity=0.339  Sum_probs=63.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCee-----E
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQP-----V  291 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~-----i  291 (591)
                      ...++|||+|||+.+|+++|+++|.+||.|..|.|+.+       |||||+|.+.++|.+|| .||+..|.|+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            34689999999999999999999999999999999865       89999999999999999 59999999998     5


Q ss_pred             EeccCc
Q 007742          292 MVKPSE  297 (591)
Q Consensus       292 ~v~~~~  297 (591)
                      +|....
T Consensus        87 ~v~~~~   92 (115)
T 3beg_B           87 RVKVDG   92 (115)
T ss_dssp             EEEECC
T ss_pred             EeccCC
Confidence            555443

>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=99.45  E-value=3.5e-13  Score=111.50  Aligned_cols=76  Identities=22%  Similarity=0.318  Sum_probs=69.6

Q ss_pred             CCcceEEEeccCCCCC-CCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          496 SPSECLLLKNMFDPAM-ETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~-~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      .++++|+|.||  |.. ++        +++|.++|+.||.|..|.+   ++|+|||+|.+.++|..|+..|+|..|+|+.
T Consensus        25 ~~~~~l~V~nl--~~~~~t--------~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   91 (110)
T 1wf1_A           25 SINSRVFIGNL--NTALVK--------KSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLAGQT   91 (110)
T ss_dssp             TCSSEEEECSC--CCSSCC--------HHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEETTEE
T ss_pred             CCCcEEEEeCC--CcccCC--------HHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            45578999999  887 77        8999999999999999998   5899999999999999999999999999999


Q ss_pred             EEEEEeCchh
Q 007742          575 ISAIFMKPED  584 (591)
Q Consensus       575 l~v~~~~~~~  584 (591)
                      |.|.|+.+..
T Consensus        92 l~V~~a~~~~  101 (110)
T 1wf1_A           92 LDINMAGEPK  101 (110)
T ss_dssp             CCEEESCCCC
T ss_pred             EEEEECCCCC
Confidence            9999997543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.45  E-value=1.6e-13  Score=110.52  Aligned_cols=76  Identities=16%  Similarity=0.271  Sum_probs=69.1

Q ss_pred             CCCcceEEEeccCCCC-CCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCe
Q 007742          495 GSPSECLLLKNMFDPA-METDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARR  573 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~-~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~  573 (591)
                      ..++++|+|.||  |. .++        +++|.++|+.||.|..|.+.   +|+|||+|.+.++|..|+..|||..|.|+
T Consensus         7 ~~~~~~l~V~nl--p~~~~t--------~~~l~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~   73 (96)
T 2kvi_A            7 IPPKSRLFIGNL--PLKNVS--------KEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIECESQEMNFGK   73 (96)
T ss_dssp             --CCEEEEEESS--TTSCCC--------HHHHHHHHTTTCCCCEEEEE---TTEEEEEESCHHHHHHHHHHHTCSSCBTT
T ss_pred             CCCCCEEEEeCC--CcccCC--------HHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCeeCCc
Confidence            457789999999  87 777        89999999999999999986   79999999999999999999999999999


Q ss_pred             EEEEEEeCch
Q 007742          574 LISAIFMKPE  583 (591)
Q Consensus       574 ~l~v~~~~~~  583 (591)
                      .|.|.|+...
T Consensus        74 ~l~V~~a~~~   83 (96)
T 2kvi_A           74 KLILEVSSSN   83 (96)
T ss_dssp             TBCEEEEECC
T ss_pred             EEEEEEcCcC
Confidence            9999998654

>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=99.45  E-value=3.2e-13  Score=117.44  Aligned_cols=80  Identities=18%  Similarity=0.127  Sum_probs=70.0

Q ss_pred             ceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEe-cCCCeeEEEEeCCHHHHHHHHHHhcccccCC--eEE
Q 007742          499 ECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVD-KRSAGFVYLRFESTEAAASAQRAMHMRWFAR--RLI  575 (591)
Q Consensus       499 ~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~-~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g--~~l  575 (591)
                      ..|+|.||  ++.++        +++|.++|++||.|..|.|. +.+.|+|||+|.+.++|..|+..|||..|.|  +.|
T Consensus        47 l~l~VgNL--~~~vt--------ed~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L  116 (164)
T 1sjr_A           47 LRIIVENL--FYPVT--------LDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL  116 (164)
T ss_dssp             EEEEECSC--CSCCC--------HHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCE
T ss_pred             EEEEEeCc--CCCCC--------HHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEE
Confidence            34789999  77777        89999999999999999885 3457899999999999999999999999965  999


Q ss_pred             EEEEeCchhhhhc
Q 007742          576 SAIFMKPEDYEAK  588 (591)
Q Consensus       576 ~v~~~~~~~~~~~  588 (591)
                      .|.|+.+.....+
T Consensus       117 ~V~~Ak~~~l~vk  129 (164)
T 1sjr_A          117 RIDFSKLTSLNVK  129 (164)
T ss_dssp             EEEECSSSSCCCC
T ss_pred             EEEEecCCccccc
Confidence            9999998865443

>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=99.44  E-value=1.1e-13  Score=117.27  Aligned_cols=80  Identities=23%  Similarity=0.277  Sum_probs=71.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ...+|||+|||+.+++++|+++|..||.|..+.++.+..++.++|||||+|.+.++|.+||. ||+. .|.|+.|.|.++
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~-~~~gr~i~V~~a  101 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQ-YMGNRFIQVHPI  101 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSB-CSTTSCBEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCC-eECCcEEEEEEC
Confidence            34899999999999999999999999999885555555689999999999999999999998 9996 699999999987


Q ss_pred             cC
Q 007742          400 TD  401 (591)
Q Consensus       400 ~~  401 (591)
                      ..
T Consensus       102 ~~  103 (124)
T 1wel_A          102 TK  103 (124)
T ss_dssp             CH
T ss_pred             CH
Confidence            53

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=3.7e-13  Score=106.93  Aligned_cols=77  Identities=14%  Similarity=0.170  Sum_probs=70.5

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      ..+.++|+|.||  |..++        +++|.++|+.||.|..|.+.   +++|||+|.+.++|.+|+..|||..|+|+.
T Consensus         6 ~~~~~~l~V~nl--p~~~t--------~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~   72 (90)
T 2dnp_A            6 SGNTWKIFVGNV--SAACT--------SQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKR   72 (90)
T ss_dssp             SCCSCCEEEESC--CTTCC--------HHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCEEEEeCC--CCCCC--------HHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            456778999999  88888        89999999999999999988   559999999999999999999999999999


Q ss_pred             EEEEEeCchh
Q 007742          575 ISAIFMKPED  584 (591)
Q Consensus       575 l~v~~~~~~~  584 (591)
                      |.|.|+.+..
T Consensus        73 l~v~~a~~~~   82 (90)
T 2dnp_A           73 INVELSTKGQ   82 (90)
T ss_dssp             CEEEESCCCC
T ss_pred             EEEEECCCCC
Confidence            9999998753

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.44  E-value=1.8e-13  Score=111.41  Aligned_cols=75  Identities=17%  Similarity=0.374  Sum_probs=70.3

Q ss_pred             eEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEE
Q 007742          500 CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIF  579 (591)
Q Consensus       500 ~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~  579 (591)
                      +|+|.||  |..++        +++|.++|+.||.|..|.+..+++|+|||+|.+.++|.+|+..|+|..|+|+.|.|.|
T Consensus         2 ~l~V~nL--p~~~t--------~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   71 (101)
T 2hvz_A            2 KVYVGNL--GTGAG--------KGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVEL   71 (101)
T ss_dssp             EEEEECC--CSSCS--------HHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEE
T ss_pred             EEEEeCC--CCCCC--------HHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEE
Confidence            6999999  88887        8999999999999999999876899999999999999999999999999999999999


Q ss_pred             eCchh
Q 007742          580 MKPED  584 (591)
Q Consensus       580 ~~~~~  584 (591)
                      +.+..
T Consensus        72 a~~~~   76 (101)
T 2hvz_A           72 STGMP   76 (101)
T ss_dssp             SSSCC
T ss_pred             ccCCC
Confidence            97754

>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=99.44  E-value=3.4e-13  Score=112.62  Aligned_cols=82  Identities=20%  Similarity=0.266  Sum_probs=71.6

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccce----EEEEE-ecCCCeeEEEEeCCHHHHHHHHHHhccc
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRV----KHIYV-DKRSAGFVYLRFESTEAAASAQRAMHMR  568 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V----~~v~l-~~~~~g~afV~F~~~e~A~~A~~~l~g~  568 (591)
                      ...++++|+|.||  |..++        +++|.++|..||.|    ..+.+ ...++|+|||+|.+.++|..|+..|||.
T Consensus        21 ~~~~~~~l~V~nL--p~~~t--------~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~   90 (115)
T 2cpx_A           21 PGEPNKVLYLKNL--SPRVT--------ERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGY   90 (115)
T ss_dssp             CCSCCSEEEEECC--CTTCC--------HHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTC
T ss_pred             CCCCCCEEEEeCC--CCCCC--------HHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            3457789999999  88888        89999999999998    45544 3456899999999999999999999999


Q ss_pred             ccCCeEEEEEEeCchhh
Q 007742          569 WFARRLISAIFMKPEDY  585 (591)
Q Consensus       569 ~~~g~~l~v~~~~~~~~  585 (591)
                      .|+|+.|.|.|+.+..-
T Consensus        91 ~~~g~~l~v~~a~~~~~  107 (115)
T 2cpx_A           91 KLYGKILVIEFGKNKKQ  107 (115)
T ss_dssp             BCSSCBCEEEECCCCSC
T ss_pred             EeCCcEEEEEEccCCCC
Confidence            99999999999987653

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=6.5e-13  Score=107.58  Aligned_cols=77  Identities=21%  Similarity=0.330  Sum_probs=70.6

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccc--cceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCC
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKY--GRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFAR  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~--G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g  572 (591)
                      ..++++|+|.||  |..++        +++|.++|+.|  |.|..|.+.   +|+|||+|.+.++|.+|+..|||..|.|
T Consensus        12 ~~~~~~l~V~nL--p~~~t--------~~~l~~~F~~~g~g~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g   78 (99)
T 2cpd_A           12 MSSVKILYVRNL--MLSTS--------EEMIEKEFNNIKPGAVERVKKI---RDYAFVHFSNREDAVEAMKALNGKVLDG   78 (99)
T ss_dssp             SSCCCEEEEESC--CTTCC--------HHHHHHHHHTTSTTCEEEEEEC---SSEEEEEESSHHHHHHHHHHHSSEEETT
T ss_pred             cCCcCEEEEeCC--CCCCC--------HHHHHHHHHhcCCcceEEEEEe---CCeEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            456789999999  88887        89999999999  999999876   7899999999999999999999999999


Q ss_pred             eEEEEEEeCchh
Q 007742          573 RLISAIFMKPED  584 (591)
Q Consensus       573 ~~l~v~~~~~~~  584 (591)
                      +.|.|.|+.+..
T Consensus        79 ~~l~v~~a~~~~   90 (99)
T 2cpd_A           79 SPIEVTLAKPVD   90 (99)
T ss_dssp             EEEEEECCCCCC
T ss_pred             cEEEEEECCCCC
Confidence            999999998764

>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=99.43  E-value=8e-14  Score=106.64  Aligned_cols=75  Identities=28%  Similarity=0.495  Sum_probs=69.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       323 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +|||+|||+.+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|..|+. +++. .+.|+.|.|.++
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-KKYH-NVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSC-CBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCC-eECCEEEEEEEC
Confidence            58999999999999999999999999999999988889999999999999999999996 5774 699999998763

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.43  E-value=6e-13  Score=110.98  Aligned_cols=74  Identities=18%  Similarity=0.253  Sum_probs=65.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccce-EEEEecCcchHHHHH-HHcCCccCC--eeEEeccC
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGV-GYIEFYDVMSVPMAI-ALSGQLLLG--QPVMVKPS  296 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~-afV~F~~~e~A~~Al-~l~g~~i~g--~~i~v~~~  296 (591)
                      -.|||+|||+.+|+++|.++|.+||.|..|.|+..      .|| |||+|.+.++|..|+ .|||..|.|  .+|.|.++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            44679999999999999999999999999998752      286 999999999999999 699999987  68999988


Q ss_pred             cccc
Q 007742          297 EAEK  300 (591)
Q Consensus       297 ~~~~  300 (591)
                      .+..
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            6543

>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=99.42  E-value=1.9e-13  Score=128.46  Aligned_cols=80  Identities=25%  Similarity=0.397  Sum_probs=75.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCC--CeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFG--PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g--~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      .++|||+|||+.+++++|+++|..||  .|..|.|+.+..++.++|||||+|.+.++|.+||..||+. .|.|+.|.|.+
T Consensus        68 ~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~-~~~Gr~l~V~~  146 (229)
T 3q2s_C           68 RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR-ELHGQNPVVTP  146 (229)
T ss_dssp             -CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTS-CBTTBCCEEEE
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC-eECCEEeEEEE
Confidence            47899999999999999999999999  9999999999889999999999999999999999999996 69999999998


Q ss_pred             ecC
Q 007742          399 VTD  401 (591)
Q Consensus       399 ~~~  401 (591)
                      ++.
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            754

>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=99.42  E-value=3.7e-13  Score=117.05  Aligned_cols=78  Identities=17%  Similarity=0.165  Sum_probs=69.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC--eeEEecc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG--QPVMVKP  295 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g--~~i~v~~  295 (591)
                      ...+|||+|||+.+|+++|+++|.+||.|..|.|+.+    ..+|||||+|.+.++|..|+ .|||..|.|  +.|+|.+
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~  120 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  120 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEE
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEE
Confidence            3467899999999999999999999999999998754    25799999999999999999 699999965  9999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +....
T Consensus       121 Ak~~~  125 (164)
T 1sjr_A          121 SKLTS  125 (164)
T ss_dssp             CSSSS
T ss_pred             ecCCc
Confidence            87653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.42  E-value=3.6e-13  Score=110.03  Aligned_cols=78  Identities=15%  Similarity=0.194  Sum_probs=70.0

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCC----HHH----HHHHHH--HhcCCe
Q 007742          322 RKLYVGNL----HFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ----LEH----AKAAQS--ALNGKL  387 (591)
Q Consensus       322 ~~l~v~nl----~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~----~~~----a~~a~~--~l~g~~  387 (591)
                      ..|||+||    |+.+++.+|+++|+.||+|.+|.++.|+.||.++|||||+|.+    +++    |..|+.  .|+|. 
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~-   81 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC-   81 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE-
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC-
Confidence            68999999    9999999999999999999999999999999999999999996    433    788887  67995 


Q ss_pred             eeCCeEEEEEEec
Q 007742          388 EIVGRTLKVSSVT  400 (591)
Q Consensus       388 ~~~g~~l~v~~~~  400 (591)
                      .|+|+.|.|....
T Consensus        82 ~I~Gr~irV~ln~   94 (136)
T 2j8a_A           82 FIMGFKFEVILNK   94 (136)
T ss_dssp             EETTEEEEEEECC
T ss_pred             eecCcEEEEEECc
Confidence            7999999998753

>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=99.42  E-value=3.3e-13  Score=106.64  Aligned_cols=78  Identities=22%  Similarity=0.301  Sum_probs=71.7

Q ss_pred             CcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEE
Q 007742          497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLIS  576 (591)
Q Consensus       497 ~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~  576 (591)
                      ..++|+|.||  |..++        +++|.++|+.| .|..+.++ .++|+|||+|.+.++|.+|+..|||..|+|+.|.
T Consensus         4 ~~~~l~V~nL--p~~~t--------~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   71 (88)
T 1wg1_A            4 GSSGILVKNL--PQDSN--------CQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLI   71 (88)
T ss_dssp             CCCCEEEESC--CSSCC--------HHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCEEEEeCC--CCCCC--------HHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEE
Confidence            4568999999  88888        89999999999 99999886 6799999999999999999999999999999999


Q ss_pred             EEEeCchhhh
Q 007742          577 AIFMKPEDYE  586 (591)
Q Consensus       577 v~~~~~~~~~  586 (591)
                      |.|++.+.+.
T Consensus        72 V~~a~~~~~~   81 (88)
T 1wg1_A           72 VQLQPTDALL   81 (88)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEcCCCceE
Confidence            9999887654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.42  E-value=4.4e-13  Score=107.97  Aligned_cols=79  Identities=19%  Similarity=0.236  Sum_probs=70.4

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      ..+.++|+|.||  |..++        +++|.++|+.||.|..+.....++|+|||+|.+.++|.+|+..|+|..|+|+.
T Consensus        13 ~~~~~~l~V~nL--~~~~t--------~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   82 (96)
T 1fjc_A           13 VRAARTLLAKNL--SFNIT--------EDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS   82 (96)
T ss_dssp             TTGGGEEEEESC--CSSCC--------HHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEE
T ss_pred             CCCCCEEEEeCC--CCCCC--------HHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            456789999999  88888        89999999999999888334456899999999999999999999999999999


Q ss_pred             EEEEEeCch
Q 007742          575 ISAIFMKPE  583 (591)
Q Consensus       575 l~v~~~~~~  583 (591)
                      |.|.|+.+.
T Consensus        83 l~v~~a~~~   91 (96)
T 1fjc_A           83 VSLYYTGEK   91 (96)
T ss_dssp             EEEEECSSS
T ss_pred             EEEEEcCCC
Confidence            999998765

>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=99.41  E-value=1.6e-13  Score=112.76  Aligned_cols=77  Identities=12%  Similarity=0.150  Sum_probs=71.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCC---eeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGP---VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~---i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ..+|||+|||+.+++++|+++|..||.   |..|.|+.+.. +.++|||||+|.+.++|..||. |++. .|.|+.|.|.
T Consensus        11 ~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~-~~~gr~i~V~   87 (107)
T 2lmi_A           11 VFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRM-YMGQRYVEVY   87 (107)
T ss_dssp             CCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTC-CSSSSCCCCE
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcc-eeCCeEEEEE
Confidence            489999999999999999999999988   89999999875 8999999999999999999997 9996 6999999998


Q ss_pred             Eec
Q 007742          398 SVT  400 (591)
Q Consensus       398 ~~~  400 (591)
                      ++.
T Consensus        88 ~a~   90 (107)
T 2lmi_A           88 EIN   90 (107)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            874

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.41  E-value=9.8e-13  Score=106.99  Aligned_cols=80  Identities=20%  Similarity=0.167  Sum_probs=70.4

Q ss_pred             CCceEEEcCCCC-----CCCHHHHHHHhccCCCeeEEEEeccCCC-CCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeE
Q 007742          320 IDRKLYVGNLHF-----NMTETQLRKLFEPFGPVELVQLPLDIET-GQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRT  393 (591)
Q Consensus       320 ~~~~l~v~nl~~-----~~~~~~l~~~f~~~g~i~~v~i~~~~~~-~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~  393 (591)
                      ++++|+|.||..     ..++++|+++|++||.|..|.|+.+..+ +.++|+|||+|.+.++|.+|+..|||+ .|.|+.
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~-~~~Gr~   85 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGR-YFGGRV   85 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTC-EETTEE
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCC-EECCcE
Confidence            458999999963     2378999999999999999999987543 578999999999999999999999998 699999


Q ss_pred             EEEEEec
Q 007742          394 LKVSSVT  400 (591)
Q Consensus       394 l~v~~~~  400 (591)
                      |.|.++.
T Consensus        86 i~v~~a~   92 (105)
T 2pe8_A           86 VKACFYN   92 (105)
T ss_dssp             CEEEECC
T ss_pred             EEEEEcC
Confidence            9999975

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.41  E-value=1.7e-12  Score=108.59  Aligned_cols=76  Identities=25%  Similarity=0.357  Sum_probs=67.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccE-EEEEeCCHHHHHHHHHHhcCCeeeCC--eEEEEEE
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGF-GFVQFAQLEHAKAAQSALNGKLEIVG--RTLKVSS  398 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~-a~Vef~~~~~a~~a~~~l~g~~~~~g--~~l~v~~  398 (591)
                      ..|||+||++.+++++|+++|++||.|..|.|+...     +|+ |||+|.+.++|..|+..|||. .|.|  +.|+|.|
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~-~i~g~~~~LrI~~  102 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQ-NIYNACCTLRIDF  102 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTC-EEETTEEEEEEEE
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCC-eecCCCcEEEEEe
Confidence            577899999999999999999999999999887542     577 999999999999999999997 6877  9999999


Q ss_pred             ecCCC
Q 007742          399 VTDHV  403 (591)
Q Consensus       399 ~~~~~  403 (591)
                      ++...
T Consensus       103 ak~~~  107 (130)
T 3zzy_A          103 SKLTS  107 (130)
T ss_dssp             CSCSS
T ss_pred             cCCCc
Confidence            97653

>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=99.41  E-value=1.7e-13  Score=108.34  Aligned_cols=76  Identities=22%  Similarity=0.291  Sum_probs=65.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      +.++|||+|||+.+|+++|+++|.+||.|..|.++.+     ++|||||+|.+.++|.+|+.. ...+.|..|.|.++.+
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecCC
Confidence            4699999999999999999999999999999999854     689999999999999765432 3446899999998866


Q ss_pred             cc
Q 007742          299 EK  300 (591)
Q Consensus       299 ~~  300 (591)
                      ..
T Consensus        78 ~~   79 (88)
T 1wf0_A           78 KH   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.41  E-value=3e-13  Score=110.27  Aligned_cols=79  Identities=28%  Similarity=0.518  Sum_probs=73.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||..+++++|+++|+.||.|..|.|+.+. ++.++|||||+|.+.++|..|+.  ++. .+.|+.|.|.++.
T Consensus         9 ~~~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            9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQI-NFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCC-EETTEECEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCC-eECCEEEEEEECC
Confidence            4899999999999999999999999999999999998 89999999999999999999996  774 7999999999886


Q ss_pred             CCC
Q 007742          401 DHV  403 (591)
Q Consensus       401 ~~~  403 (591)
                      ...
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.41  E-value=5e-13  Score=120.24  Aligned_cols=79  Identities=27%  Similarity=0.479  Sum_probs=75.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +++|||+|||+.+++++|+++|..||.|..|.|+.+. ++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.++.
T Consensus        88 ~~~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           88 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGV-PLDGRPMDIQLVA  165 (177)
T ss_dssp             CEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTC-BCSSSBCEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCC-EECCEEEEEEEec
Confidence            4899999999999999999999999999999999987 8899999999999999999999999996 6999999999986


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      .
T Consensus       166 ~  166 (177)
T 2f3j_A          166 S  166 (177)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.41  E-value=7.3e-13  Score=108.20  Aligned_cols=76  Identities=30%  Similarity=0.422  Sum_probs=67.8

Q ss_pred             CCceEEE--cCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeee-----CCe
Q 007742          320 IDRKLYV--GNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI-----VGR  392 (591)
Q Consensus       320 ~~~~l~v--~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~-----~g~  392 (591)
                      ++++|||  +||+..+++++|+++|++||.|..|.|+.      .+|||||+|.+.++|..|+..|||. .|     .|+
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~-~~~~~lg~g~   96 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGK-EVVDDLGQKI   96 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTC-EEECTTSCEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCC-EEccccCCCc
Confidence            3588999  77999999999999999999999998863      2789999999999999999999997 56     689


Q ss_pred             EEEEEEecCC
Q 007742          393 TLKVSSVTDH  402 (591)
Q Consensus       393 ~l~v~~~~~~  402 (591)
                      +|.|.++...
T Consensus        97 ~l~v~~a~~~  106 (114)
T 2cq2_A           97 TLYLNFVEKV  106 (114)
T ss_dssp             ECEEEEESCC
T ss_pred             EEEEEecccC
Confidence            9999998654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.40  E-value=7.8e-13  Score=106.49  Aligned_cols=78  Identities=31%  Similarity=0.355  Sum_probs=69.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELV-QLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v-~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ..++|||+|||+.+++++|+++|..||.|..| .|+.+..+    |.|||+|.+.++|..|+..|||. .|.|+.|.|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~-~~~g~~l~V~~   88 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGF-QLENFTLKVAY   88 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTC-BCSSCBCEEEE
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCC-EECCcEEEEEE
Confidence            35899999999999999999999999999999 57766533    34999999999999999999996 69999999999


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      +.+.
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            8764

>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=99.40  E-value=5.7e-13  Score=121.73  Aligned_cols=78  Identities=19%  Similarity=0.320  Sum_probs=72.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      .++|||+|||+.+|+++|.++|.+||.|..|.|+.+.. |.++|||||+|.+.++|..|+.+.+..+.|+.|.|.+...
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~-~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT-CCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCC-CCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            48999999999999999999999999999999998864 8999999999999999999998777899999999987654

>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=99.40  E-value=3.2e-13  Score=108.01  Aligned_cols=79  Identities=10%  Similarity=0.140  Sum_probs=69.7

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccc-eEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcc-cccCC
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGR-VKHIYVDKRSAGFVYLRFESTEAAASAQRAMHM-RWFAR  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~-V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g-~~~~g  572 (591)
                      ..+.++|+|.||  |..++        +++|.++|+.||. |..+.+.  ++|+|||+|.+.++|.+|+..||| ..|+|
T Consensus         5 ~~~~~~l~V~nL--p~~~t--------~~~l~~~F~~~G~vv~~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~g   72 (93)
T 2cqh_A            5 SSGMNKLYIGNL--SPAVT--------ADDLRQLFGDRKLPLAGQVLL--KSGYAFVDYPDQNWAIRAIETLSGKVELHG   72 (93)
T ss_dssp             CCCCCCEEEECC--CTTCC--------HHHHHHHHHHTTCCCSSCEEE--ETTEEEECCSCHHHHHHHHHHHTTTCEETT
T ss_pred             CCCCcEEEEeCC--CCCCC--------HHHHHHHHHHcCCceEEEEEc--CCCEEEEEECCHHHHHHHHHHccCCeeECC
Confidence            345678999999  88888        8999999999999 6666664  589999999999999999999999 99999


Q ss_pred             eEEEEEEeCchhh
Q 007742          573 RLISAIFMKPEDY  585 (591)
Q Consensus       573 ~~l~v~~~~~~~~  585 (591)
                      +.|.|.|+.+..-
T Consensus        73 ~~l~v~~a~~~~~   85 (93)
T 2cqh_A           73 KIMEVDYSVSKKL   85 (93)
T ss_dssp             EECEEEECCCCCC
T ss_pred             EEEEEEEccCccc
Confidence            9999999987643

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=1.7e-12  Score=104.56  Aligned_cols=80  Identities=11%  Similarity=0.129  Sum_probs=70.6

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      ..+.++|+|.||    .++        +++|.++|+.||.|..|.|. .++|+|||+|.+.++|.+|+..|||..|.|+.
T Consensus        12 ~~~~~~l~V~n~----~~t--------~~~l~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   78 (97)
T 1x5p_A           12 PRKGNTLYVYGE----DMT--------PTLLRGAFSPFGNIIDLSMD-PPRNCAFVTYEKMESADQAVAELNGTQVESVQ   78 (97)
T ss_dssp             CCCCSEEEEECS----SCC--------HHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHTTTEEETTEE
T ss_pred             CCCCCEEEEcCC----CCC--------HHHHHHHHhhCCCEEEEEec-CCCCEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            346678999996    344        89999999999999999986 57899999999999999999999999999999


Q ss_pred             EEEEEeCchhhhh
Q 007742          575 ISAIFMKPEDYEA  587 (591)
Q Consensus       575 l~v~~~~~~~~~~  587 (591)
                      |.|.|+.+.....
T Consensus        79 l~v~~a~~~~~~~   91 (97)
T 1x5p_A           79 LKVNIARKQPMLD   91 (97)
T ss_dssp             EEEECCSSCCCCC
T ss_pred             EEEEECCCCCCCC
Confidence            9999998765543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.39  E-value=1.6e-13  Score=111.77  Aligned_cols=79  Identities=24%  Similarity=0.411  Sum_probs=70.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ..+|||+|||..+++++|+++|..||.|.. .++.+..++.++|||||+|.+.++|.+|+. |+|. .|.|+.|.|.++.
T Consensus        17 ~~~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           17 PFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGL-KVFGNEIKLEKPK   93 (101)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGC-CBTTBCCEEECCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCc-EECCcEEEEEEcC
Confidence            489999999999999999999999998877 555665578899999999999999999997 9996 6999999999986


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      ..
T Consensus        94 ~~   95 (101)
T 1fj7_A           94 GR   95 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.38  E-value=6.9e-13  Score=111.20  Aligned_cols=77  Identities=29%  Similarity=0.383  Sum_probs=69.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCee--EEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVE--LVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~--~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ...+|||+|||+.+++++|+++|++| .|.  .|.|+.+.. |.++|||||+|.+.++|.+||. +++. .|.|+.|.|.
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~-~l~gR~I~V~  116 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKE-RIGHRYIEVF  116 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTC-CBTTBCCCCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCC-EECCEEEEEE
Confidence            35799999999999999999999999 666  899998875 9999999999999999999996 5664 6999999998


Q ss_pred             Eec
Q 007742          398 SVT  400 (591)
Q Consensus       398 ~~~  400 (591)
                      .+.
T Consensus       117 ~a~  119 (126)
T 2hgm_A          117 KSS  119 (126)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            774

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.37  E-value=5.7e-13  Score=111.51  Aligned_cols=77  Identities=22%  Similarity=0.223  Sum_probs=69.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCe----eEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPV----ELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i----~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      ..+|||+|||+.+++++|+++|++||.|    ..|.|+.+. ++.++|||||+|.+.++|.+||.. |+. .|.|+.|.|
T Consensus        23 ~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~-~l~gR~i~V   99 (123)
T 2dha_A           23 QVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKD-LLGKRYIEL   99 (123)
T ss_dssp             CCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTE-ESSSCEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCC-eeCCeEEEE
Confidence            4799999999999999999999999975    689898885 899999999999999999999964 885 699999999


Q ss_pred             EEec
Q 007742          397 SSVT  400 (591)
Q Consensus       397 ~~~~  400 (591)
                      ..+.
T Consensus       100 ~~a~  103 (123)
T 2dha_A          100 FRST  103 (123)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            8764

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.06  E-value=5e-14  Score=117.89  Aligned_cols=81  Identities=33%  Similarity=0.443  Sum_probs=75.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeE--------EEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVEL--------VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGR  392 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~--------v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~  392 (591)
                      .++|||+|||..+++++|+++|+.||.|..        |.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+
T Consensus         7 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~   85 (116)
T 2lcw_A            7 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK-EFSGN   85 (116)
Confidence            489999999999999999999999999998        889888778899999999999999999999999996 79999


Q ss_pred             EEEEEEecCC
Q 007742          393 TLKVSSVTDH  402 (591)
Q Consensus       393 ~l~v~~~~~~  402 (591)
                      .|.|.++...
T Consensus        86 ~l~V~~a~~~   95 (116)
T 2lcw_A           86 PIKVSFATRR   95 (116)
Confidence            9999998654

>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=99.36  E-value=2.3e-12  Score=101.71  Aligned_cols=76  Identities=13%  Similarity=0.219  Sum_probs=63.3

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccc--cCC
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRW--FAR  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~--~~g  572 (591)
                      ..+..+|+|+||  |..++        +++|.++|++||.|..|.|+..++|||||+|.+.++|.+    |+|..  +.|
T Consensus         8 ~~~~~~l~V~~L--p~~~t--------e~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g   73 (89)
T 3d2w_A            8 HHHGSKVFVGRC--TEDMT--------AEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKG   73 (89)
T ss_dssp             ---CCEEEEESC--CTTCC--------HHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETT
T ss_pred             CCCCCEEEEeCC--CCCCC--------HHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCC
Confidence            456778999999  88888        899999999999999999988899999999999999983    45665  469


Q ss_pred             eEEEEEEeCchh
Q 007742          573 RLISAIFMKPED  584 (591)
Q Consensus       573 ~~l~v~~~~~~~  584 (591)
                      +.|.|.++.++.
T Consensus        74 ~~v~v~~a~~k~   85 (89)
T 3d2w_A           74 ISVHISNAEPKH   85 (89)
T ss_dssp             EEEEEEECC---
T ss_pred             EEEEEEEcCCCC
Confidence            999999998754

>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=99.36  E-value=1.1e-12  Score=109.31  Aligned_cols=74  Identities=18%  Similarity=0.203  Sum_probs=64.5

Q ss_pred             CcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE--
Q 007742          497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL--  574 (591)
Q Consensus       497 ~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~--  574 (591)
                      ...+|+|.||  |..++        +++|.++|..||.|..|.|..+  |+|||+|.+.++|.+||+.|||..|+|+.  
T Consensus        15 ~~~~l~V~nL--p~~~t--------~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~   82 (115)
T 3beg_B           15 SENRVVVSGL--PPSGS--------WQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   82 (115)
T ss_dssp             --CCEEEEEC--CSSCC--------TTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSC
T ss_pred             CCcEEEEeCC--CCCCC--------HHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEee
Confidence            4568999999  88887        7899999999999999999765  99999999999999999999999999999  


Q ss_pred             ---EEEEEeCc
Q 007742          575 ---ISAIFMKP  582 (591)
Q Consensus       575 ---l~v~~~~~  582 (591)
                         |.|....+
T Consensus        83 ~~~i~v~~~~~   93 (115)
T 3beg_B           83 TAYIRVKVDGP   93 (115)
T ss_dssp             CCBCEEEECC-
T ss_pred             eEEEEeccCCC
Confidence               66665544

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.36  E-value=2e-12  Score=107.52  Aligned_cols=75  Identities=28%  Similarity=0.425  Sum_probs=66.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCC---CCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIET---GQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~---~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      .++|||+|||+.+++++|+++|++||.|. +.++.+..+   |.++|||||+|.+.++|..||..|++   ++|+.|.+.
T Consensus         8 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~---~~G~~~~~~   83 (114)
T 2dnl_A            8 SRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE---EDGKLYLCV   83 (114)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE---ETTEEEEEE
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh---cCCcEEEec
Confidence            48999999999999999999999999999 888777656   68999999999999999999998853   678877776


Q ss_pred             Ee
Q 007742          398 SV  399 (591)
Q Consensus       398 ~~  399 (591)
                      ..
T Consensus        84 ~~   85 (114)
T 2dnl_A           84 SS   85 (114)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=4e-12  Score=101.75  Aligned_cols=75  Identities=25%  Similarity=0.436  Sum_probs=65.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||..+++++|+++|..||.|..|  +.+..++.   ||||+|.+.++|..|+. |+|. .|.|+.|.|.++.
T Consensus         8 ~~~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            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQH-SLGGHRLRVRPRE   80 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCC-EETTEECCCBCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCe-EECCEEEEEEECC
Confidence            3799999999999999999999999999987  34443444   99999999999999998 9996 7999999998765


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      ..
T Consensus        81 ~~   82 (94)
T 2e5g_A           81 QK   82 (94)
T ss_dssp             CS
T ss_pred             cC
Confidence            43

>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=99.35  E-value=3e-12  Score=111.31  Aligned_cols=79  Identities=18%  Similarity=0.277  Sum_probs=69.4

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEE--------EEE--ecCCCeeEEEEeCCHHHHHHHHHH
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKH--------IYV--DKRSAGFVYLRFESTEAAASAQRA  564 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~--------v~l--~~~~~g~afV~F~~~e~A~~A~~~  564 (591)
                      ..++++|||+||  |..++        +++|.++|+.||.|..        +.+  ...++|+|||+|.+.++|.+|+..
T Consensus        42 ~~~~~~l~V~nL--p~~~t--------e~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~  111 (143)
T 3egn_A           42 GEPNCRIYVKNL--AKHVQ--------EKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKE  111 (143)
T ss_dssp             CSCCSEEEEEEE--CTTCC--------HHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHH
T ss_pred             CCCCCEEEEeCC--CCCCC--------HHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHH
Confidence            467789999999  88888        8999999999998865        333  345789999999999999999999


Q ss_pred             hcccccCCeEEEEEEeCch
Q 007742          565 MHMRWFARRLISAIFMKPE  583 (591)
Q Consensus       565 l~g~~~~g~~l~v~~~~~~  583 (591)
                      |||..|.|+.|.|.|+...
T Consensus       112 lng~~~~g~~l~V~~a~~~  130 (143)
T 3egn_A          112 ANGYVLFGKPMVVQFARSA  130 (143)
T ss_dssp             HTTBEETTEECEEEECCCS
T ss_pred             hCCCEeCCcEEEEEECCCC
Confidence            9999999999999998653

>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=99.35  E-value=3.2e-12  Score=104.01  Aligned_cols=81  Identities=17%  Similarity=0.263  Sum_probs=69.4

Q ss_pred             CCCceEEEcCCC--CCC--------CHHHHHHHhccCCCeeEEEEeccCCC--CCcccEEEEEeCCHHHHHHHHHHhcCC
Q 007742          319 AIDRKLYVGNLH--FNM--------TETQLRKLFEPFGPVELVQLPLDIET--GQCKGFGFVQFAQLEHAKAAQSALNGK  386 (591)
Q Consensus       319 ~~~~~l~v~nl~--~~~--------~~~~l~~~f~~~g~i~~v~i~~~~~~--~~~~g~a~Vef~~~~~a~~a~~~l~g~  386 (591)
                      .++++|+|.|+-  ..+        .+++|+++|++||.|..|.|+.+..+  +.++|+|||+|.+.++|.+|+..|||+
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            456899999993  333        34789999999999999999987643  357899999999999999999999998


Q ss_pred             eeeCCeEEEEEEec
Q 007742          387 LEIVGRTLKVSSVT  400 (591)
Q Consensus       387 ~~~~g~~l~v~~~~  400 (591)
                       .|.|++|.|.+..
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             6999999999874

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.32  E-value=2e-12  Score=120.43  Aligned_cols=79  Identities=23%  Similarity=0.375  Sum_probs=69.7

Q ss_pred             CCCCcEEEEeCCCCCC---------CHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCcc
Q 007742          217 ERDQRTVFAYQMPLKA---------TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL  286 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~---------te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i  286 (591)
                      ....++|||+|||..+         |+++|..+|.+||.|..|.|+.      ++|||||+|.+.++|..|+ .|+|+.|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4467999999999998         7999999999999999999984      4899999999999999999 6999999


Q ss_pred             ------------CCeeEEeccCccccc
Q 007742          287 ------------LGQPVMVKPSEAEKN  301 (591)
Q Consensus       287 ------------~g~~i~v~~~~~~~~  301 (591)
                                  .|+.|.|.|+...++
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             eccccccccccCCCCEEEEEEccCCCC
Confidence                        899999999976554

>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=99.31  E-value=5e-12  Score=99.65  Aligned_cols=72  Identities=18%  Similarity=0.251  Sum_probs=65.6

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccc----c-------ceEEEEEecCCCeeEEEEeCCHHHHHHHHHH
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKY----G-------RVKHIYVDKRSAGFVYLRFESTEAAASAQRA  564 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~----G-------~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~  564 (591)
                      .++++|+|.||  |..++        +++|.++|+.|    |       .|..+.+..+ +|+|||+|.+.++|.+|+ .
T Consensus         4 ~~~~~l~V~nL--p~~~t--------~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-kg~afV~f~~~~~a~~A~-~   71 (87)
T 2hzc_A            4 GSARRLYVGNI--PFGIT--------EEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-KNFAFLEFRSVDETTQAM-A   71 (87)
T ss_dssp             GGGGEEEEESC--CTTCC--------HHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-SSEEEEEESSHHHHHHHG-G
T ss_pred             CCCCEEEEeCC--CCCCC--------HHHHHHHHHHHhhhcccccCCCCcceEEEecCC-CcEEEEEcCCHHHHHHHH-h
Confidence            45678999999  88887        89999999999    8       8999988754 899999999999999999 9


Q ss_pred             hcccccCCeEEEEEE
Q 007742          565 MHMRWFARRLISAIF  579 (591)
Q Consensus       565 l~g~~~~g~~l~v~~  579 (591)
                      |||..|.|+.|.|..
T Consensus        72 l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           72 FDGIIFQGQSLKIRR   86 (87)
T ss_dssp             GTTCEETTEECEEEC
T ss_pred             cCCCEECCeEEEEeC
Confidence            999999999999873

>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=99.28  E-value=1.2e-11  Score=113.05  Aligned_cols=79  Identities=22%  Similarity=0.245  Sum_probs=71.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||+.+++++|.++|++||.|..|.|+.+. ++.++|||||+|.+.++|..|+..++.  .|.|+.|.|.+.++
T Consensus       110 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~--~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQ--KYKETDLLILFKDD  186 (193)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTTC--EETTEECEEEETTT
T ss_pred             CEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCCC--eECCEEEEEEEhHH
Confidence            799999999999999999999999999999999886 688999999999999999999965554  69999999998776


Q ss_pred             CC
Q 007742          402 HV  403 (591)
Q Consensus       402 ~~  403 (591)
                      +.
T Consensus       187 y~  188 (193)
T 2voo_A          187 YF  188 (193)
T ss_dssp             C-
T ss_pred             HH
Confidence            54

>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=99.28  E-value=1.2e-11  Score=102.52  Aligned_cols=79  Identities=20%  Similarity=0.209  Sum_probs=68.7

Q ss_pred             CceEEEcCCCCC-----CCHHHHHHHhccCCCeeEEEEeccCC----CCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC
Q 007742          321 DRKLYVGNLHFN-----MTETQLRKLFEPFGPVELVQLPLDIE----TGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG  391 (591)
Q Consensus       321 ~~~l~v~nl~~~-----~~~~~l~~~f~~~g~i~~v~i~~~~~----~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g  391 (591)
                      +++|+|.|+-..     -.+++|+++|++||.|..|.|+.+..    ++.++|+|||+|.+.++|.+|+..|||+ .|.|
T Consensus        20 s~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           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR-WFAG   98 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTC-EETT
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCC-EECC
Confidence            489999999422     23689999999999999999998753    3567899999999999999999999998 6999


Q ss_pred             eEEEEEEec
Q 007742          392 RTLKVSSVT  400 (591)
Q Consensus       392 ~~l~v~~~~  400 (591)
                      +.|.|.++.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999874

>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=99.27  E-value=4.7e-12  Score=100.01  Aligned_cols=79  Identities=18%  Similarity=0.234  Sum_probs=67.2

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEE
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI  575 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l  575 (591)
                      .++++|+|.||  |..++        +++|.++|+.||.|..|.|..+++|+|||+|.+.++|.+|+.  .+..+.|+.|
T Consensus         3 ~~~~~l~V~nL--p~~~t--------e~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l   70 (88)
T 1wf0_A            3 SGSSGVFVGRC--TGDMT--------EDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISV   70 (88)
T ss_dssp             SCCCEEEEESC--CSSSC--------HHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEE
T ss_pred             CCCcEEEEeCC--CCCCC--------HHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhc--CCceeCCEEE
Confidence            45678999999  88888        899999999999999999988889999999999999976432  1344699999


Q ss_pred             EEEEeCchhhh
Q 007742          576 SAIFMKPEDYE  586 (591)
Q Consensus       576 ~v~~~~~~~~~  586 (591)
                      .|.++.+..-.
T Consensus        71 ~v~~a~~~~~~   81 (88)
T 1wf0_A           71 HISNAEPKHNS   81 (88)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEEecCCCCCC
Confidence            99999876543

>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=99.26  E-value=5.9e-11  Score=98.22  Aligned_cols=80  Identities=23%  Similarity=0.335  Sum_probs=67.4

Q ss_pred             CCCceEEEcCCCCCC-----------CHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCe
Q 007742          319 AIDRKLYVGNLHFNM-----------TETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKL  387 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~-----------~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~  387 (591)
                      .++++|+|.||....           ++++|+++|.+||.|..|.| .+.   .++|||||+|.+.++|..|+..|||. 
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~-   87 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR-   87 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC-
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC-
Confidence            346899999995433           25899999999999999966 332   37999999999999999999999996 


Q ss_pred             eeCCeEEEEEEecCCC
Q 007742          388 EIVGRTLKVSSVTDHV  403 (591)
Q Consensus       388 ~~~g~~l~v~~~~~~~  403 (591)
                      .|.|++|.|.++.+..
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            6999999999986543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.23  E-value=1.3e-11  Score=114.92  Aligned_cols=87  Identities=13%  Similarity=0.172  Sum_probs=69.4

Q ss_pred             CCCcceEEEeccCCCCCCCCchh-hhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccccc---
Q 007742          495 GSPSECLLLKNMFDPAMETDPDF-DLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWF---  570 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~-~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~---  570 (591)
                      ....++|||+||  +..+++..+ ....+++|.++|+.||.|..|.|.. ++|||||+|.+.++|..|+..|+|..|   
T Consensus       131 ~~~~rtLfVgnL--~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~  207 (240)
T 3u1l_A          131 RKKNKTLYVGGI--DGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-SKNCGFVKFKYQANAEFAKEAMSNQTLLLP  207 (240)
T ss_dssp             CCCCCEEEEECT--TGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-GGTEEEEEESSHHHHHHHHHHHTTCCCCCT
T ss_pred             ccCCceeecCCC--ChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-CCCEEEEEeCCHHHHHHHHHHhCCCEEecc
Confidence            346778999999  554310000 0112899999999999999999874 589999999999999999999999999   


Q ss_pred             ---------CCeEEEEEEeCchh
Q 007742          571 ---------ARRLISAIFMKPED  584 (591)
Q Consensus       571 ---------~g~~l~v~~~~~~~  584 (591)
                               .|+.|.|.|+.++.
T Consensus       208 ~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          208 SDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             TSTTGGGGGGSCCCEEEECC---
T ss_pred             ccccccccCCCCEEEEEEccCCC
Confidence                     89999999998753

>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=99.22  E-value=3.4e-12  Score=103.75  Aligned_cols=71  Identities=20%  Similarity=0.314  Sum_probs=62.2

Q ss_pred             EeCCCCCCCHHHHHHHH------------hcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeE
Q 007742          225 AYQMPLKATERDVYEFF------------SKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV  291 (591)
Q Consensus       225 V~nLp~~~te~~l~~~f------------~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i  291 (591)
                      +.|||+.+++++|.+.|            ++||.|..|.|+.+.. |.++|||||+|.+.++|.+|+ .|||..+.|++|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56677777887777666            9999999999998765 789999999999999999999 699999999999


Q ss_pred             EeccC
Q 007742          292 MVKPS  296 (591)
Q Consensus       292 ~v~~~  296 (591)
                      .|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99875

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.17  E-value=1.2e-10  Score=93.33  Aligned_cols=62  Identities=15%  Similarity=0.215  Sum_probs=56.7

Q ss_pred             HHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCchhh
Q 007742          522 QGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDY  585 (591)
Q Consensus       522 ~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  585 (591)
                      +++|.++|++||.|..|.|+..++|||||+|.+.++|..|+..++|  +.|++|.|.|+.+..-
T Consensus        31 e~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           31 KDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             HHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             HHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            8999999999999999999888999999999999999999998655  6899999999887653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.17  E-value=1.2e-10  Score=88.95  Aligned_cols=83  Identities=16%  Similarity=0.255  Sum_probs=67.2

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      ++|..+|+|...  +.......+..++..+|.+.|..||.|..+.+...   .+||+|.+.++|.+|+. |||..++|+.
T Consensus         4 GPpd~tv~V~~~--~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d---~~fVtF~d~~sAlaAi~-mnG~~v~Gr~   77 (91)
T 2dnr_A            4 GSSGGTVLVSIK--SSLPENNFFDDALIDELLQQFASFGEVILIRFVED---KMWVTFLEGSSALNVLS-LNGKELLNRT   77 (91)
T ss_dssp             CCSSCEEEEEEE--CSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS---SEEEEESSHHHHHHGGG-GTTCEETTEE
T ss_pred             CCCCCeEEEEec--cCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC---CEEEEECChHHHHHHHh-cCCeEeCCeE
Confidence            566778888887  32221223445567889999999999999998743   48999999999999998 9999999999


Q ss_pred             EEEEEeCch
Q 007742          575 ISAIFMKPE  583 (591)
Q Consensus       575 l~v~~~~~~  583 (591)
                      |+|.+++++
T Consensus        78 LkV~lkt~d   86 (91)
T 2dnr_A           78 ITIALKSPS   86 (91)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999998864

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.15  E-value=8.6e-11  Score=110.40  Aligned_cols=89  Identities=27%  Similarity=0.525  Sum_probs=76.7

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEec---------CCCeeEEEEeCCHHHHHHHHHHh
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK---------RSAGFVYLRFESTEAAASAQRAM  565 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~---------~~~g~afV~F~~~e~A~~A~~~l  565 (591)
                      ...+.++.+.|++++....     .++.++|.++|++||.|..|.|..         .+.|++||+|.+.++|.+|+..|
T Consensus       121 ~~~s~v~~l~n~v~~~e~~-----~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l  195 (222)
T 3dxb_A          121 AMESTVMVLRNMVDPKDID-----DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL  195 (222)
T ss_dssp             CCBCSEEEEESSCCGGGCC-----TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             ccccccchhhcCCCHHHHH-----HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHh
Confidence            3455688899997766543     356789999999999999999852         35689999999999999999999


Q ss_pred             cccccCCeEEEEEEeCchhhhhc
Q 007742          566 HMRWFARRLISAIFMKPEDYEAK  588 (591)
Q Consensus       566 ~g~~~~g~~l~v~~~~~~~~~~~  588 (591)
                      ||+.|+|+.|.|.|++++.|.+.
T Consensus       196 ~gr~~~gr~i~~~~~~~~~f~~~  218 (222)
T 3dxb_A          196 NGRWFAGRKVVAEVYDQERFDNS  218 (222)
T ss_dssp             TTCBSSSSBCEEEECCHHHHHTT
T ss_pred             cCceECCeEEEEEEcCHHHhhhc
Confidence            99999999999999999999864

>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=99.14  E-value=2.5e-10  Score=93.88  Aligned_cols=75  Identities=17%  Similarity=0.235  Sum_probs=64.4

Q ss_pred             CceEEEcCCCCCC----------CHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeC
Q 007742          321 DRKLYVGNLHFNM----------TETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIV  390 (591)
Q Consensus       321 ~~~l~v~nl~~~~----------~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~  390 (591)
                      +++|+|.|+-...          .+++|+++|++||.|..|.|..+.    ++|+|||+|.+.++|.+|+..|||+ .|+
T Consensus         7 s~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            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGR-WFA   81 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTC-EET
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCC-EEC
Confidence            5899999994322          236889999999999999997553    5899999999999999999999998 699


Q ss_pred             CeEEEEEEec
Q 007742          391 GRTLKVSSVT  400 (591)
Q Consensus       391 g~~l~v~~~~  400 (591)
                      |+.|.|.++.
T Consensus        82 GR~i~v~~~~   91 (114)
T 3s6e_A           82 GKMITAAYVP   91 (114)
T ss_dssp             TEECEEEEEC
T ss_pred             CEEEEEEEEc
Confidence            9999999974

>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=99.09  E-value=1.8e-10  Score=113.39  Aligned_cols=80  Identities=13%  Similarity=0.155  Sum_probs=68.1

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccccc---
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWF---  570 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~---  570 (591)
                      ...|+.+|+|.|+.-+..++        +++|.++|++||.|..|.++. ++|||||+|.+.++|.+|+..|||..+   
T Consensus        14 ~~~ps~~l~VgN~gl~~~~t--------e~~L~~~F~~~G~V~~v~~~~-~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~   84 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVS--------RNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVVDD   84 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCC--------HHHHHHHHHTTSCEEEEECCT-TCSEEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             cCCCCCEEEEEcCCCCCCCC--------HHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCccccc
Confidence            35788899999952256666        899999999999999998875 799999999999999999999999987   


Q ss_pred             CCe--EEEEEEeCc
Q 007742          571 ARR--LISAIFMKP  582 (591)
Q Consensus       571 ~g~--~l~v~~~~~  582 (591)
                      .|+  .|.|.|+..
T Consensus        85 ~g~~~~ly~~~~~~   98 (345)
T 3tht_A           85 LGQKITLYLNFVEK   98 (345)
T ss_dssp             TSCEEECEEEECSS
T ss_pred             cCCceEEEEEEeec
Confidence            345  688888853

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.09  E-value=9.1e-10  Score=88.13  Aligned_cols=75  Identities=16%  Similarity=0.162  Sum_probs=61.8

Q ss_pred             CcEEEEeCCC-------CCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEE
Q 007742          220 QRTVFAYQMP-------LKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM  292 (591)
Q Consensus       220 ~~~l~V~nLp-------~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~  292 (591)
                      ..+|-|.-.+       ..+|+++|+++|.+||.|..|.|+     +.++|||||+|.+.++|..|+.. +..+.|++|.
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~-~~~~~g~~l~   83 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQN-EVGLVDNPLK   83 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHT-CCBCSSSBCE
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHh-cCCCCCCeEE
Confidence            3566665544       458999999999999999999998     46899999999999999999964 3447899999


Q ss_pred             eccCcccc
Q 007742          293 VKPSEAEK  300 (591)
Q Consensus       293 v~~~~~~~  300 (591)
                      |.|+....
T Consensus        84 V~~a~~~~   91 (100)
T 2d9o_A           84 ISWLEGQP   91 (100)
T ss_dssp             EECSSCCC
T ss_pred             EEEccCCC
Confidence            99986543

>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=98.98  E-value=1.2e-09  Score=107.59  Aligned_cols=77  Identities=30%  Similarity=0.432  Sum_probs=64.5

Q ss_pred             CCCCceEEEcC--CCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeee--CCe-
Q 007742          318 GAIDRKLYVGN--LHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI--VGR-  392 (591)
Q Consensus       318 ~~~~~~l~v~n--l~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~--~g~-  392 (591)
                      ..++.+|||+|  |+..+++++|.++|++||.|..|.|..      ++|||||+|.+.++|.+|+..|||...+  .|+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            44568999999  578999999999999999999988753      4799999999999999999999997322  345 


Q ss_pred             -EEEEEEec
Q 007742          393 -TLKVSSVT  400 (591)
Q Consensus       393 -~l~v~~~~  400 (591)
                       .|.|.|+.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             67777764

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.92  E-value=1.6e-09  Score=83.12  Aligned_cols=82  Identities=10%  Similarity=0.172  Sum_probs=65.0

Q ss_pred             cCCCcceEEEeccCCCCCCC-CchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCC
Q 007742          494 IGSPSECLLLKNMFDPAMET-DPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFAR  572 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~-~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g  572 (591)
                      .++|..+|+|..+  +.... ...+..++..+|.+.|..||.|..+.+..+.   +||+|.+.++|.+||. |+|..++|
T Consensus        11 ~GPpD~Tv~V~~~--~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~---~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           11 QGPLDATVVVNLQ--SPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---MLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             CCCTTCEEEEEES--SCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---EEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             cCCCCCeEEEEec--CCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc---EEEEEcChHHHHHHHh-cCCeeeCC
Confidence            4677788999887  32100 0112344567899999999999999887443   8999999999999999 99999999


Q ss_pred             eEEEEEEeC
Q 007742          573 RLISAIFMK  581 (591)
Q Consensus       573 ~~l~v~~~~  581 (591)
                      +.|+|.+-.
T Consensus        85 r~L~V~~k~   93 (95)
T 1ufw_A           85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEeccC
Confidence            999999854

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.82  E-value=1.7e-08  Score=82.80  Aligned_cols=78  Identities=12%  Similarity=0.040  Sum_probs=66.9

Q ss_pred             CCCcceEEEeccCCCCC-CCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCC-HHHHHHHHHHhc--cccc
Q 007742          495 GSPSECLLLKNMFDPAM-ETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFES-TEAAASAQRAMH--MRWF  570 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~-~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~-~e~A~~A~~~l~--g~~~  570 (591)
                      -++..+|+|.||  +.. ++        .++|+++|+.||.|.+|.+..... .|||+|.+ ..+|..|+..|+  |..|
T Consensus        15 ~~~G~il~v~~l--~~~~~s--------redLke~F~~~G~V~~Vd~~~g~~-tgfVrf~~~~~~A~~av~~ln~~~~~i   83 (121)
T 1owx_A           15 EKIGCLLKFSGD--LDDQTC--------REDLHILFSNHGEIKWIDFVRGAK-EGIILFKEKAKEALGKAKDANNGNLQL   83 (121)
T ss_dssp             CCCCCEEEEEES--CCSSCC--------HHHHHHHTCSSCCEEEEECCTTCS-EEEEEESSCHHHHHHHHHHTTTSCBCT
T ss_pred             ccCCeEEEEecC--CCCcCC--------HHHHHHHHHhcCCEEEEEEecCCC-EEEEEECCChHHHHHHHHHhhcCCcEE
Confidence            356678999999  666 66        899999999999999999875444 69999999 899999999994  8889


Q ss_pred             CCeEEEEEEeCch
Q 007742          571 ARRLISAIFMKPE  583 (591)
Q Consensus       571 ~g~~l~v~~~~~~  583 (591)
                      .|..+.+.....+
T Consensus        84 ~g~~~~~evL~Ge   96 (121)
T 1owx_A           84 RNKEVTWEVLEGE   96 (121)
T ss_dssp             TSSSEEEEECCHH
T ss_pred             eCcEEEEEECCCH
Confidence            9999999887643

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.76  E-value=3.6e-08  Score=75.34  Aligned_cols=74  Identities=28%  Similarity=0.392  Sum_probs=61.4

Q ss_pred             CCCCceEEEcCCCC----CCCH----HHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeee
Q 007742          318 GAIDRKLYVGNLHF----NMTE----TQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI  389 (591)
Q Consensus       318 ~~~~~~l~v~nl~~----~~~~----~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~  389 (591)
                      +|+.-+|+|..++.    .+-.    .+|.+.|.+||.|..++++.+.        +||+|.+.++|.+|+. |||. .+
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~-~v   73 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGK-EL   73 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTC-EE
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCe-Ee
Confidence            45557888877762    2323    6788999999999999998764        8999999999999997 9996 89


Q ss_pred             CCeEEEEEEecC
Q 007742          390 VGRTLKVSSVTD  401 (591)
Q Consensus       390 ~g~~l~v~~~~~  401 (591)
                      .|+.|+|..+++
T Consensus        74 ~Gr~LkV~lkt~   85 (91)
T 2dnr_A           74 LNRTITIALKSP   85 (91)
T ss_dssp             TTEEEEEEECCC
T ss_pred             CCeEEEEEeCCC
Confidence            999999998764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.74  E-value=3.7e-08  Score=80.78  Aligned_cols=76  Identities=16%  Similarity=0.229  Sum_probs=65.1

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCC-HHHHHHHHHHhc-CCeeeCCeEE
Q 007742          318 GAIDRKLYVGNLHFN-MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ-LEHAKAAQSALN-GKLEIVGRTL  394 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~-~~~a~~a~~~l~-g~~~~~g~~l  394 (591)
                      -+++..|+|+||+.. ++.++|+++|+.||.|..|.+..+..      .|||+|.+ ..+|..|+..|+ +.+.|.|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            344589999999999 99999999999999999999987642      59999999 899999999996 3367999888


Q ss_pred             EEEEe
Q 007742          395 KVSSV  399 (591)
Q Consensus       395 ~v~~~  399 (591)
                      .+...
T Consensus        89 ~~evL   93 (121)
T 1owx_A           89 TWEVL   93 (121)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            88654

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.60  E-value=1e-07  Score=73.13  Aligned_cols=71  Identities=17%  Similarity=0.192  Sum_probs=60.7

Q ss_pred             CCcEEEEeCCCCC------CCH---HHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCe
Q 007742          219 DQRTVFAYQMPLK------ATE---RDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQ  289 (591)
Q Consensus       219 ~~~~l~V~nLp~~------~te---~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~  289 (591)
                      +..+|+|.-++..      ..+   .+|.+.|.+||.|+.++++.++        +||+|.+.++|.+||.|||..+.|+
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~v~Gr   85 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKVKGR   85 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSEETTE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCeeeCCe
Confidence            4578999988743      221   4689999999999999999764        9999999999999999999999999


Q ss_pred             eEEeccCc
Q 007742          290 PVMVKPSE  297 (591)
Q Consensus       290 ~i~v~~~~  297 (591)
                      .|+|+...
T Consensus        86 ~L~V~~k~   93 (95)
T 1ufw_A           86 AVKISGPS   93 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEeccC
Confidence            99997653

>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=98.55  E-value=2e-07  Score=87.18  Aligned_cols=78  Identities=21%  Similarity=0.222  Sum_probs=65.1

Q ss_pred             ceEEEcCCC-----CCCCHHHHHHHhccCCCeeEEEEeccCC----CCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCe
Q 007742          322 RKLYVGNLH-----FNMTETQLRKLFEPFGPVELVQLPLDIE----TGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGR  392 (591)
Q Consensus       322 ~~l~v~nl~-----~~~~~~~l~~~f~~~g~i~~v~i~~~~~----~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~  392 (591)
                      ..+.+.|+-     ..-.+++|.+.|.+||.|..|.|+.+..    ++.++|++||+|.+.++|.+|+..|||+ .|.|+
T Consensus       125 ~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr-~~~gr  203 (222)
T 3dxb_A          125 TVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR-WFAGR  203 (222)
T ss_dssp             SEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTC-BSSSS
T ss_pred             ccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCc-eECCe
Confidence            456666662     2345678999999999999999985543    3488999999999999999999999998 59999


Q ss_pred             EEEEEEec
Q 007742          393 TLKVSSVT  400 (591)
Q Consensus       393 ~l~v~~~~  400 (591)
                      +|.+.+..
T Consensus       204 ~i~~~~~~  211 (222)
T 3dxb_A          204 KVVAEVYD  211 (222)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEcC
Confidence            99999874

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.46  E-value=7.7e-07  Score=69.47  Aligned_cols=76  Identities=11%  Similarity=0.082  Sum_probs=66.6

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccc-----cceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccccc
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKY-----GRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWF  570 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~-----G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~  570 (591)
                      ...++|-|.||  |.+++        ...|+.++..|     |.|..|.|..+-.| |+|+|.+...|-+|..+|+|..|
T Consensus        19 ~~~rtiaL~~i--pDtvn--------darIr~lve~~~~i~~g~i~KI~L~pDH~G-Aivef~d~~~AgKasLaL~G~ef   87 (117)
T 2l9w_A           19 ELETLICLFPL--SDKVS--------PSLICQFLQEEIHINEKDIRKILLVSDFNG-AIIIFRDSKFAAKMLMILNGSQF   87 (117)
T ss_dssp             TTTSCEEEECC--CTTCC--------HHHHHHHHHHHTCCCTTTCSEEEEETTTTE-EEEECSCHHHHHHHHHHHSSEEE
T ss_pred             cCCcEEEEecC--CCCCC--------HHHHHHHHhhhhccCccceeEEEEecCCCc-eEEEEccchhhHHHHhhcCCeee
Confidence            34678999999  88887        78899999999     99999999865454 89999999999999999999999


Q ss_pred             CCeEEEEEEeCc
Q 007742          571 ARRLISAIFMKP  582 (591)
Q Consensus       571 ~g~~l~v~~~~~  582 (591)
                      .|++|.|.-+.+
T Consensus        88 ~gr~Lr~gTv~e   99 (117)
T 2l9w_A           88 QGKVIRSGTIND   99 (117)
T ss_dssp             TTEEEEEECHHH
T ss_pred             cCeEEEecCHHH
Confidence            999999976543

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.37  E-value=2e-06  Score=67.18  Aligned_cols=71  Identities=13%  Similarity=0.200  Sum_probs=65.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccC-----CCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPF-----GPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~-----g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      ++|.|.|||..++...|+.+++++     |.|..|.+..+.      +-|+|+|.+...|.+|..+|+| .+|.|++|.+
T Consensus        22 rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G-~ef~gr~Lr~   94 (117)
T 2l9w_A           22 TLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNG-SQFQGKVIRS   94 (117)
T ss_dssp             SCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSS-EEETTEEEEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCC-eeecCeEEEe
Confidence            899999999999999999999999     999999998764      3499999999999999999999 4899999999


Q ss_pred             EEe
Q 007742          397 SSV  399 (591)
Q Consensus       397 ~~~  399 (591)
                      ...
T Consensus        95 gTv   97 (117)
T 2l9w_A           95 GTI   97 (117)
T ss_dssp             ECH
T ss_pred             cCH
Confidence            764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.87  E-value=0.00012  Score=56.86  Aligned_cols=88  Identities=15%  Similarity=0.204  Sum_probs=72.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcC-----CCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEe
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKA-----GKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMV  293 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~-----G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v  293 (591)
                      -.++|.|.|||..+.++.|.-+|+.-     |.|..|....        +-|+|+|.+.+.|+..|+...+.+.|.+|.|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV   78 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLSL   78 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEEE
Confidence            35899999999999999999999872     6888887753        4699999999999988888788999999999


Q ss_pred             ccCccccccccccCCCCCCCCCCCCCCCceEEEcCCCCCCC
Q 007742          294 KPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMT  334 (591)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  334 (591)
                      .+..+..                    ..+|++.+|++.+.
T Consensus        79 ~P~~~~~--------------------~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           79 RPAPPRA--------------------PARLLLQGLPPGTS   99 (104)
T ss_dssp             EECCCCC--------------------CCCCCCCSCCCCCC
T ss_pred             EcCCCCC--------------------cceEeeecCCCCCC
Confidence            7753321                    26888888887664

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.77  E-value=5.9e-05  Score=58.97  Aligned_cols=78  Identities=18%  Similarity=0.178  Sum_probs=62.1

Q ss_pred             ceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEE
Q 007742          499 ECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAI  578 (591)
Q Consensus       499 ~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~  578 (591)
                      ++|+|.|| ++....++    ++.+.+.++|..|+.+......+ +-.-+.|.|.++++|.+|-..||+..|.|+.|.|.
T Consensus         6 ntLiitnl-~~~vF~~~----~lk~~~e~Lf~~~~~~~tF~~lk-SFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~Y   79 (104)
T 1wey_A            6 SGLIACVA-NDDVFSES----ETRAKFESLFRTYDKDTTFQYFK-SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             CEEEEECC-CGGGGSTT----THHHHHHHHHHTTCSSCEEEEET-TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             ceEEEecC-CHHHcCCH----HHHHHHHHHHHhhCcCcceeecC-cceEEEEEeCChHHHHHHHHHhccceecCceeEEE
Confidence            47999999 44333322    23578899999999888775553 34467999999999999999999999999999999


Q ss_pred             EeCc
Q 007742          579 FMKP  582 (591)
Q Consensus       579 ~~~~  582 (591)
                      |+.+
T Consensus        80 Fgq~   83 (104)
T 1wey_A           80 FAQT   83 (104)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9764

>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=97.30  E-value=0.0011  Score=53.39  Aligned_cols=73  Identities=14%  Similarity=0.209  Sum_probs=58.8

Q ss_pred             cceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCC-eEEE
Q 007742          498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFAR-RLIS  576 (591)
Q Consensus       498 s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g-~~l~  576 (591)
                      ...|.|.++  |...         ...|..+|++||.|.....+ ....+..|.|.+..+|++||. .||..|+| -.|-
T Consensus        24 ~~wVtVFGF--p~~~---------~~~VL~~F~~~G~Iv~~~~~-~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIG   90 (119)
T 1wwh_A           24 DTWVTVFGF--PQAS---------ASYILLQFAQYGNILKHVMS-NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIG   90 (119)
T ss_dssp             GGEEEEECC--CGGG---------HHHHHHHHHTTSCEEEEEEC-SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECE
T ss_pred             CCEEEEECC--CHHH---------HHHHHHHHHhhCcEEEeccC-CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEE
Confidence            456889998  5543         57899999999999988874 356788999999999999999 49999985 6677


Q ss_pred             EEEeCch
Q 007742          577 AIFMKPE  583 (591)
Q Consensus       577 v~~~~~~  583 (591)
                      |..+..+
T Consensus        91 V~p~~d~   97 (119)
T 1wwh_A           91 VKPCIDK   97 (119)
T ss_dssp             EEECCCH
T ss_pred             EEECCCH
Confidence            7766543

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.20  E-value=0.0026  Score=49.73  Aligned_cols=74  Identities=15%  Similarity=0.168  Sum_probs=62.1

Q ss_pred             CceEEEcCCCCCC-C----HHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEE
Q 007742          321 DRKLYVGNLHFNM-T----ETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLK  395 (591)
Q Consensus       321 ~~~l~v~nl~~~~-~----~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~  395 (591)
                      +++|+|.||+..+ .    .+.+.++|..|+++......+.-      .-+.|.|.++++|.+|-..|++. .|.|+.++
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~-~f~g~~~r   77 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKT-EFLGKEMK   77 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTS-EETTEECE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccc-eecCceeE
Confidence            3789999998754 2    25788999999999888776542      35899999999999999999996 79999999


Q ss_pred             EEEecC
Q 007742          396 VSSVTD  401 (591)
Q Consensus       396 v~~~~~  401 (591)
                      |.++..
T Consensus        78 ~YFgq~   83 (104)
T 1wey_A           78 LYFAQT   83 (104)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999873

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.07  E-value=0.00046  Score=56.30  Aligned_cols=77  Identities=14%  Similarity=0.210  Sum_probs=60.5

Q ss_pred             eEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEE-Eec------------------CCCeeEEEEeCCHHHHHH
Q 007742          500 CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIY-VDK------------------RSAGFVYLRFESTEAAAS  560 (591)
Q Consensus       500 ~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~-l~~------------------~~~g~afV~F~~~e~A~~  560 (591)
                      -|.|.++  |...         ...|.++|++||.|..-. +..                  .+..+..|+|.+..+|.+
T Consensus         9 ~VtVFGF--p~~~---------~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~r   77 (132)
T 3p3d_A            9 AILVFGY--PETM---------ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVD   77 (132)
T ss_dssp             EEEEECC--CGGG---------HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHH
T ss_pred             EEEEEec--CHHH---------HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHH
Confidence            5788888  5543         578999999999997621 111                  135678999999999999


Q ss_pred             HHHHhcccccCCeEEEEEEeCchhhhhc
Q 007742          561 AQRAMHMRWFARRLISAIFMKPEDYEAK  588 (591)
Q Consensus       561 A~~~l~g~~~~g~~l~v~~~~~~~~~~~  588 (591)
                      |+. .||..|+|..|-|..+++....++
T Consensus        78 AL~-~NG~ii~G~mIGV~Py~~~~ve~l  104 (132)
T 3p3d_A           78 ALL-ENGAVFNGVLLGVIPYTKDAVERL  104 (132)
T ss_dssp             HHT-TTTCEETTEECEEEECCHHHHHHH
T ss_pred             HHH-hCCeEeCcEEEEEEECCHHHHHHH
Confidence            998 599999999999999887765543

>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=97.04  E-value=0.0043  Score=47.53  Aligned_cols=54  Identities=24%  Similarity=0.325  Sum_probs=45.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN  384 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~  384 (591)
                      ..++| ++|+.+...||.++|++||.| .|..+-+.       .|||.|.+.+.|..|+.++.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            55666 999999999999999999955 35555543       69999999999999998773

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.90  E-value=0.0055  Score=47.09  Aligned_cols=70  Identities=13%  Similarity=0.197  Sum_probs=55.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCC--CcccEEEEEeCCHHHHHHHHHHhcCCeeeCC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAAQSALNGKLEIVG  391 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~--~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g  391 (591)
                      ..|.|++||+.+|++++.+.+.....+........+.+.  ..-.-|||.|.+.+++......++|...++.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~   73 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcC
Confidence            478999999999999999999999877666555443221  2335799999999999999999999754443

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.67  E-value=0.009  Score=45.88  Aligned_cols=67  Identities=15%  Similarity=0.208  Sum_probs=54.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCC--ccceEEEEecCcchHHHHH-HHcCCccC
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR--SKGVGYIEFYDVMSVPMAI-ALSGQLLL  287 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~--~~G~afV~F~~~e~A~~Al-~l~g~~i~  287 (591)
                      .+|.|++||+.+|++++.+.+..+..+.....+..+.+..  .-.-|||.|.+.+++.... .++|..+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            5799999999999999999999998877666666543322  3457999999999998888 58988764

>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=96.54  E-value=0.012  Score=45.14  Aligned_cols=57  Identities=14%  Similarity=0.255  Sum_probs=44.6

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhc
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMH  566 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~  566 (591)
                      ....+++| ++  |.++.        ..||.++|+.||.|.--.|.   ...|||.|.+++.|..|+..+.
T Consensus        14 ~r~HVf~l-~F--P~ewK--------t~DI~~lFs~fggv~I~Wid---DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           14 KRDHVLHV-TF--PKEWK--------TSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEE-EC--CTTCC--------HHHHHHHHTTTCSCCCEEEE---TTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCeEEEE-eC--Chhhh--------hHHHHHHhhccCCEEEEEEc---CCeEEEEecCHHHHHHHHHhcc
Confidence            34456667 88  77777        89999999999965544444   4579999999999999998764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.51  E-value=0.018  Score=44.72  Aligned_cols=74  Identities=12%  Similarity=-0.039  Sum_probs=58.3

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhcc-----ccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccccc
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSK-----YGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWF  570 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~-----~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~  570 (591)
                      ....+|.|.||  |..+.        .+.|.-+|++     -|.|..+....   +-|+|+|.+.+.|+..++. .-..|
T Consensus         6 ~~~~~I~V~~l--Pp~~~--------~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k-~~H~L   71 (104)
T 2dhx_A            6 SGGVAVEVRGL--PPAVP--------DELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ-ADHEL   71 (104)
T ss_dssp             CCCCEEEEESC--CTTSC--------HHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC-SCCBS
T ss_pred             cCccEEEEECC--CCCCC--------hhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC-Cccee
Confidence            34568999999  77665        6788888876     26888988764   6789999999999988873 35778


Q ss_pred             CCeEEEEEEeCch
Q 007742          571 ARRLISAIFMKPE  583 (591)
Q Consensus       571 ~g~~l~v~~~~~~  583 (591)
                      .|..|.|.-+.+.
T Consensus        72 ~~~~LsV~P~~~~   84 (104)
T 2dhx_A           72 HGAQLSLRPAPPR   84 (104)
T ss_dssp             SSSBCEEEECCCC
T ss_pred             cCeEEEEEcCCCC
Confidence            8999998765543

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.49  E-value=0.0043  Score=47.70  Aligned_cols=54  Identities=26%  Similarity=0.336  Sum_probs=44.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN  384 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~  384 (591)
                      ..++| ++|+.+.-.||.++|++||.| .|..+-+.       .|||.|.+.+.|..|+.++.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45556 999999999999999999944 46665543       69999999999999998774

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.42  E-value=0.015  Score=46.86  Aligned_cols=72  Identities=13%  Similarity=0.143  Sum_probs=58.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC-eEEEEEEe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG-RTLKVSSV  399 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g-~~l~v~~~  399 (591)
                      ...|.|.+.|+.. ...|...|+.||.|......    .  ......|.|.+..+|.+|| ..||. .|.| ..|-|.++
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~--~~NWihI~Y~s~~~A~rAL-~kNG~-ii~g~~mIGV~p~   94 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----N--TGNWMHIRYQSKLQARKAL-SKDGR-IFGESIMIGVKPC   94 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----S--SSSEEEEEESSHHHHHHHH-TTTTC-EETTTEECEEEEC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----C--CCCeEEEEeCCHHHHHHHH-HhCCe-EecCCEEEEEEEC
Confidence            3789999999875 67888999999999888762    1  2458999999999999999 78997 4764 77777776


Q ss_pred             cC
Q 007742          400 TD  401 (591)
Q Consensus       400 ~~  401 (591)
                      .+
T Consensus        95 ~d   96 (119)
T 1wwh_A           95 ID   96 (119)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.00  E-value=0.0087  Score=46.04  Aligned_cols=54  Identities=15%  Similarity=0.270  Sum_probs=42.5

Q ss_pred             ceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhc
Q 007742          499 ECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMH  566 (591)
Q Consensus       499 ~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~  566 (591)
                      .+++| ++  |.++.        ..||.++|+.||.|.--.|.   ...|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~F--P~ewK--------t~Di~~lFs~fggv~I~Wid---DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TF--PKEWK--------TSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-EC--CTTCC--------HHHHHHHTTTSEEEEEEEEE---TTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eC--Chhhh--------hHHHHHHHhccCCEEEEEEc---CCeEEEEecCHHHHHHHHHhcc
Confidence            45666 88  77776        89999999999955433444   4579999999999999999764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.33  E-value=0.028  Score=43.37  Aligned_cols=69  Identities=10%  Similarity=0.160  Sum_probs=49.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCC--CCcccEEEEEeCCHHHHHHHHHHhcCCeeeC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIET--GQCKGFGFVQFAQLEHAKAAQSALNGKLEIV  390 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~--~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~  390 (591)
                      -.|.|+.||+.+|++++.+.+.+.-.+..........+  ...-.-|||.|.+.++.......++|.+.++
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            68999999999999999888887655433222221111  1122469999999999999999999975344

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.43  E-value=0.064  Score=43.74  Aligned_cols=76  Identities=17%  Similarity=0.087  Sum_probs=54.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEeccC-----------C-CC-CcccEEEEEeCCHHHHHHHHHHhcCCe
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELV-QLPLDI-----------E-TG-QCKGFGFVQFAQLEHAKAAQSALNGKL  387 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v-~i~~~~-----------~-~~-~~~g~a~Vef~~~~~a~~a~~~l~g~~  387 (591)
                      ..|.|.+.|+. ....|...|++||.|..- .+....           . .. .......|+|.+..+|.+|| ..||. 
T Consensus         8 ~~VtVFGFp~~-~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~NG~-   84 (132)
T 3p3d_A            8 LAILVFGYPET-MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LENGA-   84 (132)
T ss_dssp             CEEEEECCCGG-GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTTTC-
T ss_pred             eEEEEEecCHH-HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhCCe-
Confidence            57888899754 456677999999998652 221100           0 00 13568899999999999999 78997 


Q ss_pred             eeCCeEEEEEEec
Q 007742          388 EIVGRTLKVSSVT  400 (591)
Q Consensus       388 ~~~g~~l~v~~~~  400 (591)
                      .|.|..|-|.++.
T Consensus        85 ii~G~mIGV~Py~   97 (132)
T 3p3d_A           85 VFNGVLLGVIPYT   97 (132)
T ss_dssp             EETTEECEEEECC
T ss_pred             EeCcEEEEEEECC
Confidence            5999977777664

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=93.87  E-value=0.031  Score=56.85  Aligned_cols=57  Identities=19%  Similarity=0.191  Sum_probs=42.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcC
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSG  283 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g  283 (591)
                      +.|+|. .|..+++.+|.++|.+||+|.++.+..+.     .-||.|||.+.+++..++...+
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~~~  110 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNGTH  110 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSSCC
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhccC
Confidence            789997 68999999999999999999999887543     2599999999999987775433

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=93.33  E-value=0.053  Score=41.82  Aligned_cols=68  Identities=15%  Similarity=0.155  Sum_probs=47.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCC--CccceEEEEecCcchHHHHH-HHcCCccC
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSR--RSKGVGYIEFYDVMSVPMAI-ALSGQLLL  287 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g--~~~G~afV~F~~~e~A~~Al-~l~g~~i~  287 (591)
                      +-+|.|+.||+.+|++++.+.+..+-.+.....+..+.+-  ..-.-|||.|.+.+++.... ..+|..+.
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            4689999999999999988888765443322222222211  12346899999999998888 57877753

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=91.96  E-value=0.083  Score=53.72  Aligned_cols=53  Identities=21%  Similarity=0.315  Sum_probs=41.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHH
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ  380 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~  380 (591)
                      +.|+|. .|..+++.+|.+.|+.||+|..+.+..+.     .-||.|||.+.+++..++
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~  106 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQ  106 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHH
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHH
Confidence            789996 79999999999999999999999998654     369999999999888665

---

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	591
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	7e-21
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	8e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-19
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-05
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	9e-18
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-08
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-17
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-09
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-16
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	8e-16
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-15
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	7e-08
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-15
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-15
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-05
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-15
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-15
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-06
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	9e-15
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-14
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	8e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-14
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-05
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-06
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-06
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-13
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-06
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-13
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	8e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	4e-13
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-12
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-04
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-12
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-12
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	0.004
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-12
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	7e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-05
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	7e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	0.002
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-11
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	4e-11
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-11
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-04
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-09
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:) 5e-11
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:) 4e-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:) 1e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	8e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-10
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-10
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	9e-10
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-09
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	0.001
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.002
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	0.003
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-09
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	7e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	7e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-07
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-05
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	4e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	9e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	8e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	4e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.002
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	7e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-05
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	1e-04
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	7e-04
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	0.002
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	0.004
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-04
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	2e-04
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	4e-04
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	7e-04
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	0.003
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	0.004
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	3e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	5e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.001
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	0.003

>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 = 88.1 bits (217), Expect = 7e-21
 Identities = 39/183 (21%), Positives = 81/183 (44%), Gaps = 13/183 (7%)

Query: 215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMS 274
           +PE+  R +F   +  + T+  +   F + G + D  ++ D N++RS+G G++ +  V  
Sbjct: 2   EPEQL-RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 275 VPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMT 334
           V  A+      + G+ V  K + + ++  +                 +K++VG +  +  
Sbjct: 61  VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLT----------VKKIFVGGIKEDTE 110

Query: 335 ETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTL 394
           E  LR  FE +G +E++++  D  +G+ +GF FV F   +              + G   
Sbjct: 111 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYH-TVNGHNC 168

Query: 395 KVS 397
           +V 
Sbjct: 169 EVR 171

>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 = 47.3 bits (111), Expect = 8e-07
 Identities = 18/124 (14%), Positives = 45/124 (36%)

Query: 177 ELERERERERELRERERDLEMRESRRYKEKKEVVEPEADPERDQRTVFAYQMPLKATERD 236
                 E +  +  R   ++ R     +                + +F   +     E  
Sbjct: 54  TYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 113

Query: 237 VYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS 296
           + ++F + GK+  + ++ DR S + +G  ++ F D  SV   +      + G    V+ +
Sbjct: 114 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 173

Query: 297 EAEK 300
            +++
Sbjct: 174 LSKQ 177

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 82.0 bits (202), Expect = 1e-19
 Identities = 32/101 (31%), Positives = 47/101 (46%), Gaps = 7/101 (6%)

Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGF 547
           G P+E L L NM  P    D +   EI  DV +ECSKYG VK I + +          G 
Sbjct: 1   GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 60

Query: 548 VYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 588
           +++ F S      A + +  R FA R++   +  P+ Y  +
Sbjct: 61  IFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRR 101

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 5e-05
 Identities = 12/74 (16%), Positives = 29/74 (39%), Gaps = 3/74 (4%)

Query: 326 VGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAAQSAL 383
           + +  +      +R     +G V+ +++P  ++       G  FV+F  +   + A   L
Sbjct: 19  LDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78

Query: 384 NGKLEIVGRTLKVS 397
            G+ +   R +   
Sbjct: 79  TGR-KFANRVVVTK 91

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 76.1 bits (187), Expect = 9e-18
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  LYV NL   +T+ QL  +F  +G +    +  D  TG+ +G  FV++ + E A+ A 
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 381 SALNGK-LEIVGRTLKVS 397
           SALN    E   + L V 
Sbjct: 66  SALNNVIPEGGSQPLSVR 83

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 48.8 bits (116), Expect = 4e-08
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
               ++   +P   T+  +   F K G +    ++ D+ + R +GV ++ +        A
Sbjct: 5   KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 279 I-ALSGQLLLG--QPVMVK 294
           I AL+  +  G  QP+ V+
Sbjct: 65  ISALNNVIPEGGSQPLSVR 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 = 74.6 bits (183), Expect = 2e-17
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            LYVG+LH ++TE  L + F P GP+  +++  D+ T +  G+ +V F Q   A+ A   
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 383 LNGKLEIVGRTLKVS 397
           +N    I G+ +++ 
Sbjct: 62  MNFD-VIKGKPVRIM 75

>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 = 52.2 bits (125), Expect = 2e-09
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-A 280
           +++   +    TE  +YE FS AG +  +R+  D  +RRS G  Y+ F        A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 281 LSGQLLLGQPVMVKPSE 297
           ++  ++ G+PV +  S+
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 73.0 bits (179), Expect = 1e-16
 Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE-TGQCKGFGFVQFAQLEHAKAAQ 380
            K+ V N+ F   + ++R+LF  FG ++ V+LP  +  TG  +GFGFV F   + AK A 
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 381 SALNGKLEIVGRTLKVS 397
           +AL     + GR L + 
Sbjct: 69  NALCHSTHLYGRRLVLE 85

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.4 bits (115), Expect = 6e-08
 Identities = 17/93 (18%), Positives = 43/93 (46%), Gaps = 3/93 (3%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRN-SRRSKGVGYIEFYD 271
           +   ++    +    +P +A +R++ E FS  G+++ VRL      +   +G G+++F  
Sbjct: 1   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 60

Query: 272 VMSVPMAIA--LSGQLLLGQPVMVKPSEAEKNL 302
                 A         L G+ ++++ +++E  +
Sbjct: 61  KQDAKKAFNALCHSTHLYGRRLVLEWADSEVTV 93

>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 = 70.4 bits (172), Expect = 8e-16
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K+++G L +  T+  LR+ F  FG V+   +  D  T + +GFGFV F           A
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60

Query: 383 LNGKLEIVGRTLKVS 397
            +   E+  +T+   
Sbjct: 61  QSRH-ELDSKTIDPK 74

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.2 bits (130), Expect = 4e-10
 Identities = 18/72 (25%), Positives = 38/72 (52%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F   +  + T+  + E+F + G+V++  ++ D  ++RS+G G++ F D   V   +A S
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 283 GQLLLGQPVMVK 294
              L  + +  K
Sbjct: 63  RHELDSKTIDPK 74

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 69.6 bits (170), Expect = 1e-15
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           +  L V  L  +MT+ +L  LF   GP+   ++  D +TG   G+ FV F     ++ A 
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 381 SALNGKLEIVGRTLKVS 397
             LNG   +  + LKVS
Sbjct: 62  KVLNGI-TVRNKRLKVS 77

>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 = 47.7 bits (113), Expect = 7e-08
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-A 280
            +    +P   T+R++Y  F   G +   R++ D  +  S G  +++F   M    AI  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 281 LSGQLLLGQPVMVKPS 296
           L+G  +  + + V  +
Sbjct: 64  LNGITVRNKRLKVSYA 79

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.1 bits (171), Expect = 2e-15
 Identities = 53/95 (55%), Positives = 71/95 (74%)

Query: 207 KEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGY 266
           +E V+  +  ERD RTVF  Q+  +   RD+ +FFS  GKVRDVR+I DRNSRRSKG+ Y
Sbjct: 5   REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 64

Query: 267 IEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKN 301
           +EF ++ SVP+AI L+GQ LLG P++V+ S+AEKN
Sbjct: 65  VEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKN 99

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 5e-09
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 2/76 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R ++   L   +    L   F   G V  V++  D  + + KG  +V+F +++       
Sbjct: 19  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP-LAI 77

Query: 382 ALNGKLEIVGRTLKVS 397
            L G+  ++G  + V 
Sbjct: 78  GLTGQ-RLLGVPIIVQ 92

>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 = 68.8 bits (168), Expect = 3e-15
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KL V NL F +++  +++LF  FG ++   +  D  +G+  G   V F +   A  A   
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 60

Query: 383 LNGKLEIVGRTLKVSSVT 400
            NG   + GR + +  VT
Sbjct: 61  YNGV-PLDGRPMNIQLVT 77

>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 = 41.1 bits (96), Expect = 2e-05
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
           +    +    ++ D+ E F++ G ++    +    S RS G   + F        A+   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAA-VHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 282 SGQLLLGQPVMVK 294
           +G  L G+P+ ++
Sbjct: 62  NGVPLDGRPMNIQ 74

>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 = 69.3 bits (169), Expect = 3e-15
 Identities = 25/90 (27%), Positives = 39/90 (43%), Gaps = 4/90 (4%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S GG   GP G  D ++YVGNL  ++    +  +F  +G +  + L           F F
Sbjct: 1   SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAF 57

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           V+F     A+ A    +G  +  G  L+V 
Sbjct: 58  VEFEDPRDAEDAVYGRDGY-DYDGYRLRVE 86

>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 = 67.8 bits (165), Expect = 7e-15
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  LYV  L   MT+ +L +LF  +G +   ++ +D  TG  +G GF++F +   A+ A 
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 381 SALNGKLEIVGRTLKV 396
             LNG+ +  G T  +
Sbjct: 66  KGLNGQ-KPSGATEPI 80

>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 = 43.1 bits (101), Expect = 4e-06
 Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 3/77 (3%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
             ++   +P   T++++ + FS+ G++   R+++D+ +  S+GVG+I F   +    AI 
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 280 ALSGQLLLG--QPVMVK 294
            L+GQ   G  +P+ VK
Sbjct: 67  GLNGQKPSGATEPITVK 83

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 67.8 bits (165), Expect = 9e-15
 Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 3/87 (3%)

Query: 311 GTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
           G ++G  G     + V N+ F ++  ++   F  +  +         E G   G   V F
Sbjct: 1   GASSGKPG--PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 58

Query: 371 AQLEHAKAAQSALNGKLEIVGRTLKVS 397
              + A AA   LN +  I  R +K+ 
Sbjct: 59  ESRDEATAAVIDLNDR-PIGSRKVKLV 84

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.7 bits (105), Expect = 1e-06
 Identities = 9/75 (12%), Positives = 23/75 (30%), Gaps = 1/75 (1%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
             +    MP   +  ++ +FF     +     +         G   + F        A+ 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 280 ALSGQLLLGQPVMVK 294
            L+ + +  + V + 
Sbjct: 70  DLNDRPIGSRKVKLV 84

>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 = 66.6 bits (162), Expect = 2e-14
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             L V  L    TE  LR++F  +GP+  V +  D ++ + +GF FV F  ++ AK A+ 
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 382 ALNGKLEIVGRTLKV 396
             NG  E+ GR ++V
Sbjct: 70  RANGM-ELDGRRIRV 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 = 45.1 bits (106), Expect = 8e-07
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
             +  + + L  TERD+ E FSK G + DV ++ D+ SRRS+G  ++ F +V     A  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 280 ALSGQLLLGQPVMV 293
             +G  L G+ + V
Sbjct: 70  RANGMELDGRRIRV 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 = 65.9 bits (160), Expect = 3e-14
 Identities = 29/76 (38%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             L V  L  NMT+ + R LF   G +E  +L  D  TGQ  G+GFV +   + A+ A +
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 382 ALNGKLEIVGRTLKVS 397
            LNG   +  +T+KVS
Sbjct: 63  TLNGL-RLQTKTIKVS 77

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 3e-05
 Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
           +  +    +P   T+ +    F   G++   +L+ D+ + +S G G++ + D      AI
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 280 -ALSGQLLLGQPVMVKPSE 297
             L+G  L  + + V  + 
Sbjct: 62  NTLNGLRLQTKTIKVSYAR 80

>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 = 65.7 bits (160), Expect = 6e-14
 Identities = 27/88 (30%), Positives = 42/88 (47%), Gaps = 2/88 (2%)

Query: 497 PSECLLLKNMFDPA-METDPDFDLEIQGDVEEECSKYGRVKHIY-VDKRSAGFVYLRFES 554
               +++KNMF P   E DP    EI+ D+  ECSK+G+++ +   D+   G   + F  
Sbjct: 7   HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRD 66

Query: 555 TEAAASAQRAMHMRWFARRLISAIFMKP 582
            E A    + +  RWF  R I+A     
Sbjct: 67  PEEADYCIQTLDGRWFGGRQITAQAWDG 94

>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 = 41.4 bits (97), Expect = 2e-05
 Identities = 18/82 (21%), Positives = 24/82 (29%), Gaps = 8/82 (9%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
                L  N     LR     FG +  + L          G   V F   E A      L
Sbjct: 22  FEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTL 77

Query: 384 NGKLEIVGRTLKVS---SVTDH 402
           +G+    GR +        TD+
Sbjct: 78  DGR-WFGGRQITAQAWDGTTDY 98

>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 = 64.6 bits (157), Expect = 1e-13
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             LYVGNL F  TE Q+ +LF   G ++ + + LD       GF FV++     A+ A  
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 382 ALNGKLEIVGRTLKVS 397
            +NG   +  R ++  
Sbjct: 68  YINGT-RLDDRIIRTD 82

>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 = 43.8 bits (103), Expect = 3e-06
 Identities = 16/77 (20%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPM 277
           +   T++   +    TE  +YE FSK+G ++ + + +D+  + + G  ++E+Y       
Sbjct: 5   KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 278 AI-ALSGQLLLGQPVMV 293
           A+  ++G  L  + +  
Sbjct: 65  AMRYINGTRLDDRIIRT 81

>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 = 63.9 bits (155), Expect = 2e-13
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPV---ELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           L++ NL+F+ TE  L+ +F   G +    + +           GFGFV++ + E A+ A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 381 SALNGKLEIVGRTLKVS 397
             L G   + G  L+V 
Sbjct: 61  KQLQGH-TVDGHKLEVR 76

>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 = 43.1 bits (101), Expect = 4e-06
 Identities = 18/77 (23%), Positives = 31/77 (40%), Gaps = 4/77 (5%)

Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRN---SRRSKGVGYIEFYDVMSVPMAI-ALSG 283
           +    TE  +   FSK G ++   +   +N      S G G++E+        A+  L G
Sbjct: 6   LNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQG 65

Query: 284 QLLLGQPVMVKPSEAEK 300
             + G  + V+ SE   
Sbjct: 66  HTVDGHKLEVRISERAT 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 = 63.9 bits (155), Expect = 2e-13
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            KL++G L   + + Q+++L   FGP++   L  D  TG  KG+ F ++  +     A +
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 382 ALNGKLEIVGRTLKVS 397
            LNG  ++  + L V 
Sbjct: 62  GLNGM-QLGDKKLLVQ 76

>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 = 44.6 bits (105), Expect = 1e-06
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
             +F   +P    +  V E  +  G ++   L+ D  +  SKG  + E+ D+     AI 
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 280 ALSGQLLLGQPVMVKPSEAEKN 301
            L+G  L  + ++V+ +     
Sbjct: 62  GLNGMQLGDKKLLVQRASVGAK 83

>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 = 64.5 bits (157), Expect = 2e-13
 Identities = 20/91 (21%), Positives = 47/91 (51%), Gaps = 10/91 (10%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLH-FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFG 366
           S+G +      +++ ++++GNL+   + ++ +  +F  +G +    +         KGF 
Sbjct: 2   SSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFA 53

Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           FVQ+    +A+AA +  +G+  I G+ L ++
Sbjct: 54  FVQYVNERNARAAVAGEDGR-MIAGQVLDIN 83

>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 = 43.7 bits (103), Expect = 3e-06
 Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 10/92 (10%)

Query: 212 PEADPERDQRTVFAYQM-PLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
            + DP      VF   +  L   + DV   FSK GK+    +          G  ++++ 
Sbjct: 7   GKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYV 58

Query: 271 DVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKN 301
           +  +   A+    G+++ GQ + +  +   K 
Sbjct: 59  NERNARAAVAGEDGRMIAGQVLDINLAAEPKV 90

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 2e-13
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
            RKL++G L F  T+  LR  FE +G +    +  D  T + +GFGFV +A +E   AA 
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 381 SALNGKLEIVGRTLKV 396
           +A   K++  GR ++ 
Sbjct: 66  NARPHKVD--GRVVEP 79

>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 = 49.3 bits (117), Expect = 3e-08
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMS 274
           +PE+  R +F   +  + T+  +   F + G + D  ++ D N++RS+G G++ +  V  
Sbjct: 2   EPEQL-RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 275 VPMAIALSGQLLLGQPVMVK 294
           V  A+      + G+ V  K
Sbjct: 61  VDAAMNARPHKVDGRVVEPK 80

>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 = 63.5 bits (154), Expect = 3e-13
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  +YVG L   ++E  L +LF   GPV    +P D  TGQ +G+GFV+F   E A  A 
Sbjct: 9   DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 68

Query: 381 SALNGKLEIVGRTLKVS 397
             ++   ++ G+ ++V+
Sbjct: 69  KIMDMI-KLYGKPIRVN 84

>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 = 50.8 bits (121), Expect = 8e-09
 Identities = 27/93 (29%), Positives = 47/93 (50%), Gaps = 3/93 (3%)

Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
           P ++  +D  TV+   +  K +E  ++E F +AG V +  +  DR + + +G G++EF  
Sbjct: 2   PISERNQD-ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 60

Query: 272 VMSVPMAI-ALSGQLLLGQPVMVKPSEA-EKNL 302
                 AI  +    L G+P+ V  + A  KNL
Sbjct: 61  EEDADYAIKIMDMIKLYGKPIRVNKASAHNKNL 93

>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 = 62.7 bits (152), Expect = 4e-13
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K++VG L  +  E ++R+ F  FG VE ++LP+D +T + +GF F+ F + E  K     
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 383 LNGKLEIVGRTLKV 396
               +       ++
Sbjct: 61  KYHNVG--LSKCEI 72

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.5 bits (110), Expect = 2e-07
 Identities = 14/72 (19%), Positives = 28/72 (38%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F   +     E  + E+F   G+V  + L MD  + + +G  +I F +   V   +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 283 GQLLLGQPVMVK 294
              +      +K
Sbjct: 62  YHNVGLSKCEIK 73

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.4 bits (151), Expect = 6e-13
 Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 6/75 (8%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           KLY+GNL   +T   LR+LF            L  +     G+ FV +     A  A   
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 383 LNGKLEIVGRTLKVS 397
           L+GK+E+ G+ ++V 
Sbjct: 57  LSGKVELHGKIMEVD 71

>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 = 60.8 bits (147), Expect = 2e-12
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K+++G L ++ T+  L+  F  FG V    L LD  TG+ +GFGFV F + E        
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 383 LNGKLEIVGRTLKV 396
              KL   G+ +  
Sbjct: 61  KEHKLN--GKVIDP 72

>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 = 47.7 bits (113), Expect = 8e-08
 Identities = 21/72 (29%), Positives = 38/72 (52%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F   +    T++D+ ++FSK G+V D  L +D  + RS+G G++ F +  SV   +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 283 GQLLLGQPVMVK 294
              L G+ +  K
Sbjct: 62  EHKLNGKVIDPK 73

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 2e-12
 Identities = 32/76 (42%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R LYVG L   + +  L   F PFG +  +Q+PLD ET + +GF FV+F   E A AA  
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 382 ALNGKLEIVGRTLKVS 397
            +N   E+ GRT++V+
Sbjct: 66  NMNES-ELFGRTIRVN 80

>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 = 45.8 bits (108), Expect = 5e-07
 Identities = 13/84 (15%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
            +R ++   +  +  ++ ++  F   G + D+++ +D  + + +G  ++EF        A
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 279 I-ALSGQLLLGQPVMVKPSEAEKN 301
           I  ++   L G+ + V  ++  + 
Sbjct: 64  IDNMNESELFGRTIRVNLAKPMRI 87

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.1 bits (148), Expect = 2e-12
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           +  +Y G +   +T+  +R+ F PFG +  +++         KG+ FV+F+  E A  A 
Sbjct: 18  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHAI 71

Query: 381 SALNGKLEIVGRTLKVS 397
            ++NG   I G  +K  
Sbjct: 72  VSVNGT-TIEGHVVKCY 87

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 17/100 (17%), Positives = 43/100 (43%), Gaps = 9/100 (9%)

Query: 204 KEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
           + + E V  ++ P     TV+   +    T++ + + FS  G++ ++R+  ++       
Sbjct: 4   QLRFEDVVNQSSP--KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------ 55

Query: 264 VGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNL 302
             ++ F    S   AI +++G  + G  V     +   ++
Sbjct: 56  YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM 95

>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 = 60.6 bits (146), Expect = 2e-12
 Identities = 17/77 (22%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           +  L++ N   + T+  +R L +    V L      +     + F ++     E A+   
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 381 SALNGKLEIVGRTLKVS 397
             LNG  +I G TL   
Sbjct: 61  EKLNGL-KIEGYTLVTK 76

>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 = 39.0 bits (90), Expect = 1e-04
 Identities = 13/78 (16%), Positives = 27/78 (34%), Gaps = 1/78 (1%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
            T++    P   T+R++ +       V     +       S+   YI+          + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 280 ALSGQLLLGQPVMVKPSE 297
            L+G  + G  ++ K S 
Sbjct: 62  KLNGLKIEGYTLVTKVSN 79

>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 = 60.9 bits (147), Expect = 2e-12
 Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 7/89 (7%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLP-----LDIETGQCKGFGFVQFAQLEHA 376
           R+LYVGN+ F +TE  +   F     +  +        L ++  Q K F F++F  ++  
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 377 KAAQSALNGKLEIVGRTLKVSSVTDHVGT 405
             A +  +G     G++LK+    D+   
Sbjct: 62  TQAMA-FDGI-IFQGQSLKIRRPHDYQPL 88

>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 = 51.7 bits (123), Expect = 4e-09
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRL-----IMDRNSRRSKGVGYIEFYDVMSV 275
           R ++   +P   TE  + +FF+   ++  +       ++     + K   ++EF  V   
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 276 PMAIALSGQLLLGQPVMVK 294
             A+A  G +  GQ + ++
Sbjct: 62  TQAMAFDGIIFQGQSLKIR 80

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 2e-12
 Identities = 11/78 (14%), Positives = 31/78 (39%), Gaps = 3/78 (3%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPV--ELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           +L++G +       ++ +          +++      +  + +GF FV++     A  A+
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 381 SALNGK-LEIVGRTLKVS 397
             L    +++ G  + V 
Sbjct: 63  RKLMPGRIQLWGHQIAVD 80

>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 = 60.9 bits (147), Expect = 3e-12
 Identities = 32/94 (34%), Positives = 49/94 (52%), Gaps = 4/94 (4%)

Query: 304 QSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 363
           QS  +AG    GP GA    L++ +L     +  L ++F PFG V   ++ +D +T   K
Sbjct: 4   QSIGAAGSQKEGPEGA---NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 60

Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
            FGFV +     A+AA  ++NG  +I  + LKV 
Sbjct: 61  CFGFVSYDNPVSAQAAIQSMNGF-QIGMKRLKVQ 93

>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 = 35.1 bits (80), Expect = 0.004
 Identities = 16/82 (19%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
             +F Y +P +  ++D+ + F   G V   ++ +D+ +  SK  G++ + + +S   AI 
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 280 ALSGQLLLGQPVMVKPSEAEKN 301
           +++G  +  + + V+   ++ +
Sbjct: 79  SMNGFQIGMKRLKVQLKRSKND 100

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 3e-12
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           +R LY+ NL + +T  ++  +F  +GP+  +++     T + +G  +V +  +  AK A 
Sbjct: 7   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNAC 63

Query: 381 SALNGKLEIVGRTLKVS 397
             L+G   +  R L V 
Sbjct: 64  DHLSGF-NVCNRYLVVL 79

>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 = 44.6 bits (105), Expect = 2e-06
 Identities = 22/95 (23%), Positives = 42/95 (44%), Gaps = 4/95 (4%)

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
           P    R ++   +P K T  ++Y+ F K G +R    I   N+  ++G  Y+ + D+   
Sbjct: 3   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDA 59

Query: 276 PMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSA 309
             A   LSG  +  + ++V    A +   + +T  
Sbjct: 60  KNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKK 94

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.1 bits (145), Expect = 7e-12
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            K++VG L ++ T+  LRK FE FG +E   +  D +TG+ +G+GFV  A    A+ A  
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 382 ALNGKLEIVGRTLKVS 397
             N  ++  GR   V+
Sbjct: 71  DPNPIID--GRKANVN 84

>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 = 41.6 bits (97), Expect = 2e-05
 Identities = 16/89 (17%), Positives = 37/89 (41%), Gaps = 2/89 (2%)

Query: 215 DPERDQ--RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
             ++D     +F   +P   T+  + ++F   G + +  +I DR + +S+G G++   D 
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 273 MSVPMAIALSGQLLLGQPVMVKPSEAEKN 301
            +   A      ++ G+   V  +     
Sbjct: 63  AAAERACKDPNPIIDGRKANVNLAYLGAK 91

>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 = 59.2 bits (143), Expect = 7e-12
 Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 7/76 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            +L+VGNL  ++TE ++RKLFE +G    V +       + KGFGF++      A+ A+ 
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAEIAKV 62

Query: 382 ALNGKLEIVGRTLKVS 397
            L+    + G+ L+V 
Sbjct: 63  ELDNM-PLRGKQLRVR 77

>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 = 35.7 bits (82), Expect = 0.002
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 7/83 (8%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI- 279
             +F   +P   TE ++ + F K GK  +V +  D+        G+I         +A  
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKV 62

Query: 280 ALSGQLLLGQPVMVKPSEAEKNL 302
            L    L G+ + V+ +    +L
Sbjct: 63  ELDNMPLRGKQLRVRFACHSASL 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 = 59.7 bits (144), Expect = 7e-12
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R L   NL FN+TE +L+++FE    + LV      + G+ KG  +++F     A+    
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLE 71

Query: 382 ALNGKLEIVGRTLKVS 397
              G  EI GR++ + 
Sbjct: 72  EKQGA-EIDGRSVSLY 86

>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 = 38.9 bits (90), Expect = 2e-04
 Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 6/85 (7%)

Query: 214 ADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVM 273
           +   R  RT+ A  +    TE ++ E F  A ++R     +     +SKG+ YIEF    
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEA 64

Query: 274 SVPMAI-ALSGQLLLGQPVMVKPSE 297
                +    G  + G+ V +  + 
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTG 89

>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 = 58.6 bits (141), Expect = 1e-11
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           K++VG L  N T   ++  FE FG V+   L  D  T + +GFGFV F   +  +     
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 383 LNGKLEIVGRTLKV 396
           ++   EI  + ++ 
Sbjct: 60  IHFH-EINNKMVEC 72

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.6 bits (102), Expect = 2e-06
 Identities = 18/72 (25%), Positives = 32/72 (44%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
           +F   + +  T  DV  +F + GKV D  L+ D+ + R +G G++ F     V     + 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 283 GQLLLGQPVMVK 294
              +  + V  K
Sbjct: 62  FHEINNKMVECK 73

>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 = 58.6 bits (141), Expect = 1e-11
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQ-LPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
           +++GNL   + E  L   F  FG +     +  D +TG  KG+ F+ FA  + + AA  A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 383 LNGKLEIVGRTLKVS 397
           +NG+  +  R + VS
Sbjct: 61  MNGQ-YLCNRPITVS 74

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 3e-06
 Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 2/81 (2%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKV-RDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-A 280
           +F   +  +  E+ +Y+ FS  G + +  +++ D ++  SKG  +I F    +   AI A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 281 LSGQLLLGQPVMVKPSEAEKN 301
           ++GQ L  +P+ V  +  + +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>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 = 58.8 bits (142), Expect = 1e-11
 Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 3/76 (3%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             L V  L +  TE  L++ F  FG V +VQ+  D++TG  KGFGFV+F      +    
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF---TEYETQVK 65

Query: 382 ALNGKLEIVGRTLKVS 397
            ++ +  I GR     
Sbjct: 66  VMSQRHMIDGRWCDCK 81

>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 = 41.5 bits (97), Expect = 1e-05
 Identities = 19/84 (22%), Positives = 42/84 (50%), Gaps = 1/84 (1%)

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPM 277
           +    +    +P K TE+D+ E+FS  G+V  V++  D  +  SKG G++ F +  +   
Sbjct: 6   QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 65

Query: 278 AIALSGQLLLGQPVMVKPSEAEKN 301
            ++    ++ G+    K   ++++
Sbjct: 66  VMS-QRHMIDGRWCDCKLPNSKQS 88

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 4e-11
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           +K++VG +  +  E  LR  FE +G +E++++  D  +G+ +GF FV F   +       
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV- 61

Query: 382 ALNGKLEIVGRTLKV 396
                  + G   +V
Sbjct: 62  IQKYH-TVNGHNCEV 75

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 3e-06
 Identities = 15/76 (19%), Positives = 34/76 (44%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
           + +F   +     E  + ++F + GK+  + ++ DR S + +G  ++ F D  SV   + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 281 LSGQLLLGQPVMVKPS 296
                + G    V+ +
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>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 = 57.4 bits (138), Expect = 4e-11
 Identities = 30/77 (38%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           + KL+VG L F+  E  L ++F  +G +  V +  D ET + +GFGFV F  ++ AK A 
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 381 SALNGKLEIVGRTLKVS 397
            A+NGK  + GR ++V 
Sbjct: 65  MAMNGK-SVDGRQIRVD 80

>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 = 39.0 bits (90), Expect = 1e-04
 Identities = 20/86 (23%), Positives = 47/86 (54%), Gaps = 1/86 (1%)

Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
             D+  +F   +     E+ + + FSK G++ +V ++ DR ++RS+G G++ F ++    
Sbjct: 2   ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 61

Query: 277 MAI-ALSGQLLLGQPVMVKPSEAEKN 301
            A+ A++G+ + G+ + V  +    +
Sbjct: 62  DAMMAMNGKSVDGRQIRVDQAGKSSD 87

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 4e-11
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           RKL++G L F  TE  LR  +E +G +    +  D  + + +GFGFV F+ +    AA +
Sbjct: 21  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 80

Query: 382 ALNGKLEIVGRTLKVS 397
           A    ++  GR ++  
Sbjct: 81  ARPHSID--GRVVEPK 94

>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 = 51.6 bits (123), Expect = 6e-09
 Identities = 25/96 (26%), Positives = 47/96 (48%), Gaps = 1/96 (1%)

Query: 204 KEKKEVVEPEADPERDQ-RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSK 262
           K  + V       E++Q R +F   +  + TE  +  ++ + GK+ D  ++ D  S+RS+
Sbjct: 3   KTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSR 62

Query: 263 GVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA 298
           G G++ F  +  V  A+A     + G+ V  K + A
Sbjct: 63  GFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA 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 = 57.4 bits (138), Expect = 5e-11
 Identities = 18/98 (18%), Positives = 41/98 (41%), Gaps = 3/98 (3%)

Query: 300 KNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIET 359
            N+ ++  ++  +A G   A+   + +   +    E    ++ E +G VE + +  +   
Sbjct: 7   LNIYRNPQNSSQSADGLRSAVS-DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LG 64

Query: 360 GQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
               G  +V+F + E A+ A   LN +    G+ +   
Sbjct: 65  DHLVGNVYVKFRREEDAEKAVIDLNNR-WFNGQPIHAE 101

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 4e-06
 Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 2/75 (2%)

Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
           V   +   +  E    E   K G+V ++  + D       G  Y++F        A+  L
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 282 SGQLLLGQPVMVKPS 296
           + +   GQP+  + S
Sbjct: 89  NNRWFNGQPIHAELS 103

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 23/102 (22%), Positives = 37/102 (36%), Gaps = 20/102 (19%)

Query: 498 SECLLLKNMF-DPAM---------------ETDPDFDLEIQGDVEEECSKYGRVKHIYVD 541
           S+ + L N++ +P                 E    +D   +    E   KYG V+ + V 
Sbjct: 1   SQTIALLNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVC 60

Query: 542 KRSAG----FVYLRFESTEAAASAQRAMHMRWFARRLISAIF 579
                     VY++F   E A  A   ++ RWF  + I A  
Sbjct: 61  DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>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 = 57.0 bits (137), Expect = 6e-11
 Identities = 29/76 (38%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            +L+V NL +  +E  L KLF  +GP+  +  P+D  T + KGF FV F   EHA  A +
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 382 ALNGKLEIVGRTLKVS 397
            ++G+    GR L V 
Sbjct: 69  EVDGQ-VFQGRMLHVL 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 = 47.4 bits (112), Expect = 2e-07
 Identities = 22/93 (23%), Positives = 43/93 (46%), Gaps = 1/93 (1%)

Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
               +F   +   ++E D+ + FS  G + ++   +D  +++ KG  ++ F        A
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 279 I-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAG 310
              + GQ+  G+ + V PS  +K   QS  S+G
Sbjct: 67  YAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>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 = 56.6 bits (136), Expect = 8e-11
 Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           +  + V NL  +  ET L++LF PFG +  + L  D  TGQ KGF F+ F + E A  A 
Sbjct: 8   NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 381 SALNGKLEIVGRTLKVS 397
           + ++G        L V 
Sbjct: 68  AGVSGF-GYDHLILNVE 83

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 1/86 (1%)

Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
             D  T+    +     E D+ E F   G +  + L  D+ + +SKG  +I F+      
Sbjct: 5   ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 277 MAI-ALSGQLLLGQPVMVKPSEAEKN 301
            AI  +SG       + V+ ++   N
Sbjct: 65  RAIAGVSGFGYDHLILNVEWAKPSTN 90

>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 = 55.9 bits (134), Expect = 1e-10
 Identities = 26/76 (34%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             L+V ++H    E ++++ F  +G ++ + L LD  TG  KG+  V++   + A AA+ 
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 382 ALNGKLEIVGRTLKVS 397
           ALNG  EI+G+T++V 
Sbjct: 68  ALNGA-EIMGQTIQVD 82

>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 = 41.2 bits (96), Expect = 2e-05
 Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 3/82 (3%)

Query: 216 PER--DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVM 273
           P+R  +   +F   +  +A E ++ E F   G+++++ L +DR +  SKG   +E+    
Sbjct: 1   PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 60

Query: 274 SVPMAI-ALSGQLLLGQPVMVK 294
               A  AL+G  ++GQ + V 
Sbjct: 61  QALAAKEALNGAEIMGQTIQVD 82

>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 = 55.8 bits (134), Expect = 1e-10
 Identities = 26/76 (34%), Positives = 45/76 (59%), Gaps = 3/76 (3%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R LYVGNL  ++TE  + +LF   GP +  ++  +        + FV+F +   A AA +
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE--HTSNDPYCFVEFYEHRDAAAALA 66

Query: 382 ALNGKLEIVGRTLKVS 397
           A+NG+ +I+G+ +KV+
Sbjct: 67  AMNGR-KILGKEVKVN 81

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.3 bits (135), Expect = 2e-10
 Identities = 18/90 (20%), Positives = 42/90 (46%), Gaps = 2/90 (2%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G + +    +     ++GNL +++TE  +++ F       +          + KGFG+
Sbjct: 2   SSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY 61

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
            +F  L+   +A  +LN +  +  + ++V 
Sbjct: 62  AEFEDLDSLLSAL-SLNEE-SLGNKRIRVD 89

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 2e-07
 Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 1/95 (1%)

Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
           P+    T F   +P   TE  + EFF               N  R KG GY EF D+ S+
Sbjct: 11  PKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSL 70

Query: 276 PMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAG 310
             A++L+ + L  + + V  ++  ++   S  S+G
Sbjct: 71  LSALSLNEESLGNKRIRVDVADQAQD-KDSGPSSG 104

>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 = 2e-10
 Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 6/96 (6%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
            ++ V NL + +T   L ++F  FG V  +       T   +    +Q+A    A+ A+ 
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYADPVSAQHAKL 63

Query: 382 ALNGK-LEIVGRTLKVS-SVTDHVGTQDTAAKSADF 415
           +L+G+ +     TL++  S    +  +    KS D+
Sbjct: 64  SLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDY 99

>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 = 55.2 bits (132), Expect = 3e-10
 Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 9/85 (10%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLP--------LDIETGQCKGFGFVQFAQ 372
           +  +YV  L+ ++T   L   F+  G V++ +          LD ETG+ KG   V +  
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 373 LEHAKAAQSALNGKLEIVGRTLKVS 397
              AKAA    +GK +  G  LKVS
Sbjct: 68  PPTAKAAVEWFDGK-DFQGSKLKVS 91

>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 = 40.5 bits (94), Expect = 4e-05
 Identities = 16/94 (17%), Positives = 37/94 (39%), Gaps = 9/94 (9%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLI--------MDRNSRRSKGV 264
           + D + D   ++   +    T  D+ +FF + G V+  +          +D+ + + KG 
Sbjct: 1   DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 60

Query: 265 GYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE 297
             + + D  +   A+    G+   G  + V  + 
Sbjct: 61  ATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 94

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 4e-10
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           LY+  L    T+  L KL +P+G +   +  LD  T +CKG+GFV F     A+ A +AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 384 NGKLEIVGRTLK 395
                +  +  K
Sbjct: 61  KAS-GVQAQMAK 71

>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 = 53.9 bits (129), Expect = 6e-10
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + LYV NL  + +E  + K F    P             + + + FV F+  E A  A  
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHFSNREDAVEAMK 62

Query: 382 ALNGKLEIVGRTLKVS 397
           ALNGK  + G  ++V+
Sbjct: 63  ALNGK-VLDGSPIEVT 77

>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 = 53.5 bits (128), Expect = 9e-10
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           ++L+V N+ F   +  LR++F  FG +  V++  +      KGFGFV F     A  A+ 
Sbjct: 12  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRARE 69

Query: 382 ALNGKLEIVGRTLKVS 397
            L+G   + GR ++V+
Sbjct: 70  KLHGT-VVEGRKIEVN 84

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 19/86 (22%), Positives = 41/86 (47%), Gaps = 3/86 (3%)

Query: 214 ADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVM 273
           ++ +   + +    +P +  + D+ + F + GK+ DV +I +     SKG G++ F +  
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSA 62

Query: 274 SVPMAI-ALSGQLLLGQPVMVKPSEA 298
               A   L G ++ G+ + V  + A
Sbjct: 63  DADRAREKLHGTVVEGRKIEVNNATA 88

>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 = 53.6 bits (128), Expect = 1e-09
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 6/74 (8%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           +  G L   ++  QL  + E  G V+ + +P        K + F ++   E +K A   L
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTEESKRAYVTL 76

Query: 384 NGKLEIVGRTLKVS 397
           NGK  +     K++
Sbjct: 77  NGKEVVDDLGQKIT 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 = 53.1 bits (127), Expect = 1e-09
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 2/77 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKL-FEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
             +Y+ NL+  + + +L+K     F     +   L   + + +G  FV F ++  A  A 
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 381 SALNGKLEIVGRTLKVS 397
            ++ G      + +++ 
Sbjct: 64  RSMQGF-PFYDKPMRIQ 79

>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 = 53.1 bits (127), Expect = 1e-09
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             ++VG    +MTE +LR+ F  +G V  V           + F FV F      + AQS
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTF---ADDQIAQS 57

Query: 382 ALNGKLEIVGRTLKVS 397
                L I G ++ +S
Sbjct: 58  LCGEDLIIKGISVHIS 73

>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 = 35.8 bits (82), Expect = 0.001
 Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 6/81 (7%)

Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
             VF  +     TE ++ EFFS+ G V DV +             ++ F D         
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSLCG 60

Query: 281 LSGQLLLGQPVMVKPSEAEKN 301
               ++ G  V +  +E + N
Sbjct: 61  -EDLIIKGISVHISNAEPKHN 80

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 54.5 bits (130), Expect = 1e-09
 Identities = 35/104 (33%), Positives = 56/104 (53%), Gaps = 1/104 (0%)

Query: 294 KPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQL 353
           + ++ ++   Q       T   P   + R L V  +   + E QLR+LFE +GP+E V++
Sbjct: 15  QTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKI 74

Query: 354 PLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
             D ET Q +G+GFV+F     A+ A + LNG   I+ + LKV+
Sbjct: 75  VCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF-NILNKRLKVA 117

>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 = 36.8 bits (84), Expect = 0.002
 Identities = 24/116 (20%), Positives = 55/116 (47%), Gaps = 2/116 (1%)

Query: 199 ESRRYKEKKEVVEPEADPERDQ-RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRN 257
           +  + ++++ +   + +PE D  R +    +P    E  + + F + G +  V+++ DR 
Sbjct: 20  QQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE 79

Query: 258 SRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGT 312
           +R+S+G G+++F    S   AI  L+G  +L + + V  + +         + G  
Sbjct: 80  TRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDG 135

>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 = 52.3 bits (125), Expect = 2e-09
 Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 9/76 (11%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             LYV     +MT T LR  F PFG +       D+     +   FV + ++E A  A +
Sbjct: 6   NTLYVYGE--DMTPTLLRGAFSPFGNII------DLSMDPPRNCAFVTYEKMESADQAVA 57

Query: 382 ALNGKLEIVGRTLKVS 397
            LNG  ++    LKV+
Sbjct: 58  ELNGT-QVESVQLKVN 72

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 9/80 (11%)

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPM 277
           R   T++ Y      T   +   FS  G + D+ +   R         ++ +  + S   
Sbjct: 3   RKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQ 54

Query: 278 AI-ALSGQLLLGQPVMVKPS 296
           A+  L+G  +    + V  +
Sbjct: 55  AVAELNGTQVESVQLKVNIA 74

>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 = 51.7 bits (123), Expect = 3e-09
 Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 4/76 (5%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             L++ N+  +++E  L+ LF   G V    +       + +    +Q   +E A  A  
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALI 66

Query: 382 ALNGKLEIVGRTLKVS 397
            L+         L+VS
Sbjct: 67  DLHNHDLGENHHLRVS 82

>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 = 51.6 bits (123), Expect = 4e-09
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            +++ NL  ++    L   F  FG +   ++  D    +   +GFV F   E A+ A   
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERAIEK 67

Query: 383 LNGKLEIVGRTLKVS 397
           +NG   +  R + V 
Sbjct: 68  MNGM-LLNDRKVFVG 81

>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 = 39.2 bits (91), Expect = 1e-04
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 3/80 (3%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-A 280
            +F   +      + +Y+ FS  G +   +++   +   SKG G++ F    +   AI  
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQEAAERAIEK 67

Query: 281 LSGQLLLGQPVMVKPSEAEK 300
           ++G LL  + V V   ++ K
Sbjct: 68  MNGMLLNDRKVFVGRFKSRK 87

>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 = 51.3 bits (122), Expect = 7e-09
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
           G  ++ LY+ NL   +TE  L  LF  F   +   +   + TG+ +G  F+ F   E A 
Sbjct: 15  GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAW 74

Query: 378 AAQSALNGKLEIVGRTLKVS 397
            A   +NG  ++ G+ L + 
Sbjct: 75  QALHLVNGY-KLYGKILVIE 93

>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 = 51.0 bits (121), Expect = 7e-09
 Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 7/82 (8%)

Query: 322 RKLYVGNLHFNMTETQLRKLFE---PFGPVELVQLPLDIETGQC---KGFGFVQFAQLEH 375
             ++V  L   + + ++ K  E    FG +  V +                +V + + E 
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 376 AKAAQSALNGKLEIVGRTLKVS 397
           A  A   +N    + GRTLK S
Sbjct: 69  ALRAIQCVNNV-VVDGRTLKAS 89

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 7e-09
 Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R ++VGN+ +  TE QL+ +F   GPV   +L  D ETG+ KG+GF ++   E A +A  
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 382 ALNGKLEIVGRTLKVS 397
            LNG+ E  GR L+V 
Sbjct: 69  NLNGR-EFSGRALRVD 83

>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 = 44.4 bits (104), Expect = 2e-06
 Identities = 31/90 (34%), Positives = 51/90 (56%), Gaps = 3/90 (3%)

Query: 215 DP--ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
           DP  +R  R+VF   +P +ATE  + + FS+ G V   RL+ DR + + KG G+ E+ D 
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 273 MSVPMAI-ALSGQLLLGQPVMVKPSEAEKN 301
            +   A+  L+G+   G+ + V  + +EKN
Sbjct: 61  ETALSAMRNLNGREFSGRALRVDNAASEKN 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 = 51.0 bits (121), Expect = 1e-08
 Identities = 15/88 (17%), Positives = 30/88 (34%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
           E D    +       +P   T+ DV +F        +   ++  N+ +  G   ++F + 
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 273 MSVPMAIALSGQLLLGQPVMVKPSEAEK 300
                +  L  + L G+   V     E 
Sbjct: 61  DDARKSERLHRKKLNGREAFVHVVTLED 88

>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 = 47.5 bits (112), Expect = 2e-07
 Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
              ++ N+ F++T+  + +  E     E     L    GQ  G   VQF   + A+ ++ 
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE- 67

Query: 382 ALNGKLEIVGRTLKVSSVTD 401
            L+ K ++ GR   V  VT 
Sbjct: 68  RLHRK-KLNGREAFVHVVTL 86

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.8 bits (118), Expect = 1e-08
 Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 4/78 (5%)

Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
            + V NL  +  + ++ K F+  GP+  V +   ++  +   F  ++FA+ + A AA + 
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITK 59

Query: 383 LNGKLEIVGRTLKVSSVT 400
            +  +      + VS +T
Sbjct: 60  THKVVG--QNEIIVSHLT 75

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.0 bits (95), Expect = 2e-05
 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
           TV    +P    +  VY++F   G +  V +    + +++     IEF        AI  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITK 59

Query: 282 SGQLLLGQPVMVK 294
           + +++    ++V 
Sbjct: 60  THKVVGQNEIIVS 72

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.6 bits (120), Expect = 1e-08
 Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 2/89 (2%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +   P  A D  + +  L F  ++ ++ + F     V           G+  G  F
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
           VQFA  E A+ A    + +  I  R +++
Sbjct: 62  VQFASQEIAEKALK-KHKE-RIGHRYIEI 88

>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 = 50.2 bits (119), Expect = 1e-08
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 5/81 (6%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + +++ NL F+  E  L ++ + FG ++ V++ L  +T   KG  F QF   E A+   +
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 382 ALNGKL-----EIVGRTLKVS 397
           A + +      ++ GR LKV 
Sbjct: 69  AASLEAEGGGLKLDGRQLKVD 89

>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 = 37.1 bits (85), Expect = 8e-04
 Identities = 17/91 (18%), Positives = 37/91 (40%), Gaps = 7/91 (7%)

Query: 218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPM 277
            + +TVF   +   + E  + E   + G ++ VR+++  ++  SKG  + +F    +   
Sbjct: 6   TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 278 AIA-------LSGQLLLGQPVMVKPSEAEKN 301
            +A         G  L G+ + V  +     
Sbjct: 66  CLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 1e-08
 Identities = 13/76 (17%), Positives = 23/76 (30%), Gaps = 8/76 (10%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             + V NL  +    ++  L + +               + K   FV     E A+ A  
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 382 ALNGKLEIVGRTLKVS 397
             +      G+ L V 
Sbjct: 59  MFHQY-SFRGKDLIVQ 73

>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 = 49.8 bits (118), Expect = 2e-08
 Identities = 12/82 (14%), Positives = 25/82 (30%), Gaps = 12/82 (14%)

Query: 321 DRKLYVGNLHF-----NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH 375
              L     +      + T  +   LF  +      Q        +      + F+    
Sbjct: 5   SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFSNPLS 58

Query: 376 AKAAQSALNGKLEIVGRTLKVS 397
           A  A+  L+   E +G+ +K+ 
Sbjct: 59  AADARLRLHKT-EFLGKEMKLY 79

>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 = 49.3 bits (117), Expect = 4e-08
 Identities = 24/93 (25%), Positives = 43/93 (46%), Gaps = 9/93 (9%)

Query: 308 SAGGTATGPYGAID--RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGF 365
           S+G +    YG  +   +L+VG L  N +   L + F+ FG +  +         +   F
Sbjct: 2   SSGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSF 55

Query: 366 GFVQFAQLEHAKAAQSALNGK-LEIVGRTLKVS 397
            ++Q+  L+ A+AA + + G  L    R L+V 
Sbjct: 56  AYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD 88

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.4 bits (112), Expect = 1e-07
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 4/78 (5%)

Query: 322 RKLYVGNLHFNMT-ETQLRKLFEPFGPVELVQLPLDI-ETGQCKGFGFVQFAQLEHAKAA 379
           R++ + NL   +  E  LR+ FE FG +E + +P    E        F+ F   + A+ A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 380 QSALNGKLEIVGRTLKVS 397
              +N    +  R + VS
Sbjct: 65  L-QMNRS-LLGNREISVS 80

>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 = 39.3 bits (91), Expect = 9e-05
 Identities = 8/81 (9%), Positives = 28/81 (34%), Gaps = 2/81 (2%)

Query: 219 DQRTVFAYQMPLKATERDVYE--FFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
           + R +    +  +  + ++    F       +       +    +    ++ F +  S  
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 277 MAIALSGQLLLGQPVMVKPSE 297
            A+ ++  LL  + + V  ++
Sbjct: 63  RALQMNRSLLGNREISVSLAD 83

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.1 bits (111), Expect = 3e-07
 Identities = 16/91 (17%), Positives = 34/91 (37%), Gaps = 7/91 (7%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G + +    ++   ++V  L  ++ E  L +  E FG          +     K    
Sbjct: 2   SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGT------ICYVMMMPFKRQAL 55

Query: 368 VQFAQLEHAKAAQSALNGK-LEIVGRTLKVS 397
           V+F  ++ AK   +      + I G+    +
Sbjct: 56  VEFENIDSAKECVTFAADVPVYIAGQQAFFN 86

>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 = 8e-07
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 8/90 (8%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G +   P    D ++ V  L  + +   L+      G V            Q  G G 
Sbjct: 2   SSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDV-------CYADVQKDGMGM 54

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           V++ + E  + A   L+   +      + S
Sbjct: 55  VEYLRKEDMEYALRKLDDT-KFRSHEGETS 83

>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 = 44.0 bits (103), Expect = 2e-06
 Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 3/81 (3%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           +R +Y+     + T   +++  E  G V  +Q+         KG  FV F  +E AK   
Sbjct: 6   NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR-RTLHKAFKGSIFVVFDSIESAKKFV 64

Query: 381 SALNGKLEIVGRTLKVSSVTD 401
                K +     L +    D
Sbjct: 65  ETPGQKYK--ETDLLILFKDD 83

>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 = 40.1 bits (93), Expect = 4e-05
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
           +   R+V+    P  AT  D+ E+    G+V +++ +     +  KG  ++ F  + S  
Sbjct: 3   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAK 61

Query: 277 MAIALSGQLLLGQPVMVKPSE 297
             +   GQ      +++   +
Sbjct: 62  KFVETPGQKYKETDLLILFKD 82

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 44.1 bits (103), Expect = 2e-06
 Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 5/76 (6%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           + L++ NL     E  L  LF  F   + V+              FV+F     + AA+ 
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPGFKEVR-----LVPNRHDIAFVEFTTELQSNAAKE 63

Query: 382 ALNGKLEIVGRTLKVS 397
           AL G        +K++
Sbjct: 64  ALQGFKITPTHAMKIT 79

>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 = 44.4 bits (104), Expect = 2e-06
 Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 2/76 (2%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
             LY+ NL  +M E +L  + +PFG V      L   +G  +G GF +    E  +A   
Sbjct: 19  TNLYISNLPLSMDEQELENMLKPFGQVI-STRILRDSSGTSRGVGFARMESTEKCEAVIG 77

Query: 382 ALNGKLEIVGRTLKVS 397
             NGK  I       +
Sbjct: 78  HFNGK-FIKTPPGVSA 92

>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 = 35.5 bits (81), Expect = 0.002
 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 2/89 (2%)

Query: 210 VEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
            +     E+D   ++   +PL   E+++       G+V   R I+  +S  S+GVG+   
Sbjct: 8   AQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR-ILRDSSGTSRGVGFARM 66

Query: 270 YDVMSVPMAI-ALSGQLLLGQPVMVKPSE 297
                    I   +G+ +   P +  P+E
Sbjct: 67  ESTEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 6e-06
 Identities = 19/90 (21%), Positives = 36/90 (40%), Gaps = 4/90 (4%)

Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
           S+G + +         +++  L +  TE  +   F P  P+ +         G+  G   
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHI--EIGPDGRVTGEAD 59

Query: 368 VQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
           V+FA  E A AA  A +    +  R +++ 
Sbjct: 60  VEFATHEDAVAAM-AKDKA-NMQHRYVELF 87

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 19/96 (19%), Positives = 31/96 (32%), Gaps = 2/96 (2%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
            +        V    +P +ATE D+Y FFS    +R           R  G   +EF   
Sbjct: 8   SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHI--EIGPDGRVTGEADVEFATH 65

Query: 273 MSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTS 308
                A+A     +  + V +  +          +S
Sbjct: 66  EDAVAAMAKDKANMQHRYVELFLNSTAGTSGSGPSS 101

>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 = 42.2 bits (98), Expect = 7e-06
 Identities = 14/74 (18%), Positives = 26/74 (35%), Gaps = 8/74 (10%)

Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
           + +  L  ++T  ++  L   +               + KG  FV     E A+AA +  
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELK-------YCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 384 NGKLEIVGRTLKVS 397
           +    +  R L V 
Sbjct: 54  HQS-RLRERELSVQ 66

>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 = 41.9 bits (97), Expect = 1e-05
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
              L++GNL+ N +  +L+           + +     TG  + FG+V F   E  + A 
Sbjct: 13  PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKAL 71

Query: 381 SALNGKLEIVGRTLKVS 397
             L G  ++ G  +K+ 
Sbjct: 72  E-LTGL-KVFGNEIKLE 86

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 40.7 bits (94), Expect = 3e-05
 Identities = 12/85 (14%), Positives = 33/85 (38%), Gaps = 1/85 (1%)

Query: 213 EADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
           E         +F   +    +  ++    S+     D+ ++  R    ++  GY++F   
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTG-TNRKFGYVDFESA 64

Query: 273 MSVPMAIALSGQLLLGQPVMVKPSE 297
             +  A+ L+G  + G  + ++  +
Sbjct: 65  EDLEKALELTGLKVFGNEIKLEKPK 89

>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 = 41.7 bits (97), Expect = 2e-05
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 322 RKLYVGNLHF-NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
             L V NL+   +T   L  LF  +G V+ V++         K    VQ A    A+ A 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLAM 57

Query: 381 SALNGKLEIVGRTLKVS 397
           S LNG  ++ G+ ++++
Sbjct: 58  SHLNGH-KLHGKPIRIT 73

>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 = 40.6 bits (94), Expect = 3e-05
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 7/77 (9%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
           R L++  L   +TET++  L  PFG V       +I   + K   F++ A  E A    +
Sbjct: 9   RVLHIRKLPGEVTETEVIALGLPFGKVT------NILMLKGKNQAFLELATEEAAITMVN 62

Query: 382 ALNGK-LEIVGRTLKVS 397
             +     +  + + + 
Sbjct: 63  YYSAVTPHLRNQPIYIQ 79

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 1e-04
 Identities = 27/208 (12%), Positives = 71/208 (34%), Gaps = 5/208 (2%)

Query: 4   DEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSR 63
           D     +K +  Q ++K+DD        + +E S               EE+ ++G  S+
Sbjct: 92  DVDHLFQKELAAQLEKKRDD-----FCKQNQEASSDRCSGLLQVIFSPLEEEVKAGIYSK 146

Query: 64  RDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERE 123
                    +    + +  ++ R     +       + +        ++ +   ++++  
Sbjct: 147 PGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEI 206

Query: 124 RRERRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERE 183
             ER   E  +   +          +    + R      ++  E+      +L  E+ER 
Sbjct: 207 EVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERT 266

Query: 184 RERELRERERDLEMRESRRYKEKKEVVE 211
              +L+E+E+ L+    +  +  K  ++
Sbjct: 267 LALKLQEQEQLLKEGFQKESRIMKNEIQ 294

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 7e-04
 Identities = 20/200 (10%), Positives = 63/200 (31%)

Query: 7   EYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDE 66
           E   +  +++    + +  +S  +     +   S  + E       +         +  +
Sbjct: 100 ELAAQLEKKRDDFCKQNQEASSDRCSGLLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQD 159

Query: 67  DEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRE 126
            ++      R   +  +  +              +  +T  ++E+  E    + E  +  
Sbjct: 160 LKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQAS 219

Query: 127 RRDREKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERER 186
            +   + + +      +     +    Q        R +  +E ER   L+L+ + +  +
Sbjct: 220 AKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLK 279

Query: 187 ELRERERDLEMRESRRYKEK 206
           E  ++E  +   E +  + K
Sbjct: 280 EGFQKESRIMKNEIQDLQTK 299

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 0.002
 Identities = 25/212 (11%), Positives = 75/212 (35%)

Query: 10  EKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKRSRRDEDEE 69
           E      R   +D D   +K+   + + +R    +++ E   +             E+E 
Sbjct: 80  EAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSDRCSGLLQVIFSPLEEEV 139

Query: 70  NGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKERERRERRD 129
                 +        ++ +  + +  +  R+  +  E  +   + +        + ++  
Sbjct: 140 KAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTL 199

Query: 130 REKERERERDGERRSSSRSRRSSSQSRRSSSRSRRERERESERERELELERERERERELR 189
            EKE+E E +  +  S+++        +  +    E++  S +E   +L  + E +R   
Sbjct: 200 TEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQL 259

Query: 190 ERERDLEMRESRRYKEKKEVVEPEADPERDQR 221
            +E++  +    + +E+      + +    + 
Sbjct: 260 LKEQERTLALKLQEQEQLLKEGFQKESRIMKN 291

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 0.004
 Identities = 14/142 (9%), Positives = 55/142 (38%)

Query: 2   EFDEYEYLEKTVEEQRQQKQDDDSSSKKKAKREEKSERSYRKREDSEEEEEEEKSRSGKR 61
            +  +    + ++++  ++      +++  +   KS+ S        ++   EK +  + 
Sbjct: 149 GYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEV 208

Query: 62  SRRDEDEENGSRRDRDRDRDRDKERHRRDRDRDRDRGRERERETERDRERSRERREKEKE 121
            R   +    S +     + ++++   +     ++  ++   + E DR +  + +E+   
Sbjct: 209 ERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLA 268

Query: 122 RERRERRDREKERERERDGERR 143
            + +E+    KE  ++     +
Sbjct: 269 LKLQEQEQLLKEGFQKESRIMK 290

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 8/78 (10%)

Query: 322 RKLYVGNL-HFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           R +++ +         QL +L EPFG +       +          F++ A  E A+AA 
Sbjct: 9   RVVHIMDFQRGKNLRYQLLQLVEPFGVIS------NHLILNKINEAFIEMATTEDAQAAV 62

Query: 381 SALNGK-LEIVGRTLKVS 397
                    + G+ ++V 
Sbjct: 63  DYYTTTPALVFGKPVRVH 80

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.3 bits (88), Expect = 3e-04
 Identities = 20/88 (22%), Positives = 36/88 (40%)

Query: 215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMS 274
            P      V+   +P +A  + V +FF K   V D   I    + ++ G G++EF +   
Sbjct: 13  SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEAD 72

Query: 275 VPMAIALSGQLLLGQPVMVKPSEAEKNL 302
              A+    Q +  + + V P   +  L
Sbjct: 73  YKAALCRHKQYMGNRFIQVHPITKKGML 100

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.8 bits (85), Expect = 5e-04
 Identities = 10/82 (12%), Positives = 23/82 (28%), Gaps = 10/82 (12%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
           D  + V           +   F  +G +    +           +  +++     A+ A 
Sbjct: 4   DTWVTVFGFPQASAS-YILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKAL 56

Query: 381 SALNGKLEIVGRT-LKVSSVTD 401
           S  +G+        + V    D
Sbjct: 57  S-KDGR-IFGESIMIGVKPCID 76

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.2 bits (85), Expect = 0.001
 Identities = 11/77 (14%), Positives = 24/77 (31%), Gaps = 7/77 (9%)

Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
              +   NL       ++++ F  FG +        +   +      V+F +   A+ A 
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLG------RVLLPEGGITAIVEFLEPLEARKAF 63

Query: 381 SALNGKLEIVGRTLKVS 397
             L    +     L + 
Sbjct: 64  RHLAYS-KFHHVPLYLE 79

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.6 bits (81), Expect = 0.003
 Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 8/77 (10%)

Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ-LEHAKAAQ 380
              + G+L        L  LF   G ++       I+  +    G + F +  + A    
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIK------WIDFVRGAKEGIILFKEKAKEALGKA 65

Query: 381 SALNGKLEIVGRTLKVS 397
              N    +  R  +V+
Sbjct: 66  KDANNG-NLQLRNKEVT 81

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	591
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.95
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.91
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.76
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.75
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.75
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.75
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.75
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.74
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.74
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.74
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.74
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.74
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.74
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.73
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.73
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.73
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.72
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.72
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.72
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.72
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.72
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.72
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.71
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.71
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.7
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.7
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.7
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.7
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.69
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.69
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.69
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.69
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.69
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.68
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.68
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.68
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.68
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.68
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.67
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.67
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.67
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.67
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.67
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.66
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.66
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.65
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.65
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.64
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.64
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.64
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.64
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.64
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.64
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.63
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.63
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.63
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.63
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.63
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.63
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.62
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.62
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.62
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.62
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.62
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.62
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.61
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.61
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.61
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.61
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.61
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.6
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.6
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.6
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.6
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.6
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.6
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.6
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.6
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.59
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.58
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.58
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.58
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.58
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.58
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.58
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.57
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.57
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.57
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.57
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.57
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.56
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.56
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.56
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.56
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.56
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.56
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.56
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.56
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.56
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.56
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.56
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.56
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.55
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.54
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.54
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.54
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.54
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.54
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.54
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.54
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.54
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.53
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.53
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.53
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.53
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.53
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.53
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.53
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.53
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.52
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.52
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.52
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.52
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.52
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.51
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.51
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.51
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.51
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.5
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.5
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.5
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.5
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.49
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.49
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.49
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.49
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.48
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.47
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.47
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.43
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.43
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.43
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.43
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.41
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.41
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.3
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	99.29
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	99.28
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.28
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.25
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.23
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.22
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.22
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.19
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.1
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.06
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.31
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.22
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.51
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.14
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.85
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.59
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.99
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	92.56

>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=99.95  E-value=1.1e-27  Score=217.45  Aligned_cols=170  Identities=22%  Similarity=0.405  Sum_probs=150.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCccc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~~  299 (591)
                      .++|||+|||+.+|+++|.++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+.+++..+.+..+.+.+....
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhc
Confidence            47999999999999999999999999999999999999999999999999999999999999999999998888766443


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHH
Q 007742          300 KNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA  379 (591)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a  379 (591)
                      ......          ......++|||+|||..+++++|+++|..||.|..+.|+.+..++.++|||||+|.+.++|..|
T Consensus        86 ~~~~~~----------~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~A  155 (183)
T d1u1qa_          86 EDSQRP----------GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI  155 (183)
T ss_dssp             TGGGST----------TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHH
T ss_pred             cccccc----------ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHH
Confidence            332221          1122347999999999999999999999999999999999888899999999999999999999


Q ss_pred             HHHhcCCeeeCCeEEEEEEecC
Q 007742          380 QSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       380 ~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      +. +++. .|.|+.|.|.++.+
T Consensus       156 l~-~~~~-~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         156 VI-QKYH-TVNGHNCEVRKALS  175 (183)
T ss_dssp             HT-SSCE-EETTEEEEEEECCC
T ss_pred             HH-hCCC-eECCEEEEEEecCC
Confidence            95 7775 69999999998753

>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=99.91  E-value=6.7e-24  Score=192.26  Aligned_cols=167  Identities=20%  Similarity=0.338  Sum_probs=139.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|..|+..+++  .+.+..+.+.....
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~--~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH--KVDGRVVEPKRAVS   84 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSC--EETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCC--cccccchhhhhhhh
Confidence            7999999999999999999999999999999999988999999999999999999999965554  48888887776432


Q ss_pred             CCCCCcccccCCCCCCCCCCCccccHHHHHHHHHHhhhcCCccccCCcCCCCCcccCccccccccccCcCCCCCCCCCCC
Q 007742          402 HVGTQDTAAKSADFDDDDGGGLALNAQSRALLMQKLDRTGIATSIAGSLGVAPAVNGSAVNQQAISLPVVGQPAVPVPAV  481 (591)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (591)
                      .....                                                                           
T Consensus        85 ~~~~~---------------------------------------------------------------------------   89 (183)
T d1u1qa_          85 REDSQ---------------------------------------------------------------------------   89 (183)
T ss_dssp             TTGGG---------------------------------------------------------------------------
T ss_pred             ccccc---------------------------------------------------------------------------
Confidence            11000                                                                           


Q ss_pred             CCCccccccccccCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEec-----CCCeeEEEEeCCHH
Q 007742          482 TAPVIPNMAAEFIGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-----RSAGFVYLRFESTE  556 (591)
Q Consensus       482 ~~~~~~~~~~~~~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~-----~~~g~afV~F~~~e  556 (591)
                               ........++|+|.||  |..++        +++|.++|+.||.|..+.+..     .++|+|||+|.+.+
T Consensus        90 ---------~~~~~~~~~~i~V~~l--p~~~t--------e~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e  150 (183)
T d1u1qa_          90 ---------RPGAHLTVKKIFVGGI--KEDTE--------EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD  150 (183)
T ss_dssp             ---------STTTTCCCSEEEEECC--CTTCC--------HHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHH
T ss_pred             ---------ccccccccceeEEccC--CCcCC--------HHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHH
Confidence                     0001234467999999  88888        899999999999999998753     35689999999999


Q ss_pred             HHHHHHHHhcccccCCeEEEEEEeCchhh
Q 007742          557 AAASAQRAMHMRWFARRLISAIFMKPEDY  585 (591)
Q Consensus       557 ~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  585 (591)
                      +|.+|+. ++|..|.|+.|.|.++.++.-
T Consensus       151 ~A~~Al~-~~~~~~~G~~i~V~~A~~k~e  178 (183)
T d1u1qa_         151 SVDKIVI-QKYHTVNGHNCEVRKALSKQE  178 (183)
T ss_dssp             HHHHHHT-SSCEEETTEEEEEEECCCHHH
T ss_pred             HHHHHHH-hCCCeECCEEEEEEecCCccc
Confidence            9999997 789999999999999876653

>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=99.76  E-value=4.2e-19  Score=141.64  Aligned_cols=81  Identities=58%  Similarity=0.964  Sum_probs=77.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      ..++|||+|||+.+|+++|+++|..||.|.+|.|+.+..+|.++|||||+|.+.++|.+|+.|||..|.|+.|.|.++.+
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCC
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999999998755


Q ss_pred             c
Q 007742          299 E  299 (591)
Q Consensus       299 ~  299 (591)
                      .
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.1e-18  Score=137.35  Aligned_cols=82  Identities=27%  Similarity=0.440  Sum_probs=77.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +.++|||+|||+.+|+++|+++|.+||.|..|.|+.++.+|.++|||||+|.+.++|..|| .|||..|.|+.|+|.++.
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            4589999999999999999999999999999999999999999999999999999999999 699999999999999986


Q ss_pred             ccc
Q 007742          298 AEK  300 (591)
Q Consensus       298 ~~~  300 (591)
                      +..
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            643

>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=99.76  E-value=3.7e-19  Score=134.33  Aligned_cols=76  Identities=24%  Similarity=0.420  Sum_probs=73.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      |+|||+|||+.+|+++|+++|.+||.|..+.|+.++.+|.++|||||+|.+.++|.+||.+|++.|.|+.|.|..+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999998754

>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=99.75  E-value=2e-18  Score=134.36  Aligned_cols=81  Identities=25%  Similarity=0.365  Sum_probs=76.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      .++++|||+|||+.+|+++|.++|..||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|.|+.|.|.|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35689999999999999999999999999999999999999999999999999999999999 69999999999999998


Q ss_pred             cc
Q 007742          297 EA  298 (591)
Q Consensus       297 ~~  298 (591)
                      .+
T Consensus        85 ~~   86 (88)
T d1rk8a_          85 FV   86 (88)
T ss_dssp             EE
T ss_pred             cC
Confidence            65

>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=99.75  E-value=1.4e-18  Score=133.66  Aligned_cols=79  Identities=22%  Similarity=0.423  Sum_probs=75.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      .++|||+|||+.+|+++|+++|.+||.|..|.++.++.+|.++|||||+|.+.++|..|| .|||..+.|+.|.|.++.+
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            468999999999999999999999999999999999999999999999999999999999 6999999999999999864

>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=99.75  E-value=2.4e-18  Score=138.20  Aligned_cols=94  Identities=34%  Similarity=0.548  Sum_probs=87.2

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecC-------CCeeEEEEeCCHHHHHHHHHHhcc
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKR-------SAGFVYLRFESTEAAASAQRAMHM  567 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~-------~~g~afV~F~~~e~A~~A~~~l~g  567 (591)
                      ++|+++|+|.||++|..+.++..+.+|.+||+++|++||.|..|.|+.+       ..|++||+|.++++|.+|+..|||
T Consensus         1 g~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~G   80 (104)
T d1o0pa_           1 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   80 (104)
T ss_dssp             CCCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSS
T ss_pred             CCCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCC
Confidence            4689999999999999999999999999999999999999999998642       358999999999999999999999


Q ss_pred             cccCCeEEEEEEeCchhhhhc
Q 007742          568 RWFARRLISAIFMKPEDYEAK  588 (591)
Q Consensus       568 ~~~~g~~l~v~~~~~~~~~~~  588 (591)
                      +.|+|+.|.|.|++++.|.+.
T Consensus        81 r~f~gR~v~v~f~~~~~y~~~  101 (104)
T d1o0pa_          81 RKFANRVVVTKYCDPDSYHRR  101 (104)
T ss_dssp             CCSSSSCCEEEEECHHHHHHT
T ss_pred             CEECCeEEEEEEcCHHHhhhc
Confidence            999999999999999999864

>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=99.75  E-value=1.8e-18  Score=133.15  Aligned_cols=77  Identities=23%  Similarity=0.413  Sum_probs=74.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      .++|||+|||+.+|+++|.++|..||.|..|.|+.++.+|.++|||||+|.+.++|.+||.++++.|.|+.|.|..+
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEEC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEee
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999765

>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=99.74  E-value=2.4e-18  Score=135.36  Aligned_cols=81  Identities=20%  Similarity=0.423  Sum_probs=76.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ..+++|||+|||+.+|+++|.++|.+||.|.+|.++.++.+|.++|||||+|.+.++|..|+ .|||..|.|++|.|.|+
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            35789999999999999999999999999999999999999999999999999999999999 59999999999999987


Q ss_pred             cc
Q 007742          297 EA  298 (591)
Q Consensus       297 ~~  298 (591)
                      ..
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>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=99.74  E-value=3.5e-18  Score=136.40  Aligned_cols=84  Identities=21%  Similarity=0.408  Sum_probs=78.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ..+++|||+|||+.+|+++|+++|.+||.|..|.|+.++.+|.++|||||+|.+.++|..|| .||+..|.|+.|.|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45688999999999999999999999999999999999999999999999999999999999 69999999999999998


Q ss_pred             ccccc
Q 007742          297 EAEKN  301 (591)
Q Consensus       297 ~~~~~  301 (591)
                      .....
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            76543

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.3e-18  Score=134.38  Aligned_cols=79  Identities=24%  Similarity=0.389  Sum_probs=75.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-HcCCccCCeeEEeccCccc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-LSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l~g~~i~g~~i~v~~~~~~  299 (591)
                      ++|||+|||+.+|+++|.++|.+||+|..|.|+.++.||.++|||||+|.+.++|..|+. |||..|.|++|.|.++...
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            689999999999999999999999999999999999999999999999999999999995 9999999999999998653

>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=99.74  E-value=2.3e-18  Score=129.53  Aligned_cols=74  Identities=28%  Similarity=0.445  Sum_probs=71.4

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEecc
Q 007742          222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP  295 (591)
Q Consensus       222 ~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~  295 (591)
                      +|||+|||+.+|+++|.++|.+||.|..|.++.++.+|.++|||||+|.+.++|.+||.+++..|.|+.|.|..
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeE
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999864

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=3e-18  Score=131.99  Aligned_cols=76  Identities=33%  Similarity=0.484  Sum_probs=72.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEe
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV  293 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v  293 (591)
                      .+.++|||+|||+.+|+++|+++|.+||.|.+|.++.++.+|.++|||||+|.+.++|..|+ .|||..|.|+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            34689999999999999999999999999999999999999999999999999999999999 69999999999987

>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=99.74  E-value=2.3e-18  Score=131.47  Aligned_cols=76  Identities=28%  Similarity=0.439  Sum_probs=73.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       222 ~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      .|||+|||+.+|+++|.++|.+||+|..|.|+.++.+|.++|||||+|.+.++|..|| .|||..+.|++|+|.|+.
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~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            5999999999999999999999999999999999999999999999999999999999 699999999999999874

>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=99.74  E-value=2.6e-18  Score=134.43  Aligned_cols=81  Identities=23%  Similarity=0.297  Sum_probs=76.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +.++|||+|||..+|+++|+++|.+||.|..|.++.++.+|.++|||||+|.+.++|..|| .|||..|.|+.|.|.++.
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            4589999999999999999999999999999999999999999999999999999999999 599999999999999986


Q ss_pred             cc
Q 007742          298 AE  299 (591)
Q Consensus       298 ~~  299 (591)
                      +.
T Consensus        87 p~   88 (90)
T d2cq0a1          87 PS   88 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.73  E-value=6.2e-18  Score=130.09  Aligned_cols=78  Identities=21%  Similarity=0.417  Sum_probs=74.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      ++|||+|||+.+|+++|.++|++||.|..|.++.+..+|.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.+
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            57999999999999999999999999999999999999999999999999999999999 6999999999999998753

>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=99.73  E-value=6e-18  Score=135.55  Aligned_cols=82  Identities=20%  Similarity=0.436  Sum_probs=77.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ++++|||+|||+.+|+++|.++|..||.|..+.++.++.+|.++|||||+|.+.++|..|| .|||..|.|+.|.|.++.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            4578999999999999999999999999999999999999999999999999999999999 699999999999999986


Q ss_pred             ccc
Q 007742          298 AEK  300 (591)
Q Consensus       298 ~~~  300 (591)
                      +..
T Consensus        97 ~k~   99 (102)
T d2cpza1          97 SKN   99 (102)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            643

>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=99.73  E-value=2.4e-18  Score=134.38  Aligned_cols=81  Identities=16%  Similarity=0.360  Sum_probs=76.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||+.+|+++|+++|++||+|..|.++.++.+|.++|||||+|.+.++|..|+ .+||..|.|+.|.|.++.
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            3589999999999999999999999999999999999999999999999999999999999 699999999999999986


Q ss_pred             cc
Q 007742          298 AE  299 (591)
Q Consensus       298 ~~  299 (591)
                      +.
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.72  E-value=8.7e-18  Score=130.77  Aligned_cols=82  Identities=23%  Similarity=0.404  Sum_probs=75.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~  297 (591)
                      ...++|||+|||+.+|+++|+++|+.||.|..|.|+.|+.+|.++|||||+|.+.++|.+||. ++..|.|+.|.|.++.
T Consensus         6 ~~~~~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           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEECCC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEeEEEeCC
Confidence            356889999999999999999999999999999999999999999999999999999999997 3457999999999886


Q ss_pred             ccc
Q 007742          298 AEK  300 (591)
Q Consensus       298 ~~~  300 (591)
                      +..
T Consensus        85 ~k~   87 (90)
T d2cqga1          85 SKQ   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            543

>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=99.72  E-value=3e-18  Score=128.33  Aligned_cols=74  Identities=19%  Similarity=0.309  Sum_probs=70.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEecc
Q 007742          222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP  295 (591)
Q Consensus       222 ~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~  295 (591)
                      +|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||++++..|.|+.|.|..
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~   74 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEE
Confidence            59999999999999999999999999999999999999999999999999999999998888999999998864

>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=99.72  E-value=7.6e-18  Score=128.49  Aligned_cols=77  Identities=19%  Similarity=0.389  Sum_probs=73.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      .++|||+|||+.+|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+.+||+.|.|+.|.|..+
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            37999999999999999999999999999999999999999999999999999999999999999999999999754

>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=99.72  E-value=8.9e-18  Score=129.71  Aligned_cols=78  Identities=28%  Similarity=0.546  Sum_probs=72.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC--eeEEecc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG--QPVMVKP  295 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g--~~i~v~~  295 (591)
                      ..++|||+|||+.+|+++|+++|.+||+|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..+.|  .+|.|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            3578999999999999999999999999999999999999999999999999999999999 699999988  4588876


Q ss_pred             C
Q 007742          296 S  296 (591)
Q Consensus       296 ~  296 (591)
                      +
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.72  E-value=5.4e-18  Score=135.53  Aligned_cols=80  Identities=26%  Similarity=0.441  Sum_probs=76.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCccc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~~  299 (591)
                      .++|||+|||+++|+++|+++|.+||.|..+.|+.++.++.++|||||+|.+.++|.+||.++++.|.|+.|.|.++.+.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECccc
Confidence            37899999999999999999999999999999999999999999999999999999999999999999999999887654

>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=99.72  E-value=1.8e-17  Score=133.02  Aligned_cols=82  Identities=18%  Similarity=0.356  Sum_probs=75.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~  297 (591)
                      ...++|||+|||+.+|+++|.++|++||.|.+|.|+.++.+|.++|||||+|.+.++|.+||+.++..|.|+.|.|.++.
T Consensus         8 ~~~~~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           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAY   87 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEEST
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcC
Confidence            34578999999999999999999999999999999999999999999999999999999999654558999999998876


Q ss_pred             cc
Q 007742          298 AE  299 (591)
Q Consensus       298 ~~  299 (591)
                      ..
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.71  E-value=1.4e-17  Score=128.71  Aligned_cols=78  Identities=22%  Similarity=0.441  Sum_probs=73.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC--eeEEecc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG--QPVMVKP  295 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g--~~i~v~~  295 (591)
                      ..++|||+|||+.+|+++|+++|.+||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..+.|  ++|.|.+
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            4578999999999999999999999999999999999999999999999999999999999 699999876  8899987


Q ss_pred             C
Q 007742          296 S  296 (591)
Q Consensus       296 ~  296 (591)
                      +
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=8.6e-18  Score=131.68  Aligned_cols=81  Identities=25%  Similarity=0.525  Sum_probs=76.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +.++|||+|||+.+|+++|.++|.+||.|..+.++.+..+|.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.
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            4688999999999999999999999999999999999999999999999999999999999 699999999999999875


Q ss_pred             cc
Q 007742          298 AE  299 (591)
Q Consensus       298 ~~  299 (591)
                      +.
T Consensus        84 ~~   85 (90)
T d1x5sa1          84 KS   85 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.71  E-value=1.5e-17  Score=131.00  Aligned_cols=82  Identities=23%  Similarity=0.500  Sum_probs=75.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCC-CCCccceEEEEecCcchHHHHH-HH-cCCccCCeeEEec
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRN-SRRSKGVGYIEFYDVMSVPMAI-AL-SGQLLLGQPVMVK  294 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~-~g~~~G~afV~F~~~e~A~~Al-~l-~g~~i~g~~i~v~  294 (591)
                      ..+++|||+|||+.+|+++|+.+|.+||.|..|.|+.+.. +|.++|||||+|.+.++|..|| .| ||..|.|++|.|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            3568899999999999999999999999999999998754 7999999999999999999999 57 8999999999999


Q ss_pred             cCccc
Q 007742          295 PSEAE  299 (591)
Q Consensus       295 ~~~~~  299 (591)
                      |+...
T Consensus        86 ~A~~~   90 (94)
T d2cpha1          86 WADSE   90 (94)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            98654

>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=99.71  E-value=8.6e-18  Score=128.81  Aligned_cols=78  Identities=17%  Similarity=0.230  Sum_probs=67.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      ++|||+|||+.+|+++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|..|+ .|||..+.|++|.|.++.|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            79999999999999999999999999999989888888999999999999999999999 6999999999999998864

>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=99.70  E-value=2.8e-18  Score=138.49  Aligned_cols=82  Identities=34%  Similarity=0.589  Sum_probs=77.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      .++|||+|||+.+|+++|.++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++..
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            478999999999999999999999999999999999999999999999999999999999 6899999999999999865


Q ss_pred             ccc
Q 007742          299 EKN  301 (591)
Q Consensus       299 ~~~  301 (591)
                      ...
T Consensus        88 ~~~   90 (104)
T d1p1ta_          88 EKN   90 (104)
T ss_dssp             TTH
T ss_pred             CCC
Confidence            443

>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=99.70  E-value=2.9e-17  Score=128.40  Aligned_cols=81  Identities=23%  Similarity=0.463  Sum_probs=74.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||..+|+++|.++|..||+|..|.++.+..+  .+|||||+|.+.++|..|+ .+||..|.|+.|+|.+
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            445689999999999999999999999999999999998765  4899999999999999999 6999999999999999


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +.++
T Consensus        83 a~~~   86 (90)
T d2cqia1          83 ATTP   86 (90)
T ss_dssp             CCCT
T ss_pred             cCCC
Confidence            8643

>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=99.70  E-value=1.8e-17  Score=125.63  Aligned_cols=75  Identities=21%  Similarity=0.380  Sum_probs=70.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       222 ~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +|||+|||+.+|+++|+++|.+||.|..|.++.++ +|.++|||||+|.+.++|..|+ .|||..+.|++|.|.++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999886 6899999999999999999999 699999999999998753

>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=99.70  E-value=3.7e-17  Score=125.62  Aligned_cols=79  Identities=32%  Similarity=0.496  Sum_probs=75.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..|++.|||. .|.|++|.|.++++
T Consensus         3 t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~-~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           3 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGI-TVRNKRLKVSYARP   81 (82)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCC-EECCEEEEEEEcCC
Confidence            68999999999999999999999999999999998889999999999999999999999999996 79999999999864

>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=99.70  E-value=3.7e-17  Score=139.42  Aligned_cols=82  Identities=24%  Similarity=0.470  Sum_probs=77.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||+.+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|| .|||..|.|+.|.|.++.
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            3478999999999999999999999999999999999999999999999999999999999 599999999999999986


Q ss_pred             ccc
Q 007742          298 AEK  300 (591)
Q Consensus       298 ~~~  300 (591)
                      ...
T Consensus       121 ~~~  123 (139)
T d1u6fa1         121 SGH  123 (139)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.69  E-value=1.1e-17  Score=129.53  Aligned_cols=81  Identities=14%  Similarity=0.233  Sum_probs=71.1

Q ss_pred             CCcEEEEeCCCCCCC-HHHHHHHHhcCCCeeEEEEeec-CCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          219 DQRTVFAYQMPLKAT-ERDVYEFFSKAGKVRDVRLIMD-RNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       219 ~~~~l~V~nLp~~~t-e~~l~~~f~~~G~i~~v~~~~d-~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      +.++|||+|||+.+| +++|+++|++||.|..|.|+.+ ..+|.++|||||+|.+.++|.+||+|||..|.|+.|.|.++
T Consensus         3 e~~~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           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            468999999999986 5669999999999999998764 56899999999999999999999999999999999999988


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      .++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.69  E-value=1.3e-17  Score=125.94  Aligned_cols=75  Identities=24%  Similarity=0.409  Sum_probs=72.1

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       222 ~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      +|||+|||+.+|+++|+++|..||.|..+.++.++.+|.++|||||+|.+.++|.+||++||+.|.|++|.|.++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999754

>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=99.69  E-value=7.2e-17  Score=126.86  Aligned_cols=84  Identities=23%  Similarity=0.493  Sum_probs=75.9

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEE
Q 007742          214 ADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVM  292 (591)
Q Consensus       214 ~~~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~  292 (591)
                      .+.....++|||+|||+.+|+++|.++|..||+|..|.++.+..+  ++|||||+|.+.++|..|+ .|||..|.|+.|.
T Consensus         5 ~~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~--~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~   82 (93)
T d2cq3a1           5 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIE   82 (93)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC--CcceeEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344556789999999999999999999999999999999988653  7999999999999999999 6999999999999


Q ss_pred             eccCccc
Q 007742          293 VKPSEAE  299 (591)
Q Consensus       293 v~~~~~~  299 (591)
                      |.++.+.
T Consensus        83 V~~A~~r   89 (93)
T d2cq3a1          83 VNNATAR   89 (93)
T ss_dssp             EEECCSS
T ss_pred             EEecCcC
Confidence            9998654

>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=99.69  E-value=9.5e-17  Score=128.44  Aligned_cols=84  Identities=30%  Similarity=0.445  Sum_probs=78.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ++++.+|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|..||..|||. .|.|+.|.|.
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~-~~~g~~i~V~   93 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGF-QIGMKRLKVQ   93 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCC-EECCEEEEEE
Confidence            345678999999999999999999999999999999999889999999999999999999999999996 6999999999


Q ss_pred             EecCC
Q 007742          398 SVTDH  402 (591)
Q Consensus       398 ~~~~~  402 (591)
                      ++.+.
T Consensus        94 ~a~~k   98 (102)
T d2cpza1          94 LKRSK   98 (102)
T ss_dssp             CCCCS
T ss_pred             EeCCC
Confidence            98654

>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=99.69  E-value=7.8e-17  Score=125.22  Aligned_cols=80  Identities=33%  Similarity=0.542  Sum_probs=76.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ..+|||+|||..+++++|.++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.|+.
T Consensus         7 ~~~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_           7 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA-EIMGQTIQVDWCF   85 (88)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEESE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCC-EECCEEEEEEEec
Confidence            379999999999999999999999999999999999889999999999999999999999999996 7999999999986


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      .
T Consensus        86 ~   86 (88)
T d1rk8a_          86 V   86 (88)
T ss_dssp             E
T ss_pred             C
Confidence            4

>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=99.68  E-value=1.9e-17  Score=127.49  Aligned_cols=77  Identities=26%  Similarity=0.435  Sum_probs=71.8

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeeE-EEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          223 VFAYQMPLKATERDVYEFFSKAGKVRD-VRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       223 l~V~nLp~~~te~~l~~~f~~~G~i~~-v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      |||+|||+++|+++|.++|.+||.|.. +.++.+..+|.++|||||+|.+.++|..|| .|+|..+.|++|.|.++.+.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            799999999999999999999999866 478889999999999999999999999999 59999999999999998653

>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=99.68  E-value=7.6e-17  Score=125.66  Aligned_cols=80  Identities=40%  Similarity=0.671  Sum_probs=76.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||+.+++++|+++|++||+|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++.
T Consensus         5 ~~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           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVNLAK   83 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTE-EETTEEEEEEECC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCC-EECCEEEEEEEeC
Confidence            489999999999999999999999999999999999888999999999999999999999999995 7999999999986


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      +
T Consensus        84 p   84 (89)
T d2cqba1          84 P   84 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=4.3e-17  Score=125.61  Aligned_cols=77  Identities=19%  Similarity=0.319  Sum_probs=72.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~  297 (591)
                      .++|||+|||+.+|+++|.++|+.||+|..|.|..+. +|.++|||||+|.+.++|.+||++++..+.|+.|.|.+..
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            5899999999999999999999999999999998775 6899999999999999999999999999999999998764

>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=99.68  E-value=1e-16  Score=123.20  Aligned_cols=79  Identities=37%  Similarity=0.536  Sum_probs=75.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||+.+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++++
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~-~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGL-RLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-EETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEeeC
Confidence            57999999999999999999999999999999998888999999999999999999999999996 79999999999864

>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=99.68  E-value=6.2e-17  Score=123.37  Aligned_cols=77  Identities=31%  Similarity=0.521  Sum_probs=73.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       323 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .|||+|||+.+++++|+++|+.||+|..|.|+.+..++.++|||||+|.+.++|..|++.|+|. .+.|++|+|.+++
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~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFD-VIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTC-EETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCC-EECCEEEEEEEeC
Confidence            5999999999999999999999999999999999889999999999999999999999999997 6999999999874

>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=99.68  E-value=4.2e-17  Score=126.15  Aligned_cols=76  Identities=25%  Similarity=0.435  Sum_probs=70.7

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCC---CccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSR---RSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       223 l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g---~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      |||+|||+.+|+++|+++|++||.|..|.|+.++.++   .++|||||+|.+.++|..|+ .|||..|.|+.|.|.++..
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            7999999999999999999999999999999987765   46899999999999999999 6999999999999998743

>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=99.67  E-value=1.8e-16  Score=124.44  Aligned_cols=80  Identities=30%  Similarity=0.455  Sum_probs=75.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +++|||+|||+.+++++|.++|++||+|..|.|+.+..++.++|||||+|.+.++|..|++.|||. .|.|++|.|.++.
T Consensus         7 s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~-~~~gr~i~V~~a~   85 (93)
T d1h2vz_           7 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGT-RLDDRIIRTDWDA   85 (93)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTS-EETTEECEEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEcC
Confidence            479999999999999999999999999999999999889999999999999999999999999996 6999999999975


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      .
T Consensus        86 ~   86 (93)
T d1h2vz_          86 G   86 (93)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.67  E-value=1.5e-16  Score=124.28  Aligned_cols=81  Identities=33%  Similarity=0.488  Sum_probs=76.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ..+|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..||+.|+|. .|.|+.|.|.+++
T Consensus         8 ~~~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           8 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGF-GYDHLILNVEWAK   86 (90)
T ss_dssp             SEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTC-EETTEECEEEESS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCC-EECCEEEEEEeee
Confidence            378999999999999999999999999999999999888999999999999999999999999996 7999999999987


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      +.
T Consensus        87 p~   88 (90)
T d2cq0a1          87 PS   88 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.67  E-value=2.4e-16  Score=125.56  Aligned_cols=82  Identities=37%  Similarity=0.596  Sum_probs=77.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +.+|||+|||+.+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|..||+.|||. .|.|+.|.|.++.
T Consensus         8 ~~~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_           8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQ-VFQGRMLHVLPST   86 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTE-ESSSCEEEEEECC
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCC-EECCEEEEEEECC
Confidence            478999999999999999999999999999999999889999999999999999999999999996 7999999999987


Q ss_pred             CCC
Q 007742          401 DHV  403 (591)
Q Consensus       401 ~~~  403 (591)
                      ...
T Consensus        87 ~~~   89 (99)
T d1whwa_          87 IKK   89 (99)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            643

>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=99.67  E-value=1.2e-16  Score=125.42  Aligned_cols=81  Identities=35%  Similarity=0.583  Sum_probs=76.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|++|.|.++.
T Consensus         9 ~~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           9 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMI-KLYGKPIRVNKAS   87 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSC-BCSSCBCEEEETT
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCC-EECCEEEEEEEcC
Confidence            479999999999999999999999999999999999889999999999999999999999999996 6999999999986


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      +.
T Consensus        88 ~~   89 (93)
T d1x5ua1          88 AH   89 (93)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.67  E-value=2e-16  Score=121.58  Aligned_cols=75  Identities=35%  Similarity=0.591  Sum_probs=71.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      +++|||+|||+.+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||. .|.|++|.|
T Consensus         9 ~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~gr~i~V   83 (83)
T d2cqca1           9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM-ELDGRRIRV   83 (83)
T ss_dssp             GGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTE-EETTEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCC-EECCEEeEC
Confidence            479999999999999999999999999999999999888999999999999999999999999995 799999987

>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=99.67  E-value=1.1e-16  Score=128.94  Aligned_cols=84  Identities=31%  Similarity=0.474  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecC-CCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR-NSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~-~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~  294 (591)
                      +..+.++|||+|||+.+|+++|+++|..|| |+.+.++.+. .+|.++|||||+|.+.++|.+|+.||+..|.|+.|.|.
T Consensus        11 p~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVD   89 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEE
Confidence            344569999999999999999999999999 6777777655 57889999999999999999888999999999999999


Q ss_pred             cCcccc
Q 007742          295 PSEAEK  300 (591)
Q Consensus       295 ~~~~~~  300 (591)
                      ++....
T Consensus        90 ~a~~~~   95 (104)
T d1wi8a_          90 VADQAQ   95 (104)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            886543

>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=99.66  E-value=1.9e-16  Score=126.31  Aligned_cols=82  Identities=22%  Similarity=0.401  Sum_probs=74.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHc------CCccCCee
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALS------GQLLLGQP  290 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~------g~~i~g~~  290 (591)
                      .++++|||+|||+.+|+++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|..|| .+|      |..|.|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            35689999999999999999999999999999999999999999999999999999999999 465      56688999


Q ss_pred             EEeccCccc
Q 007742          291 VMVKPSEAE  299 (591)
Q Consensus       291 i~v~~~~~~  299 (591)
                      |.|.++.+.
T Consensus        86 l~v~~a~~k   94 (98)
T d1x4ha1          86 LKVDLAVTR   94 (98)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEECCCC
Confidence            999988653

>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=99.66  E-value=1.5e-16  Score=127.60  Aligned_cols=84  Identities=18%  Similarity=0.372  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCee--------EEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCcc
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVR--------DVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL  286 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~--------~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i  286 (591)
                      .....++|||+|||+.+|+++|.++|..||.|.        .+.+..+..+|.++|||||+|.+.++|..|| .|||..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            344678999999999999999999999999873        5777788889999999999999999999999 6999999


Q ss_pred             CCeeEEeccCccc
Q 007742          287 LGQPVMVKPSEAE  299 (591)
Q Consensus       287 ~g~~i~v~~~~~~  299 (591)
                      .|+.|.|.++...
T Consensus        84 ~gr~i~V~~a~~~   96 (101)
T d2cpea1          84 QGSKLKVSLARKK   96 (101)
T ss_dssp             TTEECEEECSSCC
T ss_pred             CCEEEEEEEcCCC
Confidence            9999999998654

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.3e-16  Score=129.53  Aligned_cols=80  Identities=24%  Similarity=0.436  Sum_probs=72.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ...+++|||+|||+.+|+++|.++|.+||.|.+|.+..+   +.++|||||+|.+.++|..|+ .|||..|.|+.|.|.+
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   80 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY   80 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999999865   557999999999999999999 6999999999999998


Q ss_pred             Cccc
Q 007742          296 SEAE  299 (591)
Q Consensus       296 ~~~~  299 (591)
                      +...
T Consensus        81 a~~~   84 (114)
T d2f9da1          81 YNAN   84 (114)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            7543

>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=99.65  E-value=9.7e-17  Score=125.03  Aligned_cols=78  Identities=24%  Similarity=0.437  Sum_probs=72.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~  298 (591)
                      ..+|||+|||+.+|+++|+++|..||.|..+.|+.+..  .++|||||+|.+.++|..|| .|||..|.|+.|.|.++.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            36899999999999999999999999999999998864  47899999999999999999 6999999999999998865


Q ss_pred             c
Q 007742          299 E  299 (591)
Q Consensus       299 ~  299 (591)
                      .
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.65  E-value=3.7e-16  Score=122.89  Aligned_cols=82  Identities=35%  Similarity=0.636  Sum_probs=74.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccC-CCCCcccEEEEEeCCHHHHHHHHHHh-cCCeeeCCeEEEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDI-ETGQCKGFGFVQFAQLEHAKAAQSAL-NGKLEIVGRTLKVSS  398 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~-~~~~~~g~a~Vef~~~~~a~~a~~~l-~g~~~~~g~~l~v~~  398 (591)
                      +.+|||+|||+.+++++|+++|..||.|..|.|+.+. .+|.++|||||+|.+.++|..||..| ||. .|.|++|.|.+
T Consensus         8 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~-~~~Gr~l~V~~   86 (94)
T d2cpha1           8 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHST-HLYGRRLVLEW   86 (94)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCC-BSSSCBCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCc-EECCEEEEEEE
Confidence            4789999999999999999999999999999998774 37889999999999999999999998 775 69999999999


Q ss_pred             ecCCC
Q 007742          399 VTDHV  403 (591)
Q Consensus       399 ~~~~~  403 (591)
                      +....
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87543

>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=99.64  E-value=3.4e-16  Score=118.46  Aligned_cols=76  Identities=30%  Similarity=0.519  Sum_probs=72.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       323 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .|||+|||+.+++++|+++|++||+|..|.|..+. ++.++|||||+|.+.++|..|++.|||. .+.|++|.|.+++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGV-PLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTC-EETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEee
Confidence            59999999999999999999999999999999886 8889999999999999999999999997 6999999999874

>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=99.64  E-value=1.9e-16  Score=122.07  Aligned_cols=79  Identities=28%  Similarity=0.560  Sum_probs=75.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ..|||+|||..+++++|+++|++||+|..|.|+.++.+|.++|||||+|.++++|..|+..|||. .|.|++|.|.++..
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~-~l~g~~l~V~~A~~   80 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM-QLGDKKLLVQRASV   80 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSC-CCSSSCCEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEECCC
Confidence            47999999999999999999999999999999999889999999999999999999999999996 69999999999864

>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=99.64  E-value=3.1e-16  Score=126.05  Aligned_cols=82  Identities=15%  Similarity=0.157  Sum_probs=75.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~  297 (591)
                      .....|||+|||+.+|+++|+++|..+|.|..+.++.+..++.++|||||+|.+.++|.+|+.+|+..|.|+.|.|.++.
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEECC
Confidence            34568999999999999999999999999998778888888999999999999999999999999999999999998776


Q ss_pred             cc
Q 007742          298 AE  299 (591)
Q Consensus       298 ~~  299 (591)
                      ..
T Consensus        93 ~~   94 (104)
T d1wg5a_          93 RA   94 (104)
T ss_dssp             TT
T ss_pred             HH
Confidence            54

>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=99.64  E-value=2e-16  Score=126.33  Aligned_cols=80  Identities=24%  Similarity=0.485  Sum_probs=73.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ....++|||+|||+.+|+++|.++|.+||.|..+.++.+. ++.++|||||+|.+.++|.+|| .|||..|.|+++.|.+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            3456899999999999999999999999999999998874 6899999999999999999999 6999999999999877


Q ss_pred             Cc
Q 007742          296 SE  297 (591)
Q Consensus       296 ~~  297 (591)
                      +.
T Consensus        94 ~~   95 (101)
T d1x5oa1          94 TE   95 (101)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>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=99.64  E-value=2.4e-17  Score=128.75  Aligned_cols=81  Identities=12%  Similarity=0.237  Sum_probs=73.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      +....+|||+|||+.+|+++|+++|..||.|..+.++.+ .+|.++|||||+|.+.++|..||+|||..|.|+.|.|.++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEec
Confidence            335679999999999999999999999999998888654 5789999999999999999999999999999999999987


Q ss_pred             cc
Q 007742          297 EA  298 (591)
Q Consensus       297 ~~  298 (591)
                      ..
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.64  E-value=5.1e-16  Score=119.79  Aligned_cols=78  Identities=35%  Similarity=0.488  Sum_probs=72.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC--eEEEEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG--RTLKVSS  398 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g--~~l~v~~  398 (591)
                      .++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..|++.|||. .+.|  ++|.|.+
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~~~l~V~~   84 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV-IPEGGSQPLSVRL   84 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-CCTTCSSCCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCC-EeCCCCeEEEEEE
Confidence            368999999999999999999999999999999999889999999999999999999999999996 5766  8899987


Q ss_pred             e
Q 007742          399 V  399 (591)
Q Consensus       399 ~  399 (591)
                      +
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.64  E-value=2.9e-16  Score=120.08  Aligned_cols=79  Identities=22%  Similarity=0.309  Sum_probs=67.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|..|+..|||. .|.|++|.|.++.+
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~-~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL-KIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTC-EETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEccC
Confidence            68999999999999999999999999988888777778899999999999999999999999996 79999999998754

>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=99.63  E-value=4.2e-16  Score=120.15  Aligned_cols=77  Identities=31%  Similarity=0.542  Sum_probs=71.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCC--eEEEEEEe
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVG--RTLKVSSV  399 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g--~~l~v~~~  399 (591)
                      ++|||+|||+.+++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|..|++.|||. .+.|  ++|.|.|+
T Consensus         7 ~~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           7 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ-KPSGATEPITVKFA   85 (85)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC-CCTTCSSCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCC-EeCCCCEEEEEEeC
Confidence            68999999999999999999999999999999999888999999999999999999999999997 5887  56888774

>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=99.63  E-value=6.5e-16  Score=118.51  Aligned_cols=79  Identities=14%  Similarity=0.231  Sum_probs=72.3

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccccc-CC
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWF-AR  572 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~-~g  572 (591)
                      ..+|+++|+|.||  |..++        +++|.++|+.||.|..|.+....+|+|||+|.+.++|..|+..|||..| +|
T Consensus         4 ~~pP~~tl~V~nL--p~~~t--------~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~   73 (83)
T d2b0ga1           4 EQPPNQILFLTNL--PEETN--------EMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPT   73 (83)
T ss_dssp             CCSCCSEEEEESC--CTTCC--------HHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTT
T ss_pred             CCCCCCEEEEECC--CCCCC--------HHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCC
Confidence            3577889999999  88887        8999999999999999999877889999999999999999999999998 57


Q ss_pred             eEEEEEEeCc
Q 007742          573 RLISAIFMKP  582 (591)
Q Consensus       573 ~~l~v~~~~~  582 (591)
                      +.|.|.|++.
T Consensus        74 ~~i~v~~akk   83 (83)
T d2b0ga1          74 HAMKITFAKK   83 (83)
T ss_dssp             CBCEEEECCC
T ss_pred             cEEEEEEecC
Confidence            9999999863

>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=99.63  E-value=6.8e-17  Score=129.89  Aligned_cols=84  Identities=17%  Similarity=0.330  Sum_probs=77.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEec
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK  294 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~  294 (591)
                      +..++++|||+|||..+|+++|.++|..||.|..+.++.+..+|.++|||||+|.+.++|..|| .|||..|.|+.|.|.
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   93 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE   93 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3445789999999999999999999999999999999988888999999999999999999999 699999999999999


Q ss_pred             cCccc
Q 007742          295 PSEAE  299 (591)
Q Consensus       295 ~~~~~  299 (591)
                      ++.+.
T Consensus        94 ~ak~k   98 (102)
T d2cpxa1          94 FGKNK   98 (102)
T ss_dssp             ECCCC
T ss_pred             eCCCc
Confidence            98654

>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=99.63  E-value=3.7e-16  Score=117.02  Aligned_cols=74  Identities=19%  Similarity=0.274  Sum_probs=68.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      .+|||+|||+.+|+++|+++|..||.|..|.++.++..  .+|||||+|.+.++|.+||.+|+..|.|++|.|...
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            47999999999999999999999999999999998764  468999999999999999999999999999999653

>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=99.63  E-value=4.6e-16  Score=122.67  Aligned_cols=75  Identities=21%  Similarity=0.328  Sum_probs=69.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||..+|+++|.++|.+||.|.+|.++.+      +|||||+|.+.++|..|+ .|||..|.|+.|+|.|+.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3579999999999999999999999999999999864      789999999999999999 699999999999999986


Q ss_pred             cc
Q 007742          298 AE  299 (591)
Q Consensus       298 ~~  299 (591)
                      ..
T Consensus        91 ~~   92 (96)
T d1x4ga1          91 ES   92 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.63  E-value=6e-16  Score=123.05  Aligned_cols=78  Identities=22%  Similarity=0.436  Sum_probs=73.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||+.+++++|+++|+.||.|..|.|+.+..+|.++|||||+|.+.++|.+|+ .|||. .|.|+.|.|.+++
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 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQ-RLLGVPIIVQASQ   95 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTE-EETTEEEEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCC-EECCEEEEEEECC
Confidence            378999999999999999999999999999999999889999999999999999999999 59995 7999999999864

>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=99.63  E-value=1.6e-15  Score=129.15  Aligned_cols=81  Identities=40%  Similarity=0.615  Sum_probs=76.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||+.+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..||..|||. .|.|+.|.|.++.
T Consensus        42 ~~~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          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF-NILNKRLKVALAA  120 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTE-ECSSCEEEEEESS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCC-EECCEEEEEEEcC
Confidence            478999999999999999999999999999999999889999999999999999999999999995 7999999999986


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      ..
T Consensus       121 ~~  122 (139)
T d1u6fa1         121 SG  122 (139)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.62  E-value=4.4e-16  Score=123.36  Aligned_cols=89  Identities=28%  Similarity=0.475  Sum_probs=79.0

Q ss_pred             CCCcceEEEeccCCCCCC-CCchhhhhHHHHHHHHhccccceEEEEEec-CCCeeEEEEeCCHHHHHHHHHHhcccccCC
Q 007742          495 GSPSECLLLKNMFDPAME-TDPDFDLEIQGDVEEECSKYGRVKHIYVDK-RSAGFVYLRFESTEAAASAQRAMHMRWFAR  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~-~~~~~~~~~~edl~~~f~~~G~V~~v~l~~-~~~g~afV~F~~~e~A~~A~~~l~g~~~~g  572 (591)
                      ...+++|+|.||++|..+ .++.++.+|.++|.++|++||.|..|.+.. .+.|+|||+|.+.++|.+|+..|||+.|+|
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~g   84 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG   84 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECC
Confidence            457789999999888764 356678899999999999999999998854 468999999999999999999999999999


Q ss_pred             eEEEEEEeCch
Q 007742          573 RLISAIFMKPE  583 (591)
Q Consensus       573 ~~l~v~~~~~~  583 (591)
                      ++|.|.|+.+.
T Consensus        85 r~i~v~~~~g~   95 (99)
T d2dita1          85 RQITAQAWDGT   95 (99)
T ss_dssp             EECEEEECCSC
T ss_pred             EEEEEEEeCCc
Confidence            99999998654

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=1.2e-16  Score=119.29  Aligned_cols=70  Identities=20%  Similarity=0.394  Sum_probs=67.2

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEE
Q 007742          223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVM  292 (591)
Q Consensus       223 l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~  292 (591)
                      |||+|||+.+|+++|.++|.+||.|..+.++.++.++.++|||||+|.+.++|..|+ .|||..|.|+.|+
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            799999999999999999999999999999999999999999999999999999999 6999999998764

>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=99.62  E-value=1.1e-15  Score=118.69  Aligned_cols=79  Identities=34%  Similarity=0.516  Sum_probs=72.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +.+|||+|||+.+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..||+.++   .|+|+.|.|.++.
T Consensus         8 ~~~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           8 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH---MIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE---EETTEEEEEECCC
T ss_pred             CCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC---ccCCEEeEEEeCC
Confidence            4789999999999999999999999999999999998899999999999999999999996433   5899999999876


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      +.
T Consensus        85 ~k   86 (90)
T d2cqga1          85 SK   86 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>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=99.62  E-value=1.5e-15  Score=118.42  Aligned_cols=78  Identities=35%  Similarity=0.579  Sum_probs=71.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +++|||+|||..+++++|+++|+.||+|..|.|+.+..+  .+|||||+|.+.++|..|+..|+|. .|.|+.|.|.++.
T Consensus         8 ~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~-~~~g~~i~v~~a~   84 (90)
T d2cqia1           8 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGR-KILGKEVKVNWAT   84 (90)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTE-EETTEEEEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCC-EECCEEEEEEEcC
Confidence            489999999999999999999999999999999887544  4789999999999999999999995 7999999999986


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      +
T Consensus        85 ~   85 (90)
T d2cqia1          85 T   85 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=1e-15  Score=117.39  Aligned_cols=77  Identities=32%  Similarity=0.582  Sum_probs=72.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ++|||+|||+.+++++|.++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|++ +++. .|.|+.|.|..+.
T Consensus         7 ~~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           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPH-KVDGRVVEPKRAV   83 (84)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSC-EETTEECEEEECC
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCC-EECCEEEEEEeee
Confidence            789999999999999999999999999999999999899999999999999999999995 6775 6999999998763

>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=99.62  E-value=5e-16  Score=121.42  Aligned_cols=81  Identities=37%  Similarity=0.676  Sum_probs=76.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      .+|||+|||+.+++++|+++|++||.|..|.++.+..++.++|||||+|.+.++|..|+..|+|. .|.|+.|.|.++..
T Consensus         6 ~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~-~~~g~~l~V~~a~~   84 (90)
T d1x5sa1           6 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGK-SVDGRQIRVDQAGK   84 (90)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTC-CTTSCCCEEEEEEC
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCC-EECCEEEEEEEcCC
Confidence            78999999999999999999999999999999988888999999999999999999999999996 79999999999865


Q ss_pred             CC
Q 007742          402 HV  403 (591)
Q Consensus       402 ~~  403 (591)
                      ..
T Consensus        85 ~~   86 (90)
T d1x5sa1          85 SS   86 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.62  E-value=2.7e-15  Score=117.68  Aligned_cols=79  Identities=32%  Similarity=0.599  Sum_probs=72.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||+.+++++|+++|..||+|..|.++.+.  +.++|||||+|.+.++|..|+..|||. .|.|+.|.|.+++
T Consensus        11 ~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~-~~~g~~l~V~~A~   87 (93)
T d2cq3a1          11 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGT-VVEGRKIEVNNAT   87 (93)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTC-EETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCC-EECCEEEEEEecC
Confidence            4789999999999999999999999999999998875  336899999999999999999999996 7999999999987


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      +.
T Consensus        88 ~r   89 (93)
T d2cq3a1          88 AR   89 (93)
T ss_dssp             SS
T ss_pred             cC
Confidence            64

>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=99.61  E-value=4.4e-16  Score=124.61  Aligned_cols=81  Identities=22%  Similarity=0.278  Sum_probs=72.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      .....+|||+|||+.+|+++|+++|..||. +.|.++.+.. |..+|||||+|.+.++|.+||++|++.|.|+.|.|.++
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~-g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPD-GRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSS-SCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecC-CcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            445689999999999999999999999984 5777777754 78999999999999999999999999999999999887


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      ...
T Consensus        90 ~~~   92 (102)
T d1weza_          90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.61  E-value=1.3e-15  Score=120.08  Aligned_cols=78  Identities=21%  Similarity=0.326  Sum_probs=70.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ...++|||+|||+.+|+++|+++|..||.|..+.+..+   +.++|||||+|.+.++|..|| .||+..|.|++|+|.++
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            34589999999999999999999999999999887654   457899999999999999999 69999999999999997


Q ss_pred             cc
Q 007742          297 EA  298 (591)
Q Consensus       297 ~~  298 (591)
                      ..
T Consensus        89 ~~   90 (95)
T d1x4aa1          89 RS   90 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.61  E-value=2.9e-16  Score=126.15  Aligned_cols=82  Identities=16%  Similarity=0.210  Sum_probs=73.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCcc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEA  298 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~~  298 (591)
                      ...+|||+|||+.+|+++|.++|..||.|..+.++....+|.++|||||+|.+.++|.+||.+|+..|.|+.|.|.++..
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECH
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECCH
Confidence            34679999999999999999999999999876666666789999999999999999999999999999999999987654


Q ss_pred             cc
Q 007742          299 EK  300 (591)
Q Consensus       299 ~~  300 (591)
                      ..
T Consensus        87 ~~   88 (103)
T d2cpya1          87 ED   88 (103)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>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=99.61  E-value=1.9e-15  Score=120.95  Aligned_cols=80  Identities=35%  Similarity=0.504  Sum_probs=74.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .++|||+|||+.+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|..|++.+++  .|.|+.|.|.++.
T Consensus        10 ~~~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          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP--IIDGRKANVNLAY   87 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC--EETTEECEEEEST
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC--cCCCEEEEEEEcC
Confidence            36799999999999999999999999999999999988899999999999999999999988876  4899999999875


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      ..
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=99.61  E-value=7.7e-16  Score=118.31  Aligned_cols=78  Identities=31%  Similarity=0.572  Sum_probs=71.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEE-EEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecCC
Q 007742          324 LYVGNLHFNMTETQLRKLFEPFGPVELV-QLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH  402 (591)
Q Consensus       324 l~v~nl~~~~~~~~l~~~f~~~g~i~~v-~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~~  402 (591)
                      |||+|||+.+++++|+++|++||.|..+ .++.+..++.++|||||+|.+.++|..|+..|+|. .|.|++|.|.++.+.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~-~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQ-YLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTC-EETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCc-EECCEEEEEEEecCC
Confidence            7999999999999999999999998654 77888888999999999999999999999999996 799999999998643

>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=99.60  E-value=1.7e-15  Score=120.73  Aligned_cols=79  Identities=32%  Similarity=0.563  Sum_probs=73.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||+.+++++|+++|.+||.|..+.|+.+..++.++|||||+|.+.++|..|| .+++. .|.|+.|.|.++.+
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al-~~~~~-~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPH-SIDGRVVEPKRAVA   98 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHH-TSCSE-EETTEEEEEECCSS
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHH-HhCCC-eECCEEEEEEECcc
Confidence            78999999999999999999999999999999999888999999999999999999999 57885 69999999998865


Q ss_pred             C
Q 007742          402 H  402 (591)
Q Consensus       402 ~  402 (591)
                      .
T Consensus        99 k   99 (103)
T d1x4ba1          99 R   99 (103)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.60  E-value=5.8e-16  Score=124.61  Aligned_cols=79  Identities=41%  Similarity=0.735  Sum_probs=74.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||+.+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|..|++.|+|. .|.|+.|.|.++..
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~-~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGR-EFSGRALRVDNAAS   87 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSB-SCSSSCBEEEETTC
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCC-EECCEEEEEEECCC
Confidence            68999999999999999999999999999999999888999999999999999999999999996 69999999998753

>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=99.60  E-value=3.7e-16  Score=121.45  Aligned_cols=76  Identities=18%  Similarity=0.332  Sum_probs=68.8

Q ss_pred             CCcEEEEeCCCCCCCHHHH---HHHHhcCCCeeEEEEeecCCCCCcc---ceEEEEecCcchHHHHH-HHcCCccCCeeE
Q 007742          219 DQRTVFAYQMPLKATERDV---YEFFSKAGKVRDVRLIMDRNSRRSK---GVGYIEFYDVMSVPMAI-ALSGQLLLGQPV  291 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l---~~~f~~~G~i~~v~~~~d~~~g~~~---G~afV~F~~~e~A~~Al-~l~g~~i~g~~i  291 (591)
                      +.++|||+|||+.+|+++|   .++|.+||.|..|.++.++.++.++   |||||+|.+.++|..|+ .|||..+.|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3467999999999999999   6789999999999999998776554   99999999999999999 699999999999


Q ss_pred             Eec
Q 007742          292 MVK  294 (591)
Q Consensus       292 ~v~  294 (591)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            873

>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=99.60  E-value=8.5e-16  Score=121.54  Aligned_cols=82  Identities=21%  Similarity=0.308  Sum_probs=71.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCC-eeEEEEeecC-CCCCccceEEEEecCcchHHHHH-HHcC--CccCCeeEEec
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGK-VRDVRLIMDR-NSRRSKGVGYIEFYDVMSVPMAI-ALSG--QLLLGQPVMVK  294 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~-i~~v~~~~d~-~~g~~~G~afV~F~~~e~A~~Al-~l~g--~~i~g~~i~v~  294 (591)
                      +|+|||+|||..+|+++|.++|..||. |..|.++.+. .+|.++|||||+|.+.++|..|+ .|++  ..+.|++|.|.
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            378999999999999999999999996 8999999875 46889999999999999999999 5654  45679999999


Q ss_pred             cCccccc
Q 007742          295 PSEAEKN  301 (591)
Q Consensus       295 ~~~~~~~  301 (591)
                      |+.+...
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9976443

>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=99.60  E-value=5.2e-16  Score=120.18  Aligned_cols=77  Identities=12%  Similarity=0.163  Sum_probs=68.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ...+|||+|||+.+|+++|.++|..||.|....++.+..+|.++|||||+|.+.++|.+|+ .||+..|.|++|.|..
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3577999999999999999999999999977544455567999999999999999999999 6999999999999975

>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=99.60  E-value=1.6e-15  Score=117.08  Aligned_cols=76  Identities=29%  Similarity=0.548  Sum_probs=70.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCC---CcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG---QCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       324 l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~---~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      |||+|||+.+++++|+++|++||.|..|.|+.+..++   .++|||||+|.+.++|..|++.|||. .|.|+.|.|.++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~-~~~g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGH-TVDGHKLEVRISE   79 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTC-EETTEECEEECSS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCC-EECCEEEEEEECC
Confidence            7999999999999999999999999999999876554   46899999999999999999999996 6999999999874

>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=99.60  E-value=1e-15  Score=118.02  Aligned_cols=75  Identities=25%  Similarity=0.382  Sum_probs=69.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +.++|||+|||+.+++++|+++|.+||.|..|.++.+      +|||||+|.+.++|..|+ .|||..|.|+.|.|.++.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3478999999999999999999999999999999854      689999999999999999 699999999999999986


Q ss_pred             cc
Q 007742          298 AE  299 (591)
Q Consensus       298 ~~  299 (591)
                      ..
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=8.8e-16  Score=115.08  Aligned_cols=74  Identities=30%  Similarity=0.583  Sum_probs=68.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       323 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      .|||+|||+.+++++|.++|++||+|..|.|+.++.++.++|||||+|.+.++|..||+ +++. .|.|+.|.|..
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~-~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEH-KLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCC-CBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCC-EECCCEEEeeE
Confidence            48999999999999999999999999999999999899999999999999999999995 7775 69999998854

>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=99.60  E-value=2.2e-15  Score=123.46  Aligned_cols=79  Identities=19%  Similarity=0.329  Sum_probs=72.0

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEec--CCCeeEEEEeCCHHHHHHHHHHhcccccCCe
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK--RSAGFVYLRFESTEAAASAQRAMHMRWFARR  573 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~--~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~  573 (591)
                      ..+++|+|+||  |..++        +++|.++|+.||.|..|.+..  .++|+|||+|.+.++|..|+..|||..|+|+
T Consensus         5 ~~~r~l~V~nL--p~~~t--------e~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr   74 (114)
T d2f9da1           5 EVNRILYIRNL--PYKIT--------AEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNR   74 (114)
T ss_dssp             TCCSEEEEESC--CTTCC--------HHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEECC--CCCCC--------HHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            45678999999  88888        899999999999999999864  4689999999999999999999999999999


Q ss_pred             EEEEEEeCchh
Q 007742          574 LISAIFMKPED  584 (591)
Q Consensus       574 ~l~v~~~~~~~  584 (591)
                      .|.|.|+.+..
T Consensus        75 ~l~V~~a~~~~   85 (114)
T d2f9da1          75 YLVVLYYNANR   85 (114)
T ss_dssp             ECEEEECCHHH
T ss_pred             EEEEEEcCCCc
Confidence            99999987654

>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=99.60  E-value=3e-15  Score=113.77  Aligned_cols=76  Identities=25%  Similarity=0.531  Sum_probs=71.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +.|||+|||+.+|+++|+++|+.||.|..+.+..+..++.++|||||+|.+.++|.+|+ .|+|. .|.|+.|.|..+
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 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYH-TVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCC-EETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCC-EECCEEEEEEEC
Confidence            79999999999999999999999999999999999889999999999999999999998 68996 699999999865

>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=99.59  E-value=6.3e-16  Score=116.30  Aligned_cols=76  Identities=26%  Similarity=0.458  Sum_probs=70.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      +.|||+|||+.+++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|.+|++ +++. .++|+.|.|..+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~-~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRH-ELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTC-CCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCC-EECCeEEEEEEC
Confidence            369999999999999999999999999999999999899999999999999999999995 7886 699999999764

>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=99.58  E-value=3.8e-15  Score=114.48  Aligned_cols=77  Identities=23%  Similarity=0.295  Sum_probs=71.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      ++|||+|||..+++++|.++|+.||+|..|.|..+. ++.++|||||+|.+.++|..|| .++|. .|.|+.|.|.+..+
T Consensus         7 rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al-~~~~~-~~~g~~l~v~~~~d   83 (85)
T d1zh5a2           7 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFV-ETPGQ-KYKETDLLILFKDD   83 (85)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHH-TCCCC-EETTEECEEEEGGG
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHH-HHCCC-EECCEEEEEEEcCC
Confidence            799999999999999999999999999999998775 8889999999999999999999 57885 79999999998755

>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=99.58  E-value=2.5e-15  Score=118.35  Aligned_cols=77  Identities=17%  Similarity=0.246  Sum_probs=70.4

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEE
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI  575 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l  575 (591)
                      ++.++|+|+||  |..++        +++|.++|+.||.|.+|.+.. .+|+|||+|.+.++|..|+..|||..|+|+.|
T Consensus        16 ~~~~~l~v~nL--~~~~t--------e~~L~~~F~~fG~i~~v~i~~-~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l   84 (96)
T d1x4ga1          16 PKNCTVYCGGI--ASGLT--------DQLMRQTFSPFGQIMEIRVFP-EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVV   84 (96)
T ss_dssp             SSCCEEEEECC--SSCCC--------HHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCEEEEcCC--CCCCC--------HHHHHHHHHHhCCceEEEEEe-cceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            44568999999  88777        899999999999999999985 48999999999999999999999999999999


Q ss_pred             EEEEeCch
Q 007742          576 SAIFMKPE  583 (591)
Q Consensus       576 ~v~~~~~~  583 (591)
                      .|.|+.+.
T Consensus        85 ~v~~ak~~   92 (96)
T d1x4ga1          85 KCYWGKES   92 (96)
T ss_dssp             EEECCCCC
T ss_pred             EEEEcCCC
Confidence            99998753

>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=99.58  E-value=1.5e-15  Score=120.10  Aligned_cols=78  Identities=23%  Similarity=0.420  Sum_probs=68.6

Q ss_pred             CCCCCCCcEEEEeCCC-CCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeE
Q 007742          214 ADPERDQRTVFAYQMP-LKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV  291 (591)
Q Consensus       214 ~~~~~~~~~l~V~nLp-~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i  291 (591)
                      .++....++|||+||| ..+++++|+++|.+||.|..|.|        ++|||||+|.+.++|.+|| .|||..|.|+.|
T Consensus         9 ~~~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (98)
T d1wf2a_           9 TDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVL   80 (98)
T ss_dssp             CCCSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEEC
T ss_pred             CCCCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3444556889999997 56789999999999999999988        3789999999999999999 599999999999


Q ss_pred             EeccCccc
Q 007742          292 MVKPSEAE  299 (591)
Q Consensus       292 ~v~~~~~~  299 (591)
                      .|.++...
T Consensus        81 ~V~~a~~~   88 (98)
T d1wf2a_          81 DINLAAEP   88 (98)
T ss_dssp             EEEETTSC
T ss_pred             EEEECCCC
Confidence            99998653

>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=99.58  E-value=2.1e-15  Score=117.27  Aligned_cols=78  Identities=26%  Similarity=0.439  Sum_probs=71.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      .+|||+|||+.+++++|+++|+.||.|..+.|+.+.  +.++|||||+|.+.++|..|++.|||. .|.|+.|.|.+++.
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 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGM-LLNDRKVFVGRFKS   85 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEE-EETTEEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCC-EECCEEEEEEECCC
Confidence            579999999999999999999999999999998875  346899999999999999999999995 79999999999865


Q ss_pred             C
Q 007742          402 H  402 (591)
Q Consensus       402 ~  402 (591)
                      .
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.58  E-value=5.1e-16  Score=126.48  Aligned_cols=83  Identities=22%  Similarity=0.350  Sum_probs=74.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccC
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~  296 (591)
                      ....++|||+|||+.+|+++|.++|..||.+..+.++.+..+|.++|||||+|.+.++|.+||.+||..|.|+.|.|.++
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEc
Confidence            34567999999999999999999999999998776777777899999999999999999999999999999999999876


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      ...
T Consensus        95 ~~~   97 (112)
T d1wela1          95 TKK   97 (112)
T ss_dssp             CHH
T ss_pred             ChH
Confidence            543

>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=99.58  E-value=2.7e-15  Score=115.99  Aligned_cols=75  Identities=17%  Similarity=0.293  Sum_probs=67.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||+.+|+++|+++|.+||.|..+.+.      .++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            45899999999999999999999999998877764      45899999999999999999 699999999999999986


Q ss_pred             cc
Q 007742          298 AE  299 (591)
Q Consensus       298 ~~  299 (591)
                      +.
T Consensus        81 P~   82 (86)
T d2cpda1          81 PV   82 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.57  E-value=7.6e-15  Score=116.79  Aligned_cols=82  Identities=29%  Similarity=0.494  Sum_probs=74.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcC-----CeeeCCeEEE
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG-----KLEIVGRTLK  395 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g-----~~~~~g~~l~  395 (591)
                      .++|||+|||+.+++++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|..||+.|++     ...+.|+.|.
T Consensus         8 ~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~   87 (98)
T d1x4ha1           8 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLK   87 (98)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEE
Confidence            47899999999999999999999999999999999888899999999999999999999999873     2468999999


Q ss_pred             EEEecCC
Q 007742          396 VSSVTDH  402 (591)
Q Consensus       396 v~~~~~~  402 (591)
                      |.++.+.
T Consensus        88 v~~a~~k   94 (98)
T d1x4ha1          88 VDLAVTR   94 (98)
T ss_dssp             EECCCCC
T ss_pred             EEECCCC
Confidence            9998653

>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=99.57  E-value=8.8e-16  Score=119.14  Aligned_cols=77  Identities=22%  Similarity=0.317  Sum_probs=68.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEeccCc
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~~~~  297 (591)
                      ..+++|||+|||+.+|+++|+++|.+||.|..|.+.     ..++|||||+|.+.++|..||. +++.|.|++|.|.++.
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCC
Confidence            356899999999999999999999999999999775     3468999999999999999985 7888999999999986


Q ss_pred             ccc
Q 007742          298 AEK  300 (591)
Q Consensus       298 ~~~  300 (591)
                      +..
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.57  E-value=2.6e-15  Score=122.06  Aligned_cols=78  Identities=15%  Similarity=0.178  Sum_probs=70.5

Q ss_pred             cceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEE
Q 007742          498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISA  577 (591)
Q Consensus       498 s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v  577 (591)
                      +.+|+|.|| +|..++        +++|.++|+.||.|..|.|..+.+|+|||+|.++++|.+|++.|||..|.|+.|.|
T Consensus         2 ~~~l~V~nL-~p~~~t--------e~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v   72 (109)
T d2adca1           2 NSVLLVSNL-NPERVT--------PQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRI   72 (109)
T ss_dssp             CSEEEEESC-CTTTCC--------HHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCEEEEeCC-CcccCC--------HHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            468999999 334466        89999999999999999998888999999999999999999999999999999999


Q ss_pred             EEeCchh
Q 007742          578 IFMKPED  584 (591)
Q Consensus       578 ~~~~~~~  584 (591)
                      .|+....
T Consensus        73 ~~s~~~~   79 (109)
T d2adca1          73 TLSKHQN   79 (109)
T ss_dssp             ECCSCCC
T ss_pred             EECCCCC
Confidence            9986543

>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=99.57  E-value=1.6e-15  Score=118.60  Aligned_cols=79  Identities=18%  Similarity=0.396  Sum_probs=70.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHH----HHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEe
Q 007742          219 DQRTVFAYQMPLKATERDVYE----FFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV  293 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~----~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v  293 (591)
                      ++++|||+|||+.+|+++|++    +|.+||.|..|.+..   ++.++|||||+|.+.++|..|+ .+||..+.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            568999999999999999864    579999999988764   4668999999999999999999 69999999999999


Q ss_pred             ccCcccc
Q 007742          294 KPSEAEK  300 (591)
Q Consensus       294 ~~~~~~~  300 (591)
                      .++....
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9986543

>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=99.57  E-value=5.3e-15  Score=113.33  Aligned_cols=77  Identities=26%  Similarity=0.358  Sum_probs=68.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeee-CCeEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI-VGRTLKV  396 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~-~g~~l~v  396 (591)
                      .|++++|||+|||..+++++|.++|+.||.|..|.++.+.     +|||||+|.+.++|..|+..|+|. .| .|+.|.|
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~-~~~~~~~i~v   78 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGF-KITPTHAMKI   78 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTC-BSSTTCBCEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCc-EeCCCcEEEE
Confidence            4556899999999999999999999999999999997543     689999999999999999999996 45 5799999


Q ss_pred             EEec
Q 007742          397 SSVT  400 (591)
Q Consensus       397 ~~~~  400 (591)
                      .|++
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9975

>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=99.56  E-value=1.6e-15  Score=117.32  Aligned_cols=73  Identities=16%  Similarity=0.213  Sum_probs=66.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      .+|||+|||+.+|+++|.++|.+||.|..+.++.       .|||||+|.+.++|.+|| .|||..|.|+.|.|.+....
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            3699999999999999999999999999999864       389999999999999999 69999999999999887544


Q ss_pred             c
Q 007742          300 K  300 (591)
Q Consensus       300 ~  300 (591)
                      .
T Consensus        74 ~   74 (87)
T d3begb1          74 V   74 (87)
T ss_dssp             E
T ss_pred             c
Confidence            3

>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=99.56  E-value=1.3e-14  Score=114.20  Aligned_cols=80  Identities=25%  Similarity=0.414  Sum_probs=71.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      ...+++|||+|||+.+++++|+++|..||.|..+.+..+   +.++|||||+|.+.++|..||..|||. .|.|++|.|.
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~-~~~g~~l~V~   86 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGY-DYDGYRLRVE   86 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTC-EETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCC-EECCEEEEEE
Confidence            344578999999999999999999999999999887643   456899999999999999999999996 7999999999


Q ss_pred             EecC
Q 007742          398 SVTD  401 (591)
Q Consensus       398 ~~~~  401 (591)
                      +++.
T Consensus        87 ~a~~   90 (95)
T d1x4aa1          87 FPRS   90 (95)
T ss_dssp             CCCC
T ss_pred             eccC
Confidence            8754

>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=99.56  E-value=3e-15  Score=113.50  Aligned_cols=74  Identities=18%  Similarity=0.283  Sum_probs=67.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ..+++|||+||+  +|+++|+++|++||.|..|.+..      .+|||||+|.+.++|..|+ .|||..|.|++|+|.|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET------TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc------CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456899999996  89999999999999999999874      4689999999999999999 79999999999999998


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      .++
T Consensus        75 ~~~   77 (79)
T d2bz2a1          75 RKQ   77 (79)
T ss_dssp             CSS
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=99.56  E-value=9e-15  Score=117.03  Aligned_cols=81  Identities=33%  Similarity=0.477  Sum_probs=73.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCee--------EEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVE--------LVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGR  392 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~--------~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~  392 (591)
                      ..+|||+|||..+++++|.++|..||.|.        .+.+..+..++.++|||||+|.+.++|..||+.|||. .|.|+
T Consensus         8 ~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~-~~~gr   86 (101)
T d2cpea1           8 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK-DFQGS   86 (101)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC-EETTE
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC-EECCE
Confidence            47999999999999999999999999874        4566677778899999999999999999999999996 69999


Q ss_pred             EEEEEEecCC
Q 007742          393 TLKVSSVTDH  402 (591)
Q Consensus       393 ~l~v~~~~~~  402 (591)
                      .|.|.+++..
T Consensus        87 ~i~V~~a~~~   96 (101)
T d2cpea1          87 KLKVSLARKK   96 (101)
T ss_dssp             ECEEECSSCC
T ss_pred             EEEEEEcCCC
Confidence            9999998653

>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=99.56  E-value=2.6e-15  Score=113.00  Aligned_cols=75  Identities=29%  Similarity=0.519  Sum_probs=70.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       323 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      .|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|..|++ |||. .|.|++|.|..+
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-IHFH-EINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSC-CBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCC-EECCeEEEEEEC
Confidence            48999999999999999999999999999999988889999999999999999999995 9996 699999999764

>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=99.56  E-value=5.6e-15  Score=114.74  Aligned_cols=77  Identities=22%  Similarity=0.279  Sum_probs=69.0

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEE-ecCCCeeEEEEeCCHHHHHHHHHHhccccc-CCe
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYV-DKRSAGFVYLRFESTEAAASAQRAMHMRWF-ARR  573 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l-~~~~~g~afV~F~~~e~A~~A~~~l~g~~~-~g~  573 (591)
                      +|+++|+|+||  |..++        +++|.++|+.||.|..+.+ ....+|+|||+|.+.++|..|+..|||..+ +|+
T Consensus         8 pPs~tL~V~NL--p~~~t--------e~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~   77 (88)
T d2adca2           8 PPSATLHLSNI--PPSVS--------EEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENH   77 (88)
T ss_dssp             CSCSEEEEECC--CTTCC--------HHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CCCCEEEEECC--CCCCC--------HHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCC
Confidence            56789999999  88888        8999999999999987754 556789999999999999999999999988 599


Q ss_pred             EEEEEEeCc
Q 007742          574 LISAIFMKP  582 (591)
Q Consensus       574 ~l~v~~~~~  582 (591)
                      .|.|+|++.
T Consensus        78 ~l~v~~sk~   86 (88)
T d2adca2          78 HLRVSFSKS   86 (88)
T ss_dssp             BCEEEECSS
T ss_pred             EEEEEeCCC
Confidence            999999875

>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=99.56  E-value=1.3e-15  Score=120.33  Aligned_cols=79  Identities=27%  Similarity=0.378  Sum_probs=70.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEecc
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKP  295 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~  295 (591)
                      ..+.++|||+|||+.+|+++|+++|.+||.|..+..     +|.++|||||+|.+.++|..|+ .|||..|.|++|.|.+
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345699999999999999999999999998876542     5788999999999999999999 6999999999999999


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +.+..
T Consensus        88 a~~k~   92 (96)
T d1fjca_          88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             eCCCC
Confidence            87643

>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=99.56  E-value=5.8e-15  Score=120.00  Aligned_cols=75  Identities=19%  Similarity=0.425  Sum_probs=68.4

Q ss_pred             CcEEEEeCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          220 QRTVFAYQMPL-KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       220 ~~~l~V~nLp~-~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      +++|||+|||+ .+|+++|.++|+.||.|..|.|+.++     +|||||+|.+.++|.+|| .|||..|.|+.|.|.++.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57999999965 59999999999999999999998763     689999999999999999 699999999999999975


Q ss_pred             cc
Q 007742          298 AE  299 (591)
Q Consensus       298 ~~  299 (591)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.56  E-value=3.8e-15  Score=117.68  Aligned_cols=80  Identities=19%  Similarity=0.234  Sum_probs=73.3

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      ..++++|||+||  |..++        +++|+++|..||.|..+.....++|+|||+|.+.++|..|+..|||..|+|+.
T Consensus        13 ~~~~~~l~V~nL--~~~~t--------e~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~   82 (96)
T d1fjca_          13 VRAARTLLAKNL--SFNIT--------EDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS   82 (96)
T ss_dssp             TTGGGEEEEESC--CSSCC--------HHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEE
T ss_pred             CCCCCEEEEeCC--CCCCC--------HHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEE
Confidence            345678999999  88888        89999999999999888877778999999999999999999999999999999


Q ss_pred             EEEEEeCchh
Q 007742          575 ISAIFMKPED  584 (591)
Q Consensus       575 l~v~~~~~~~  584 (591)
                      |.|.|+.++.
T Consensus        83 i~V~~a~~k~   92 (96)
T d1fjca_          83 VSLYYTGEKG   92 (96)
T ss_dssp             EEEEECSSSC
T ss_pred             EEEEEeCCCC
Confidence            9999998764

>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=99.56  E-value=3.9e-15  Score=121.50  Aligned_cols=80  Identities=16%  Similarity=0.229  Sum_probs=72.7

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEE
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI  575 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l  575 (591)
                      ...++|+|+||  |..++        +++|.++|+.||.|..|.|. ..+|+|||+|.+.++|.+|++.|||..|.|++|
T Consensus         8 r~~~~l~V~nL--p~~~t--------~~~L~~~F~~fG~I~~v~l~-~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l   76 (111)
T d1whxa_           8 RSKTVILAKNL--PAGTL--------AAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPL   76 (111)
T ss_dssp             EEEEEEEEESC--CTTCC--------HHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCEEEEECC--CCCCC--------HHHHHhhhhccCCccEEEee-ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeE
Confidence            34568999999  88888        89999999999999999886 468999999999999999999999999999999


Q ss_pred             EEEEeCchhhh
Q 007742          576 SAIFMKPEDYE  586 (591)
Q Consensus       576 ~v~~~~~~~~~  586 (591)
                      .|.|+....+.
T Consensus        77 ~v~~a~~~~~~   87 (111)
T d1whxa_          77 YLEWAPIGVFG   87 (111)
T ss_dssp             EEEEEETTTTC
T ss_pred             EEEECCCCccc
Confidence            99999876654

>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=99.56  E-value=4e-15  Score=114.81  Aligned_cols=79  Identities=27%  Similarity=0.416  Sum_probs=68.1

Q ss_pred             CceEEEcCCCCCCC-HHHHHHHhccCCCeeEEEEecc-CCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          321 DRKLYVGNLHFNMT-ETQLRKLFEPFGPVELVQLPLD-IETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       321 ~~~l~v~nl~~~~~-~~~l~~~f~~~g~i~~v~i~~~-~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      .++|||+|||+.++ +++|+++|++||.|..|.|+.+ ..++.++|||||+|.+.++|..|+ .|||. .|.|+.|.|.+
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al-~~n~~-~~~gr~l~V~~   81 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRS-LLGNREISVSL   81 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTE-EETTEEEEEEE
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHH-hcCCC-EECCEEEEEEE
Confidence            37999999999876 5679999999999999998764 457889999999999999999999 59995 79999999999


Q ss_pred             ecC
Q 007742          399 VTD  401 (591)
Q Consensus       399 ~~~  401 (591)
                      +++
T Consensus        82 a~~   84 (86)
T d2ghpa3          82 ADK   84 (86)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.56  E-value=1.5e-15  Score=113.42  Aligned_cols=74  Identities=28%  Similarity=0.501  Sum_probs=68.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       323 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      .|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||+ +++. .+.|+.|.|..
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~-~i~g~~i~vk~   74 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYH-NVGLSKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSC-CBTTBCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCC-EECCEEeEEEE
Confidence            48999999999999999999999999999999998899999999999999999999995 4554 59999998864

>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=99.56  E-value=1.5e-15  Score=115.46  Aligned_cols=73  Identities=19%  Similarity=0.282  Sum_probs=65.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCC-ccCCeeEEeccCcc
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQ-LLLGQPVMVKPSEA  298 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~-~i~g~~i~v~~~~~  298 (591)
                      .+|||+|||+.+|+++|.++|.+||.|..+.++.      ++|||||+|.+.++|..|+ .|||. .|.|++|.|.++.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4699999999999999999999999998776654      4789999999999999999 69986 59999999999875


Q ss_pred             c
Q 007742          299 E  299 (591)
Q Consensus       299 ~  299 (591)
                      .
T Consensus        76 k   76 (80)
T d2cqha1          76 K   76 (80)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.56  E-value=3.4e-15  Score=121.85  Aligned_cols=74  Identities=18%  Similarity=0.254  Sum_probs=67.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSE  297 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~  297 (591)
                      ..++|||+|||+.+|+++|.++|..||.|..|.|.      ..+|||||+|.+.++|..|| .|||..|.|+.|.|.|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            35799999999999999999999999999999874      45799999999999999999 699999999999998875


Q ss_pred             c
Q 007742          298 A  298 (591)
Q Consensus       298 ~  298 (591)
                      .
T Consensus        83 ~   83 (111)
T d1whxa_          83 I   83 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.55  E-value=6.8e-15  Score=116.24  Aligned_cols=81  Identities=20%  Similarity=0.324  Sum_probs=69.6

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEE
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI  575 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l  575 (591)
                      ....+|||.|| +|..++        +++|.++|++||.|..|.|.   +|||||+|.+.++|.+|+..|||..|.|+.|
T Consensus        13 ~~~~~lfV~nL-~~~~~~--------~~~L~~~F~~~G~i~~~~i~---rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (98)
T d1wf2a_          13 SMNSRVFIGNL-NTLVVK--------KSDVEAIFSKYGKIVGCSVH---KGFAFVQYVNERNARAAVAGEDGRMIAGQVL   80 (98)
T ss_dssp             SCCCCEEEEEE-CTTTCC--------HHHHHHSSTTSSCEEEEEEE---TEEEEEEESSHHHHHHHHHTTTTCEETTEEC
T ss_pred             CCCcEEEEeCC-CcccCC--------HHHHHHHHhhcCCEEEEEEe---CCeEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34457999999 224555        78899999999999999884   7999999999999999999999999999999


Q ss_pred             EEEEeCchhhhhc
Q 007742          576 SAIFMKPEDYEAK  588 (591)
Q Consensus       576 ~v~~~~~~~~~~~  588 (591)
                      .|.|+.+......
T Consensus        81 ~V~~a~~~~~~~~   93 (98)
T d1wf2a_          81 DINLAAEPKVNRS   93 (98)
T ss_dssp             EEEETTSCCCCSS
T ss_pred             EEEECCCCCCCCC
Confidence            9999987654443

>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=99.54  E-value=4.9e-15  Score=114.96  Aligned_cols=75  Identities=23%  Similarity=0.344  Sum_probs=68.0

Q ss_pred             ceEEEcCCCCCCCHHHH---HHHhccCCCeeEEEEeccCCCCCc---ccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEE
Q 007742          322 RKLYVGNLHFNMTETQL---RKLFEPFGPVELVQLPLDIETGQC---KGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLK  395 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l---~~~f~~~g~i~~v~i~~~~~~~~~---~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~  395 (591)
                      ++|||+|||+.+++++|   .++|.+||+|..|.|+.++.++.+   .|||||+|.+.++|..|++.|||. .|.|+.|+
T Consensus         9 n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~-~~~gr~lk   87 (89)
T d2cpia1           9 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNV-VVDGRTLK   87 (89)
T ss_dssp             SCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTE-EETTEEEE
T ss_pred             CEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCC-EECCEEEE
Confidence            68999999999999999   678999999999999988766544   489999999999999999999996 79999999


Q ss_pred             EE
Q 007742          396 VS  397 (591)
Q Consensus       396 v~  397 (591)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.54  E-value=9.5e-15  Score=113.41  Aligned_cols=78  Identities=21%  Similarity=0.247  Sum_probs=68.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeee-CCeEEEEE
Q 007742          319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI-VGRTLKVS  397 (591)
Q Consensus       319 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~-~g~~l~v~  397 (591)
                      |++++|||+|||+.+++++|+++|.+||.|..+.+...    ..+|+|||+|.+.++|..|+..|+|. .+ +|++|.|.
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~-~i~~g~~l~v~   82 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNH-DLGENHHLRVS   82 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTC-BSSSSCBCEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCC-EecCCCEEEEE
Confidence            34689999999999999999999999999988777543    35789999999999999999999996 45 68999999


Q ss_pred             EecC
Q 007742          398 SVTD  401 (591)
Q Consensus       398 ~~~~  401 (591)
                      +++.
T Consensus        83 ~sk~   86 (88)
T d2adca2          83 FSKS   86 (88)
T ss_dssp             ECSS
T ss_pred             eCCC
Confidence            9864

>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=99.54  E-value=6.9e-15  Score=113.71  Aligned_cols=77  Identities=23%  Similarity=0.283  Sum_probs=68.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEE-EEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELV-QLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v-~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ....|+|.|||+.+++++|+++|..||.+... .+..+ .++.++|+|||+|.+.++|..|+..||+. .+.|++|.|..
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~-~l~gr~i~v~l   85 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDR-PIGSRKVKLVL   85 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTC-EETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCC-EECCEEEEEEE
Confidence            34789999999999999999999999988664 44444 58899999999999999999999999997 79999999975

>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=99.54  E-value=8.8e-15  Score=110.83  Aligned_cols=75  Identities=12%  Similarity=0.174  Sum_probs=67.9

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEE
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI  575 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l  575 (591)
                      ..+++|+|+|+  +  ++        +++|+++|++||.|..+.+.. .+|+|||+|.+.++|..|+..|||..|+|+.|
T Consensus         3 ~~~~ti~V~~~--~--~t--------e~~L~~~F~~~G~I~~v~~~~-~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   69 (79)
T d2bz2a1           3 RKGNTLYVYGE--D--MT--------PTLLRGAFSPFGNIIDLSMDP-PRNCAFVTYEKMESADQAVAELNGTQVESVQL   69 (79)
T ss_dssp             CCCCEEEEECS--S--CC--------HHHHHHHHSTTCCCSCEEEET-TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBC
T ss_pred             CCCCEEEEECC--C--CC--------HHHHHHHHhccCccceeeecc-CCCEEEEEEcccHHHHHHHHHhCCCEECCEEE
Confidence            45678999998  5  34        899999999999999999874 58899999999999999999999999999999


Q ss_pred             EEEEeCch
Q 007742          576 SAIFMKPE  583 (591)
Q Consensus       576 ~v~~~~~~  583 (591)
                      .|.|+.++
T Consensus        70 ~V~~a~~~   77 (79)
T d2bz2a1          70 KVNIARKQ   77 (79)
T ss_dssp             EEEECCSS
T ss_pred             EEEEecCC
Confidence            99999865

>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=99.54  E-value=7.1e-15  Score=113.21  Aligned_cols=76  Identities=20%  Similarity=0.367  Sum_probs=69.8

Q ss_pred             cceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEE
Q 007742          498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISA  577 (591)
Q Consensus       498 s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v  577 (591)
                      .+.|+|+||  |..++        +++|.++|+.||.|..|.+.. .+|+|||+|.+.++|..|+..|||..|+|+.|.|
T Consensus         8 ~~~l~V~nL--p~~~~--------~~~l~~~F~~~G~i~~i~~~~-~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V   76 (86)
T d2cpja1           8 RSRLFVGNL--PPDIT--------EEEMRKLFEKYGKAGEVFIHK-DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   76 (86)
T ss_dssp             TTEEEEESC--CTTCC--------HHHHHHHTSTTCCCSEEEEET-TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CCEEEEECC--CCCCC--------HHHHHHHHHHhCCceEeeeec-ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            456999999  88887        899999999999999999875 4899999999999999999999999999999999


Q ss_pred             EEeCchh
Q 007742          578 IFMKPED  584 (591)
Q Consensus       578 ~~~~~~~  584 (591)
                      .|+....
T Consensus        77 ~~A~~~~   83 (86)
T d2cpja1          77 RFACHSA   83 (86)
T ss_dssp             EESSCCS
T ss_pred             EECCCcC
Confidence            9998753

>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=99.54  E-value=4e-15  Score=112.96  Aligned_cols=75  Identities=32%  Similarity=0.472  Sum_probs=67.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEecC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTD  401 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~~  401 (591)
                      .+|||+|||..+++++|.++|.+||.|..+.+..      .+|||||+|.+.++|..|++.|||.+.+.|++|.|.++.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999987665553      4789999999999999999999997679999999999875


Q ss_pred             C
Q 007742          402 H  402 (591)
Q Consensus       402 ~  402 (591)
                      .
T Consensus        76 k   76 (80)
T d2cqha1          76 K   76 (80)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.54  E-value=2.6e-14  Score=114.55  Aligned_cols=79  Identities=18%  Similarity=0.176  Sum_probs=69.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH-H--cCCccCCeeEE
Q 007742          216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L--SGQLLLGQPVM  292 (591)
Q Consensus       216 ~~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~-l--~g~~i~g~~i~  292 (591)
                      ...++++|||+|||+.+|+++|.++|..||.|..|.+.+      .+|||||+|.+.++|..|+. +  ++..+.|++|.
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~------~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe------cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            345679999999999999999999999999999999874      47899999999999999993 4  56678999999


Q ss_pred             eccCcccc
Q 007742          293 VKPSEAEK  300 (591)
Q Consensus       293 v~~~~~~~  300 (591)
                      |.++..+.
T Consensus        85 v~~s~~~~   92 (104)
T d1wexa_          85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEcCCCc
Confidence            99986543

>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=99.54  E-value=2.3e-15  Score=112.07  Aligned_cols=70  Identities=33%  Similarity=0.577  Sum_probs=66.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEE
Q 007742          324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTL  394 (591)
Q Consensus       324 l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l  394 (591)
                      |||+|||..+++++|.++|.+||+|..+.+..+..++.++|+|||+|.+.++|..|++.|||. .|.|+.|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~-~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS-GVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHH-TCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCC-EECCEEC
Confidence            799999999999999999999999999999999889999999999999999999999999996 6888865

>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=99.53  E-value=1.4e-15  Score=122.07  Aligned_cols=82  Identities=27%  Similarity=0.398  Sum_probs=75.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ++++|||+|||..+++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|..|+..|||. .|.|+.|.|.++
T Consensus        17 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          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGY-KLYGKILVIEFG   95 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTC-BCSSCBCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCC-EECCEEEEEEeC
Confidence            4589999999999999999999999999998888877778899999999999999999999999995 799999999998


Q ss_pred             cCC
Q 007742          400 TDH  402 (591)
Q Consensus       400 ~~~  402 (591)
                      +..
T Consensus        96 k~k   98 (102)
T d2cpxa1          96 KNK   98 (102)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            753

>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=99.53  E-value=2.5e-16  Score=123.16  Aligned_cols=78  Identities=19%  Similarity=0.422  Sum_probs=69.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEe-----ecCCCCCccceEEEEecCcchHHHHHHHcCCccCCeeEEec
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLI-----MDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVK  294 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~-----~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~i~v~  294 (591)
                      +++|||+|||+.+|+++|+++|+.||.|..+.+.     .+..++.++|||||+|.+.++|..|+.|||..+.|+.|+|.
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCB
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEEC
Confidence            3789999999999999999999999987665553     34567889999999999999999999999999999999997


Q ss_pred             cCc
Q 007742          295 PSE  297 (591)
Q Consensus       295 ~~~  297 (591)
                      .+.
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            554

>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=99.53  E-value=8.9e-15  Score=116.61  Aligned_cols=77  Identities=29%  Similarity=0.494  Sum_probs=70.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      .++|||+|||+.+++++|+++|+.||.|..+.+..+. ++.++|||||+|.+.++|.+|+..|||. .|.|+++.|.++
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~-~i~gr~~~v~~~   94 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGK-FIKTPPGVSAPT   94 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTC-CCCCCTTSCCCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCC-EECCcCCccCCC
Confidence            3789999999999999999999999999999988775 8889999999999999999999999997 699998877654

>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=99.53  E-value=6.1e-15  Score=115.16  Aligned_cols=81  Identities=19%  Similarity=0.374  Sum_probs=69.5

Q ss_pred             CcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEec--CCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK--RSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       497 ~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~--~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      |+++|+|+||  |..++++    +|.+.|.++|+.||.|..|.+..  ..+|+|||+|.+.++|..|+..|||..|+|+.
T Consensus         2 P~~tl~V~nL--p~~~t~~----dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~   75 (91)
T d1nu4a_           2 PNHTIYINNL--NEKIKKD----ELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   75 (91)
T ss_dssp             CCSEEEEESC--CTTSCHH----HHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCEEEEeCC--CCCCCHH----HHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            5789999999  8887732    23455677899999999998854  35899999999999999999999999999999


Q ss_pred             EEEEEeCch
Q 007742          575 ISAIFMKPE  583 (591)
Q Consensus       575 l~v~~~~~~  583 (591)
                      |.|.|+..+
T Consensus        76 l~v~~ak~~   84 (91)
T d1nu4a_          76 MRIQYAKTD   84 (91)
T ss_dssp             CEEEECSSC
T ss_pred             EEEEEeCCC
Confidence            999999865

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=2.4e-14  Score=111.03  Aligned_cols=81  Identities=20%  Similarity=0.302  Sum_probs=71.8

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhc--ccccC
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMH--MRWFA  571 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~--g~~~~  571 (591)
                      .+.|+++|+|+||  |..++        +++|.++|+.||.|..+.+.. .+|+|||+|.+.++|..|+..|+  +..++
T Consensus         4 ~~~Ps~~l~V~nL--p~~~t--------~~~L~~~f~~~G~i~~v~~~~-~~~~afV~f~~~e~A~~a~~~~~~~~~~~~   72 (88)
T d2cq1a1           4 DGAPSRVLHIRKL--PGEVT--------ETEVIALGLPFGKVTNILMLK-GKNQAFLELATEEAAITMVNYYSAVTPHLR   72 (88)
T ss_dssp             CSSCCSEEEEESC--CTTCC--------HHHHHHTTTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCEET
T ss_pred             CCCCCCEEEEeCC--CCCCC--------HHHHHHHHhcccccccccccc-cceEEEEEeCCHHHHHHHHHHHccCCCccC
Confidence            4678999999999  88887        899999999999999998874 57899999999999999998764  56799


Q ss_pred             CeEEEEEEeCchhh
Q 007742          572 RRLISAIFMKPEDY  585 (591)
Q Consensus       572 g~~l~v~~~~~~~~  585 (591)
                      |++|.|.|++.++.
T Consensus        73 g~~l~v~~sk~~~l   86 (88)
T d2cq1a1          73 NQPIYIQYSNHKEL   86 (88)
T ss_dssp             TEECEEEECSCSSC
T ss_pred             CCEEEEEECCCCCC
Confidence            99999999987653

>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=99.53  E-value=1.4e-14  Score=111.91  Aligned_cols=77  Identities=18%  Similarity=0.275  Sum_probs=69.8

Q ss_pred             CcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEE
Q 007742          497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLIS  576 (591)
Q Consensus       497 ~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~  576 (591)
                      ..++|+|+||  |..++        +++|.++|+.||.|..+.+. .++|+|||+|.+.++|..|+..|||..|+|+.|.
T Consensus         7 ~~k~l~V~nL--p~~~t--------e~~l~~~F~~~g~i~~~~~~-~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~   75 (86)
T d2cpda1           7 SVKILYVRNL--MLSTS--------EEMIEKEFNNIKPGAVERVK-KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIE   75 (86)
T ss_dssp             CCCEEEEESC--CTTCC--------HHHHHHHHHTTSTTCEEEEE-ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCCEEEEcCC--CCCCC--------HHHHHHhhcccceeeeEEEc-cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEE
Confidence            3468999999  88888        89999999999999888775 4689999999999999999999999999999999


Q ss_pred             EEEeCchh
Q 007742          577 AIFMKPED  584 (591)
Q Consensus       577 v~~~~~~~  584 (591)
                      |.|+.|..
T Consensus        76 V~~akP~~   83 (86)
T d2cpda1          76 VTLAKPVD   83 (86)
T ss_dssp             EECCCCCC
T ss_pred             EEeccCCC
Confidence            99988754

>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=99.53  E-value=9.9e-15  Score=112.93  Aligned_cols=81  Identities=21%  Similarity=0.272  Sum_probs=69.1

Q ss_pred             CcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEE
Q 007742          497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLIS  576 (591)
Q Consensus       497 ~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~  576 (591)
                      .+.+|+|.||  |..++        +++|.++|..|| +..+.+. ..+|+|||+|.+.++|+.|+..|||..|+|+.|.
T Consensus         4 ~s~~i~V~nL--p~~~t--------~~~l~~lF~~~G-~~~~~~~-~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~   71 (88)
T d1wg1a_           4 GSSGILVKNL--PQDSN--------CQEVHDLLKDYD-LKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLI   71 (88)
T ss_dssp             CCCCEEEESC--CSSCC--------HHHHHHHTCSSC-CCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCEEEEeCC--CCccC--------hHHHHHHHHhcC-ceeeeee-ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            4568999999  88888        899999999999 3334443 4689999999999999999999999999999999


Q ss_pred             EEEeCchhhhhcc
Q 007742          577 AIFMKPEDYEAKF  589 (591)
Q Consensus       577 v~~~~~~~~~~~~  589 (591)
                      |.|++.+.....-
T Consensus        72 V~~a~~~~~~~~~   84 (88)
T d1wg1a_          72 VQLQPTDALLCSG   84 (88)
T ss_dssp             EEECCCCCCCSCC
T ss_pred             EEEcCCCCCCCCC
Confidence            9999877654443

>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=99.53  E-value=1.1e-14  Score=114.93  Aligned_cols=75  Identities=16%  Similarity=0.225  Sum_probs=68.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ....+|||+|||+.+++++|.++|.+||.|..+.+.       .+|||||+|.+.++|..|| .|||..|.|+.|.|.+.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~-------~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ-------KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE-------TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhccccccccc-------ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            456889999999999999999999999999999886       3589999999999999999 69999999999999887


Q ss_pred             ccc
Q 007742          297 EAE  299 (591)
Q Consensus       297 ~~~  299 (591)
                      ...
T Consensus        86 ~~~   88 (98)
T d1wg4a_          86 RVY   88 (98)
T ss_dssp             EEE
T ss_pred             ecC
Confidence            544

>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=99.52  E-value=8.9e-15  Score=118.25  Aligned_cols=78  Identities=17%  Similarity=0.149  Sum_probs=69.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCcc--CCeeEEecc
Q 007742          219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL--LGQPVMVKP  295 (591)
Q Consensus       219 ~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i--~g~~i~v~~  295 (591)
                      +..+|||+|||+.+|+++|.++|.+||.|..|.++.++    .+|||||+|.+.++|..|| .|||..|  .|..|.|.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            45789999999999999999999999999999998764    4899999999999999999 6999988  578888888


Q ss_pred             Ccccc
Q 007742          296 SEAEK  300 (591)
Q Consensus       296 ~~~~~  300 (591)
                      +....
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            76543

>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=99.52  E-value=3.2e-14  Score=114.08  Aligned_cols=81  Identities=21%  Similarity=0.180  Sum_probs=72.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ...+|||+|||+.+++++|+++|..+|.|..+.++....++.++|+|||+|.+.++|.+|+ .||+. .|.|+.|.|.++
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~-~~~~~-~i~gR~i~V~~~   91 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKE-RIGHRYIEIFKS   91 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHH-TTTTC-CSSSSCCEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHH-hhCCC-EEcceEEEEEEC
Confidence            3468999999999999999999999999888666666668899999999999999999999 58996 599999999988


Q ss_pred             cCC
Q 007742          400 TDH  402 (591)
Q Consensus       400 ~~~  402 (591)
                      +..
T Consensus        92 ~~~   94 (104)
T d1wg5a_          92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            654

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.9e-14  Score=111.56  Aligned_cols=77  Identities=18%  Similarity=0.258  Sum_probs=68.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH---HcCCccCCeeEEe
Q 007742          217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA---LSGQLLLGQPVMV  293 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~---l~g~~i~g~~i~v  293 (591)
                      ..++++|||+|||+.+|+++|.++|.+||.|..+.++.+      +|||||+|.+.++|..|+.   +++..+.|++|.|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            457799999999999999999999999999999998743      5799999999999999984   4678899999999


Q ss_pred             ccCccc
Q 007742          294 KPSEAE  299 (591)
Q Consensus       294 ~~~~~~  299 (591)
                      .++..+
T Consensus        79 ~~sk~~   84 (88)
T d2cq1a1          79 QYSNHK   84 (88)
T ss_dssp             EECSCS
T ss_pred             EECCCC
Confidence            998643

>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=99.52  E-value=1.5e-14  Score=108.12  Aligned_cols=70  Identities=14%  Similarity=0.260  Sum_probs=62.3

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccCccc
Q 007742          223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAE  299 (591)
Q Consensus       223 l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~~~~  299 (591)
                      |||+|||+.+|+++|+++|.+|| +..+.+      +..+|||||+|.+.++|.+|+ .|||..+.|++|.|.++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 444443      456899999999999999999 69999999999999988543

>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=99.52  E-value=4.4e-14  Score=113.44  Aligned_cols=80  Identities=24%  Similarity=0.528  Sum_probs=69.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccC-CCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEE
Q 007742          320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDI-ETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSS  398 (591)
Q Consensus       320 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~-~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~  398 (591)
                      ++.+|||+|||+.+++++|+++|+.|| |..+.++.+. .++.++|||||+|.+.++|.+|+ .||+. .|.|+.|.|.+
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~-~~~gr~l~V~~   90 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE-SLGNKRIRVDV   90 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTC-EETTEECEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCC-EECCEEEEEEE
Confidence            458999999999999999999999999 6667666554 46788999999999999998777 69996 79999999999


Q ss_pred             ecCC
Q 007742          399 VTDH  402 (591)
Q Consensus       399 ~~~~  402 (591)
                      +...
T Consensus        91 a~~~   94 (104)
T d1wi8a_          91 ADQA   94 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.51  E-value=2.1e-14  Score=107.22  Aligned_cols=74  Identities=23%  Similarity=0.304  Sum_probs=66.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ++|||+|||+.+++++|+++|..||.|..|.|..+..  ...+||||+|.+.++|.+|+ .+++. .|+|+.|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAI-TKTHK-VVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHH-TTTTC-EETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHH-HhcCc-EECCEEEEEEEC
Confidence            4799999999999999999999999999999988763  34579999999999999999 68997 699999999865

>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=99.51  E-value=2.4e-14  Score=113.09  Aligned_cols=76  Identities=13%  Similarity=0.225  Sum_probs=68.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCC--eeEEec
Q 007742          218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLG--QPVMVK  294 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g--~~i~v~  294 (591)
                      .+.++|||+|||+.+|+++|+++|.+||.|..|.++++      ++||||+|.+.++|..|+ .||+..|.|  .+|.|.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            35689999999999999999999999999999998753      679999999999999999 699999977  479998


Q ss_pred             cCccc
Q 007742          295 PSEAE  299 (591)
Q Consensus       295 ~~~~~  299 (591)
                      |+...
T Consensus        89 ~ak~~   93 (97)
T d1whya_          89 FAKSG   93 (97)
T ss_dssp             ECCCC
T ss_pred             eCCCC
Confidence            88653

>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=99.51  E-value=4.5e-15  Score=115.60  Aligned_cols=78  Identities=23%  Similarity=0.369  Sum_probs=70.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ..+|||+|||+.+++++|+++|+.||.|..+.|+.+ .+|.++|||||+|.+.++|..|| .|||. .|.|+.|.|.+++
T Consensus        13 ~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al-~~~g~-~~~g~~i~V~~ak   89 (91)
T d1fjeb1          13 PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKAL-ELTGL-KVFGNEIKLEKPK   89 (91)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHH-HGGGE-EETTEEEEEECCC
T ss_pred             CcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHH-hcCCc-EECCEEEEEEecC
Confidence            478999999999999999999999999988887654 48889999999999999999999 59995 7999999999875


Q ss_pred             C
Q 007742          401 D  401 (591)
Q Consensus       401 ~  401 (591)
                      .
T Consensus        90 ~   90 (91)
T d1fjeb1          90 G   90 (91)
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=99.51  E-value=3.3e-14  Score=113.48  Aligned_cols=81  Identities=22%  Similarity=0.330  Sum_probs=70.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEE
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS  397 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~  397 (591)
                      .....+|||.|||+.+|+++|+++|..+|.+ .|.++.+. ++..+|||||+|.+.++|..|+ .||+. .|.|+.|.|.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al-~~~~~-~i~gR~I~V~   87 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKA-NMQHRYVELF   87 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSC-CSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEec-CCcceEEEEEEECCHHHHHHHH-HcCCC-EECCEEEEEE
Confidence            3445799999999999999999999999855 67777665 6889999999999999999999 58996 6999999999


Q ss_pred             EecCC
Q 007742          398 SVTDH  402 (591)
Q Consensus       398 ~~~~~  402 (591)
                      +++..
T Consensus        88 ~s~~~   92 (102)
T d1weza_          88 LNSTA   92 (102)
T ss_dssp             EECCC
T ss_pred             EcCCC
Confidence            87654

>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=99.50  E-value=6.6e-14  Score=108.19  Aligned_cols=74  Identities=18%  Similarity=0.223  Sum_probs=64.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +++|||+|||+.+++++|+++|.+||. ..+.+      +..+|||||+|.+.++|..|+..|||. .|.|+.|.|.+++
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~-~~~G~~l~V~~a~   76 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQY-SFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTE-EETTEEEEEEECC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcCc-eeeee------eccCCceEEEECCHHHHHHHHHHhCCC-EECCEEEEEEEcC
Confidence            478999999999999999999999993 22333      235789999999999999999999995 7999999999986


Q ss_pred             CC
Q 007742          401 DH  402 (591)
Q Consensus       401 ~~  402 (591)
                      ..
T Consensus        77 ~~   78 (88)
T d1wg1a_          77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.50  E-value=5.8e-14  Score=104.79  Aligned_cols=72  Identities=22%  Similarity=0.390  Sum_probs=65.0

Q ss_pred             EEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEe
Q 007742          501 LLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFM  580 (591)
Q Consensus       501 l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~  580 (591)
                      |+|+||  |..++        +++|.++|++|| +..+.+. .++|+|||+|.+.++|.+|+..|||..|.|++|.|+|+
T Consensus         1 i~V~nL--p~~~t--------~~~l~~~F~~~g-~~~~~~~-~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a   68 (75)
T d1wi6a1           1 ILIRGL--PGDVT--------NQEVHDLLSDYE-LKYCFVD-KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQ   68 (75)
T ss_dssp             EEEECC--CTTCC--------HHHHHHHTTTSC-EEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CEEeCC--CCcCC--------HHHHHHHHhccc-ccceeec-ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEe
Confidence            799999  88888        899999999999 5555554 47999999999999999999999999999999999999


Q ss_pred             Cchh
Q 007742          581 KPED  584 (591)
Q Consensus       581 ~~~~  584 (591)
                      +.+.
T Consensus        69 ~~d~   72 (75)
T d1wi6a1          69 PTDA   72 (75)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            8764

>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=99.50  E-value=1.3e-13  Score=110.45  Aligned_cols=81  Identities=20%  Similarity=0.211  Sum_probs=70.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcC-CeeeCCeEEE
Q 007742          317 YGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG-KLEIVGRTLK  395 (591)
Q Consensus       317 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g-~~~~~g~~l~  395 (591)
                      ..+++.+|||.|||+.+++++|+++|.+||.|..|.+...      +|+|||+|.+.++|..|+..|++ .+.+.|++|.
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            3445689999999999999999999999999999998753      68999999999999999998853 2568999999


Q ss_pred             EEEecCCC
Q 007742          396 VSSVTDHV  403 (591)
Q Consensus       396 v~~~~~~~  403 (591)
                      |.|++.+.
T Consensus        85 v~~s~~~~   92 (104)
T d1wexa_          85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEcCCCc
Confidence            99987543

>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=99.50  E-value=1.2e-14  Score=112.56  Aligned_cols=79  Identities=18%  Similarity=0.234  Sum_probs=71.7

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEE
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI  575 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l  575 (591)
                      ..+++|||.||  |..++        +++|+++|++||.|..|.++..++|||||+|.+.++|+.|+.  ++..|+|+.|
T Consensus         3 ~~s~~lfV~nL--p~~~t--------e~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l   70 (88)
T d1wf0a_           3 SGSSGVFVGRC--TGDMT--------EDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISV   70 (88)
T ss_dssp             SCCCEEEEESC--CSSSC--------HHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEE
T ss_pred             CCCCEEEEeCC--CCCCC--------HHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEe
Confidence            35678999999  88888        899999999999999999988899999999999999999985  8889999999


Q ss_pred             EEEEeCchhhh
Q 007742          576 SAIFMKPEDYE  586 (591)
Q Consensus       576 ~v~~~~~~~~~  586 (591)
                      .|.++.++.-.
T Consensus        71 ~v~~a~~k~~~   81 (88)
T d1wf0a_          71 HISNAEPKHNS   81 (88)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999876543

>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=99.49  E-value=7e-15  Score=113.69  Aligned_cols=73  Identities=15%  Similarity=0.185  Sum_probs=66.6

Q ss_pred             eEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEE
Q 007742          500 CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIF  579 (591)
Q Consensus       500 ~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~  579 (591)
                      .|+|+||  |..++        +++|.++|++||.|..+.+..  .|+|||+|.+.++|.+||..|||..|.|+.|.|.|
T Consensus         2 rvfV~nl--p~~~~--------~~~l~~~F~~~G~v~~~~i~~--~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~   69 (87)
T d3begb1           2 RVVVSGL--PPSGS--------WQDLKDHMREAGDVCYADVYR--DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   69 (87)
T ss_dssp             CEEEEEC--CSSCC--------TTHHHHHHGGGSCEEEEEECT--TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             eEEEECC--CCcCC--------HHHHHHHHhhhcccccccccc--cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeE
Confidence            5999999  88888        799999999999999998864  58999999999999999999999999999999988


Q ss_pred             eCchh
Q 007742          580 MKPED  584 (591)
Q Consensus       580 ~~~~~  584 (591)
                      +..+.
T Consensus        70 ~~~~~   74 (87)
T d3begb1          70 IRVKV   74 (87)
T ss_dssp             CEEEE
T ss_pred             EecCc
Confidence            76543

>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=99.49  E-value=2.2e-14  Score=113.26  Aligned_cols=82  Identities=16%  Similarity=0.254  Sum_probs=72.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCC-eeEEEEeccC-CCCCcccEEEEEeCCHHHHHHHHHHhcCC-eeeCCeEEEEEE
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGP-VELVQLPLDI-ETGQCKGFGFVQFAQLEHAKAAQSALNGK-LEIVGRTLKVSS  398 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~v~i~~~~-~~~~~~g~a~Vef~~~~~a~~a~~~l~g~-~~~~g~~l~v~~  398 (591)
                      +.|||+|||..+++++|+++|+.||+ |..|.|+.+. .++.++|||||+|.+.++|..|++.|++. +.+.|+.|.|.+
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            57999999999999999999999996 8999998874 35788999999999999999999998753 457899999999


Q ss_pred             ecCCC
Q 007742          399 VTDHV  403 (591)
Q Consensus       399 ~~~~~  403 (591)
                      +++..
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            97543

>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=99.49  E-value=2.7e-14  Score=112.69  Aligned_cols=76  Identities=14%  Similarity=0.169  Sum_probs=69.9

Q ss_pred             CcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeEEE
Q 007742          497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLIS  576 (591)
Q Consensus       497 ~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~  576 (591)
                      ...+|+|.||  |..++        +++|.++|+.||.|..+.|.  .+|+|||+|.+.++|.+||+.|||..|.|+.|.
T Consensus        14 ~~~~i~V~Nl--p~~~~--------~~~L~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~   81 (98)
T d1wg4a_          14 SDFRVLVSGL--PPSGS--------WQDLKDHMREAGDVCYADVQ--KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGE   81 (98)
T ss_dssp             CSCEEEEECC--CSSCC--------HHHHHHHHTTSSCEEEEEEE--TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSC
T ss_pred             CCCEEEEECC--CCCCC--------HHHHHHHHHhhccccccccc--ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            4567999999  88888        89999999999999999987  468999999999999999999999999999999


Q ss_pred             EEEeCchh
Q 007742          577 AIFMKPED  584 (591)
Q Consensus       577 v~~~~~~~  584 (591)
                      |.|+.+..
T Consensus        82 v~~~~~~~   89 (98)
T d1wg4a_          82 TSYIRVYP   89 (98)
T ss_dssp             EEEEEEEC
T ss_pred             EEEEecCC
Confidence            99987654

>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=99.49  E-value=5e-14  Score=111.26  Aligned_cols=78  Identities=22%  Similarity=0.337  Sum_probs=70.1

Q ss_pred             CCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCC--
Q 007742          495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFAR--  572 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g--  572 (591)
                      .+|+++|+|.||  |..++        +++|+++|++||.|..+.+.. .+++|||+|.+.++|..|++.|||..|.|  
T Consensus        14 ~~Ps~tl~V~nL--p~~~t--------~~~l~~~f~~~G~i~~~~~~~-~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~   82 (97)
T d1whya_          14 ANPTTRLWVGGL--GPNTS--------LAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFPLGGPD   82 (97)
T ss_dssp             CCCCSCEEEECC--CSSCC--------HHHHHHHHHTTSCEEEEEECS-SSCCEEEEESSHHHHHHHHHHHTTCBCSSSS
T ss_pred             CCCCCEEEEcCC--CCCCC--------HHHHHHHHHhhcccceEeeec-cccEEEeccCCHHHHHHHHHHhCCCEeCCCc
Confidence            356789999999  88787        899999999999999999874 48899999999999999999999999976  


Q ss_pred             eEEEEEEeCch
Q 007742          573 RLISAIFMKPE  583 (591)
Q Consensus       573 ~~l~v~~~~~~  583 (591)
                      +.|.|.|+...
T Consensus        83 ~~l~v~~ak~~   93 (97)
T d1whya_          83 RRLRVDFAKSG   93 (97)
T ss_dssp             CBCEEEECCCC
T ss_pred             eEEEEEeCCCC
Confidence            58999998754

>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=99.48  E-value=4.3e-14  Score=114.18  Aligned_cols=81  Identities=20%  Similarity=0.157  Sum_probs=70.9

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEe-cCCCeeEEEEeCCHHHHHHHHHHhccccc--CC
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVD-KRSAGFVYLRFESTEAAASAQRAMHMRWF--AR  572 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~-~~~~g~afV~F~~~e~A~~A~~~l~g~~~--~g  572 (591)
                      .+...|+|+||  |..++        +++|.++|++||.|..|.+. ...+|+|||+|.+.++|..|+..|||..|  .|
T Consensus         5 s~~~~v~V~NL--~~~vt--------e~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~   74 (108)
T d2adba1           5 SPVLRIIVENL--FYPVT--------LDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNAC   74 (108)
T ss_dssp             CCEEEEESCSC--CSTTH--------HHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTC
T ss_pred             CCeEEEEEeCc--CCCCC--------HHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCC
Confidence            45667999999  88887        89999999999999998774 34689999999999999999999999998  58


Q ss_pred             eEEEEEEeCchhhh
Q 007742          573 RLISAIFMKPEDYE  586 (591)
Q Consensus       573 ~~l~v~~~~~~~~~  586 (591)
                      +.|.|.|+.++...
T Consensus        75 ~~l~v~~s~~~~~~   88 (108)
T d2adba1          75 CTLRIDFSKLTSLN   88 (108)
T ss_dssp             CCCEEEECSSCSCC
T ss_pred             cEEEEEecCCcccc
Confidence            89999998776543

>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=99.47  E-value=4e-14  Score=113.41  Aligned_cols=77  Identities=26%  Similarity=0.287  Sum_probs=68.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      .+|||+|||+.+++++|.++|..||.|..+.++....+|.++|+|||+|.+.++|..|| .||+. .|.|+.|.|.++.
T Consensus         9 ~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al-~~n~~-~i~gr~i~V~~~~   85 (103)
T d2cpya1           9 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RLHRK-KLNGREAFVHVVT   85 (103)
T ss_dssp             CEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHG-GGCSE-EETTEEEEEEEEC
T ss_pred             eEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHH-hcCCC-eECCcEEEEEECC
Confidence            78999999999999999999999998876544444458999999999999999999999 59995 7999999998864

>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=99.47  E-value=4.2e-14  Score=111.95  Aligned_cols=78  Identities=19%  Similarity=0.221  Sum_probs=68.8

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHH---HcCCccCCeeEE
Q 007742          217 ERDQRTVFAYQMPLK-ATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA---LSGQLLLGQPVM  292 (591)
Q Consensus       217 ~~~~~~l~V~nLp~~-~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~---l~g~~i~g~~i~  292 (591)
                      ...+++|||+|||.. +|+++|.++|+.||.|..|.++.+      +|||||+|.+.++|..|+.   +++..|.|+.|.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            345689999999985 899999999999999999999753      6899999999999999983   788899999999


Q ss_pred             eccCcccc
Q 007742          293 VKPSEAEK  300 (591)
Q Consensus       293 v~~~~~~~  300 (591)
                      |.++....
T Consensus        89 V~~s~~~~   96 (99)
T d1x4fa1          89 VDLSEKYK   96 (99)
T ss_dssp             EEEECSCS
T ss_pred             EEEcCCcc
Confidence            99886543

>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=99.43  E-value=1.8e-13  Score=105.73  Aligned_cols=77  Identities=6%  Similarity=0.069  Sum_probs=67.6

Q ss_pred             CCCcceEEEeccCCCCC-CCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHh--cccccC
Q 007742          495 GSPSECLLLKNMFDPAM-ETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAM--HMRWFA  571 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~-~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l--~g~~~~  571 (591)
                      ..++++|+|.||  |.. +|        +++|.++|+.||.|..|.+.. .+++|||+|.+.++|..|+..|  ++..++
T Consensus         5 ~~~sr~v~v~nl--~~~~~t--------~~eL~~lF~~fG~I~~i~i~~-~k~~afV~f~~~~~A~~A~~~l~~~~~~~~   73 (89)
T d1x4da1           5 VETRRVVHIMDF--QRGKNL--------RYQLLQLVEPFGVISNHLILN-KINEAFIEMATTEDAQAAVDYYTTTPALVF   73 (89)
T ss_dssp             CCCCCEEEEESC--CCSSSH--------HHHHHTTTGGGSCEEEEEECS-SSSCEEEEESSHHHHHHHHHHHHHSCCEET
T ss_pred             CCCCcEEEEECC--CCCcCC--------HHHHHHHHHhhCCeEEEEeec-cceEEEEEEcchhhHHHHHHHHhhCCCccC
Confidence            467889999999  654 44        899999999999999999874 4789999999999999999976  566799


Q ss_pred             CeEEEEEEeCc
Q 007742          572 RRLISAIFMKP  582 (591)
Q Consensus       572 g~~l~v~~~~~  582 (591)
                      |++|.|.|++.
T Consensus        74 gr~l~V~~s~~   84 (89)
T d1x4da1          74 GKPVRVHLSQK   84 (89)
T ss_dssp             TEECEEEEECC
T ss_pred             CceEEEEECCC
Confidence            99999999874

>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=99.43  E-value=1.3e-13  Score=109.81  Aligned_cols=78  Identities=15%  Similarity=0.082  Sum_probs=68.0

Q ss_pred             CCCcEEEEeCCCCCC-CH----HHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeE
Q 007742          218 RDQRTVFAYQMPLKA-TE----RDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV  291 (591)
Q Consensus       218 ~~~~~l~V~nLp~~~-te----~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i  291 (591)
                      ..+.+|||+||+..+ ++    ++|..+|..||.|+.+.+++      ++|||||+|.+.++|..|+ .|||..|.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            346899999999876 33    56999999999999999973      5789999999999999999 699999999999


Q ss_pred             EeccCccccc
Q 007742          292 MVKPSEAEKN  301 (591)
Q Consensus       292 ~v~~~~~~~~  301 (591)
                      +|.|+.....
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999865443

>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=99.43  E-value=8.2e-14  Score=113.13  Aligned_cols=78  Identities=23%  Similarity=0.287  Sum_probs=69.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       321 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      ..+|||+|||+.+|+++|.++|+.+|.+..+.++....+|.++|+|||+|.+.++|..|+ .|||. .|+|+.|.|..+.
T Consensus        18 ~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al-~~~~~-~i~gR~i~V~~~~   95 (112)
T d1wela1          18 GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQ-YMGNRFIQVHPIT   95 (112)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHH-TSCSB-CSTTSCBEEEEEC
T ss_pred             CeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHH-HcCCC-cCCCEEEEEEEcC
Confidence            479999999999999999999999998876555555568999999999999999999999 59996 6999999998764

>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=99.43  E-value=2e-13  Score=107.90  Aligned_cols=78  Identities=17%  Similarity=0.297  Sum_probs=67.9

Q ss_pred             CCCcceEEEeccCCCCC-CCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHH--HhcccccC
Q 007742          495 GSPSECLLLKNMFDPAM-ETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQR--AMHMRWFA  571 (591)
Q Consensus       495 ~~~s~~l~v~Nl~~p~~-~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~--~l~g~~~~  571 (591)
                      ..++++|+|.||  |.. ++        +++|.++|+.||.|..|.+.. .+|+|||+|.+.++|..|+.  .+++..|+
T Consensus        15 ~~~~~~l~v~nL--p~~~~t--------e~~l~~~F~~fG~V~~v~~~~-~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~   83 (99)
T d1x4fa1          15 QELGRVIHLSNL--PHSGYS--------DSAVLKLAEPYGKIKNYILMR-MKSQAFIEMETREDAMAMVDHCLKKALWFQ   83 (99)
T ss_dssp             SCCCCEEEEESC--CCSSCC--------SHHHHTTTTTTSCCSEEEEET-TTTEEEEECSSHHHHHHHHHHHHHSCCCSS
T ss_pred             CCCCCEEEEeCC--cCCccC--------HHHHHhhhccccceeEEEEee-cCCcEEEEecchHHHHHHHHHHhcCCceEC
Confidence            456789999999  653 55        689999999999999999874 57999999999999999998  46788899


Q ss_pred             CeEEEEEEeCch
Q 007742          572 RRLISAIFMKPE  583 (591)
Q Consensus       572 g~~l~v~~~~~~  583 (591)
                      |+.|.|.|++..
T Consensus        84 gr~l~V~~s~~~   95 (99)
T d1x4fa1          84 GRCVKVDLSEKY   95 (99)
T ss_dssp             SSCCEEEEECSC
T ss_pred             CEEEEEEEcCCc
Confidence            999999998654

>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=99.41  E-value=3.7e-13  Score=104.00  Aligned_cols=75  Identities=21%  Similarity=0.260  Sum_probs=66.5

Q ss_pred             CCceEEEcCCCCC-CCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHh--cCCeeeCCeEEEE
Q 007742          320 IDRKLYVGNLHFN-MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL--NGKLEIVGRTLKV  396 (591)
Q Consensus       320 ~~~~l~v~nl~~~-~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l--~g~~~~~g~~l~v  396 (591)
                      ++++|||+|||.. +|+++|.++|++||.|..|.+..+      +++|||+|.+.++|..|+..|  ++ +.+.|++|.|
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~-~~~~gr~l~V   79 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTP-ALVFGKPVRV   79 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSC-CEETTEECEE
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCC-CccCCceEEE
Confidence            3589999999986 789999999999999999999754      468999999999999999977  45 4799999999


Q ss_pred             EEecC
Q 007742          397 SSVTD  401 (591)
Q Consensus       397 ~~~~~  401 (591)
                      .|++.
T Consensus        80 ~~s~~   84 (89)
T d1x4da1          80 HLSQK   84 (89)
T ss_dssp             EEECC
T ss_pred             EECCC
Confidence            99864

>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=99.41  E-value=1.3e-13  Score=109.85  Aligned_cols=83  Identities=18%  Similarity=0.144  Sum_probs=69.3

Q ss_pred             CCcceEEEeccCCCCCC-CCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE
Q 007742          496 SPSECLLLKNMFDPAME-TDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL  574 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~-~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~  574 (591)
                      ..+..|||.||  ...+ +.+    ++.++|..+|+.||.|..+.+. .+.++|||+|.+.++|.+|+..|||..|+|+.
T Consensus         3 ~~~~~L~v~nl--~~~v~~~d----~~k~~l~~lF~~~G~i~~~~~~-k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~   75 (104)
T d1weya_           3 SGSSGLIACVA--NDDVFSES----ETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFLGKE   75 (104)
T ss_dssp             SCCCEEEEECC--CGGGGSTT----THHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEETTEE
T ss_pred             CCCceEEEEeC--CchhcCcH----HHHHHHHHHhcccccceEEEEe-cCCCEEEEEECCHHHHHHHHHHhcccccCCCE
Confidence            35568999999  4332 221    2257899999999999999887 46889999999999999999999999999999


Q ss_pred             EEEEEeCchhh
Q 007742          575 ISAIFMKPEDY  585 (591)
Q Consensus       575 l~v~~~~~~~~  585 (591)
                      |.|.|+.....
T Consensus        76 l~v~~a~~~~~   86 (104)
T d1weya_          76 MKLYFAQTLHI   86 (104)
T ss_dssp             CEEECCCCSSC
T ss_pred             eEEeecccCCC
Confidence            99999976543

>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=99.30  E-value=2.6e-12  Score=101.59  Aligned_cols=79  Identities=13%  Similarity=0.209  Sum_probs=65.1

Q ss_pred             CCCcceEEEec--cCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhccccc-C
Q 007742          495 GSPSECLLLKN--MFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWF-A  571 (591)
Q Consensus       495 ~~~s~~l~v~N--l~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~-~  571 (591)
                      ..|+.+|+|.|  |  |..++        +++|.++|++||.|..|.+.. .+++|||+|.+.++|..|+..|||+.+ .
T Consensus        15 ~~pt~~l~V~ng~L--~~~vt--------e~~L~~~F~~~G~i~~i~~~~-~k~~aFV~f~~~e~A~~A~~~lng~~i~~   83 (101)
T d2cq2a1          15 SYATQSLVVANGGL--GNGVS--------RNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVVD   83 (101)
T ss_dssp             SSCCSEEEEETCTG--GGTCC--------HHHHHHHHHHHSCEEEEECCT-TCSCEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CCCCceEEEECCCC--CCCCC--------HHHHHHHHHhhCcccEEeecc-CccEEEEEECCHHHHHHHHHHhCCCCCCC
Confidence            45677888866  9  88887        899999999999999998874 588999999999999999999999987 3


Q ss_pred             --Ce--EEEEEEeCchh
Q 007742          572 --RR--LISAIFMKPED  584 (591)
Q Consensus       572 --g~--~l~v~~~~~~~  584 (591)
                        +.  +|.++|+..-+
T Consensus        84 ~~~~~i~~~~~~~~~~~  100 (101)
T d2cq2a1          84 DLGQKITLYLNFVEKVQ  100 (101)
T ss_dssp             TTSCEEECEEEEESCCC
T ss_pred             CCCcEEEEEEEeeeecc
Confidence              33  34456665543

>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=99.29  E-value=1.5e-13  Score=109.38  Aligned_cols=75  Identities=20%  Similarity=0.188  Sum_probs=68.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHH-HHcCCccCCeeEEeccC
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      ..++|.+++..+++++|.++|++||.|..|.|+.+ .+|.++|||||+|.+.++|.+|+ .|||..+.|++|.|.++
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            44778888888999999999999999999999876 57999999999999999999999 69999999999999765

>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=99.28  E-value=3.1e-13  Score=107.54  Aligned_cols=76  Identities=18%  Similarity=0.218  Sum_probs=69.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEe
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSV  399 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~  399 (591)
                      ..++|.+++..+++++|.++|++||.|..|.|+.+. ++.++|+|||+|.+.++|.+|+..|||+ .|.|++|.|.+.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~-~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNR-WFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTC-EETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCC-EECCEEEEEEEC
Confidence            357778888889999999999999999999998774 8999999999999999999999999997 699999999875

>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=99.28  E-value=4.2e-14  Score=110.18  Aligned_cols=79  Identities=29%  Similarity=0.519  Sum_probs=67.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEe-----ccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEE
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLP-----LDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV  396 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~-----~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v  396 (591)
                      +.|||+|||..+++++|+++|+.||.|..+.+.     .+..++.++|||||+|.+.++|..|+ .|||. .|.|+.|.|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~-~~~Gr~l~V   79 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGI-IFQGQSLKI   79 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSC-CSSSSCCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCc-EECCEEEEE
Confidence            789999999999999999999999987665543     23346678999999999999999999 59996 799999999


Q ss_pred             EEecCC
Q 007742          397 SSVTDH  402 (591)
Q Consensus       397 ~~~~~~  402 (591)
                      ..++++
T Consensus        80 ~r~k~~   85 (90)
T d1u2fa_          80 RRPHDY   85 (90)
T ss_dssp             BCTTCC
T ss_pred             CCCCCC
Confidence            766543

>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=99.25  E-value=4.5e-12  Score=95.24  Aligned_cols=73  Identities=14%  Similarity=0.175  Sum_probs=62.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCcchHHHHHHHcCCccCCee-EEeccCcc
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQP-VMVKPSEA  298 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~e~A~~Al~l~g~~i~g~~-i~v~~~~~  298 (591)
                      .+.|+|+|+|+.++++.| .+|.+||.|.++.+.      ..+|||||+|.+.++|.+||.+||..|.|+. |.|.+...
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCCC
Confidence            368999999999986555 689999999999874      4578999999999999999999999999985 56877654


Q ss_pred             c
Q 007742          299 E  299 (591)
Q Consensus       299 ~  299 (591)
                      +
T Consensus        77 k   77 (81)
T d1wwha1          77 K   77 (81)
T ss_dssp             H
T ss_pred             h
Confidence            3

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=5.1e-12  Score=100.68  Aligned_cols=81  Identities=17%  Similarity=0.267  Sum_probs=68.1

Q ss_pred             CCCceEEEcCC--CCCC--------CHHHHHHHhccCCCeeEEEEeccCCC--CCcccEEEEEeCCHHHHHHHHHHhcCC
Q 007742          319 AIDRKLYVGNL--HFNM--------TETQLRKLFEPFGPVELVQLPLDIET--GQCKGFGFVQFAQLEHAKAAQSALNGK  386 (591)
Q Consensus       319 ~~~~~l~v~nl--~~~~--------~~~~l~~~f~~~g~i~~v~i~~~~~~--~~~~g~a~Vef~~~~~a~~a~~~l~g~  386 (591)
                      +++++|+|.||  |..+        ..++|++.|++||.|..|.|+.+..+  ....|++||+|.+.++|.+|+..|||+
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            45689999999  4433        23679999999999999999876533  345689999999999999999999998


Q ss_pred             eeeCCeEEEEEEec
Q 007742          387 LEIVGRTLKVSSVT  400 (591)
Q Consensus       387 ~~~~g~~l~v~~~~  400 (591)
                       .|+|+.|.|.+..
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             5999999999975

>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=99.22  E-value=9.1e-12  Score=100.82  Aligned_cols=71  Identities=14%  Similarity=0.080  Sum_probs=60.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCccceEEEEecCc-chHHHHH-HHcCCccCCeeEEeccC
Q 007742          220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV-MSVPMAI-ALSGQLLLGQPVMVKPS  296 (591)
Q Consensus       220 ~~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~G~afV~F~~~-e~A~~Al-~l~g~~i~g~~i~v~~~  296 (591)
                      .-.+||+|||+.+|+++|+++|.+||+|..|.|+.      .+|||||.|.+. ++|..|+ .+|+..+.+..+.|.+.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~------~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR------GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT------TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEec------CCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            45569999999999999999999999999999984      378999999986 6788888 79998887776666544

>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=99.22  E-value=8.5e-12  Score=98.52  Aligned_cols=67  Identities=28%  Similarity=0.413  Sum_probs=57.9

Q ss_pred             CCceEEEcC--CCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCe
Q 007742          320 IDRKLYVGN--LHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGR  392 (591)
Q Consensus       320 ~~~~l~v~n--l~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~  392 (591)
                      ++.+|+|.|  ||..+|+++|+++|++||.|..|.+..+      ++||||+|.+.++|..|+..|||...+.++
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~~~~   85 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDL   85 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCCCCC
Confidence            347888855  9999999999999999999999988754      579999999999999999999997444543

>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=99.19  E-value=4.3e-11  Score=94.10  Aligned_cols=77  Identities=21%  Similarity=0.311  Sum_probs=65.5

Q ss_pred             CceEEEcCC--CCCC---------CHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeee
Q 007742          321 DRKLYVGNL--HFNM---------TETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEI  389 (591)
Q Consensus       321 ~~~l~v~nl--~~~~---------~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~  389 (591)
                      +++|+|.||  |..+         .+++|.+.|++||.|..|.+..+    ..+|+|||+|.+.++|..|+..|||. .|
T Consensus         8 ~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~-~~   82 (99)
T d2dita1           8 ERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGR-WF   82 (99)
T ss_dssp             CCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTC-EE
T ss_pred             ccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCc-EE
Confidence            489999999  4432         23689999999999999988754    46799999999999999999999997 69


Q ss_pred             CCeEEEEEEecCC
Q 007742          390 VGRTLKVSSVTDH  402 (591)
Q Consensus       390 ~g~~l~v~~~~~~  402 (591)
                      +|++|.|.+....
T Consensus        83 ~gr~i~v~~~~g~   95 (99)
T d2dita1          83 GGRQITAQAWDGT   95 (99)
T ss_dssp             TTEECEEEECCSC
T ss_pred             CCEEEEEEEeCCc
Confidence            9999999987543

>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=99.10  E-value=5e-11  Score=96.34  Aligned_cols=70  Identities=13%  Similarity=0.074  Sum_probs=60.1

Q ss_pred             eEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCH-HHHHHHHHHhcccccCCeEEEEE
Q 007742          500 CLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFEST-EAAASAQRAMHMRWFARRLISAI  578 (591)
Q Consensus       500 ~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~-e~A~~A~~~l~g~~~~g~~l~v~  578 (591)
                      .+||+||  |..+|        +++|+++|+.||.|.+|.|+. ++|||||.|.+. ++|..|+..|+|..+.++.+.|.
T Consensus        13 ~~fvgnL--~~~~t--------ee~Lk~~F~~fG~V~~v~i~~-~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~   81 (113)
T d1owxa_          13 LKFSGDL--DDQTC--------REDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   81 (113)
T ss_dssp             EEEEESC--CSSCC--------HHHHHHHTCSSCCEEEEECCT-TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             EEEECCC--CCCCC--------HHHHHHHHHhcCChheEEEec-CCceEEEEecCcHHHHHHHHHHhcCCceecCceEEE
Confidence            3589999  88887        999999999999999999985 589999999985 78999999999998876665555


Q ss_pred             Ee
Q 007742          579 FM  580 (591)
Q Consensus       579 ~~  580 (591)
                      +.
T Consensus        82 ~~   83 (113)
T d1owxa_          82 WE   83 (113)
T ss_dssp             EE
T ss_pred             Ee
Confidence            53

>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=99.06  E-value=1.9e-10  Score=86.19  Aligned_cols=73  Identities=14%  Similarity=0.229  Sum_probs=60.7

Q ss_pred             ceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCeE-EEE
Q 007742          499 ECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRL-ISA  577 (591)
Q Consensus       499 ~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~-l~v  577 (591)
                      .-|+|.++  |...         .++|..+|+.||.|.++.+.. .+|+|||+|.+.++|.+|+. |||..|+|+. |.|
T Consensus         5 ~wV~V~G~--p~~~---------~~~il~~F~~~G~I~~~~~~~-~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV   71 (81)
T d1wwha1           5 TWVTVFGF--PQAS---------ASYILLQFAQYGNILKHVMSN-TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGV   71 (81)
T ss_dssp             GEEEEECC--CGGG---------HHHHHHHHHTTSCEEEEEECS-SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEE
T ss_pred             cEEEEECC--ChHH---------HHHHHHHHHhhhhhheEEecC-CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEE
Confidence            45999999  6554         356667899999999998864 58999999999999999996 9999999985 568


Q ss_pred             EEeCchh
Q 007742          578 IFMKPED  584 (591)
Q Consensus       578 ~~~~~~~  584 (591)
                      ..+..+.
T Consensus        72 ~~~~~k~   78 (81)
T d1wwha1          72 KPCIDKN   78 (81)
T ss_dssp             EECCCHH
T ss_pred             EeCCChh
Confidence            8776654

>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=98.31  E-value=1.5e-06  Score=59.87  Aligned_cols=64  Identities=17%  Similarity=0.184  Sum_probs=57.1

Q ss_pred             hhHHHHHHHHhccccceEEEEEecC--CCeeEEEEeCCHHHHHHHHHHhcccccCCeEEEEEEeCc
Q 007742          519 LEIQGDVEEECSKYGRVKHIYVDKR--SAGFVYLRFESTEAAASAQRAMHMRWFARRLISAIFMKP  582 (591)
Q Consensus       519 ~~~~edl~~~f~~~G~V~~v~l~~~--~~g~afV~F~~~e~A~~A~~~l~g~~~~g~~l~v~~~~~  582 (591)
                      .+|.+.|...|.+||.|.++.|...  ..-.|-|...+.++|..|+..||.+++++++|.|+|++.
T Consensus         7 kelqq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1           7 KELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            4668899999999999999999544  345789999999999999999999999999999999863

>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=98.22  E-value=9.3e-07  Score=64.24  Aligned_cols=82  Identities=13%  Similarity=0.257  Sum_probs=62.8

Q ss_pred             cCCCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhcccccCCe
Q 007742          494 IGSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARR  573 (591)
Q Consensus       494 ~~~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~g~~~~g~  573 (591)
                      +++|..+|.|.=. ++....+..+.+.+..+|.+.|..||.|.-|.+.   .+..+|+|.+-++|.+|+. |+|.++.|+
T Consensus        11 qGPpDgTIvV~i~-~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv---~d~mwVTF~dG~SAL~al~-l~g~~v~G~   85 (95)
T d1ufwa_          11 QGPLDATVVVNLQ-SPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRIN---QGQMLVTFADSHSALSVLD-VDGMKVKGR   85 (95)
T ss_dssp             CCCTTCEEEEEES-SCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEE---TTEEEEECSCSHHHHHHHH-GGGSEETTE
T ss_pred             cCCCCcEEEEEec-cCCccccccCCHHHHHHHHHHHhhCCeEEEEEEe---CCeEEEEECCcHHHHHHhc-cCCeEEcce
Confidence            4566677777433 2222112244556688999999999999999876   4467999999999999998 899999999


Q ss_pred             EEEEEEe
Q 007742          574 LISAIFM  580 (591)
Q Consensus       574 ~l~v~~~  580 (591)
                      +|+|+.-
T Consensus        86 ~l~It~~   92 (95)
T d1ufwa_          86 AVKISGP   92 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEecC
Confidence            9999864

>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=97.51  E-value=0.00013  Score=52.84  Aligned_cols=74  Identities=24%  Similarity=0.369  Sum_probs=57.9

Q ss_pred             CCCCCCceEEEcCCCCCCCH---------HHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCC
Q 007742          316 PYGAIDRKLYVGNLHFNMTE---------TQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK  386 (591)
Q Consensus       316 ~~~~~~~~l~v~nl~~~~~~---------~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~  386 (591)
                      ..+|+.-+|.|.-..+...+         .+|.+.|..||+|.-|++..+        ..+|+|.+-++|.+|+ .|+|.
T Consensus        10 ~qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al-~l~g~   80 (95)
T d1ufwa_          10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVL-DVDGM   80 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHH-HGGGS
T ss_pred             ccCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHh-ccCCe
Confidence            34555667877544433222         468889999999999999865        4999999999999999 89995


Q ss_pred             eeeCCeEEEEEEe
Q 007742          387 LEIVGRTLKVSSV  399 (591)
Q Consensus       387 ~~~~g~~l~v~~~  399 (591)
                       ++.|+.|.|...
T Consensus        81 -~v~G~~l~It~~   92 (95)
T d1ufwa_          81 -KVKGRAVKISGP   92 (95)
T ss_dssp             -EETTEEEEEECC
T ss_pred             -EEcceEEEEecC
Confidence             899999999743

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.14  E-value=0.0012  Score=45.22  Aligned_cols=61  Identities=28%  Similarity=0.270  Sum_probs=51.1

Q ss_pred             HHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhcCCeeeCCeEEEEEEec
Q 007742          336 TQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVT  400 (591)
Q Consensus       336 ~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~g~~l~v~~~~  400 (591)
                      +-|.+.|.++|+|..+.+.... .+.  -.|-|...+.++|..|+..|+-. .|+++.|.|.+++
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg~--~~A~V~v~~~q~A~~~v~~LhR~-KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DYQ--LKAVVQMENLQDAIGAVNSLHRY-KIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-STT--CCEEEEESSHHHHHHHHHHHTTE-EETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CCc--EEEEEEcCCHHHHHHHHHHHHHH-hcCCeEEEEEEec
Confidence            3466788999999999986543 333  35999999999999999999995 8999999999875

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.85  E-value=0.0031  Score=46.42  Aligned_cols=69  Identities=13%  Similarity=0.197  Sum_probs=55.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCC--CcccEEEEEeCCHHHHHHHHHHhcCCeeeC
Q 007742          322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAAQSALNGKLEIV  390 (591)
Q Consensus       322 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~--~~~g~a~Vef~~~~~a~~a~~~l~g~~~~~  390 (591)
                      +.|.|+.||+.+|++++.+.+.+.|.+........+.+.  ..-.-|||.|.+.+++......++|.+.++
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            478999999999999999999999998877665543332  223569999999999999999999975344

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.59  E-value=0.0049  Score=45.32  Aligned_cols=67  Identities=15%  Similarity=0.208  Sum_probs=55.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCC--ccceEEEEecCcchHHHHH-HHcCCccC
Q 007742          221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRR--SKGVGYIEFYDVMSVPMAI-ALSGQLLL  287 (591)
Q Consensus       221 ~~l~V~nLp~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~--~~G~afV~F~~~e~A~~Al-~l~g~~i~  287 (591)
                      .+|.|+.||+.+|++++.+.+...|.+.....+..+.+-.  .-.-|||.|.+.+++.... ..+|..+.
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            5799999999999999999999999988877777554422  2357899999999998888 58888763

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.99  E-value=0.016  Score=42.52  Aligned_cols=59  Identities=19%  Similarity=0.269  Sum_probs=47.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeccCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 007742          318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN  384 (591)
Q Consensus       318 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~v~i~~~~~~~~~~g~a~Vef~~~~~a~~a~~~l~  384 (591)
                      .+.-..||.-.+|..+...+|.++|++||.|.--.| -+.       -|||...+.++|..++..+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-ddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cCc-------eEEEEecCHHHHHHHHHHhc
Confidence            344578999999999999999999999998854344 332       59999999999999886654

>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=92.56  E-value=0.25  Score=35.94  Aligned_cols=58  Identities=14%  Similarity=0.246  Sum_probs=46.0

Q ss_pred             CCcceEEEeccCCCCCCCCchhhhhHHHHHHHHhccccceEEEEEecCCCeeEEEEeCCHHHHHHHHHHhc
Q 007742          496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMH  566 (591)
Q Consensus       496 ~~s~~l~v~Nl~~p~~~~~~~~~~~~~edl~~~f~~~G~V~~v~l~~~~~g~afV~F~~~e~A~~A~~~l~  566 (591)
                      +...-||...+  |....        ..+|+++|+.||.|.-..|.   ...|||.-.+.++|..+++.+.
T Consensus        13 p~RdHVf~~tF--P~~Wk--------~~dI~~lFSpfG~V~VswId---dTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTF--PKEWK--------TSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEEC--CTTCC--------HHHHHHHHTTTCSCCCEEEE---TTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeC--Ccccc--------hhHHHHHhcCCCceEEEEec---CceEEEEecCHHHHHHHHHHhc
Confidence            34456888888  77766        78999999999988766664   3368999999999998887654